Is the Blueprint the Building? Studies on the Use of Social Representation Theory, Information Theory, Folkscience, Metaphor and Language to Understand Student Comprehension of Metaphors in the Domain of Gene Expression

DISSERTATION

Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University

By Andrea Michele Graytock Graduate Program in Education

The Ohio State University 2011

Dissertation Committee: David L. Haury, Advisor Antoinette Errante Laura Wagner

Copyrighted by Andrea Michele Graytock 2011

Abstract

Learning about gene expression can be hampered by the multiple steps of the process as well as the technical terms used to represent the process. Technical terms and explanations are based on the metaphors of language, code, containers, gift-giving, computer programs, and construction. The effective use of metaphor depends on the background of the audience and their familiarity with base concepts of the metaphors in use. Inappropriate metaphors also interfere with new information projection from the metaphor to new information. A series of three qualitative studies was carried out to determine non-science students‘ interpretation of commonly-used theory constitutive metaphors. For Study 1students were asked to interpret the metaphors DNA IS A

LANGUAGE, DNA IS A CODE, DNA IS A CARRIER OF INFORMATION, and DNA IS A COMPUTER

PROGRAM. Using Corbin & Strauss‘s Grounded Theory, similar action/interactional strategies from interpretations of participants were grouped to form concepts and consequences of those concepts were noted. Concepts that reflected a similar theme were combined to form categories. These categories reflected the conceptual understanding of each metaphor. For Study 2, students were asked to explain the meaning of the base concepts language and code and the target DNA. Then they were asked to explain the meaning of the metaphors that use those concepts; DNA IS A CODE and DNA IS A

LANGUAGE. The same coding procedure from Study 1 was used. For Study 3, students were asked to provide the base for a self-generated metaphor using ―DNA‖, ―RNA‖, ii

―Proteins‖, ―Transcription‖, ―Translation‖, and ―Ribosome‖ as the targets. Additionally, they were asked to provide an explanation of their metaphors. Bases were coded for concepts and explanations were coded for action/interactional strategies and consequences from which concepts and categories were developed. Using categories developed from action/interactional strategy concepts from Study 1, students, when they conceptualized DNA as a language, wrote of DNA as involved in internal dialogue with cells, molecules, or the body either as a participant in communication or used as a medium of communication between cells or body parts; DNA as a private language that one or a very few individuals could understand; requires experts to understand it or translate it; and, like language, is made up of smaller components that can be combined.

As a code, DNA was made up of individual components in a particular sequence was the most common interpretation. When asked to define both the base and target before being asked to interpret the metaphor, students used the features associated with the base. The most important features for language were that it was a means of interpersonal communication and there are different languages and one must know the language to understand it. These features were used to interpret the DNA IS A LANGUAGE metaphor.

The categories and concepts were similar to those of Study 1 but the interpersonal feature was most common. Codes were defined by their components and the sequence. These features were used in the interpretation of the metaphor. Similar categories and concepts were developed from interpretations of both studies. Most interpretations, for all of the metaphors interpreted, were not the features used in the development of the code, language, carrier, and computer program metaphors. It was suggested that there are key

iii features used to interpret scientific metaphors, especially theory-constitutive metaphors, and suggest the concept ―Keystone Concepts‖ to highlight this fact. Students also used these ―one-dimensional metaphors‖ to explain two and three dimensional processes and structures.

iv

I would like to thank my sister, Kathleen, and my parents, Andrew and Marie. There constant support, emotionally and financially over the years has made my academic pursuits possible. It is to them that I dedicate this dissertation.

v

Acknowledgments

I would like to thank my advisor, Dr. David Haury, for his enthusiasm, support, insightful conversations, and willingness to let me explore uncharted territory for this dissertation project. I would also like to thank my committee members, Dr. Antoinette

Errante and Dr. Laura Wagner for their expertise and discussions of my work-in-progress and for their enthusiasm and support in my explorations of metaphor interpretation and use of qualitative methods. I would like to thank my brother, Andy, for our discussion about computing, computer programs and computers that aided in my understanding and analysis of DNA IS A COMPUTER PROGRAM and computer-related explanations from Study

3. I would like to also thank all of my colleagues and students over the years for their discussions about science teaching and where the problems may lie. I would like to thank

The Ohio State University Biology Department and Dr. John Cogan for allowing me to ask his Biology 101 class to participate in this research project. I would like to thank all of the Biology 101 students who gave of their time to help me with this research. Finally,

I would like to thank Michael Gee for his technical expertise in uploading the studies onto Carmen.

vi

Vita

1986…………………………………………..B.S. Chemistry, Marywood College

1992…………………………………………..M.S. Toxicology, St. John‘s University

1992 to 1999………………………………….Keystone College/Keystone Junior College

Professional Tutor

1994 to 1999…………………………………..Keystone (Junior) College

Adjunct Instructor, Allied Health,

Sciences, and Math Division

1996 to1997 ………………………………….Scranton Preparatory School,

Biology Teacher

1999 to 2001…………………………………..The Ohio State University

College of Biological Sciences, Molecular,

Cellular, Developmental Biology Program

2002 to Present………………………………..The Ohio State University, College of

Education and Human Ecology,

Department of Teaching and Learning

September 2002 to Present……………………Otterbein (College) University

Senior Lecturer, Department of Biology

and Earth Science, Department of

Education vii

September 2002 to Present…………………….Columbus State Community College

Instructor, Biological Sciences

Publications:

Jones, C.B., McIntosh, J., Hustig, H., Graytock, A., & Hoyt, D.G. (2001). Regulation of Bleomycin-induced DNA Breakage and Chromatin Structure in Lung Epithelial Cells by Integrins and Poly (ADP-Ribose) Polymerase. Molecular Pharmacology, 59, 69-75.

Graytock, A.M., & Grove, T.L. (2008). Microbiology for Nursing Students. 1st Edition, Kearney, NE.

Graytock, A.M., & Grove, T.L. (2009). Microbiology for Nursing Students. 2nd Edition, Kearney, NE.

Fields of Study

Major Field: Education

Focus: Science

viii

Table of Contents

Abstract ...... ii

Acknowledgments ...... vi

Vita ...... vii

List of Tables...... xi

List of Figures ...... xii

Chapter 1: The Problem ...... 1

Chapter 2: Literature Review ...... 27

Chapter 3: Design and Method ...... 92

Research Purpose and Hypotheses…………………………………………………92

Study Rationale and theoretical Framework ...... 94

Design and Procedures ...... 98

Sampling ...... 103

Chapter 4: Analysis ...... 106

Chapter 5: Study 1 ...... 121

Chapter 6: Conclusions for Study 1...... 173

Chapter 7: Study 2. ……………………………………………………………………191

ix

Chapter 8: Conclusions for Study 2……………………………………………………247

Chapter 9: Conclusions for Study 1 and Study 2………………………………………253

Chapter 10: Study 3……………………………………………………………………258

Chapter 11: Conclusions for Study 3…………………………………………………..278

Chapter 12: General Conclusions……………………………………………………...287

References……………………………………………………………………………..313

Appendix A: Metaphors as part of Misconception…………………………………….324

Appendix B: A list of base concepts provided for Study 3……………………………328

x

List of Tables

Table 1. Classification of DNA IS A LANGUAGE Categories …….. …………………….155

Table 2. Category ‗Transfer‘, Sub-category Modes of transfer analysis of what

‗Information‘ is transferred by DNA ………………………………………………...... 161

Table 3. Summary of the number of responses for each aspect of information……….162

Table 4. The number of responses given for the meaning of information for responses that used the two meanings of carry, hold/contain and transfer………………………..163

Table 5. Coding of DNA definition responses: the use of Double Helix……………...201

Table 6. Percent of base concept categories for the six targets DNA, Transcription,

RNA, Translation, Proteins and Ribosomes for Study 3 shared across the 6 target concepts…………………………………………………………………………………259

Table 7. Categories from Transcription base concepts from all responses. Totals are given for both the concepts and action…………………………………………………261

xi

List of Figures

Figure 1. DNA as information metaphorical representation leading to DNA as information that results in development of Biological Information Theory……………. 62

Figure 2. The Knowledge Vee developed by Gowin (1984)……….. ………………….68

Figure 3. Career of Gene Expression Metaphors………………………………………..80

Figure 4. Different sectors of the public, represented by the spheres A and B, are likely to hold divergent versions of vernacular science knowledge and conceptual bases for metaphor development………………………………………………………...84

Figure 5. Two types of reasoning about the physical world…………………………….85

Figure 6. Combining Social Representation Theory and Career of Metaphor to demonstrate how Career of Metaphor compliments the ideas of social representation…86

Figure 7. Resolution of an incongruity between the horizons of the scientific term/metaphor and the students.…………………………………………………………89

Figure 8. Model developed with implications and questions raised by the model……...93

Figure 9. Summary of the proposed studies for this research project…………………105

Figure 10. The general process for the development of a grounded theory from data to concept development, the formation of categories that comprise a grounded theory………………………………………………………………………………… 108

Figure 11. Categories, sub-categories and concepts from students‘ action/interactional strategies developed from responses to DNA IS A COMPUTER PROGRAM………………..121

xii

Figure 12. Sub-categories, concepts and consequences that made up the category ‗Write‘ in the DNA IS A COMPUTER PROGRAM responses……………………...123

Figure 13. DNA IS A COMPUTER PROGRAM action/interactional strategy concepts and the consequences of those strategies that formed the categories ‗Download/

Install‘ and ‗Run/Execute‘……………………………………………………………...131

Figure 14. Summary of the action/interactional strategy concepts and the consequences of those strategies for the category Output, Sub-category

Functions developed from student responses to the DNA IS A COMPUTER PROGRAM metaphor………………………………………………………………………………..134

Figure 15. Compilation of the categories, action/interactional strategy concepts and their consequences that formed those categories developed from student explanations of the metaphor DNA IS A LANGUAGE……………………………………..142

Figure 16. Internal Dialogue Category formed from action/interactional strategy concepts from student interpretations of the DNA IS A LANGUAGE metaphor…………..143

Figure 17. Uses/Aspects of Language Category formed from action/interactional strategy concepts from student interpretations of the DNA IS A LANGUAGE metaphor….146

Figure 18. Action/interactional strategies that were used to develop the category

Private Language from student explanations of the metaphor DNA IS A LANGUAGE……148

Figure 19. Action/interactional strategy concepts and their consequences that define the category ‗Order‘ for the interpretation of the metaphor DNA IS A

LANGUAGE………………………………………………………………………………150

Figure 20. Action/interactional strategy concepts and consequences of the

xiii

Categories ―Know language to understand‘, ‗Translate‘, ‗Code‘, and ‗Purpose.‘……..152

Figure 21. Results of coding for concepts of DNA IS A CARRIER OF

INFORMATION metaphor for explanation of ‗Information‘ including the consequences of those concepts………………………………………………………...159

Figure 22. Action/interactional strategy concepts and the categories developed from them for interpretations of the metaphor DNA IS A CODE………………………….164

Figure 23. Action/interactional strategy concepts for the category ‗Form.‘…………...166

Figure 24. Action/Interactional strategy concepts for the category Decipher/Decode...169

Figure 25. Action/Interactional strategy concepts that formed the Categories codes for, What is encoded, Communication…………………………………………………171

Figure 26. Concept map developed from responses to define the base concept

―language.‖ Categories are in blue boxes and action/interactional strategy concepts used to form the category are shown in the black boxes……………………..196

Figure 27. Most prevalent links from the Language group concept map……………..199

Figure 28. Comparison of metaphor use and reference to the structure of DNA

between students who used the metaphor Double Helix and those that did not…….…204

Figure 29. Concept map showing the relationship between responses to define

DNA that contain the metaphor ‗Double Helix‘ with additional metaphors…………...206

Figure 30. Concept map showing the relationship between responses to define

DNA that used at least one metaphor but did not contain the metaphor

‗Double Helix.‘………………………………………………………………………....207

Figure 31. The general process of encoding and decoding a plaintext message

xiv including processes performed by both the sender and receiver……………………….210

Figure 32. Define code responses that related to the process of encoding, transmittance and decoding……………………………………………………………..213

Figure 33. Responses to Code showing action/interactional strategy concepts and the categories formed from those concepts………………………………………...214

Figure 34. Pie Chart for Categories and Concepts from Action/interactional

strategies of DNA IS A LANGUAGE responses……………………………………………221

Figure 35 Action/Interactional Strategy concepts and their consequences for the category Internal Dialogue developed from responses to the metaphor DNA IS A

LANGUAGE ……………………………………………………………………………...222

Figure 36. Uses/Aspects of language category and the action/interactional strategy concepts used to form the category…………………………………………………….227

Figure 37. Action/Interactional strategy concepts and Private language, know language to, code, order and translate categories for DNA IS A LANGUAGE……………..230

Figure 38. Categories and action/interactional strategy concepts that form them from the responses to the DNA IS A CODE metaphor…………………………………….233

Figure 39. The category ‗Form‘ developed from action/interactional strategies from the explanations of DNA IS A CODE………………………………………………..234

Figure 40. Concepts that made up the Category Decipher with the consequences of the actions/interactions of DNA as a code…………………………………………...239

Figure 41. Category Information was developed from the action/interactional strategies contains, tell/give and information identified………………………………..241

xv

Figure 42. Category Codes for developed from action/interactional strategy concepts from interpretations of DNA IS A CODE………………………………………..243

Figure 43. Categories Communication and Types of. And concepts developed from interpretations to DNA IS A CODE…………………………………………………..245

Figure 44. Features of code used by students to interpret the metaphor DNA IS

A CODE…………………………………………………………………………………..250

Figure 45. Code is used as an example of information transfer within a communication system………………………………………………………………….251

Figure 46. Comparison of Categories and action/interactional strategy concepts for the metaphor DNA IS A LANGUAGE A: Study 1, B: Study 2…………………………254

Figure 47. Comparison of Categories and action/interactional strategy concepts for the metaphor DNA IS A CODE A:Study 1, B: Study 2……………………………….255

Figure 48. Analysis of ‗Code‘ metaphor identifying the Keystone Concept………….298

Figure 49. Keystone concepts used in the development and interpretation of the metaphor DNA IS A CODE………………………………………………………………..299

Figure 50. Sequence of events from parent to offspring and development of the immature form to the mature form showing where the 1-D metaphors are appropriate……………………………………………………………………………302

xvi

CHAPTER 1: THE PROBLEM

It is a well-established fact that language is not only our servant, when we wish to express- or even conceal- our thoughts, but that it may also be our master, overpowering us by means of the notions attached to the current words. Wilhelm Johannsen, 1911

Brief for American Association for the Advancement of Science et al. as Amici Curiae 7-8 ("Science is not an encyclopedic body of knowledge about the universe. Instead, it represents a process for proposing and refining theoretical explanations about the world that are subject to further testing and refinement" (emphasis in original, Ruling Daubert vs Merrell Dow Pharmaceutical, 1993)

Metaphors are used by scientists in the development of models as they attempt to understand and explain new phenomena, in hypothesis formulation, to aid in interpretation of results, and for neologisms of terminology for a new phenomenon.

These constitute what Boyd refers to as theory-constitutive metaphors. They are other-generated metaphors that are not only heuristic in nature, but also rhetorical. As

Brown argues, they are not bridges to understanding but are a framework for model development; the metaphor remains as framework for further interpretation and terminology.

As time passes from this initial metaphor formulation, hypothesis formulation and testing and development of terminology, the metaphorical nature of the model is

1 lost and both the model and terminology are viewed as literal. Bowdle and Gentner refer to this phenomenon as career of Metaphor.

When individuals not part of this domain attempt to understand the model of the phenomenon completed with its metaphor-derived terminology, they may encounter difficulty. Part of the difficulty may lie in not recognizing the metaphorical nature of the model and terminology. DNA IS A CODE is understood to be a fact. As such, any potential exploration of how DNA might be like a code or even why the association came to be may not seem evident.

Metaphors frame interpretation of natural phenomena. The originators of the metaphors understood the phenomenon based on the metaphors. When we later attempt an understanding of the phenomenon, we accept the models as facts. Learning facts bereft of an appreciation of how they are developed not only presents a distorted understanding of the nature of science but add to the challenge of intelligible, plausible and fruitful conceptual understanding of the phenomenon.

It is the intent of this research to begin to determine undergraduate, non- science majors‘ understanding of commonly used theory-constitutive and non-theory- constitutive metaphors in the domain of gene expression; the production of proteins by a cell using DNA. The domain is replete with both categories of metaphors that we can trace to the origins of the field of molecular biology in the 1940s; conceptual metaphors that give rise to these metaphors can be traced back even further in the field of genetics and prior to that, studies of heredity and embryology. These metaphors

2 had a very specific interpretation and use. This is what allowed them the heuristic value they enjoyed.

As will be explained in the ensuing chapters, use of metaphor in science is very different from metaphor use in a common or literary manner. Whereas common or literary use invites creative interpretation to explore potential new avenues of understanding between what an individual understands, known as the base of the metaphor, and what is less known, the target, scientific use of metaphor is restricted in which associations are acceptable for understanding of a natural phenomenon. Mary

Hesse‘s theory of positive, neutral and negative analogy provides a framework for us to understand how metaphor is productively used by scientists.

Why might students‘ interpretation of gene expression metaphors not coincide with their use by biologists? Although part of the answer lies with not recognizing the metaphoric nature of statements such as DNA IS A CODE, part of the answer may lie in how both groups-although neither is monolithic- understand the base of these metaphors. Which features of the base is part of the conceptual understanding of the base does influence which features are available for similarity relations between the base and the target of a metaphor. Conceptual understanding of the base is based on the experience of the individual. Some bases may be more familiar to students than others, for example language might be more familiar than are codes. So interpretation of DNA IS A LANGUAGE and DNA IS A CODE depends on understanding of the base.

What is learned about DNA is directly related to features of the base available for comparison. If the features used by the scientist to gain understanding of DNA are not

3 part of the conceptual understanding of the bases by students, their interpretations will be based on their understanding and will not include the features used by the scientists in model development and terminology. This disconnect may hinder conceptual understanding of the domain of gene expression.

Is this the case? Student understanding of these metaphors has not been studied before. So the role of other-generated gene expression metaphors in conceptual understanding is not understood. This study makes the first steps towards determining student understanding of these metaphors. Is their interpretation complimentary to scientific use? How do they interpret them? What is their conceptual understanding of the role of DNA based on use of these metaphors?

In order to gain insight into students‘ understanding of commonly-used gene expression metaphors, I will utilize the methods of Grounded Theory first established by Glaser and Strauss (1967) and later elaborated by Strauss and Corbin (1990, 1998,

2008). Grounded Theory methods are inductive and address both the collecting and analyzing of the collected data to ―build a middle-range theoretical framework to explain the collected data‖ (Charmaz, 2000, p. 509). The methods were particularly useful as I had no initial data, theory, or understanding of student interpretations of these metaphors. Although Strauss and Corbin take an objectivist stance to grounded theory which ―assumes that different observers will discover‖ an external world that

―can be described, analyzed, explained and predicted‖ and ―described it in similar ways‖ (Charmaz, 2000, p. 524) and I have used their methods in this research.

4

To gain an understanding of how student understanding of other –generated gene expression metaphors influences conceptual understanding of the role that DNA plays, I will first develop the problem in more detail using the problem-solving algorithm developed by Althusser. Following this analysis of the problem, I will review literature from the fields I used to understand and situate the problem and that contributed to the theoretical framework for understanding student understanding of other-generated gene expression metaphors. This will include within the field of education, conceptual change and meaningful learning; constructivism; metaphor theory; metaphor use in science; historical roots of gene expression metaphors and why this knowledge is important in informing us about potential instructional methods; the central dogma; the public understanding of science and metaphor use; social representation theory; hermeneutics and pragmatism. Next, I will summarize the research purpose and hypotheses, design and procedures, then how the analysis of the collected data will proceed. Finally the results from each of three studies will be discussed followed by conclusions for each study separately followed by conclusions for all three studies. I will conclude with suggestions for the use of results from these initial studies in classes that study DNA and gene expression.

Choosing the Problem

I once saw an ad. It consisted of two pictures, side-by-side. The picture on the left was a pile of sand with the caption ―information.‖ The picture on the right was of an elaborate sand castle, with the caption ―knowledge.‖ This ad summarized in two pictures and two words my view of education. Information consists of the

5 experiences, words, and descriptions of concepts we present to students. Knowledge is the result of their ability to understand information (intelligible), see the possibility that the sand can be made into a castle (plausible) and finally build the sand castle

(information becomes knowledge, is fruitful). Much of what we present to students is a pile of sand and for many students remains a pile of sand.

The final goal of the solution to the problem involves determining what characteristics of the understanding must be changed, what characteristics cannot be changed and what the main technical characteristic that must be improved is.

The questions the life scientists ask and the models they propose and test are, when all is said and done, put simply as: these are solutions to problems of how organisms carry out life functions including development and heredity. These ultimate questions have not changed since Aristotle and have been variously studied in the course of Western history by theologians, natural philosophers, biologists and now life sciences plus cooperation from physics and chemistry. The scope of biology was clearly laid out as early as 1866 by Spencer when he wrote that, ―the entire Science of

Life, must consist in a detailed interpretation of all these functional and structural phenomena in their relations to the phenomena of the environment. Immediately or mediately, proximately or remotely, every trait exhibited by organic bodies, as distinguished from inorganic bodies, must be referable to this continuous adjustment between their actions and the actions going on around them‖ (p. 95). Different organisms have varying solutions to problems of energy production, nutrient utilization, development and reproduction. There are similarities between some of

6 these organisms, but what life scientists have always tried to find out, no matter the era or what they were called or called themselves, was and is how does life solve these problems? And ultimately answer the question: What is Life?

Recent conceptual understanding in Life Science takes our explanations of these processes to the molecular level that started in the early 20th century with the recognition of the importance of proteins within a cell. Proteins play a key role in living things due to their versatility in structure based on the order of building block units, called amino acids. Even though nucleic acids, specifically DNA, has seemed to have taken center stage in molecular biology since 1953, even Crick recognized their importance and highlighted this when he wrote, ―[I]n the protein molecule Nature has devised a unique instrument in which an underlying simplicity is used to express great subtlety and versatility; it is impossible to see molecular biology in proper perspective until this combination of virtues has been clearly grasped‖ (1958, p. 139).

We must continue to decide what the focus within Life Science education should be: DNA structure and function or proteins. Currently DNA holds a place of prominence within Life Science as genetic explanations for such diverse processes as human disease states, nutrition and resistance of crops, resistance of bacteria to antimicrobials are explained at the level of DNA. Although there is no doubt that

DNA does indeed play a role in these and other processes of living things, continued over-emphasis on this molecule may contribute to a lack of understanding of the structure and function of living things.

7

The search for the hereditary ―stuff‖ did include DNA, but it did not start with it. Yet the focus within science education has been with DNA starting in the 1960s (as reflected in changes in emphasis in textbooks as is noted by Gaster, 1990).Our understanding of the nucleic acid concept of gene that is the role of DNA in heredity and development is only 50 years old. Before that, a summary of the search for the hereditary ―stuff‖ included the determination that heredity involved cells, then of what part of the cell is involved, to the nucleus or cytoplasm is important, to the nucleus is important, to chromosomes within the nucleus are important, to is it nucleic acid or nucleoprotein that is important, to it‘s the nucleoprotein that‘s important to its DNA that is important and in the process discarding inheritance of acquired traits and vitalism.

The search for the determinants of what made one species different from another involved the recognition of the importance of proteins. Then the questions guiding research became, how do the proteins in the cells of a species arise? How are they synthesized? What are they made up of? What makes one protein different from another protein? Since there was a focus on structure and specificity, proteins were thought to act as 3-D templates for the formation of the same protein.

Several key features about proteins about proteins made in the late 1940s and early 1950s seemed to be important in the need for a cell to possess a linear template versus a 3-D template. The key features are: the order of amino acids of any single protein (called the sequence), such as insulin, is the same in every molecule of that protein (Sanger during the years 1953-1956), different proteins have a different

8 number of amino acids, and sequences of proteins from individuals of the same species are identical. The question then became, how is the cell able to produce proteins with the same sequence of amino acids and for organisms to produce proteins with consistent sequences? With Beadle and Tatum‘s one-(protein) gene-one enzyme hypothesis (1945) that one gene controls the production of one enzyme, Dounce‘s hypothesis papers on the proposed role of DNA and RNA in protein synthesis during the years 1952 and 1953 based on Boivin and Vendreley‘s (1948) and Brachet‘s work with RNA in the cytoplasm of the cell and with Watson and Crick‘s publication of the structure of DNA in 1953, DNA became the likely template, although not readily accepted as such. This is a brief conceptual history of the place of DNA in the function of cells. The direction of focus started with the previously discussed properties of proteins with the search always for the template molecule, and not here‘s

DNA we wonder what it does. Yet our focus of instruction is ‗here‘s DNA and here‘s what it does‘, not the ‗protein to what is the template route‘ which was the actual course of molecular biology.

Conceptually these are two different problems: search for a template versus here‘s a molecule what role does it have based on its structure. Does the order of presentation of DNA and protein matter as far as conceptual understanding is concerned? If protein didn‘t have the structural properties it has there would be no need for a linear template molecule (DNA). Yet we present the molecule as most important and proteins get made, in the format of the Central Dogma of Molecular

Biology (Dounce, 1953; formally by Crick, 1958): DNA RNA  Protein rather

9 than the actual conceptual history previously stated. There is a need for investigation within the domain of gene expression education to determine the merits and drawbacks of both approaches.

The focus on the role of DNA as a template for the synthesis of proteins began in the 1950s and the search for a mechanism was formulated In the discourse of information including codes and language metaphors.

The problems faced by living things became out intellectual problems. The work of these individuals was resolving the ―how do they‖ problems of living things by asking questions about these problems, proffering solutions to the problems posed then providing empirical evidence to support a particular explanation. At the turn of the 20th century in the United States, biologists, chemists and physicists cooperated to solve the ‗mystery of life‘ by altering both methodical and ontological approaches of the past and taking a more problem solving approach and a more mechanistic and engineering view of life leading to one of the most successful research programs in the history of modern science (Kay, 1993). If we do not frame the study of heredity and development in this problem solving terms then we are, to paraphrase Marian

Ravenwood in ‗Indiana Jones‘, dragging our students all over the academic world collecting our little bits of terminological junk.‖

What characteristic must be changed to help students understand and use scientific metaphors?

10

The characteristic that must be changed is student understanding of gene expression metaphors and metaphorical statements including the function of DNA in the process of protein synthesis. Included in this understanding is determining how these metaphors help in thinking about gene expression and the role of DNA in the cell. Because protein synthesis is part of an interrelated system whose end result is to carry out cellular functions including metabolism – synthesis of biological molecules for use in the cell or for release from the cell and energy production especially the synthesis of ATP. Do these metaphors contribute to an understanding of these functions in both prokaryotic and eukaryotic cells? All types of eukaryotic cells (eg. animal eukaryotic cells versus fungal eukaryotic cells)? Do they help us understand the functioning of multicellular organisms? Secondly, how are metaphors that were developed and used by scientists for their model-building work to explain protein synthesis useful or helpful to those individuals not involved in this enterprise? Do the metaphors used when teaching and learning about DNA and gene expression need to be improved to aid comprehension of the concepts? Do currently used metaphors interfere with comprehension of gene expression and also to further solving problems involving DNA? Are the roles of DNA and genes conflated?

Which characteristic of scientific metaphors cannot be changed?

The characteristic that cannot be changed are the scientific metaphors themselves. Scientific metaphors used in the development of models of gene expression were just that: the basis of model development, research program direction including questions asked and hypotheses developed, and scientific terminology

11 related to these processes in an act of catachresis. They are, as Boyd (1993) refers to them, Theory-constitutive metaphors. As such, they cannot be abandoned completely regardless of learner comprehension of them.

Although student comprehension of metaphors is important and their lack of understanding of these metaphors may lead to lack of intelligibility and plausibility of certain aspects of gene expression, the central role metaphor played and continues to play in gene expression model development including terminology, precludes that we must determine the role metaphor plays in student comprehension of gene expression concepts.

Since metaphors are of conceptual importance not only for scientists who develop and use them but for the understanding of those concepts by everyone else, an understanding of the following must be considered when attempting to develop learning aids for gene expression:

1. to show that metaphors are used by scientists in their cognitive development of

solutions to problems of protein synthesis including its regulation. Models and

scientific terms have a metaphorical basis; metaphors are integral to model

development, not peripheral to it. They are a foundation for conceptual

understanding, not a bridge that once crossed is ever considered again.

2. Metaphors of these models and terms are comprehensible (‗Intelligible‘ in

conceptual change theory terminology) and an understanding of this fact both by

students and instructors can lead to an increased understanding of these models

and terms.

12

3. Once the models and terms and the underlying metaphors are brought to the

forefront, we are then in a position to be able to show how relations suggested by

the metaphor lead to hypotheses and further testing/refinement of the current

metaphorically-based model. Mary Hesse‘s concept of neutral analogy will play a

role here.

4. We are then in a position to use metaphors as vital to instruction of gene

expression:

a. To help as a scaffold to help in meaningful learning of gene expression

models and origins of terms- to find the signified and referent of a sign- by

explaining the metaphors or metaphors it was derived from. Ausubel‘s

concept of advance organizer fits how metaphors can be introduced and

used to structure further instruction on gene expression.

b. Show the metaphorical basis of scientific thought when scientists are

developing models, hypotheses and terms, that is, the uses of metaphor in

science (Hoffman, 1985). This is part of what it means to ‗think like a

scientist‘.

If this instruction in the uses of metaphor and the metaphorical basis of models and terms cannot be accomplished what other more general problem can be solved to reach the final result of student comprehension of gene expression and the role of

DNA in the cell? Certainly we may make a logical attempt. We first need to evaluate the aptness of currently-used metaphors to current students. This is different from an evaluation of the aptness of these same metaphors to scientists and instructors.

13

Bypass Approach to Scientific Metaphors: Develop new metaphors

We might develop new metaphors that highlight important features and relationships of DNA, gene expression and cellular function using concepts for comparison that students are familiar with and have no pre-conceived notions about their meaning because they have heard them prior to instruction.

Determine where currently-used metaphors cannot be extended to cover current findings. Additional new metaphors would highlight these ‗holes‘ in the currently- used models, holes that result because of what scientists have learned since the origin of the coding and information metaphors. These new entities and relationships could better be understood in terms of the new, apt metaphor or metaphors. These would include the role of RNAs, which in the original metaphors played a nominal if not subservient role to DNA and the role of protein products of genes in development and normal routine functioning of cells. These include: classes of RNA (snoRNAs, RNAi, piwi-RNAs), non-coding regions of DNA, splicing of eukaryotic primary mRNA transcripts, polygenic traits (multiple genes influence one trait), pleiotrophy (one gene influencing many traits), chromosome territories

(Mishteli, 2011), and regulation of expression. This reasoning is based on Hesse‘s concept of neutral analogy. What are the properties that we are not certain if they belong to the primary system/target or the secondary system/base or both?

14

Related to this point is to determine how current metaphors may interfere with student understanding of current findings? Can aspects of currently-used metaphor bases be used to understand current findings?

To take a different slant on the problem of metaphor comprehension, would a visual representation be useful in helping communicate the concepts of DNA and gene expression compared to words-only presentation or a presentation of visual plus words? According to Lakoff (1993, p. 32), ―the locus of metaphor is not in language, but in the way we conceptualize one mental domain in terms of another.‖ How can we best aid in this ―conceptualizing‖?

Bypass Approach: Number of Metaphors used and time to learn using them

An additional consideration of the metaphor problem is to consider the number of metaphors that are used in the communication and models of gene expression. At one end of the spectrum is to consider the sheer number of metaphors used to explain

DNA function. Would student understanding of DNA function and gene expression improve if the number of metaphors used during instruction decreased progressively and ultimately to zero, where we would use no metaphors to communicate gene expression concepts? This would mean that the current cadre of metaphors that includes DNA as code, blueprint, information, script, plan, language, book, master molecule, computer program would be pruned either progressively until we had a repertoire of a few apt metaphors or develop purely non-metaphorical explanations of gene expression.

15

The flip side of this numbers game is to increase the number of metaphors used to communicate gene expression. This would involve adding metaphors where there were holes in currently-used metaphors and/or adding metaphors that are not necessarily used by scientists in their models but helpful to students from a conceptual understanding viewpoint. This could occur either with or without pruning away those that have lost utility or are in some way redundant in meaning with more apt metaphors. This addition of new metaphors is a viable approach if at least two criteria are met:

1. if the new metaphor(s) allow mappings to new research findings, such as the roles of the various classes of RNA and regulation at the DNA

2. act as a general conceptual metaphor that accommodates all that is known about gene expression, if this is even possible as no metaphor can be expected to map all relations to a help us understand a target.

Now to consider the time aspect that metaphor use allows for comprehension/ meaningful learning of gene expression concepts. How could we minimize the time it takes to conceptually understand (intelligible and plausible) gene expression metaphors to time zero? It is here that part of the time problem becomes the difficulty in using metaphors based on whether they are self-generated versus other-generated.

According to Carroll & Mack (1999), self-generated metaphors are developed spontaneously and without apparent effort that is without additional processing demands. There are two recognized problems with self-generated metaphors (Gentner

& Gentner, 1980). The first is that they may be inappropriate for learning within a

16 domain. Secondly, no one metaphor will be sufficient to understand all the properties of an object.

Other-generated metaphors are as the name implies generated by someone other than the user to be used by the person who generated the metaphor plus others.

Understanding other-generated metaphors imposes a learning burden on the user that

―must tradeoff favorably with the savings in the learning burden derived from employing the metaphor subsequently.‖ (Carroll & Mack, 1999, p. 396) Part of the problem is that hearers may not recognize the metaphor as being a metaphor (see) or they may recognize that a metaphor is being used but may not know how to do so

(exploit) the connections spontaneously or consider the possibility that the metaphor might be useful to understand the concepts.

In deciding whether to use other-generated theory-constitutive metaphors or student-generated metaphors, we must consider the pragmatics of the learning situation: ―who will use the metaphor (the goals and needs of the learner) and for what ends was it designed‖ (Carroll & Mack, 1999, p. 397). This relates to the context of discovery versus the context of use.

At the other end of the time spectrum is increasing the time it takes to learn a metaphor. To consider increasing the time it takes to learn a metaphor would not be practical. It is not an efficient way to learn (devote more cognitive resources without return) and we would encounter a motivation problem.

Which problem to solve: Explain currently-used metaphors or develop new ones?

17

When providing instruction in the role of DNA in the cell and gene expression, current educational practice presents scientific terms and models (explanations of phenomena) as facts bereft of the creative nature of both; that is their metaphorical basis and sociohistorical past. We may present the ‗who did what and why‘ but not the wrong paths taken, conceptual framework the researcher was working from, who they were working with, who funded the research and why it was funded, or whose ideas held more intellectual sway for the community than others, the ―Matthew effect.‖ (Merton in Brown, 2003) This is no doubt messy, but closer to the way gene expression models were developed.

Without the metaphorical basis of the framework of gene expression, we are asking students to learn scientific concepts in this domain as facts and an interrelation of facts (eg. ‗DNA makes RNA during transcription‘ or ‗DNA codes for proteins‘) without the background for the interpretation and meaning of the facts. The metaphorical nature of models and terms is not given attention in introductory college biology classrooms or textbooks.

Although conceptual change and constructivism guide science instruction as plausible explanations for how people learn science, the metaphorical basis of gene expression and DNA function have not been incorporated into these frameworks.

Inquiry as a method of instruction is given a high priority, but questions guiding inquiry do not necessarily come from an exploration of neutral analogy.

Understanding scientific metaphors as part of scientific thinking

18

Brown (2003) has written about the metaphorical basis of scientific knowledge in physics, chemistry and biology and discusses the role of metaphor in science education and the observation of a lack of establishing conceptual understanding. He suggests how conceptual metaphor can lead to good science teaching practice in a generalized manner that I proffer does not go far enough in integrating understanding of metaphor into that practice. Considering the keystone position he gives metaphor, this was disappointing. But it is a start in recognizing that metaphor can guide instruction.

Within this approach is to follow the reasoning of Hoffman (1983, p. 333) who noted, ―Progress on a theoretical level often consists of deliberately exploring the implications of metaphors to expose assumptions or weaknesses and to suggest alternatives.‖ This is in line with how I envision the role of metaphor in gene expression instruction.

Develop new metaphors

Alternatively, the use of new metaphors by instructors is used to better illustrate a concept, as a method to improve comprehension but does not highlight metaphor/analogy as the basis of much of scientific thinking (Petrie & Oshlag, 1993).

From a conceptual change standpoint Posner et al. (Posner et al. 1982, Strike &

Posner, 1992) stress the importance of metaphor and analogy to ―lend initial meaning and intelligibility to new concepts‖ (Posner et al., 1982, p. 214).

Initial meaning is a good objective, but we must begin to view a good metaphor as setting the stage for higher level of conceptual change such as those

19 elaborated by Thagard (1990). Scientific metaphors, especially theory-constitutive metaphors, need to be viewed as frameworks and not as bridges. The view of metaphor as a framework envisions building a concept/model upon the metaphorical framework and as such the metaphorical basis of the model does not go away and can be detected no matter the complexity of the model build from the framework (Brown,

2003). This is opposed to the bridge conception of metaphor which views the metaphor as a heuristic device, bridging the individual to a new meaning, and then is of no further utility (Brown, 2003).

Petrie and Oshlag (1993) suggest the four step process of anomaly, metaphor, activity, and correction of the activity as a process for acquiring radically-new knowledge and can be viewed as a pragmatic process of conceptual change

(dissatisfaction, intelligible, plausible, fruitful). The metaphor development here is guided and developed by the teacher based on student understanding. They suggest that later during instruction understanding of concepts may be assessed by student- generated metaphors. Student generated metaphors require knowledge of the target domain.

Which problem to pursue?

In attempting to make a decision here, it is useful to consider an extremely important part of the creative process: formulating the Ideal Final Result (IFR;

Altshuller, 2007). Then one works from the Ideal state to determine the element of the problem that can be changed and how that change will lead to the IFR and how that element relates to other elements that are involved in the problem.

20

For the currently-used metaphors, the IFR is stated as follows: The base of a metaphor allows the hearer to increase the intelligibility and plausibility of the function of DNA by itself providing a familiar domain from which to make connections to the unfamiliar target domain (DNA) when students are learning about the target domain (DNA) from teachers, textbooks, and supplemental materials (either visual or written) being told a metaphor is being used and being allowed to develop base concepts before interpretation occurs.

At this point in the development of a method of instruction for gene expression and DNA function, the original problem I posed, working with the existing metaphors with an eye towards pursuing the by-pass where older metaphors are deficient would seem like a logical place to begin. We must also keep this fact in mind about theory-constitutive/scientific metaphors: as opposed to literary metaphors where individuals are familiar with both base and target and the metaphor helps additional relations to come to light without explication from the author of the metaphor, scientific metaphors require explication. Students are learning about the target and as such may have little or no conceptual understanding of the target.

To begin to solve this problem, I suggest starting with determining, what in the hermeneutic tradition is known as an incongruity, student understanding of currently- used DNA metaphors including understanding of the base concepts of these metaphors and if they think the metaphors are or have been helpful to help them understand the function of DNA, that is, the aptness of the metaphors. Then, based on understanding and their use of these metaphors, their bases and aptness from the student point of

21 view, determine what interventions in metaphor interpretation may be needed so that student use of the metaphor and instructor/science use of the metaphor are in line. To achieve what Gadamer has called a fusing of the horizon to resolve incongruities between horizons of a text and the horizon of the interpreter of that text that will lead to an ‗event of understanding‘. In our case the text are the metaphorical expressions and theory-constitutive metaphors.

Instead of scrapping the established scientific metaphors, we can do what

Altshuller (2007) calls ‗compensation‘, that is, to compensate for the ‗evils‘ of a technology/process in order to extract something useful from it instead of eliminating it. The question becomes, how can we use established metaphors in order to understand gene expression in the present since models and terminology are based on the original metaphors? This is also important as the limitations of older metaphors and heuristics based on the centrality of DNA to cellular structure and function are recognized as impediments to conceptual understanding of cells and mutlicellular organisms (Biro, 2004; Shapiro, 2009) in light of findings about the role of chromatin structure, the location of chromosomes within a eukaryotic cell‘s nucleus, epigenetics or the role of the interaction between genes and the environment (Van Speybroeck,

2000), the role of various classes of Ribonucleic Acids (RNAs) from the last decades of the 20th century and into the 21st century.

What metaphorical frameworks will be useful in the future? Shapiro (2009, p.

23) argues that ―‖any successful 21st-century description of biological functions will include control models that incorporate cellular decisions based on symbolic

22 representation‖, that DNA cannot be central in this reconceptualization, and further suggests two basic ideas based on empirical knowledge of cellular information processing upon which future conceptualizations can be constructed: first, ―sensing, computation, and decision-making are central features of cellular functions; and secondly, the cell is an active agent utilizing and modifying the information stored in its genome.‖ The conceptualization of DNA as a master molecule, boss, sole possessor of information, in complete control of everything that happens within and between cells has no part in these proposed ―ideas.‖ The unidirectional ‗flow of information‘, plan, blueprint, recipe and script metaphorical conceptualizations of

DNA will no longer suffice for continued conceptual development of the role of DNA in the cell; they are a hindrance in absolutist, deterministic interpretations. Seen as playing a role in construction (plan, blueprint) or baking (recipe) or performing a play

(script), the proposals of Shapiro can be used to re-direct metaphorical use of these bases so that a more accurate explanation of the role of DNA in a much larger context of cell function can be developed. To use the script base: we need to recast DNA in a different role. At the heart of his argument is information, computing and decision- making; all metaphorical in nature.

How could this be practically realized? A potential solution is derived from

Carroll & Mack‘s (1999) attention to pragmatics, who will use it and the ends for which it was designed, conceptual change theory‘s suggestion to use metaphor and analogy to improve intelligibility of a concept, Gadamer‘s fusing of the horizons, and

Ausubel‘s idea of the advance organizer. Using this conceptual framework plus, when

23 the IFR is analyzed further, the element that is easiest, from my perspective, to change to improve student intelligibility and plausibility of gene expression metaphors relates to the base of those metaphors.

When we look at the bases for the commonly used theoretically-constitutive metaphors of DNA and gene expression, many are over a half century old and may not be in many people‘s active, working pool of concepts. In the classroom, students may be unfamiliar or inadequately familiar with the base concepts for the metaphor for them to useful for an adequate comparison to be made to the target. The goal should be to use the metaphors as they were designed: for thinking about the problem of how proteins are synthesized and what role DNA plays in this process rather than rote stating of what the relations between base and target are. This is not in the spirit of the utility of metaphor. Scientific metaphors are for thinking; for seeing relations, to see positive and negative analogy and investigate neutral analogy (Hesse): the process of model building and model testing and catachresis that result from this endeavor.

Knowledge of the base concepts would help achieve this goal. This is, after all, an aspect of ‗thinking like a scientist.‘

A component of adequate base utilization is to recognize that a metaphor is being employed. Boyd (2003) reminds us that scientific metaphors invite comparison. Sometimes the invitation is not obvious. Informed by work of Gentner we need to explicitly state that a metaphor is being used and we should look for relationships.

24

How can experience with base concepts be developed? Library, including internet, research would allow students to find information about base concepts.

Practical experience with the base concepts that utilize and highlight the concepts in positive analogy with the target will allow those concepts to available when target concepts are presented.

Scale of Future Applications

When considering the implications of determining how to use scientific metaphors to aid understanding of the role of DNA in the cell, we must extend beyond the college classroom for although that will be the focus of this project, individuals who do not study or use gene expression concepts in their daily work include the super majority of individuals in the population. In addition to potentially affecting all of these individuals, we consider how gene expression and DNA function are communicated to these individuals. When these metaphors are used, and not explained as is common practice, can the promulgator of the material expect comprehension as s/he intended when s/he spoke or wrote using the metaphor? Gene expression concepts and their use continue to expand as scientists apply these concepts to solving a myriad of problems facing humans. Non-gene scientist individuals learn of breakthroughs using these concepts through magazines, internet sites, popular non- fiction books, TV documentaries and visual representations that serve to support conversation about a DNA/gene-based topic. For students, in addition to all of these sources are textbooks and support sites for textbooks.

25

The scope of the need for a conceptual understanding of DNA function is far- reaching to all aspects of human communication. A conceptual understanding of DNA function is also imperative for an individual‘s understanding of gene-based medical therapies, disease states, biotechnology, genetic engineering, the relationship of living things to the environment (living and non-living components), evolution and the implications of evolution such as antibiotic resistant bacteria. If we expect our citizens to understand these applications and to incorporate the continuing expansion of understanding of the minutia of how gene expression occurs by scientists, a firm conceptual understanding of the models on which the models of gene expression, that is their metaphorical basis would seem to be a place to investigate. Is an understanding of theory-constitutive metaphors important to conceptual understanding of DNA function and gene expression?

26

CHAPTER 2: REVIEW OF THE LITERATURE

Literature Review Some Education Theory: Meaningful Learning and Conceptual Change

As the spider spins its threads, every subject spins his relations to certain characters of the things around him, and weaves them into a firm web which carries his existence. (J. von Vexküll, 1934)

Students do not come to the classroom as blank slates. They have acquired information on many concepts to explain the world around them; some of them are in line with currently accepted scientific explanations, some are not. The ones that are not ‗in line‘ are referred to by science educators and researchers as misconceptions, misunderstandings, naïve conceptions, or alternative conceptions. What is an effective approach to help students learn canonical science concepts in light of the recognition that misconceptions exist and influence learning? The learning model called conceptual change provides a body of work which attempts to understand how science is learned and how it can be effectively taught.

Conceptual change learning theories-that is, the seminal work of Posner,

Strike, Hewson, and Gertzog (1982) and the subsequent work to add to the understanding of conceptual change-attempt to address what learning is and what it depends on. That is, the conditions that are necessary for conceptual change to occur, the factors (academic and psychological) that come into play when students are 27 confronted with current scientific explanations of concepts that may or may not agree with their currently held concepts (their conceptual ecology) which may affect the ability of the student to engage in the conceptual change process, how these factors can be addressed in order to facilitate conceptual change, teaching strategies for conceptual change, and duration and transfer of the newly acquired concept. What is generally agreed upon within this tradition is that learning science was seen as conceptual change rather than the accumulation of bits of information (Asoko et. al.,

1991).

Ponser et. al (1982) proposed a theory for conceptual change and Strike &

Posner (1992) revised the original theory that describes how to structure learning to allow for accommodation of a concept in a learning situation by requiring instructors to do two main things: focus on a learner‘s conceptual ecology and determine how that ecology structures learning. They explained four conditions necessary for this accommodation to occur, though not necessarily in the order presented and not to be interpreted as a ―magic ritual‖ that guarantees success in all situations (Strike &

Posner, 1992). The four conditions they presented are: 1. Dissatisfaction, 2.

Intelligible, 3. Plausible, and 4. Fruitful.

Intelligibility involves, at the most superficial level, ―an understanding of the component terms and symbols used and the syntax of the mode of representation‖

(Posner et. al, 1982, p, 216). But intelligibility involves more than this. It also requires ―constructing or identifying a coherent representation of what a passage or theory is saying‖ with representations in the form of propositions, images, and

28 networks of interrelated propositions and/or images (p. 216). The representation of the information determines one‘s future ability to use the new ideas. If the student is able to see that the new concept makes sense and might explain his/her past experiences, then s/he will be likely to explore it further. The student need not necessarily believe it.

Metaphors and analogies were suggested as important to ―lend initial meaning and intelligibility to new concepts‖ (Posner et. al, 1982, p.214) with the caveat that previously learned misleading metaphors in a student‘s conceptual ecology -Toulmin‘s

(1972) term for a person‘s central concepts that are linked to prior experience, images and models that are available for making new concepts intelligible- contribute to misconceptions. Strike & Posner (1992) have suggested replacing the misleading metaphor with a sounder one as a way of remediation of misconceptions with a metaphorical basis.

In addition to determining the metaphors students use for a concept in an attempt to get to the root of misconceptions, I would further suggest determining student understanding of gene expression and DNA function metaphors that the teacher will use as part of instruction, including those that may be used as advance organizers (Ausubel). Both of these approaches, Strike & Posner and mine, is the logic behind Studies 1, 2, and 3 of this research and is a directly related to their suggestion for the use of conceptual change theory: ―One needs to discover the features of a student‘s conceptual ecology, find the trouble point and introduce into the student‘s experience something that is appropriate‖ (p. 159). They further suggest:

29

―For the immature student, a strategy that is attentive to the student‘s collection of metaphors‖ – and I suggest interpretation of scientific metaphors- ―may be more important than a frontal assault on the misconception‖ (p. 159). I will be testing this suggestion in Study 3.

Plausibility is when the new concept can be seen as useful to solving problems.

This results from the new concept being consistent with current concepts, experiences, knowledge, metaphysical beliefs and epistemological commitments.

Paul Thagard (1990, pp. 267-269) has worked from the premise that conceptual change is more than a simple belief revision and has described revision of concepts from the very modest to the most radical. Although Posner and colleagues‘ was viewed as radical conceptual change, it did not include exactly what occurred to the conceptual structuring of concepts, that is, how one could classify conceptual change that was occurring. Thagard‘s analysis attempts this and is based on the core concept that conceptual organization is hierarchical in which ―kind and part-whole hierarchies serve to structure most of our conceptual system, providing the backbones off of which other conceptual relations hang―(p. 264). The 8 degrees, from the routine to the most serious are:

1. Adding a new instance which involves a change to the structure of a concept.

2. Adding a new weak rule.

3. Adding a new strong role that plays a frequent role in problem-solving and explanation.

4. Adding a new part-whole relation.

30

5. Adding new kind relationships. Organizes concepts in tree-like hierarchies. This is similar to that proposed by Novak (1982) in creating concept mapping.

6. Adding a new concept.

7. Reorganizing hierarchies by branch jumping, that is, shifting a concept from one branch of a hierarchical tree to another. Such branch jumping is common in scientific revolutions (Kuhnian sense).

8. Tree switching, that is, changing the organizing principle of a hierarchical tree.

Changes 1 -3 can be interpreted as straightforward belief revision. However, changes

4-8 are not belief revision by an alteration of conceptual structure. Branch jumping and tree-switching cannot be made on a piecemeal basis and involve the most severe form of conceptual change.

Using Thagard‘s analysis, metaphors are part of a categorization process; categorization, being taken in the sense of categories is used to classify and make inferences meaning reasoning from and about those classes (Diesendruck, 2003; Keil,

1989, p. 103).

I must mention a position that science educators, based on empirical evidence, holds: that misconceptions are durable, very difficult to alter and infers with the formation of scientific conceptions. The role of misconceptions in concept formation is an interesting one. It is my observation from reading the papers from molecular biology in the first seven decades of the 20th century that the idea that we hold that the formation of a ‗valid‘ conception comes from a revision of the history concerning

‗genes‘ , chromosomes, continuity of life (heredity), development and the search for a

31 physical basis for these physical realities. I will use the concept of gene as an example. We must remember that ―gene‖ was a placeholder term for a correspondence between the presence of a physical entity within cells, the identity of which has been altered over time because the term gene was never a signifier of a concrete entity; there was a search for what the gene was. So T. H. Morgan could proceed with his research program using Drosophila without knowing or caring what the physical gene was. Beadle could state the one gene-one enzyme hypothesis with the conception that the gene was a nucleoprotein, not nucleic acid. It is only through a backward rewriting of discovery that every time the word gene is mentioned, we interpret it as the DNA gene. However, this did not happen until the early 1960s and then not all at once. But Morgan‘s and Beadle‘s contributions played a key role in our understanding of heredity and the role of chromosomes and ―genes‖.

Kay (1993) argues that it is ―[T]he introduction of sharp discontinuities between ―wrong ideas‖ and ―correct theories‖ and the emphasis on crucial experiments as necessary and sufficient conditions for scientific success have tended to obscure the subtle and gradual contributions that marked Beadle‘s intellectual program‖ (p. 210). And I would add Morgan and others who worked on this problem.

This account gives an inaccurate view of what science is and how conceptual change in science actually occurs. We, as science educators, should pay attention to the actual reinterpretation and revised explanations of these early investigators based on the concepts they were using. We would have a more accurate picture of conceptual change and one not based on the revisionist reinterpretation of this early work. The

32 alternative is a fictional account that is bereft of an understanding of how conceptual change actually occurred within molecular biology; it is of no use to help us understand how to present concepts to non-molecular biologists.

What I also find interesting about the ability to do a revisionist rewriting of

―gene‖ is this: if there was not an underlying consistent conceptual framework that was at the heart of all of this work, we could never go back and change the physical object that was the protein gene, then the nucleoprotein gene finally to the nucleic acid gene concept. It is the underlying conceptual framework, and I might add metaphorically-based- that we should focus on. It seems that through the work in molecular biology it is this that was consistent.

In light of this discussion I must ask: How do misconceptions really affect concept development? Misconceptions are really only mis-conceptions when viewed in hindsight.

Problems with Determining Conceptual Development within Science

An example from the history of genetics will help to make my next point. The history of the molecular basis of heredity is traced back to Gregor Mendel and his quantitative experiments with garden peas to determine the laws of inheritance of traits by offspring from parents. Like many scientists who contributed to our conceptual understanding of heredity, Mendel had training in physics and mathematics, including statistics. From that tradition he knew that to truly understand a physical phenomenon one needed to determine the underlying laws governing the process; this involved experimentation and mathematical analysis of the data.

33

Something physical that was responsible for a phenomenon had to be tracked and the also one had to keep track of the number of the physical thing over generations. The problem was, although the physical traits of pea plants could be followed, the physical

‗stuff‘ responsible for these traits was not known. So what Mendel did was to quantify the inheritance of traits and infer a physical ‗stuff‘ which he called ‗factors‘ was responsible for each different trait, such as purple flowers of white flowers. He had no conception of what the physical stuff was and could not since the science of the day was not at this level of understanding.

In the early 1900s when Mendel‘s original papers were ‗discovered‘ by

Bateson, de Vries, Correns and Tschermak, these workers but Correns in particular, read more in to Mendel‘s work than what was originally there. ―With their understanding of cell structure and function ―read more into Mendel‘s account than was actually there‖ (Mayr, 1982, p. 725). With a greater understanding of the molecular basis of heredity, each generation re-writes the importance of Mendel‘s work but unfortunately we lose perspective on the actual conceptual changes that occurred at each stage of development of understanding heredity.

Another example is with Beadle‘s ‗one gene-one enzyme‘ hypothesis. When

Beadle and Tatum performed their Neurospora nutrition experiments, the view of the gene held by them, and all molecular biologists was that the gene was a nucleoprotein.

However, after the 1950s and 1960s when the structure of DNA was published and the mechanism of protein synthesis was determined, DNA became the gene, and in the

‗one gene-one enzyme‘ hypothesis, the gene became DNA.

34

For science educators the revised view of the role of DNA and ‗one gene-one enzyme‘ does little to help us understand the nature of conceptual change and the role of misconceptions in science concept learning. Because when all is said and done,

Beadle had the wrong conception of the molecular basis of what the gene was, yet was able to determine a truism that survives to this day and explains a great many gene- protein relationships. How did this happen? Obviously we must think about the conceptual relationship between gene and the product of the gene. From Beadle we learn that a vague notion of gene as a physical template for a protein will get you a fairly accurate understanding of the role of genes in a cell. And just because s student indicates that there is a relationship between a specific gene and a specific protein we cannot assume that understanding extends to the molecular basis of gene as DNA.

This additional conceptual understanding does not add to an overall understanding of the role genes play as templates for a protein. Where the lack of understanding of gene as DNA segment becomes evident is when we ask how DNA is able to ‗specify‘ a particular protein. But his briefest of examples hopefully begins to get us to think about the role of misconceptions in conceptual understanding and also the need to use the ‗actual‘ history of molecular biology to provide insights into what may be a productive sequence for instruction. And from a nature of science perspective, this messiness is the way science proceeds. Not as represented by what I will call ‗the press release‘ version of science, the version that makes science look exceptionally logical, straightforward and a bit of awe at its efficiency. Science proceeds in fits and starts and what we would look back and classify as misconceptions were not a

35 hindrance to components of conceptual understanding in the field of molecular biology. With only the press release version of science we have no true understating of how scientific conceptual development proceeds. And consequently we miss an opportunity to help students overcome many of the same conceptual boundaries scientists encountered. We must reinvent the wheel. There is no need to do this. Let the true history of biology be a guide.

Epistemological Positions: Constructivism and Cognitivism

I accept conceptual change as a model with which to frame teaching and learning of science. But what is conceptual change changing? That is, what epistemic commitment does one have that is the goal of change? Are concepts data, information or knowledge? Is there an established reality that exists and learning is the creation of increasingly more accurate models of the object and the world as the cognitivist position holds (Georg van Krogh, 1998) or is it that it cannot be known ―as a set of truths because of the fallibility of the human experience‖ (von Glasserfeld, 1989) so that objectivity is not possible and all knowledge is socially negotiated and individual learners knowledge is a result of interaction with objects interpreted within the framework of extant knowledge as the constructivist would hold (Asoko eta al., 1991).

From the cognitivist stance, knowledge is explicit, is able to be encoded, stored and then transmitted to others. From the constructivist stance, knowledge cannot be transmitted directly from one person to another but is actively constructed by the learner (Asoko et al., 1991; von Glasserfeld, 1989).

36

A break is necessary to more clearly define a few terms so that I may make my epistemological stance clear. I have found the use of the terms ‗knowledge‘ and

‗information‘ in the education literature to be rather vague. However, when trying to determine what it is exactly that we present to students during instruction, how this should be presented and then whether we expect students to either receive or construct was not very clear. But it needs to be. We engage in communication, but the particulars of this communication are vague. If we are not clear about the particulars of communication, how can we logically proceed to improve teaching and learning?

So, a brief diversion to the literature of those who have clearly articulated what knowledge is: information theorists and knowledge/information management. Yes, we can learn from business.

According to information theory and from this knowledge/information management, information is data that has been given structure and knowledge is information within a particular context that has been given meaning through the act of interpretation that organizes the data, giving it structure or context and as a result, meaning (Devlin, 1999; Glazer, 1998). (Go back to the sand castle metaphor.)

The knower, or learner in the case of education, is integral to the process of knowledge creation; a leaner in a particular context. According to these theories, what is to be measured is the knower not the known (knowledge) and this is done by measuring the ‗meaning‘ of a piece of information to the knower (Glazer, 1998). The rating of the aptness and utility of gene expression metaphors is an attempt to

37 determine the meaning of the information to the students; an attempt to measure the knower.

Knowledge Management has also determined which aspects of information are attended to by knowers; these 6 are:

1. Context – knowers use contextual properties of data to place value on information

2. Framing/Problem Representation – a particularly interesting aspect of framing

and representation is within preference judgments: individuals tend to weight the

negative properties of stimuli more heavily than positive ones.

3. Configural Effects/Gestalts- this aspect deals with pattern recognition and

analogical processing. Included in this aspect is the determination that the

presence or absence of features including how they can be used for prediction of

the other is used to identify configurations. Studies of categorization and

category formation study these phenomena. Analogue methods are sensory and

are important for ‗real-time‘ performance. They also rely on ―the existence of

‗targets‘ to match incoming data‖; this is the basis of pattern recognition. And

although a hallmark of experts, novices will detect patterns in data that aren‘t

there, called ‗illusory correlations‘ (p. 180).

4. Fuzzy Aspects of Data- this aspect is related to focusing on the pattern and not the

details. Membership in categories is a matter of degrees rather than a yes/no

binary opposition.

38

5. Dynamics of Temporal Context- the meaning of data will have different meaning

on different occasions. Knowers use real-time feedback to determine if

information is relevant, and if so, change their behavior.

6. Network Externalities – the value of information varies depending on who else

knows it (p. 181). Knowledge access is important, not ownership or control.

The configural effects/gestalt aspect is informative for metaphor use that is part of instruction. Metaphor theorists have determined that it is the overall relations rather than specific one-to-one mappings that individuals use to make sense of metaphors

(eg. Lakoff & Johnson, 1980a). Brown (2003) notes the gestalt aspect of metaphor use in science. Pattern recognition is based on ‗targets‘, familiar scenarios to which the incoming data can be matched is the basis of metaphor utilization. The target of the metaphor (not the same as the ‗target‘ in memory) must be matched to existing familiar scenarios, that is not there or are not structures enough for pattern recognition to occur, the learner will not understand the metaphor and consequently not alter the conceptual framework to which the target is a part. It also suggests that students will see the overall pattern as the basis for the comparison and not necessarily the fine details of one-to-one mappings. If the metaphor is employed by the instructor to the overall pattern, no further explication of one-to-one relationships need necessarily be made. However, if the metaphor is the source of model building and testing, the teacher must know that it is highly unlikely that the student will engage in this type of analysis on his/her own; metaphor theory also supports this conclusion (Gentner).

The purpose of Study 1, 2, and 3 includes the understanding that students have of

39

DNA function metaphors. Analysis of responses will determine if the understanding

is that of an overall pattern, one-to-one correspondences or a combination of both.

What is the epistemic stance of this researcher? I take the position of the realist, the stance held by both the constructivist and the cognitivist: there is a real world comprised of objects and association between those patterns. Data can be gathered about those objects and associations in the form of empirical observations; we have access to this real world of objects through our senses and the instruments that we use to extend our senses. However, what we delineate to study, how we choose to study those delineations and then how we interpret and give meaning to those objects of study and the associations within and between those objects are idiosyncratic due to the past experiences, including culture, of each individual.

As we will see, research within life sciences was informed by those individuals who did the research. Their ontological and epistemological commitments guided choice of object of study, questions asked, methods chosen and final interpretations.

One would be remiss not to acknowledge this fact of human knowledge generation.

DNA is DNA, but its function is a matter for negotiation, for negotiated social construction. This is the information of science. This is what we present to students.

DNA is not a master molecule. We, through social negotiation, have made it that. It could easily function in some other manner.

Scientific explanation may have reached such a fine degree of detail that we lose sight of the worldviews we have and continue to imbue in the molecule. We can present the ‗what is‘ definitions of the inert acidic biopolymeric molecule within the

40 nucleus of eukaryotic cells that consists of four different nucleotides, and that the order has a role in the amino acid sequence of a particular protein but when we explain the ‗how‘ this occurs, we enter more deeply into individual construction of knowledge for here, more than any other aspect of scientific explanation we hit the realm of the use of metaphor, metaphors that take advantage of objects and associations that we have previously formed. These vary from individual to individual, so interpretation of metaphor will necessarily vary from individual to individual (Blasko, 1999). It is how much and what effect this difference has on understanding of scientific explanation of

DNA function that needs to be explored. So no I have not put myself into an epistemiological box; that would be limiting. I look at the content of the boxes and see what is useful to understand a problem.

Metaphor

Although researchers from different domains including psychology, linguistics, and philosophy have contributed to developing theories of metaphor construction and use, I will focus on those researchers who have influenced thought about the use of metaphor by scientists; these individuals have not specifically theorized about metaphor use in scientific thinking or science metaphors.

Max Black (1962, 1993) developed many ideas about metaphor that added to our understanding of the nature of metaphor: Successful metaphors are not riddles but are not interpretable based on the meaning of the words alone. So not any two nouns can be placed together to create meaning. The concept of metaphor theme as an abstraction of the metaphorical statement which can be used, adapted, and modified by

41 others. The idea of metaphors as ‗cognitive instruments‘ that are ―indispensable for perceiving connections that, once perceived, are then truly present‖ (1993, p. 37, italics original). They help us to see aspects of reality that we would not otherwise have access to. And that metaphor is one, among many other, cognitive devices for

―showing how things are‖, to create perspectives and we can therefore talk about their correctness or incorrectness but never about their truth or falsity.

Black defines several categories of metaphors. Dead metaphors ―are not metaphors at all, but merely an expression that no longer has a pregnant metaphorical use‖ (1993, p. 25). The dead metaphor may be ‗resuscitated‘ where it is possible to restore the metaphorical utility of the dead metaphor to make it ‗active‘ (1993, p. 25).

Two aspects of metaphor are emphasis and resonance. A metaphor is emphatic ―to the degree that its producer will allow no variation upon or substitute for the words used‖ especially for the ―focus‖ which is the ―salient word or expression‖ that gives the literal expression its ―metaphorical force‖ (1993, p. 26). The importance of emphatic metaphors is their ―unstated implications‖. Resonant metaphors allow for implications to be elaborated upon by the receiver. These are not mutually exclusive. In fact,

Black calls metaphors that are highly emphatic and resonant as ‗strong metaphors‘

(1993, p. 26).

Black (1962, 1993) developed the Interactive View of Metaphor and because it is the source for theoretical development of views of metaphor use in science especially by Mary Hesse and Richard Boyd, I will state Black‘s preferred summary of the interaction view (1993, pp. 27-28).

42

1. A metaphorical statement has two distinct subjects to be identified as the

―primary‖ subject and the ―secondary‖ one.

2. The secondary subject is to be regarded as a system rather than an individual thing.

3. The metaphorical utterance works by ―projecting upon‖ the primary subject a set of ―associated implications,‖ comprised in the implicative complex, that are predicable of the secondary subject.

4. The maker of a metaphorical statement selects, emphasizes, suppresses, and organizes features of the primary subject by applying to it statements isomorphic with members of the secondary subject‘s implicative complex.

5. In the context of a particular metaphorical statement, the two subjects interact in the following way: (a) the presence of the primary subject incites the hearer to select some of the secondary subject‘s properties; and (b) invites him to construct a parallel implication-complex that can fit the primary subject; and (c) reciprocally induces parallel changes in the secondary subject.

Also influential in the thinking of the use of metaphor in science have been the works of George Lakoff and Mark Johnson (1980 a, b, 1993). They have argued that human thought processes are largely metaphorical that our linguistic expressions are reflections of these metaphors and have sought to classify linguistic expressions in to metaphorical categories such as: orientational metaphors that make use of human spatial orientation such as good and more is up; ontological metaphors that make use of our experiences with physical objects onto objects or events such as we view events

43 and actions as objects, activities as substances and states as containers- these give us metaphorical models; and conceptual metaphors with subcategories within these.DNA

IS THE CODE OF LIFE is an ontological metaphor and GENES ARE IN DNA is a container metaphor. PROMOTERS ARE UPSTREAM OF A GENE is an orientational metaphor that treats a linear biological molecule like a stream or river.

An additional useful observation Lakoff & Johnson have made deals with the use of multiple metaphors for a concepts and the resulting consistency or coherence of those metaphors. They have found that different ―metaphorical structurings of a concept serve different purposes by highlighting different aspects of the concept‖, if there is an overlapping of purposes, there is a coherence, and that ―complete consistency across metaphors is rare; coherence, on the other hand, is typical‖ (1980a, p. 96). The collection of related ideas taken as a whole to understand an experience is known as an experiential gestalt or image schema (Lakoff & Johnson, 1980)

These ideas are important in our exploration of gene expression and DNA function metaphors because there are many metaphorical expressions and ontological and conceptual metaphors used by scientists and non-scientists for these processes.

We should look for coherence across these metaphors as this would add to intelligibility of the gene expression concepts for students. Non-coherent metaphors would add to confusion.

A note on terminology of the components of a metaphor or metaphorical expression and how they will be written for this work is important since many terms

44 referring to the same components are used depending on the field studying the metaphors.

Metaphor refers to a conceptual metaphor and is usually written in uppercase small capitals, such as LIFE IS A JOURNEY, DNA IS A LANGUAGE, and DNA IS A CODE.

Metaphorical expressions are ―individual linguistic expressions that are sanctioned by mapping‖ of the metaphor. These expressions are written in italics and examples include dead-end street, nucleotide alphabet and genetic code or are sentences such as

‗life is a journey‘ and ‗DNA is the genetic code‘; the single speech marks indicating also words or phrases that we wish to discuss further. These expressions are understood via a set of correspondences referred to by a metaphor. (Chanteris-Black,

2004, p. xv; Lakoff, 1993, p. 209)

Metaphors take the form ‗A is B‘ where ‗A‘, that which is less known or more abstract, is called the target or tenor. ‗B‘ is more well-known to the author or listener and is called the base or vehicle. I will refer to ‗A‘ as the target and ‗B‘ the base of the metaphor. For example, for the metaphor DNA IS A LANGUAGE DNA is the target and language is the base. We wish to understand less-well known concept of DNA in terms of the more familiar concept of language.

Metaphor Use in Science

When a science approaches the frontiers of its knowledge, it seeks refuge in allegory or in analogy. Erwin Charaff, 1958

In practice there is no such thing as a theory, there is only theorizing. Hoffman, 1985, p. 366

45

Hoffman (1985, p. 331) has suggested that scientific metaphors appear in a variety of forms:

1. Basic ―root‖ metaphors or metaphor themes. These form the basis of entire theories or points of view. Included from molecular biology would be the information metaphor and code metaphor.

2. Specific metaphorical hypotheses or principles.

3. Metaphor-based images or mental models.

4. Metaphor-based substantive models which generate functional or causal relationships.

5. Metaphor-based abstract or mathematical ―models‖.

6. Metaphor-based analogies in which specific relations are fleshed out. Mary

Hesse(1966) and Gentner and Jeziorski (1993) further develop this form.

What functions do scientific metaphors have? Hoffman (1985, pp. 332-333) has suggested the following:

1. To suggest: hypotheses, hypothetical concepts, entities, relations, events, and

observational terms.

2. To predict and describe new phenomena or cause-effect relations.

3. To give meaning to new theoretical concepts for unobservable or unobserved

events.

4. To suggest new laws or principles.

5. To suggest new models or refinement of old ones.

6. To suggest new research methods or ideas for experiments of hypothesis tests.

46

7. To suggest choice between alternative hypotheses or theories, often a choice

between more and less fruitful metaphors.

8. To suggest new models for analyzing data.

9. To contrast theories or theoretical assumptions.

10. To provide scientific explanations in the form of metaphoric redescriptions.

11. To suggest alterations or refinements in a theory.

12. To suggest new theories, theoretical systems or worldviews.

Brown (2003) performs a very nice analysis of the categories of metaphor used in the physical and life sciences. He uses Lakoff & Johnson‘s analysis of metaphor as a basis for his analysis. He concludes that the following are categories of metaphor used to explain various aspects of entities and processes in the physical world and form part of science‘s models and terminology.

1. Change is expressed as a change from one location (state) to another with changes seen as proceeding in steps which he terms the ‗location metaphor‘. In addition to this, ―impediments to change as seen as ‗barriers‘― to be overcome and ―systems that do not change are viewed as isolated from factors that could produce change‖ (p. 45).

Expressions will use words that are related to how this change in location occurs: slow, fast, multistep, rate, and speed attend location metaphors.

2. Causation ―is an action taken to achieve a desired purpose‖ and ―the cause of the action is why the action will achieve the intended purpose. In reasoning about change, people often resort to teleology, the idea that there are purposes underlying change‖

47

(p. 48). Although abhorred in science, teleological explanations can be found in the scientific literature not just used by students trying to understand natural processes.

3. Container metaphors involve an in-out orientation that is related to our experiences of our bodies as having discrete boundaries.DNA CONTAINS THE GENETIC

INFORMATION invokes the container metaphor with information inside of the container

DNA. In this expression, the focus is on the container DNA (called container locative). If one wanted to focus on the information aspect, the expression is rearranged to read GENETIC INFORMATION IS IN DNA (called content locative). Both expressions are used with the form employed dependent on the focus of the discussion or explanation.

4. Our conceptual system is grounded in a ―core set of discrete experiences‖ that arise from direct physical experiences that are termed directly emergent concepts (p.

40).

5. ―When attempting to understand systems of increasing complexity, metaphors based on physical experience will no longer suffice and interactions between components derive from social constructs, with their attendant greater complexities‖

(p. 126). The linear structure of proteins as composed of amino acids is compared to language with words (individual amino acids) in a particular order (syntax) that result in a meaningful expression of complete chain of amino acids (sentence). However, to get to its final functional state, the protein must be folded by proteins called chaperones (social comparison).

48

An additional insight based on conceptual metaphor theory is the following:

―truth is a product of human reasoning. It follows that science does not proceed by discovering preexisting truths about the world. Rather, it consists in observing the world and formulating truths about it‖ (Brown, 2003, p. 51). Maxwell (quoted in

Hoffman, 1985, p. 355) states, ―the search for the rational foundations of science in the sense of justification for empiricism is doomed to fail and philosophy should turn to descriptive accounts of the conditions to be fulfilled by significant knowledge.‖

Todes (2002) presents a detailed analysis of the development of one specific conceptual metaphor in the history of science: mechanistic imagery and the use of the factory metaphor by Ivan Pavlov in his studies of the digestive system. In the mid

1800s, when Pavlov began his studies, physiology was influenced by two schools of thought: anatomical-vivisectional which offered explanations of physiological phenomena in terms of ‗life force‖, basically, vitalism and physico-vivisectional which held that explanations had to be in terms of ―the same physical and chemical processes that governed the inorganic realm‖ (Todes, 2002, p. 51). Pavlov‘s teacher,

Tsion Ilya Fadeevich was of the physico-vivisectional school and had a great influence on Pavlov‘s thinking about physiology; Fadeevich was influenced by his teacher,

Claude Bernard. Bernard and his followers wanted to rid physiology of any vitalistic explanation, hence the use of mechanistic imagery in their theorizing such as the heart is a pump. Pavlov‘s use of the factory as analogous to the functioning of the digestive system was in this mechanistic vein.

49

But, here we encounter a problem with Pavlov‘s factory metaphor as Todor states, ―It bears emphasis that Pavlov‘s notions about the factory were based not on any actual experiences but entirely on an idealized image‖ (2002, p. 159). He viewed factories as regular and precise, powerful, efficiently coordinated to achieve a particular goal; factories of the time were just the opposite. This idealized image formed the conceptual basis for his explanations of the digestive system, and as a heuristic used in the design of experiments and in the interpretation of the results of those experiments and formed the foundation for his addresses to scientific organizations and in published papers and dissertations of his doctoral students, a foundation that became more developed and established over time.

Although Pavlov was guided by the factory metaphor and many explanations of physiological phenomena were developed using it – conditional and unconditional reflexes being one- where does that leave others who listened to and tried to make sense out of what Pavlov was explaining? His idealized image was counter to the reality of factories, and if one had experience with factories, the knowledge constructed would be based on that experience not Pavlov‘s view. How are we to know how someone used a base for a metaphor? What features were important and why? Such information is generally not articulated by the generator of the metaphor and the metaphor is subject to multiple interpretations depending on the hearer‘s experiences with the base.

It seems that where scientific metaphor use differs from the use of metaphors for every-day, non-science-based is that the investigation of relationships, positive,

50 negative and neutral analogy- to use Hesse‘s terms- is explicit rather than implicit in their interpretation. The relevance of a metaphor to understanding a physical reality may not be obvious. This also may be the case for non-scientific uses, as Gentner‘s work has shown, but even if students are informed that a metaphor is used for a scientific concept, the relationships that were drawn to understand reality may not be obvious. Students need to be taught how science uses its metaphors.

Gregory Bateson (1972) recognized the value of analogy in his anthropological work. He argues that advances in scientific thought progresses best when there is a balance between what he refers to as ‗loose thinking‘ and ‗strict thinking‘. Loose thinking allows one to ―think new thoughts‖, to entertain new ways to view a problem that are not possible with more strict and rigid thinking. Choice of a good analogy allows the researcher additional routes for investigation -conceptual frames- to play ―hunches‖ that result from going down these roads. It is their abstract nature that aids thinking. For Bateson the best analogies are those that are at the same level of abstraction as your problem. He also warns about the use of terms, both those already in existence and those that you may coin from your analogies and suggest to avoid pitfalls of misuse of analogy and terminology:

One is to trains scientists to look among the older sciences for wild analogies to their own material, so that their wild hunches about their own problems will land them among strict formulations. The second method is to train them to tie knots in their handkerchiefs whenever they leave some matter unformulated – to be willing to leave the matter so for years, but still leave a warning sign in the very terminology they use, such that these terms will forever stand, not as fences hiding the unknown from future investigators, but rather as signposts which read: ―UNEXPLORED BEYOND THIS POINT.‖ (p. 87, emphasis original)

51

An example of the concepts of loose and strict thinking can be found in the theorizing about the possible mechanism of protein synthesis in the 1960s; loose thinking firmly within the realm of metaphor and analogy. Jean Brachet (1960) reviews current understanding of the mechanism of protein synthesis and the proposed steps that involve amino acids and the ribosome. He summarizes the first two steps in a very matter-of-fact manner which alludes to the confidence that the community had about those events. As far as the third step, Brachet writes, ―[T]here is no lack of hypotheses about this ultimate step of protein synthesis: the most probable one is that the ribosomal nucleic acid carries a ‗code‘, which it has received from the nuclear deoxyribonucleic acid; this code would be inscribed, in the ribonucleic acid molecule, in the form of a specific base sequence and it would be translated, in the finished protein, as a corresponding, specific amino acid sequence‖ (p. 196).

Several observations can be made about Brachet‘s writings. First, that the

CODE metaphor is firmly a part of theorizing about the role of DNA. Secondly, the use of the ‗GIFT-GIVING‘ and ‗CONTAINER‘ metaphors to think about the relationship between DNA and RNA when he writes that ―the ribosomal nucleic acid carries a

‗code‘ (CONTAINER metaphor), which it has received from the nuclear deoxyribonucleic acid‖ where the verb ‗received‘ indicates the giving and receiving of something; the metaphoric ‗code‘. Also note that ‗code‘ is in single quotes indicating that Brachet recognized here the metaphorical nature of the term. Thirdly, the use of

‗translation‘ as a term for the event and relationship between RNA and protein. The language and information metaphors, which made their inroads into molecular biology

52 discourse starting in the 1940s is now firmly part of protein synthesis terminology; notice, no quotes around translation. Also within this trope is the phrase ―this code would be inscribed, in the ribonucleic acid molecule‖ we see ‗inscribed‘, again a metaphorical statement within the INFORMATION and LANGUAGE metaphors.

The use of metaphors within biological scientific discourse also highlights a problem that philosophers of science have had with biological explanation versus physical science explanation. Namely, biological science explanations include functional generalizations and no exceptionless strict laws. The functional terminology also is laden with anthropomorphism and human interests which biologists cannot easily forgo and still do biology (Rosenberg, 2001). As Rosenberg

(2001, p. 742) notes, ―‘Plants‘, ‗animal‘, ‗heart‘, ‗valve‘, ‗cell‘, ‗membrane‘,

‗vacuole‘—these are all functional notions. Indeed ‗gene‘ is a functional notion.‖

These functional notions are derived, to some extent, from the use of metaphors and as we have seen, what metaphors do very well is highlight relationships especially functional relationships.

That metaphorical models are used in biology should not be in doubt. An additional argument that philosophers of biological science purport is that there are not laws used in biology, but models. As Elliot Sober states, ―Biologists don‘t usually call them laws; models is the preferred term. When biologists specify a model of a given kind of process, they describe the rules by which a system of a given kind changes‖ (Sober, 1993, p. 15 quoted in Rosenberg, 2001, p. 745). These models are different from models of the physical sciences. Models in biology define systems.

53

They attempt to ―construct the logical relations that arise from various assumptions about the world‖ (Lewontin, 1980 quoted in Rosenberg, 2001, p. 747). They are an

―as if set of conditional statements‖ (Lewontin, 1980 quoted in Rosenberg, 2001, p.

747). The use of metaphors reflects the attempt to construct ‗logical relations‘ which is why biological thought could not either effectively or efficiently occur without them. This history of the life sciences is permeated by metaphorical models that attempt to determine relationships between functional individuals.

As life science educators, we should recognize the cognitive basis of explanations within our science and include this mode ‗scientific thinking‘ in our instruction if we are to accurately present the work of life scientists and the basis of the current explanations, models and terminology. This fact should also be included in general discussions of scientific reasoning that upon closer analysis reflects more the thinking tools of physical scientists than life scientists; they are not exactly transferrable from one domain of science to another and we should stop teaching as if they were.

Historical Roots of Gene Expression Metaphors

New metaphors and words increase the stock of available reality. Mark Edmunson

Those of us within science tend to have a Kuhnian perspective on the historical development of a scientific concept, namely there is no history at least none that we consciously recall in our day-to-day work (Fuller, 2003). Concepts and theories are well-established and most work is mere refining, normal science.

54

However, a closer look at the papers from the earliest period of molecular biology will bear witness to the prolific use of metaphor in the early stages of conceptual development of gene expression, what I refer to in general as a Historical

Institutionalized Metaphors. These metaphors were used by the molecular biologists of the period to communicate the process of gene expression to each other and to focus on aspects of the process that they were elucidating. But also, perhaps, guided them to hypotheses based, sometimes on the metaphor and sometimes not on the metaphor.

Additionally, remnants of the initial metaphor remain in later discussion of the concepts but stripped of the original referents of the initial metaphors. Understanding of the metaphor in order to understand the concept at a later time may be difficult because of loss of the original well-developed metaphor.

Since metaphor is an integral part of the thinking about scientific concepts

(Boyd, 1993; Brown, 2003; Gentner & Jeziorski, 1989; Hoffman, 1985; Pinker, 2007), an analysis of the major concepts of the early period of the development of gene expression and the metaphors used to communicate them to the present would seem to give insights not only into the nature of scientific thinking about gene expression but also to consider if they are still the best metaphors to use when communicating them to current students and non-scientists. Considering the important place gene expression plays in modern medicine and biotechnology, determining the most effective mode or modes of communication of concepts should be a priority for the science education of gene expression. Pinker (2007) writes that since the mind uses these metaphors to understand inaccessible concepts, like gene expression, I argue that

55 understanding the role of metaphor in science should be a priority for science education researchers. And not just as an occasional ‗pedagogical device‘ but as the main method for understanding scientific concepts. As Ortony (1975, p. 45) writes,

―Metaphors are necessary and not just nice.‖

The importance of metaphors in communicating ideas may be rooted in the human propensity for storytelling. Lakoff argues that there are three main categories of metaphors that are used by humans: war, gift-giving, and journey. These metaphors underlie the social nature of humans. Our stories are for others and about others (Hsu, 2008). In reality, explaining how genes work is story-telling–‗telling‘ the gene story- and metaphors are a useful way to relate to others how a gene works, using relationships they are already familiar with: war, gift-giving and journey and the metaphors that are developed from them.

Genes may be non-living chemical entities, but we talk about them as if they have human intentionality and motives, known as ‗theory of mind‘; this is one of the characteristics of a narrative as compared to a straight-forward explanation. We imagine thinking beings everywhere, even triangles (Heider & Simmel, 1944), so why not imbue biological molecules with intentions and motives. We have ‗selfish genes‘

(Orgel & Crick, 1980; Orgel, Crick, & Sapienza, 1980), DNA has ‗commands‘

(Judson, 1996), is also ‗ignorant‘ (Dover, 1980) and ‗parasitic‘ (Orgel & Crick, 1980).

Lakoff & Johnson (1980) refer to this phenomenon as ‗personification‘ and is used because it ―allows us to make sense of phenomena in the world in human terms-terms that we can understand on the basis of our own motivations, goals, actions, and

56 characteristics‖ (p. 34). What we must be aware of is that the choice of personal characteristics for DNA influences how we view DNA, that is, the metaphorical model we have of DNA influences how we think about DNA (sensu Lakoff & Johnson,

1980).

We must also consider the fact that scientific thinking does not occur in a value free, conceptually neutral vein. Current theories have a history to them and are very much influenced by the culture, events and individuals at the time of the foundational researches (sensu Kay, 1993; Spanier, 1995). These facts must be taken into account when evaluating the utility of a framework on which concepts for some piece of physical reality are presented to non-scientists.

Metaphors are relied upon for the building, evaluation and discussion about theories and models in biology. However, metaphors used when a concept was being developed are time and place oriented and may not hold the same explanatory utility during a different time and to a different population than from the one for which it was initially developed (Lakoff & Johnson, 1980; Charteris-Black, 2004; Peters, 1975).

One of the more important concepts within modern biology is the synthesis of polypeptides from a specific order of nucleotide bases of DNA, called a gene, or more specifically, Gene-D (Moss, 2003). The initial work on this concept, called gene expression, is said to have begun with the publishing of the structure of DNA in 1953 by James Watson and Francis Crick (Watson & Crick, 1953). Shortly thereafter, in order to more efficiently and effectively guide the study and prediction of the components and sequence of events that comprise gene expression, Crick developed

57 what he called the Central Dogma (Crick, 1958; Judson, 1996, p. 184).

Parenthetically, even though the idea of DNA makes RNA makes protein is part of

Crick‘s Central Dogma, the idea was put forth a decade earlier by an editor of

Experientia who wrote an English abstract of the paper written in French by André

Boivin and Roger Vendrely (Boivin & Vendrely, 1947; Judson, 1996, p. 244) and then stated in what was called the ‗Template Hypothesis‘ by Dounce (1953).

Crick saw the Dogma as a heuristic device, along with his ‗Sequence

Hypothesis‘, as is evident from his writing about it: ―I have found them to be of great help in getting to grips with these very complex problems‖ (Crick, 1958, p. 152). He further stated that ―[T]heir speculative nature is emphasized by their names. It is an instructive exercise to attempt to build a useful theory without using them. One generally ends up in a wilderness‖ (Crick, 1958, p. 152). In fact he is very explicit about the purpose of the Central Dogma: ―The purpose of the Dogma was to the state that ―genetic information moves from nucleic acids to protein, and most importantly that no information can get back the other way, from protein to the genetic message‖

(Crick, 1957; 1970; Judson, 1996, p. 184). Seems simple enough, but since its initial use, the Central Dogma and ‗information‘ have been misunderstood and misused so much so that Crick needed to clarify what he meant as early as 1970.

From a cultural perspective, the individuals who worked on molecular biology and made the major contributions in the field in the 1950s through 1970s came from the World War II and the subsequent Cold War eras. Metaphors and paradigms used to describe DNA, genes, and protein synthesis have a distinctive ring of secrecy,

58 martial overtones, control from a strong leader, codes and code breaking that would be expected from scientists of the era especially since many of these early molecular biologists came from a physics background and worked on projects directly related to the war effort (Kay, 2003). The Russian physicist George Gamow was particularly influential in forming the ‗coding problem‘, the attempt to determine the exact relationship between bases of DNA and amino acids of a protein. Gamow used the information discourse and framed heredity ―as information transfer, operating via a code, much like an enemy code or a cryptogram‖ (pp. 128-129).

In fact, an influential book for many of these scientists, What is Life?, was written by a physicist, Erwin Schrödinger. This is a physicist‘s view of what features the hereditary molecule should have. Schrödinger, like many of these physicists- turned-molecular biologists, Francis Crick included, was not a biologist and knew very little about the cell (Judson, 1995). Their paradigms, assumptions and base concepts for metaphors would be different from scientists who were working with living organisms. Additionally, the physicist-turned-molecular biologist was looking for the equivalent of ‗atom‘ in physics; DNA became the ‗atom‘ of molecular biology. This view was developed by Neils Bohr (1933a, 1933b) when he stated his anti-vitalistic view that, ―no well-defined limit can be drawn for the applicability of physical ideas to the phenomenon of life‖ (1933b, p. 458) opening the door for a physical understanding of life. Bohr‘s student, Max Delbrϋk, was inspired to take up the applications of physical methods to solve, as he called it, The Riddle of Life (1970). Discussions with a geneticist, Timofeeff-Ressovsky, in Berlin influenced his desire to ―get at the

59 chemical nature of the gene‖ (Delbrϋk, 1970, p. 1312) so much so that he, in time, started the Phage Group eventually based at Caltech to investigate the nature of the gene and is considered the father of molecular biology.

The metaphor ‗genetic information‘ is an interesting one because it implies a flow of information. The flow of information, including a very specific definition of

‗information‘, is the purview of Information theory that had its initial input in the

1940s but information theory had no ‗explicit part in working out those discoveries‖ of gene expression (Judson, 1996, p. 249). On the other hand, Kay (2003, pp. 105-107) argues that information theory (especially the telecommunication theory of Claude

Shannon with Norbert Weiner, the developer of cybernetics, and with Warren Weaver) played an influential role in molecular biology in the 1940s especially to Max

Delbrück and Jacques Monod (used cybernetic theory and information to guide his work that would lead him and collaborators to propose messenger RNA and gene regulation in the lac operon). With John von Neumann‗s theory of computing applied to biological entities and also influenced by communication theories, genes became an

―information tape‖ (p. 111) and, as a result of communications and discussions with geneticist Joshua Lederberg, information entered into the discourse of biology and in the early 1950s ―the DNA template signified as the locus of information storage and transmission‖ (p. 114). In fact, there was a realization during the 1950s that

Information Theory could, in some way, be used to understand the role of DNA; what was known to that point about the role of DNA, a primer on Information Theory, and how Information Theory could be applied to guide research to uncover this role was

60 discussed by participants at ‗Symposium on Information Theory in Biology‘ that was held at the end of October, 1956 (Yockley, H.P., Platzman, R. L., & Quastler, H.,

1958). In fact at that time, information ―was embodied in the extreme specificity of proteins and nucleic acids‖ (Judson, 1996, p. 249) and is relatively speaking still thought of that way today.

But we must think about this: was the use of ‗information‘ in early molecular biology metaphorical or technical, applying Information Theory and what is the relationship between the ‗information‘ metaphor and Information Theory? We can glean the relationship if we look at known users of Information Theory in the 1950s.

Gamow and Yĉas (1958) described the relationship of information and the cell as a factory in this way.

Speaking about information storage and transfer in a living cell, one always likes to compare the cell with a large factory. The cell nucleus is the manager‘s office, directing the work of the factory, and the chromosomes are the file cabinets in which all blueprints and production plans are stored. The cytoplasm is the cell itself with the workers and machinery carrying out the actual production. If something goes wrong with the information stored in the chromosome, the corresponding enzymes will also do the wrong thing (p. 63)

Here is an interesting case in the history of science where a well-established theory was used rather than developing a theory of the role of DNA within a cell de novo. But, to conceptualize this role, Gamow and Yĉas used the factory metaphor and did it in a manner where we can extract the positive analogy between a factory and the cell. I would propose this: that in order to be able to apply Information Theory, the metaphorical relationship that chromosomes played a role in information storage and transfer first had to be established. Without this positive analogy, one could not apply

61

Information Theory. Figure 1 depicts this progression. Perhaps this provides a lesson for us for how to develop a specific conceptual representation for DNA, information storage, based on a pedestrian conception of information, but then move on to apply an extended conception of information that is part of a technical Information Theory.

Information Communication Metaphor

DNA

Information Can Use

Target

Information Bases Theory Formation of DNA IS INFORMATION metaphor

Information Information Metaphor Theory

Biological Information Theory

Figure 1. DNA as information metaphorical representationleading to DNA as information that results in development of Biological Information Theory.

62

Even though ‗information ‗ was used in molecular biology as a metaphor,

Information Theory had a very specific use in theories of communication which molecular biologists have extended; that of information does not have meaning. As

Weaver stated,‖ The word ‗information‘ in this theory is used in a special sense and must not be confused with its ordinary usage. In particular, information must not be confused with meaning‖ (quoted in Kay, 2003, p. 98-99).

Quastler (1958) defined the Information Theory use of ‗information‘ as ―in a message, for example, as a type of event, is the measure of the amount of knowledge

(intelligence) which a message of this sort ideally can convey through the medium of symbolic representation. The only condition for representation is that a complete system of translation, a code, be agreed upon‖ (pp. 5-6) and that ―information theory is concerned with the general laws which govern the possibility of translating one king of information into another‖ (p. 7); ―the term ‗information‘ in the technical sense covers a good deal more than in everyday language‖ (p. 7).

Quastler (1958) also makes another interesting point about information, and one that is embodied in the idea of DNA as a ‗carrier of information.‘ ―Information is not a disembodied something; it is always related to some actual carrier – a thing or an event‖ and that ―information theory applies equally to all kinds of carriers of information. And to provide a bit more detail to what an information carrier can be, he additionally writes: ―In formal language, one refers to the information carriers as elements of discourse, or points in sample space, or configurations of properties‖ (p.

63

7). Talk about carte blanche to apply both ‗information‘ and ‗carrier of information‘ to DNA!

As many of the details of gene expression began to be determined, it was evident that gene expression was much more complicated than the simple flow of information Dogma presented by Crick. The Dogma at best asserts what happens in protein synthesis, but does nothing to indicate how protein synthesis occurs or how phenotype follows from the functional protein. In fact if presented with the Central

Dogma, one would gain little information about protein synthesis beyond the involvement of DNA, RNA and proteins and a sequence indicated by arrows.

An additional problem that occurred as a result of using the Dogma as a working model to guide a research program is that molecular biology which focuses on the structure, function and interrelationships of macromolecules of cell became dominated by DNA and further became conflated with molecular genetics. Who is responsible for this? Two molecular biologists who, as Doyle (1993) argues, had demonstrated that DNA itself cannot build an organism and that genes are regulated, namely Francois Jacob and Jacques Monod. Jacob and Monod each wrote books published in 1970 at the time of the Lysenko affair in Russia and Marks (2006) points out were as much a rhetorical strategy as communicating a groundbreaking scientific discovery. Their terminology and ―key metaphorical formulations‖ (Marks, 2006, p.

88) were ―reinforcing a largely reductionist and somewhat mechanistic view of the world‖ (p. 89). It was due to their rhetorical strategy that the ‗Master Molecule‘ view of DNA was retained in light of possible dethronement by the lac operon model of

64 gene regulation and ―external influences such as the growth and development of the organism in a particular environment are downplayed, if not discounted‖ (Marks,

2006, p. 89). As a result, ‗DNA defines the organism.‘

Thus began the ‗hegemony of the gene‘ (Silva, 2005) or as Chantrenne (1963, p. 29) called it ―the almighty genome.‖ We live with the ‗DNA as Master Molecule‘ paradigm to this day. In lieu of research into gene networks, the role of various

RNAs, and non-genetic forms of inheritance, it may be time to retire the ‗Master

Molecule‘ and ‗source of information‘ metaphor, and replace it with a more apt metaphor that captures the role of DNA within the cell as part of an interconnected whole at the molecular level, perhaps a ‗Wisdom of the Hive‖ (Seeley, 1996) metaphor would be more apt. This conception is in line with the Developmental

Systems Theory (Oyama, 2002).

But change takes time, so if we must remain with the information metaphor we should find a more productive use for it. Information Theory can be applied not only to gene expression but also to the teaching and learning of gene expression.

There is no research showing that a domain must be taught as it was discovered.

There is no reason why an incomplete application of the flow of genetic information as embodied in the Central Dogma need be the focal point of instruction within the domain of gene expression. If the Central Dogma is presented as a ‗flow of genetic information‘, then we had better present it in terms of a flow of information or the metaphor is not a very apt one.

65

A problem that educators encounter when teaching and students encounter when trying to understand gene expression is the prolific use of metaphor by scientists. These metaphors may not be obvious, as most metaphor use is not obvious, or they may now be accepted as technical terms that have lost their link to the concepts used to help scientists understand a new domain in the early stages of research. The problem is that both students and their instructors may not be aware of these metaphors, the ontology on which they are based, or the original use of the metaphor that now is lost in technical terms of gene expression and that this lack of awareness may hinder effective instruction in the domain of gene expression and as a result in the efficient learning of gene expression concepts by students.

Why should it matter how metaphors are viewed? Because all metaphors have a history

As much as science would like to appear to construct theories of the physical world independent of culture and time, this is not the case. Ontological perspectives guide the assumptions and language, including metaphors, of theories and models that explain concepts and regularities in the physical world. In this vein, Martin (in

Spanier, 1995, p. 79) notes that ―explanatory models of single purpose, centralized control, and natural hierarchies characterize Western physiology. Similar ―prior commitments‖ are apparent in molecular biology in overvaluing control, heredity, and

DNA.‖ An additional model used in the sciences includes modern industrialism that see ―production as the goal of all systems‖ (Spanier, 1996, p. 81). These tacit assumptions lead to false dichotomies, such as nature-nurture‘ present in molecular

66 biology as used by molecular genetics and all disciplines that theoretically rely on genetics in their explanations. The psychologist Allan Newell (1973) warned of the problems with research based on dichotomies and warned that ―you can‘t play 20 questions with nature and win‖. The point being that this worldview, this ontological metaphor (Lakoff & Johnson, 1980), is one of many that could portray DNA and gene expression and specific conclusions about nature are made based upon it. Other worldviews, such as a non-hierarchical equal cooperation amongst players would work as well and better represent the role of DNA within a cell.

No model of learning more clearly situates the importance of understanding scientific concepts within their historical and conceptual development and how they are linked to current research that the Vee heuristic developed by D. Bob Gowin shown in Figure 2 (Novak & Gowin, 1984; Gowin & Alvarez, 2005).

The left side of the ‗V‘ describes the conceptual and theoretical aspects of the investigation. The aspect of this side that is usually forgotten when discussing and teaching biology is the ontology/worldview that is guiding the research. This can get one into trouble when ontological perspectives are not addressed as influencing an investigation. In the present case of the information metaphor, a lack of understanding of the implications of the information metaphor and when and under the circumstances it was derived allow aspects of the original base information/code metaphor that should not be applied to the target of the metaphor, namely gene expression to be

67

Figure 2. The Knowledge Vee developed by Gowin (1984). The left side of the Vee focuses on the theoretical and conceptual aspects of an investigation. The right side focuses in the Methodological aspects of an investigation. The center presents the focus question of the investigation and the new question(s) generated as a result of the current investigation.

taken as self-evident that they need not be addressed when explaining gene expression and when proposing new research projects.

68

The prevailing metaphor used in molecular biology for gene expression and the role of DNA is that of the INFORMATION metaphor, but LANGUAGE, CODE,

CONSTRUCTION, and CONTAINER are a few of the other dominant metaphoric categories used to discuss gene expression, genes and DNA.

The origin of the CODE metaphor can be traced back to Schrödinger, but the question of what is passed from parent to offspring and what is the cause that imparts order on matter goes back to Aristotle and his theory of epigenesis with the organism as a self organizing means unto itself (Moss, 2003). With the 17th century natural philosophers the cause of the organization shifted to God and a design from without explanation. The 17th century also saw the rise of preformationism which held that smaller version of the organisms unfolded from within as preformed miniatures, like

Russian nested dolls. Epigeneticist thinking continued through Descartes and his followers.

The question of how simple matter leads to organized and adapted life forms took a turn in the 19th century with Kant and Blumenbach and the idea of teleomechanism which sought ―principles by which new life-forms are produced from some purposefully organized germ‖ (Moss, 2003, p. 12). The major idea of Kant was that of Keime und anlagen. Keime expressed preformationist ideas of preformed parts and anlagen expresses epigeneticist ideal of ‗organizational layout‘ or ‗disposition.‘

From the teleomechanist tradition of seeking mechanisms of development were Schleiden and Schwann who developed a cell theory based on observations of plant and animal cells and focused on the center, the nucleus, following the ontology

69 that morphogenesis proceeded from the center to the periphery. Virchow‘s maxim of

‗all cells from cells‘ and Haeckel‘s embryological work to experimentally determine the mechanism of development are also in the teleomechanist tradition (Moss, 2003).

August Weisman separated keime from anlagen when he proposed that germ cells and somatic cells are separate and that germ cells are not influenced by life experience.

For biology in the United States at the turn of the 19th to the 20th centuries, the epigeneticist and preformationists traditions were embodied in Charles Otis Whitman and Edmund Beecher Wilson. Whitman argued that study should focus on the role of the cytoplasm in differentiation, not the nucleus (epigenesist) and Wilson argued that study should focus on the nucleus on the developing cytoplasm (particulate preformationist) (Moss, 2003).

Two of the discoverers of Mendel‘s work on inheritance, deVries and

Bateson, were of the morphological tradition. deVries‘ Theory of Intracelluar

Pangenesis held that ―organisms are composed of unit-characters that are distinct in transmission as much as in development‖ (Moss, 2003, p. 26) that linked transmission and development; the origin of the ‗genes for…‘ mentality. Bateson described allelomorphs as an ―encapsulated piece of organismic form‖ (Moss, 2003, p. 26).

The third of the Mendel-finders, Johannsen, was opposed to the morphological tradition and felt the need to define exactly what was inherited. He proposed the terms

‗genotype‘ and ‗phenotype‘ to make the distinction clear (Johannsen, 1911). For him, heredity was about passing on genes, not morphological characters. Phenotype was

70 the result of the genotype reacting with environmental conditions. He warned:

―Hence the talk of the ―genes for any particular character‖ ought to be omitted, even in cases where no danger of confusion ought to exist‖ (Johannsen, 1911, p. 147).

The early 1900s saw a search for an explanation for the cause of the order and adaptedness of an organism. Old epigeneticist and preformationist ideas would not do. A ―new preformationism‖ (Oyama, 2002; Moss, 2003) that located within the gene the instructions for its use developed and the jargon for describing this was

―codes and information‖. The science to explain in physicochemical terms how the genotype contains within itself the instructions for making an organism was molecular genetics populated mainly by former physicists and chemists with very little to no knowledge of the cell (Judson, 1996; Moss, 2003).

These are the historical foundations upon which modern biology was built.

We would like to present the history of science as one of progressivism; what we know and how we think is somehow more advanced than that of an earlier era. But as the brief overview of the ontological history of the study of inheritance illustrates, all ideas have a history and although the terms used to describe a natural phenomenon may change over time, the underlying worldview upon which they are developed has not. It is from this informed perspective of our ontological history of genetics that this study was informed and designed.

The Central Dogma is a Nucleic Acid-Centric View of Protein Synthesis: A

Bottom-Up Explanatory Strategy

71

One of the original metaphors for the role of DNA in gene expression is the

INFORMATION metaphor. The manner in which information is viewed in molecular biology is very different from the way information is viewed by the field of knowledge management and information theory. In Information Theory, Devlin presents information as the representation plus the procedure for encoding/decoding; called the Information Equation. Using this equation, genetic information can be thought of as the representation (DNA) plus procedure for encoding/decoding (RNAs, polymerases, ribosome, and additional proteins). DNA is not the information it is the representation of the information. What is the information? The primary sequence of a polypeptide is the order of amino acids. The information is not the representation.

The order of amino acids in a polypeptide is not the DNA.

In fact, the information metaphor has gotten out of hand. Crick realized this when he wrote to Howard Temin in 1978 and wrote: ―I do not subscribe to the view that all ―information‖ is necessarily located in nucleic acids. The central dogma only applied to residue-by-reside [sequence] information‖ (quoted in Strasser, 2006, p.

507). Crick was explicit that he meant information as sequence between nucleotides of nucleic acids and amino acids of proteins in his original statement of the dogma in

1957. Maynard-Smith sees it differently when he writes that genetic information implies ―intentionality‖ and that the genome, the totality of an organism‘s DNA ―is not a description of the adult form, but a set of instructions on how to make it: it is a recipe, not a blueprint‖ (2000, p. 187).

72

It seems biologists and now the lay public can‘t let go of the INFORMATION metaphor seeing it as a theory of DNA function and a ―basic generalization of molecular biology‖ (Šustar, 2007) despite of attempts by philosophers of science to convince us otherwise (Sarkar, 1996; Sarkar, 2000; Griffith, 2001), instead of Crick‘s original intent which philosophers of science have argued is a valid interpretation of the Dogma (Stegmann, 2005).

As a result of my researches into the conceptual history of molecular biology- including work before the term was coined by Warren Weaver in 1938 while at the

Rockefeller Foundation-during the 20th century, I have, when considering how all of this history of ideas and explanations should be presented to students, come to these realizations that results in a question that I was the crux of investigations that lead to

DNA as the genetic material holder of information in Crick‘s sense: proteins were determined to be of key importance to a cell‘s functioning and that the building block components, amino acids, were in a specific order (sequence) in all molecules of a specific protein, say insulin; amino acid sequence was important to proper protein function, an observation made early in the 20th century from studies of hemoglobin and its relationship to sickle cell disease and hinted at by early immunological studies that showed that size was not important to differentiate similar proteins from different species because, based on Karl Landsteiner‘s work, the ability of serum antibodies to distinguish proteins was based on chemical structure; and that the amount of protein was not constant (Borsook & Keighley, 1935), but there was a turnover in the number

73 and types of certain proteins (Schoenheimer, 1939; after the argument of Campbell &

Work, 1953).

From these ‗facts‘ we are then led to ask: Where do proteins come from‖ that is, how are they synthesized so that the number and type of each protein changes over time but the sequence of amino acids in any one type of protein molecule remains constant? If we begin with this question rather than with DNA we are providing a plausible explanation/solution to a problem central to cell functioning (protein complement) that is based on empirical observations. If we do not begin with the empirical observations about proteins especially amino acid sequence consistency and protein turnover, then I ask, why look for or explain the functioning of a ―template‖?

As Campbell & Work (1953, and based on lectures given by Work before Watson &

Crick published their structure of DNA in April) argued: ―Thus it is reasonable to suppose that each type of cell possesses the enzymic mechanisms capable of exact control of the amino acid composition and sequence of all its proteins (p. 997).

Although they envisioned the ‗enzymic mechanisms‘ as being performed by proteins and unique for each cell type, Dounce (1953) followed shortly with a proposal that deoxyribonucleic acid is a template and that ribonucleic acid was synthesized from the

DNA which acted also as a template for protein synthesis (Dounce, 1953a, 1953b).

This DNA to RNA to Protein hypothesis would later be stated by Crick in 1958 in the famous Symposia paper and coined as the ‗Central Dogma‘.

74

Currently, we proceed from a ‗this is what is passed from parent to offspring and this is what it does‘ approach. But, why do chromosomes matter in a living cell?

That is why it is a necessity that they are passed on.

This will also set the conceptual stage for the concept of gene regulation, a solution to the problem of when to express a particular gene so that the level of protein is at a level for cell function.

Importantly for this study is how does a focus on DNA through the metaphors for its function lead to a misunderstanding of the need for DNA as a template in protein synthesis?

Of Signs, Signifier, Signified and Referents

Within molecular biology, one cannot help but be struck by, what at times, seems to be, an overwhelming number of technical terms. And not only this problem but the fact that many are confusing in that the referent is not clear to them. My students do and have done so for nearly 18 years and have told me in no uncertain terms about it. Needless to say, I was curious about the origin of scientific terms.

My researches into metaphors have provided part of the answer. But one cannot investigate the origins of the scientific explanations about heredity and the molecular basis of inheritance without wondering about the central term: gene.

Gene is a sign, when pronounced is the signifier and when we know the conceptual basis of the sign that is the signified. Gene is an interesting term (sign) because it was used as a placeholder when coined in 1909 by Wilhelm Johannsen for the ―material basis of an independently heritable character‖ (Mayr, 1982, p. 736).

75

There was no identified physical entity for what gene signified. But in order to talk about heredity of a physical stuff, you needed a term that all researchers could use when talking about this material basis of a character. To this day, there is not one single referent for gene; there are many gene concepts, many concepts that make up the signified, for the term gene. Gene from its inception as a technical term was a sign in search of a referent. Campbell and Work (1953, p. 1000) even suggested that

―[T]he conception of gene is essentially an abstract idea and it may be a mistake to try to clothe this idea in a coat of nucleic acid or protein.‖ How is a listener, especially a novice, to understand which ‗gene‘ is being referred to when s/he hears the signifier

‗gene‘? We have inherited the vague notions of a referent for gene and hence this contributed to conceptual learning of what genes specifically are and what they specifically do; an incomplete structure –function relationship.

On the other side is the sign DNA. To try to understand the function of

DNA, that is the signified; metaphors were and continue to be employed. Here, we have a referent in search of a signified. A very different conceptual challenge than what a student faces with ‗gene‘. From a conceptual change perspective using

Thaggard‘s analysis of types of conceptual change discussed previously, the referent and sign in search of a conceptual explanation would be at his level of 6 on the 1-8 scale, with 8 being the most serious change. This would be a serious revision to conceptual structure. The functions of DNA, the signified, the conceptual explanation, are communicated through metaphor and as we have seen not just a single metaphor.

76

We would hypothesize that it should be challenging for students to incorporate these various conceptions of DNA.

This is not the only conceptual challenge faced by students. Understanding the relationship between the terms DNA, gene, and chromosome involve adding part- whole structure relations; 4 on Thaggard‘s scale. Depending upon the past instruction and learning by the student, this may have involved starting with DNA or gene relationship then chromosome as the highest structure composed of both DNA and proteins. Or they may have start with chromosome then to a single molecule of DNA combined with proteins then to the relationship of gene to DNA. Then onto this conceptual structure is added the role of DNA/genes/chromosomes in inheritance.

Students must add additional conceptual explanation to the signified of DNA and genes and chromosomes. This involves branch jumping in which ―kind relations organize concepts in a tree-like hierarchy‖ (Thaggard, 1990, p. 268). If this jumping is in various stages of reorganization, we may see this reflected in vague explanations involving relations between the structural terms and inheritance concepts not fully developed (as canonical science has explained them). We should be able to see this in student descriptions of the meanings of metaphors.

An additional question that must be asked with reference to adding concepts through the use of metaphors is how do all of these additions to the signification interact with each other? I can envision four types of interactions through an analogy with the classes of drug interactions. A synergistic effect would ‗enhance‘ understanding so that pre-existing concepts would make a new concept intelligible and

77 at the same time make the new conceptual structure plausible and/or fruitful. This includes Thaggard‘s view of concept ‗differentiation‘ in which one concept becomes two distinct concepts. Neutral effect is one in which new concepts have no effect on pre-existing conceptual framework or vice versa. In metaphor use, if a student encounters a new metaphor and this does not add to a revised understanding the existing concepts, the metaphor may be viewed as useless by the student. For example, DNA IS A PLAN and DNA IS A BLUEPRINT may mean the same thing to a student and add nothing to conceptual understanding. Additive effect is a sum-of- parts effect which is similar to assimilation in which a concept of the target of a metaphor is added without rearrangement of the existing conceptual framework such as Thaggard‘s change 1 adding a new instance that changes the structure of a concept.

This is similar to Thaggard‘s analysis of ‗coalescence ‗of concepts; two concepts become one. And lastly, a subtractive effect in which the original conceptual understanding is made less intelligible because of the introduction of the new metaphor or concept. This obviously is to be avoided but at present time have no way of knowing for any one student what these may be.

Public Understanding of Science/Sociology

On Metaphor Use

Metaphors and attributes in everyday understanding are not applied because they reflect some truth about a phenomenon, but because they are good to think with. (Wagner et al., 1995)

As scientists come to understand the target phenomenon in greater depth and detail, they highlight the aspects of the metaphor that ought to be taken seriously and pare away the aspects that should be ignored…The metaphor evolves into a technical term for an abstract concept that subsumes both the target phenomenon and the source phenomenon. (Pinker, 2007, pp. 257-258).

78

Here we stand today with gene as both CODE and INFORMATION; gene as a particular sequence of nucleotides and defined by its phenotype, or rather, predictive value for the likelihood of a particular trait. The question is this: is it possible to develop a conceptual framework that will provide a solid foundation upon which concepts of cellular and developmental biology can be built? Separate the Gene-P from the Gene-D concepts?

In helping students to understand the concepts of gene expression, we are confronted with the use of scientific terms that are derived from metaphors developed at the time when a particular problem was being systematically studied. Metaphors are used extensively within science in an attempt to understand new domains of knowledge, although after time the initial metaphor is lost.

Metaphor choice is based on similarity of the base (known, understandable concept) to the target (that which requires an explanation for how the system works) and is based on ―noticing relations among parts even if the parts themselves are very different‖ (Pinker, 2008, p. 254). It follows that metaphor choice is time and culture- dependent because it ―bonds people in a joint act of meaning creation‖ (Charteris-

Black, 2004, p. 12). After a period of time within a community, the metaphors become conventional ways of referring to something (Charteris-Black, 2004, p. 18).

A theory to explain this ―Career of a Metaphor‖ was proposed by Bowdle and Gentner

(2005); their theory is visually presented in Figure 3. An important part of their theory that is relevant to the INFORMATION/CODE/LANGUAGE metaphors of gene expression

79 is that of the dead metaphor in which the link between target and base is lost and the target is the metaphor.

Phenomenon of physical reality – Literal Protein synthesis Target How does it Concept happen?

then is Metaphoric Technical To explain the Category Term phenomenon

As the link between Base and Develop Find Literal Target is lost, Metaphors Concept Base Metaphoric Category becomes a Technical Term; the metaphor is Work with these dead. metaphors – are Novel Metaphors

Then becomes within the Molecular Biology community becomes

Conventional Metaphor

Figure 3. Career of Gene Expression Metaphors. Technical terms associated with gene expression can trace their existence back to the target of a metaphor. As the metaphor becomes conventional, the link between Base and Target is lost and the Metaphor becomes a Dead Metaphor, a technical term.

As a note on the choice of the base concept for a metaphor, lack of knowledge about the concept may lead to a poor base being chosen to accurately represent the 80 phenomenon in question. Case in point: the DNA is a CODE metaphor is actually a poor choice for the nucleotide base sequence of DNA and Crick realized this (Judson,

1996). More accurately, he commented, that DNA is a cipher, not a code, but that

DNA is a code sounded better than DNA is a cipher; and it has stuck, incorrect as it is!

A cipher is ―a secret or disguised manner of writing, whether by characters arbitrarily invented (app. the earlier method), or by an arbitrary use of letters or characters in other than their ordinary sense, by making single words stand for sentences or phrases, or by other conventional methods intelligible only to those possessing the key; a cryptograph. Also, anything written in cipher, and the key to such a system‖ (Oxford

English Dictionary, 2008) and a code is ―any system of symbols and rules for expressing information or instructions in a form usable by a computer or other machine for processing or transmitting information‖ (Oxford English Dictionary,

2008).

Apparently, there is confusion as to the distinction between code and cipher, even though cipher is rarely, if ever, used in scientific discourse; they are used synonymously. An article published in the largest circulating newspaper in the United

States, USA Today (Sternberg, 2008), about the publishing of the genomes of two of the organisms that cause malaria in humans, Plasmodium vivax and Plasmodium falciparum, states that scientists had ―deciphered the genetic code of falciparum malaria‖ and other teams had ―decoded‖ vivax and Plasmodium knowlesi. The author of the article mixes CIPHER and CODE metaphors in the first quote and in the second quote, states that two specific organisms were decoded. Organisms are not

81 decoded; they are not codes. Moreover, codes are decoded, not deciphered. The base concepts of code and cipher are not being accessed.

Because of the attention in the philosophy of science literature on the utility of the INFORMATION metaphor in biology (Godfrey-Smith, 2000; Griffiths, 2001;

Maynard Smith, 1999; Moss, 2003; Oyama, 2000; Sarkar, 1996, 2000; Stegman,

2005) and research showing the ‗hegemony of genetic thinking‘ (Silva, 2005) in contemporary culture, I would suggest that the INFORMATION metaphor is a dead metaphor for gene expression and the function of genes. I suggest that metaphors and subsequent metaphoric categories, that is technical terms, we work with are from an historically different time and that what gene expression was to practicing scientists, that is what it was like (a simile-metaphor) MAY NOT BE applicable to students in the 21st century without the background knowledge of the scientist who developed the metaphor; the background is important to an understanding of metaphor argument.

Whether or not a scientific theory has ―intuitive appeal… has to do with how well its metaphors fit one‘s experience‖ (Lakoff & Johnson, 1980, p. 19). According to

Conceptual Change Theory (Posner, et. al., 1982), this would mean that the conception is plausible.

But we must consider not only scientific metaphors for a phenomenon but also what happens to these metaphors when they are introduced to the lay public. ‗Brute facts‘ are not what are solely transmitted to the public, but facts explained by use of metaphors that are then coped with by the public through the formation of additional metaphors.

82

Scientific information along with these metaphors of genetics and gene expression make their way into public discourse mostly through the media which includes news, movies, magazines and documentaries (Silva, 2005; Wagner, 1998,

2002; Christidou et al., 2004). Scientific information is viewed by the public as threatening or unfamiliar. To deal with this information, society participates in a process of representation of the event through images, metaphors or symbols, what

Wagner and colleagues (2002) have described as ‗collective symbolic coping.‘

Collective symbolic coping is viewed as a social representation within the framework of the social psychology theory called Social Representation Theory first introduced by Moscovici (1976) to explain the views of the French public when psychoanalysis was first introduced. Wagner and colleagues (1999) have elaborated these early ideas into a present form of the theory. It is based on the conclusion that ―…social psychological phenomena and processes can only be properly understood if they are seen as being embedded in historical, cultural and macrosocial conditions. By doing so it attempts to overcome the shortcomings of those currently widespread theories and approaches in social psychology which are based on methodological individualism and on an epistemology which functionally separates the subject from the object‖ (Farr, 1996 in Wagner et al, 1999, pp. 95-96).

From this perspective, Wagner has sought to explain lay metaphoric and iconic representations and explanations of natural phenomena that seem at odds with currently accepted scientific explanations of the same phenomena. He has termed this lay knowledge ‗Vernacular Science Knowledge‘ (2007) and sees as its purpose a

83 common belief system in discourse with other members of that community so that there may be several version of vernacular science knowledge held by different discourse communities, referred to as section of the public.

Different sections of the public hold different version of vernacular science knowledge and concepts that can serve as metaphor bases. Only those metaphors that a section holds are available for use to construct and understand metaphors. In Figure

4, metaphors used by Professional Science for a target domain, such as DNA/genes, are effective for the Section of Public A because they hold the same base concepts.

Section of Public B however does not hold the same base concepts and would not understand the target domain in terms of the metaphor used by Professional Science.

Shared metaphors for a target object in reality

Figure 4. Different sectors of the public, represented by the spheres A and B, are likely to hold divergent versions of vernacular science knowledge and conceptual bases for metaphor development and interpretation. Here, Public A and Professional Science shared metaphors for a target object in reality so that communication between these spheres using the shared metaphors have meaning. Public B does not share metaphor bases with Science so those scientific metaphors will have less communicative power.

The relationship between vernacular scientific knowledge, based on everyday cognition, and scientific knowledge, a specialized knowledge outside the realm of 84

Local Rules of Communication LAY

Representations are not primarily reproductions OF facts in the world BUT are Social elaborations for Knowledge of Social groups serving to the Physical maintain the World stability of their social world. Knowledge is bound to social context (Wagner, 2007).

Local Rules of Communication SCIENCE SPECIALIZED

Figure 5. Two types of reasoning about the physical world.

85 everyday cognition, is what helps to explain sometimes disparate explanations of the same natural phenomena. Figure 5 summarizes these two types of knowledge including their reason d’être.

Folk biology and Social Representation Theory

The models of representation in social psychology, developed to explain groups, seem to be related to ideas proposed by researchers in the study of folkscience that is lay explanations and categorizations of natural phenomena that are more individual in nature.

Figure 6. Combining Social Representation Theory and Career of Metaphor to demonstrate how Career of Metaphor compliments the ideas of social representation. Social Representation Theory is depicted on the outer red circle (after Wagner et al., 1999, p. 98, Figure 1) and Career of Metaphor is depicted on the inner blue circle. 86

It is known that no two individuals within a group share exact representations.

There may be shared representations between individuals as the result of the new social representation (Figure 6) but individual differences in representation due to we may each reach a moment of insight where we get the ‗causal gist‘ (Keil, 2003b) of a phenomenon and so stop searching for details. We cannot possible grasp all the details of every causal relationship in the world, so we stop at the gist.

The original LANGUAGE, CODE, CONTAINER metaphors present from the early years of molecular biology are with us as technical terms such as transcription, translation, code, sequence, and information. Understanding the physical word will always involve the use of metaphor. Our metaphors help us to understand abstract concepts by using concrete physical concepts. We should begin to try to understand how we use metaphor in science and more importantly, how we use metaphor and which metaphors we choose to use when communicating the concepts of science to students and non-scientists. Additionally, we must also realize that ―just because you use a metaphor, doesn‘t mean you think metaphorically‖ (Pinker, 2008).

Hermeneutics/Pragmatism – Fusing of the Horizons

Although Social representation Theory is useful to explain the discord in understanding of scientific information, it does not in itself suggest how this discord may be breached. However, hermeneutics does just that. Hermeneutics deals with the problems of interpretation of linguistic expressions and texts that result from words having more than one meaning, are polysemic, ‗cumulative entities, and determining

87 the context in which they are used and to be interpreted. The definition of words may seem explicit and unambiguous; this is not the case for as Ricoeur notes: language is

―a warehouse of meanings indigenous to its concomitant culture‖ (quoted in Peters,

1978, p. 363) and with reference to metaphor, the word is both more and less than the sentence. It is only when they are part of a sentence that words have actual meaning

(Peters, 1978).

Gadamer (1975) expanded Husserl‘s concept of horizon of consciousness to include the viewpoint which ―circumscribes and includes everything within it‖ including what we are focusing on (Peters, 1975). Additionally, horizon ―refers to that corona of associations and meanings that a word has accumulated in the linguistic tradition‖ and ―although in the background are present when a word is used literally‖

(p. 365). When an interpreter encounters a word/text that is strange and not understood, an incongruity exists between the two horizons, the interpreter and the text. Interpretation is how the incongruity is resolved. What is necessary is to merge the two horizons in an event of understanding, a ‘fusing of the horizons.‘ What is particularly important here, and one which science educators must take note, is that the interpreter (our student) cannot leave his/her horizon behind and enter into the horizon of the word/text. The horizon of the student must be broadened so that it fuses with the word/text (Figure 7, p.89).

For our present problem, there are three points to consider: first, it is important to recognize this framework as a plausible context in which to view student

88

Horizon of Horizon of a Scientific the Term or Incongruity Interpreter Metaphor Exists (Student)

Resolved through INTERPRETATION

Horizon is Horizon of Horizon of broadened so it a Scientific the eventually fuses Term or Interpreter with that of the scientific term/ Metaphor (Student) metaphor

2 Horizons merge in an EVENT of understanding

Figure 7. Resolution of an incongruity between the horizons of the scientific term/metaphor and the students. A fusing of the horizons in an event of understanding is needed.

89 problems when learning about gene expression and DNA function; secondly, is there actually an incongruity between the horizon of the scientific terms/metaphors and the horizon of the student?; and lastly, how does the instructor facilitate an ‗fusing of the horizons in an event of understanding‘ for the student?

There is an additional set of horizons that are involved when a metaphor is used. In actuality, the horizon of the term/metaphor is broken into the components of a metaphor, namely, base and target. Which of the meanings of the target and base that are focused upon will have influence on interpretation is dependent upon the

‗metaphorical context‘ of the interpreter (Peters, 1975, p. 365). Which meanings of the horizon of the base and target will the interpreter bring to the metaphor? Peters points out that in the interpretation of a metaphor: ―a word being said always carries with it its own horizon of that which is unsaid‖ (p. 366). It is the unsaid that allows for the range of possible interpretations and for instructors the unsaid allows for misinterpretations.

It is helpful to situate the problem within this hermeneutic framework due to fact that I see student difficulty in understanding gene expression as a problem of interpretation. It suggests a potential solution; that of determining if an incongruity exists. This means determining if students find gene expression metaphors intelligible and if so, then a fusing of horizons is needed which included further elaboration of the intent and use of the metaphor by science. This framework additionally points to a possible source of misconceptions.

90

Suggestions: Do the data bear these out?

Based on the analyses of the problem and the literature, I propose five suggestions to teachers when they use other-generated gene expression metaphors.

We will determine if the suggestions are supported by the results of the studies to be discussed.

1. Inform students that a metaphor is being used and that they can derive understanding of some aspect of DNA or gene expression from understanding and using the metaphor. (Carroll & Mack, 1999; Gentner)

2. Determine how students interpret the metaphor before you use it during instruction. This will allow the instructor to determine idiosyncratic interpretations and be certain that students realize how you and science are interpreting the same metaphor. (Strike & Posner, 1992)

3. Determine what students know about the base of the metaphor. Not just do you know the word, but what are the relationships and properties of the base that are available for students to make links to the target.

4. Work with interpreting the metaphors. Show students how the metaphor was used and how metaphorical expressions led to our current terminology.

5. Develop advance organizers to give students experience with relevant aspects of base concepts that are used as positive analogies to the target (Ausubel).

91

CHAPTER 3: DESIGN AND METHODS

Research Purpose and Hypotheses

Based on the model developed and the implications of that model (summarized in Figure 8, p. 93), the purposes of this research will be to:

1. Develop a model of learning and teaching in the domain of gene expression that focuses on language, specifically metaphor development and use, based on career of metaphor, Social Representation theory, Information theory, Communication theory,

Causal Status theory, Illusion of Explanatory Depth, Operations Research and contributions to the understanding of gene expression by philosophers of science.

2. State the implications of this model.

3. State questions that the model raises.

4. Test implications of the model.

a. Student understanding of gene expression metaphors.

b. Understanding of base concepts of those metaphors.

c. Metaphors students develop for gene expression will use base concepts that

reflect current culture referents.

92

Develop a Theory-based Determine Conceptual Model Implications of the Model Raises these Questions Test these Model Cognitive Linguistics Dimensions of the Model – Metaphor Development, Choice and Use Implications if gene expression metaphors are dead ▪Lakoff 1. Knowledge of base concepts should be ▪Chanteris-Black limited ▪ Hesse 2. Connection between base concepts and • Social Representation Theory target concepts is lost – recognition of the – Social representation of 1. What is students’ metaphor as a metaphor and students knowledge of the base aspects of the world memorize technical terms but without concepts of the ▪Wagner understanding • Career of Metaphor commonly used gene 3. Use of the technical term does not lead to expression metaphors? ▪Bowlde & Gentner nor necessarily indicate understanding of 2. Are any of the commonly • Illusion of Explanatory Depth gene expression used gene expression ▪Keil & Rosenbilt • Causal Status Theory metaphors dead? ▪Ahn 3. Do students consider • Cognitive Polyphasia/ Multiple 1. Instructors use metaphors for gene gene expression Representation expression that students do not understand metaphors to be apt? ▪Moscovici 2. Students have several explanations for the Why or why not? ▪Clark role of DNA in gene expression (cognitive 4. What metaphors would • Information Theory polyphasia) students use to explain ▪Devlin 3. Current metaphors for DNA and gene gene expression? • Communication Theory expression lead to a distorted view of the role 5. What is the difference in ▪Silva of DNA, gene expression, the regulation of the understanding of • Operations Research gene expression and are poor conceptual DNA and gene ▪Werzbicki bases for adding advanced concepts of expression between • Philosophy of Biology regulation, transcription and translation students who have been ▪Sarkar 4. The Flow of Information metaphor as currently instructed in the base ▪Fantini employed does not use salient alignable concepts of a metaphor ▪Maynard-Smith differences of information flow which leads to and those who have not? ▪Stegman a shallow use of information base concepts ▪Strasser ▪Sustar

Figure 8. Model developed with implications and questions raised by the model

93

Study Rationale and Theoretical Framework

How can the theories of social representation, public understanding of genetic

science, metaphor use and life of metaphor and Information Theory inform science

education researchers studying how students understand and learn about genetics and

gene expression?

1. By understanding that students come to formal education with ideas (metaphors,

images, symbols) about genes and gene expression influenced primarily by their culture

that includes the mass media and particular ethnic representations of reality in addition to

any formal science instruction the student may have had.

2. Scientists who teach these students use a set of metaphors that includes the

standard set that is part of their Metaphoric Categories (technical terms) for genes and

gene expression. Each also, according to the work of Moscovici (1961/1976) on

‗Cognitive polyphasia‘ and Clark (2003) on the use of multiple representation of an event

in a person‘s mind, but ‗which‘ used depends on the purpose for the representation, holds

more than one metaphoric representation of gene and gene expression to be used for

different occasions, such as talking with colleagues or to the lay public. And, it would be

interesting to investigate, if each holds a different metaphorical representation depending

on which role gene is playing.

3. Coming from different social groups, the objectified representation of the

scientist/teacher is most likely not the same as the objectified representation of the

student.

94

4. The scientist/teacher must understand that the base accessed when s/he uses a

metaphor may not be the same base concepts accessed by the student.

5. Perceived misconceptions are, in my estimation, related to problems of metaphor

use and it makes little sense to gauge student understanding of a concept, such as genes

and gene expression, influenced by the Deficit-Model that is, based only on knowledge of

facts. They are, as Martins and Ogborn (1997) argue, related to construction and use of

metaphorical models. The student will not understand the function of genes any better by

regurgitating facts; underlying metaphors must be addressed. For example, in Martins &

Ogborn‘s interviews with British primary school teachers, one teacher remarked: ―The

coding here is called a gene…the sequence itself is gene…it means gene is not something

physical is it?...It‘s a code…got it from the DNA‖ (p. 59). This is a problem of gene

being ‗subject‘ and ‗object‘. The scientific community‘s metaphors for genes are used by

this teacher, ‗Gene as code‘, but exactly what a code is and how DNA can be a code is

not evident. Additional examples of misconceptions/previous ideas on genes and gene

expression that can be interpreted as problems of metaphor use can be found at Consulta

de Ideas Previas (statements from students interpreted as metaphors are found in

Appendix A).

6. Presenting genes and gene expression within an Information Flow Analysis

scheme would present DNA (gene) as a passive player in gene expression and serve to

highlight the role of organelles and enzymes in the process. Work on understanding

student (and teacher) conceptions that result from the DNA AS MASTER MOLECULE

metaphor may help to explain why this interpretation of DNA may lead to problems

95 incorporating concepts such as epigenetic inheritance systems such as paramutation in plants (Ashe & Whitelaw, 2006), gene regulation as performed by micoRNAs (miRNAs)

(Nilsen, 2007), non-coding RNAs (ncRNAs), antigens and antisense agents, riboswitches and gene networks (Ansari, 2007) or how it is possible for genotype to remain unchanged but a change in environmental conditions can lead to different traits, such as work by

Kaiser and colleagues on the relationship of atmospheric oxygen concentration to the tracheal system of beetles (Kaiser et al., 2007) that the DNA AS MASTER metaphor would not easily accommodate; it would be difficult to project new information (Bowdle &

Genter, 2005), such as those discussed above, from the base concepts of the metaphor of

BLUEPRINT,INFORMATION, MESSAGE because DNA possesses none of the properties of these bases. As Moss (2003, p.71) states: ―Construed as language, DNA could just as well (and I would suggest better) be analyzed as context-dependent ―utterance‖ than as some form of primordial Holy Writ.‖ Context determines significance of a word, not vice versa.

7. Recent research has shown that genes work, or rather gene products, in networks

(Ansari, 2007). Perhaps a model for understanding gene networks and the role of DNA is the ISO/OSI model of seven layers of computer networks (Wierzbicki, 2007) developed in the early 1980s. The seven layers are: physical layer, transmission layer, network layer, transport layer, session layer, presentation layer, and application layer. Of course this model, which when applied to gene networks would act as a metaphor, is important because it highlights the fact that ―the function of such complex network not only cannot be explained by, but are also fully independent of the functions of its lowest, physical

96 layer, by the way of electronic switching elements work, repeat and process signals. On each higher layer, new functions and properties of the network emerge‖ (p. 614). Guess at which layer DNA would be? Yes, the physical layer. Not much understanding of the complexity and emergent properties can be gained by focusing on the physical layer,

DNA. If any metaphor of DNA and genes would be consistent with function, the physical layer of a system would be a better one than codes and information. Hubbard holds this stance and states that because of the interaction of components involved in protein synthesis ―It is wrong to single out any one substance or event as causal to any other‖ (in Spanier, 1995, p. 93).

97

Design and Procedure

Overview

The study was comprised of two major Parts, ―Is the Metaphor Dead?‖ and

―Resurrect the dead Metaphor‖. Students from previously-existing sections of introductory biology courses for non-majors at two central Ohio colleges and universities were randomly assigned to one of the studies discussed below; no students was asked to participate in more than one study. Students choose to participate if they wished.

―Is the Metaphor Dead?‖ looks at non-biology majors‘ understanding of commonly used DNA and gene expression metaphors and is comprised of three separate studies:

Study 1. ‗Are the gene expression metaphors dead?‘ seeks to determine student understanding of DNA and gene expression metaphors by asking them to explain how the target is or is not like the base. For example, if the student is presented with the metaphor

DNA IS A CODE, s/he will be asked how DNA is like a code. One Hundred seven students participated in this study.

Study 2. ‗Understanding of old metaphors of gene expression‘ asks a different group of students to explain 8 base concepts and then explain the meaning of the metaphor of which it is a part. Ninety-six students participated in this study.

Study 3. For ‗New Metaphors‘, a different group of students will be asked to provide their own, unique metaphors for six target concepts related to gene expression: DNA,

RNA, Protein, Transcription, Translation, and Ribosome. One hundred- twelve students participated in this study.

98

The second part of the research seeks to determine if incorporating a deciphering activity that highlights important concepts of the base term CODE of the metaphor DNA IS

A CODE will help students structure an understanding of the relationship between the major players involved in gene expression. This part is a quasi-experimental design in which an existing class is randomly assigned to one of two groups, the deciphering activity group and the group that does not perform the deciphering activity.

The following sections will discuss in detail the design of each study just introduced and the format of the stimuli with which students will be presented. Appendix

3 includes the form each task will take and the instructions that will be presented to students. The tasks are based on a survey with open-ended responses to each metaphor with the exception of aptness ratings which using a set scale. Stimuli for Part 1 will be available to students on their internet course management system. They will access the site if they wish to participate and type in their responses (explanations) of the metaphors.

Is the metaphor dead?

Since metaphor is the basis of our explanations of physical phenomena, it is here we should begin the search. How are gene expression and the role of DNA transmitted by instructors and understood by students within the ontology of information used and understood by students of modern day biology?

Study 1. Are gene expression metaphors dead?

Rationale: If the link between the target and base are lost, then the metaphor is dead. If students are not able to provide an explanation that links between the base information/language metaphors and the target concepts, then the metaphor is dead as a

99 link between target and base and base and Metaphoric Category. Alternatively, the student may have no idea how the base concept is related to the structure or function of the target concepts.

Task 1: Using the format of Gentner (1988, p. 55) in which stimuli were framed as

―How is _____ like a _____?‖, subjects were asked to respond to the following stimuli:

1. DNA is a computer program. How is DNA like a computer program?

2. DNA a code. How is DNA like a code?

3. DNA carries information. How is DNA like a carrier of information?

4. DNA is a language. How is DNA like a language?

Study 2: Understanding of Old Metaphors of Gene Expression

Rationale: Students who do not provide explanations for Task 1 may not understand the features of the base of the metaphor to extend to a target (Gentner, 1988, p. 49).

According to Gentner (1988), the objects used in the base of a metaphor may have both attributional and relational features that are used in the metaphor. Attributional features are used for appearance matches, relational features are used as analogues. Use of both attributional and relational features in a metaphor is called a double metaphor (Gentner,

2988).

I have argued that a possible explanation for students‘ difficulty with gene expression may be related to the fact that scientific terms for gene expression are dead metaphors that have lost the initial link between base and target concepts. Two hypotheses follow:

100

1. If the link between base and target is gone, the features students focus on when interpreting the metaphor should be the wrong features to focus on for the way the metaphor was intended to function.

2. If the metaphor is ―out-of-date‖, features of the base object should be few.

Task: To determine if students understand features of the base to extend to the target, three separate tasks will be used to ascertain students‘ understanding of the base concepts for gene expression.

The tasks, based on Gentner (1986, 1988) are:

Task 1: Write out descriptions of objects contained in the metaphor. Subjects will be asked:

a. Write down everything you know about…

i. DNA

ii. Code

iii. Language

Task 2: Interpret the metaphor

―Write down what meaning you think the following statements were meant to convey.‖

1. DNA is a computer program. How is DNA like a computer program?

2. DNA a code. How is DNA like a code?

Study 3: New Metaphors

Rationale: Students may understand gene expression by using alternative metaphors than the standard metaphors used by scientists and instructors. As was discussed above

(Martins & Ogborn, 1997), the use of metaphors used by scientists by a student does not

101 mean that the student understands the concepts that underlie those metaphors. However, it may not follow that if a student does not correctly use scientists‘ metaphors she does not understand gene expression concepts. How would we be able to determine how a student understands gene expression concepts without depending on their use of standard gene expression metaphors and technical terms derived from them?

Task: Subjects will come up with metaphors for a. transcription b. Translation c. DNA d. RNA e. Proteins f. Ribosome

In the form of: ―______is like ______because it ______‖ where the first blank will be the concepts a-f. Explain the choice you made.

Presentation of Stimuli

Students were randomly assigned (by software that is part of the Carmen system) to one of five study groups; three of the studies are discussed in this work. Each group of participants was presented with the statements for Study 1 or Study 2. Participants in

Study 3 were asked to provide metaphors for the six target concepts. No student participated in more than one Study.

Participants accessed the statements for the studies on their secure course web site: Carmen at Ohio State. A letter explaining the study and what they were asked to

102 do and a consent form appeared before the actual metaphor statements or target concepts

(depending on the study) are presented to the participant.

Sampling

The subjects for the proposed study were college students who were non-science majors enrolled in Introductory Biology course. These students were presented with instruction in DNA and gene expression at some level as these concepts were included in the United State‘s National Science Education Standards (Center for Science,

Mathematics, and Engineering Education, 1996) and the Academic Content Standards for the State of Ohio

(http://education.ohio.gov/GD/Templates/Pages/ODE/ODEDetail.aspx?page=3&TopicRe lationID=1705&ContentID=834&Content=51519); individual state science standards were based on the National Standards. Students also encounter gene expression concepts through media, as was discussed above.

Non-science majors make up the majority of a student population at most

American colleges and universities. Although the proposed model and its implications are hypothesized to hold for science majors as well as non-majors, non-majors will be chosen for the current study as they represent the majority of college undergraduates.

Institutions will be chosen whose students represent the top high school graduates and one whose students are accepted on an open admission policy. The choice of these institutions will allow for a broad cross-section of subjects in an attempt to determine metaphor use and understanding of as many sectors of the public (by sex, age, and racial and ethnic background) as possible.

103

Permission to work with students at The Ohio State University‘s (OSU)

Introductory Biology (Biology 101), was obtained.

About The Ohio State University

The Ohio State University is a land grant university with a main campus in

Columbus, Ohio and 5 regional campuses throughout Ohio. OSU employs a competitive admissions process that evaluates a student‘s college prep curriculum, SAT or ACT scores and high school performance with 91% of students ranked in the top quarter of their high school graduating class and 57% in the top 10% of their class; eighty-nine percent of incoming freshmen scored 1090 or above on SAT Reading and Math

(http://undergrad.osu.edu/domesticfreshman.html). Undergraduate enrollment is approximately 39, 000 of which 57 % are male and 43% are female, eighty percent are white, 7 % black, 3% Hispanic, 3% international, and 5% Asian; 92% percent of undergraduates are less than 25 years of age (http://oaa.osu.edu/irp/CollegePortrait.pdf).

All demographics and statistics were for the student population at the time of this study.

OSU Biology 101 is a 5 credit hour (quarter schedule) course that meets for one and one-half hours of lecture and 3 hours of laboratory per week. It is described as a course that teaches the ―[B]asic principles of biology; topics include nature of science, organismal diversity, evolution, ecology, genetics, reproduction, cell structure and function‖ and is intended for students not ―seeking an undergraduate degree in one of the biological sciences‖

(http://buckeyelink2.osu.edu/cbulletin/cdescription.aspx?dnum=075&cnum=101&cdec=

%20%20&cpre=%20&yrq=20092). Biology 101 is offered each of four quarters per

104 academic year. Enrollment in three lecture sections is large, typically 1300-1500 students per quarter with an approximate 60 -70 lab sections of up to 24 students each. Sections of the course will be randomly assigned to a study (1, 2, or 3) and a set of metaphors; see

Figure 10 for the overall sampling protocol).

One section of Biology 101 was chosen for participation in the study. The section was based on class size, course content (heavily molecular biology) and cooperation of the course instructor. Students were randomly assigned to one of five study groups using Carmen course management system.

Figure 9 presents a summary of the proposed studies for this research project.

Figure 9. Summary of the proposed studies for this research project.

105

CHAPTER 4: ANALYSES

The studies were designed using qualitative research methodology, specifically the Grounded Theory of Anselm Strauss and Juliet Corbin (1990).This method was chosen for several reasons: first, the goal of Grounded Theory is in the development of a theory of a specific phenomenon by determining and fully describing the dimensions and properties of categories used to formulate the theory. My overall future goal is to understand how metaphors help and/or hinder understanding of gene expression and the role of DNA in this process; second, as the name indicates, any concepts and categories that contribute to the theory you develop must be grounded in the data and you must be able to justify the categories by direct reference to the data; third, in line with conceptual change theory, we must understand how students conceptually understand a domain, identify how this is either congruent or incongruent with canonical scientific concepts, then develop methods to help students refine their conceptual understanding to mirror scientific explanations. We must understand the current conceptual understanding of students. Grounded Theory was seen as useful in an attempt to uncover students‘ conceptual understanding of gene expression through an interpretation of the metaphors commonly used in instruction and Theory –Constitutive Metaphors. The following sections describe the analysis of the student responses within the criteria of analyzing and evaluating the quality of qualitative data.

106

Coding

Student responses from Study 1, Study 2 and Study 3 and the statements from scientific papers and interview statements will be coded with two theoretical points in mind. The first point is that metaphors are constructed by linking a base to a target. Both the base and the target are composed of several concepts that may be linked as either an attributional sense as appearance matches (Gentner, 1988) or a relational sense where base and target share ―common relational structure‖ (Gentner, 1988, p. 48). Base and target concepts in each of the responses to each of the nine gene expression statements will be coded as either attributional, relational or both. This is related to an underlying ontology within the biological sciences- structure and function. That is, the function of a molecule, organelle, cell, tissue, organ, organ system is related to their structure.

The second point is that within each of these three codes (attributional, relational, and both) there may be concepts and certain of these concepts form categories that may indicate a pattern of thinking about the target of each metaphor that does not emerge from coding the data using only the three codes. Using the process of developing a grounded theory (Corbin & Strauss, 1990) as summarized in Figure 10, each of the three codes will be code using open coding and axial coding. The categories that result from this process are what are important for developing a grounded theory. Categories ―are the cornerstones of a developing theory‖ (Corbin & Strauss, 1990, p. 7). Concepts from the coding process may be different in the form they take but may be part of the same process; these concepts would form a category (Corbin & Strauss, 1990).

107

Datum Datum Datum Datum Datum Datum Datum

Concept Concept Concept Concept

Abstract Abstract Category Category

Figure 10. The general process for the development of a grounded theory from data to concept development, the formation of categories that comprise a grounded theory.

108

How the Coding was Accomplished

Axial and Open coding occurred as part of the same process of analysis. For

Studies 1 and 2, I would read the responses for each metaphor and for Study 2 for the explanations of the base concepts. This would give me a feel for what the students were saying about each metaphor or base concept. For example, as part of Study 2, while reading through students responses to explain the base concept ‗Language‘, I noticed that language was often described as a means of communication, the idea that humans, peopleused it also occurred frequently. I made note of these regularities when I began to closely read each individual response more closely. These were treated as phenomena of language that needed to be specified such as who did the communicating, how was communication carried out, and what form did the communication take.These were treated as action/interactional strategies (using The

Paradigm Model) which the phenomenon langauge was ―handled, managed, or carried out‖ (Strauss & Corbin, 1990, p. 97). Additionally, to further specify language, I looked for the consequences of those action/interactional strategies. Phrases that indicated a result of a certain action/interactional strategy and were indicated by such phrases as ‗so that‘, ‗in order for or inorder to‘, ‗then‘, ‗so‘, ‗to‘, and ‘results in.‘

Occasionally, but it was a rare occurrence, additional relationships that further established a category could be found in responses. Causal conditions, context and intervening conditions further refine relationship of concepts that make up a category.

109

Validity in Qualitative Research

Validity has ―to do with description and explanation and whether or not the explanation fits the description― (Denzin & Lincoln, 2000, p. 393) or put another way

―the trustworthiness of inferences drawn from the data‖ (Eisenhart & Howe, 1992, p.

644 in Freeman et. al., 2007). In order to ensure validity, all claims made must be based on the data as interpreted through the theoretical framework discussed, that is, be empirically grounded.

Corbin & Strauss (1990, pp. 17-20) discuss the criteria for empirical grounding of the findings. They are:

Criterion #1: Are concepts generated? Concepts must be grounded in theory and be put to use in the development of the theory.

Criterion #2: Are the concepts conceptually related? Are the linkages between the concepts grounded in the data?

Criterion #3: Are there many conceptual linkages and are the categories well developed? Do the categories have conceptual density? A grounded theory should tightly relate categories and sub-categories in terms of conditions, context, actions/inactions and consequences in order to give the theory explanatory power.

Criterion #4: Is there much variation built into the theory?

Criterion #5: Are there broader conditons that affect the phenomenon under study built into its explanation? Conditions noted in the explanation should not be restricted to the ones that bear directly on the phenomenon, but include macroscopic sources such as culture, values, social movements, etc.

110

Criterion #6: Has ―process‖ been taken into account? Changes must be linked to the conditions that give rise to it.

Criterion #7: Do the theoretical findings seem significant and to what extent?

Significance meaning the theory‘s importance in stimulating further studies and explaining a range of phenomena and does the researcher look beyond trivial and well- known phenomena when determining what the data indicate.All claims made from the analysis of the data will be evaluated with reference to these criteria.

Criteria for judging the Adequacy of the Research Process

Corbin and Strauss (1990) have discussed seven criteria that are used to judge the adequacy of the research process in the development of a grounded theory. The seven criteria are, as written in Corbin and Strauss (p. 16):

Criterion #1: How was the original sample selected? On what grounds (selective sampling)?

Criterion #2: What major categories emerged?

Criterion #3: What were some of the events, incidents, actions, and so on that indicated some of these major categories?

Criterion #4: On the basis of what categories did theoretical sampling proceed? That is, how did theoretical formulations guide some of the data collection?

Criterion #5: What were some of the hypotheses pertaining to relations among categories? On what grounds were they formulated and tested?

111

Criterion #6: Were the instances, when hypotheses did not hold up against what was actually seen? How were discrepancies accounted for? How did they affect hypotheses?

Criterion #7: How and why was the core category selected? Was the selection sudden or gradual, difficult or easy? On what grounds were the final analytical decisions made? How did extensive ―explanatory power‖ in relation to the phenomena under study and ―relevance‖ figure in the decision?

These criteria must be included in a discussion that uses a grounded theory.

Included in this discussion will be the early stages of the study during which papers and interviews with scientists involved in the development of the explanations of

DNA and gene expression were selected and analyzed for metaphors and thought processes thatinformed the selection of specific base concepts of metaphors that became standard within molecular biology and the series of three studies with students from a university in central Ohio.

The Current Metaphors of Molecular Biology

In order to determine the metaphors that are commonly used to communicate gene expression concepts, I have read the papers from 1950s that cover the major discoveries in gene expression, Horace Freeland Judson‘s book The Eighth Day of

Creation that resulted from interviews with 128 of the scientists of the time working on gene expression, Genes IX , Genetics for Dummies. These sources include those who worked on gene expression, what they wrote and said they did, a commonly used

112 college textbook and a book that simplifies concepts. The following is a list of the commonly used metaphors:

Code – began with Schrödinger‘s CODE-SCRIPT (1944)

Language metaphor

o Transcription- messages are transcribed

o Translation- sequence of bases of nucleic acids translated into amino acid

sequence language of proteins by special pieces of biochemical machinery

(Crick, HFJ, p. 179)

o Nucleic acids and proteins as alphabetic languages – sequence of bases,

amino acid sequences (Crick, HFJ, p. 179); proteins with amino acids as

letters of an alphabet arranged in words within the message (Herman R.

Branson, 1956 from use of information theory)

o Copying

o Library – including ‗genomic libraries‘ of plasmids that include genome

fragments

o Proof-reading

o Duplication

o Message- also from information theory

o Expression of the genes (Crick, HFJ, p. 180)

o Read a book – ―Information coded in the template is read by transfer

RNA‖ (Chantrenne, 1963)

Instruction

113

Gift-giving + container- ―…once ‗information‘ is passed into a protein it cannot

get out again.” (Crick, 1957)

Ribosome as tape recorder

Codon code for amino acids

Translation analogy to finding correct parking space

DNA as a plan

Container- ‗mRNA is responsible for carrying DNA‘s message‘; ‗strand holds the

gene‘s information‘ ; ―Moving the genetic information from DNA to protein:

(HFJ, p. 241);

Message – messages of genes

DNA as template- (Watson & Crick, Nature paper ―Each chain then acts as a

template for the information‖, HFJ, p. 159)

Information

Architect‘s plan- Schrödinger

Script – Schrödinger

Code of life, carrier of life, secret of life

DNA as blueprint (HFJ, p. 7)

DNA as master substance in the cell (HFJ, p. 7)

DNA carry specificity, information is already in the genes (Delbruck, HFJ, p. 40)

Construction – ―use the sequence of code information for amino acids to build

proteins‖ (Delbruck, HFJ, p. 153)

―D.N.A. is a code. That is, the order of bases (the letters) makes one gene

114

different from another.‖ (Crick in letter to son Michael, 1953, HFJ, p. 153)

DNA as code – ―the precise sequence of the bases is a code which carries the

genetical information.‖ (Watson & Crick Nature paper, HFJ, p. 159)

Container metaphor: ―sequence of bases carried the information‖ (HFJ, p. 159)

―how genes are switched on and off‖ (HFJ, p. 163)

War metaphor- includes the use of codes, implies secrecy

Industrial manufacturing metaphor including superior/inferior status,

boss/employee: ―determine the molecular machinery by which the commands of

the DNA are translated into proteins‖ (HFJ, p. 190)

Computer program (HFJ, p. 194)

Analysis of National Science Education Standards

Life Science Standards include sections on Reproduction and Heredity; an interesting relationship, to be sure. Reproduction is an actual physical process whereas heredity is a metaphorical description of one aspect of reproduction, namely, a focus on the DNA/chromosomes specifically the fact that there is an equal contribution from the male and female parent (during sexual reproduction) to the zygote. This fact is discussed within the human concept of inheritance; it is a metaphor that involves the giving of a material substance from parents to children. The metaphor actually made more sense in the 1600s and 1700s when it was thought that only the male contributed to the formation of the child as inheritance was from fathers, not both father and mother. But it is metaphorical, so the metaphor was extended to current conceptions of passing material goods from parents to offspring 115

When reading the standards for grades 5-8, genetic information is stated in terms of the container metaphor and the gift-giving metaphor. Under ‗Reproduction and Heredity‘ content standard it states, ―Hereditary information is contained in genes, located in the chromosomes of each cell‖ (p. 157, italics added). The use of inside/outside is a spatial concept related to the metaphorical thinking where genes are seen as repositories of ‗information.‘ However, this is not technically correct.

Although DNA is a 3-dimensional molecule, its 3-dimensional property is not related to its role in indicating the order of amino acids of a polypeptide. It is a direct linear- to-linear correspondence. Metaphorical expressions such as ‗gene mapping‘ and the directional terms ‗upstream‘ and ‗downstream‘ of a gene correctly reflect this linear,

2-dimensional, function of the nature of genes as sections of nucleotides along a longer chain of nucleotides, the chromosome. Although DNA and genes are referred to in both these senses, linear and spatial/container, only the former is technically correct. The latter may be related to DNA and genes being metaphorically referred to as the ‗Book of Life‘. Books have information, words, ideas, in them. We do not have a common way to express the relationship between books and information content other than spatial. There is no corresponding linear metaphor to express this relationship between a book and the location of information. The Standards are written around two uses for ‗genetic information‘, one is heredity and the second is protein synthesis. Perhaps because the focus is on the use of ‗information‘ in its hereditary capacity, the gift-giving and container metaphors more easily express these concepts. However, upon analysis of the language used to communicate both these

116

‗uses‘ of ‗genetic information‘ in the 9-12th grade standards, the metaphors remain.

For example, in the ‗Molecular Basis of Heredity‘ standards, we find the following standard with the metaphors used in bold:

In all organisms, the instructions (information) for specifying the characteristics (blueprint, plan) of the organism are carried in (container) DNA, a large polymer formed from subunits of four kinds (A, G, C, and T). The chemical and structural properties of DNA explain how the genetic information (information) that underlies heredity (inheritance) is both encoded (Code) in (Container)genes (as a string of molecular ''letters" (alphabet and language; note quotes to indicate known metaphorical nature)) and replicated (by a templating (Copy by impression) mechanism). Each DNA molecule in a cell forms a single chromosome. (p.185, emphasis mine)

We can also see the error in extending ‗instructions‘ to have meaning when we read in the first sentence, ―the instructions for specifying the characteristics of the organism‖, where the information here is for the characteristics, implying a direct one- to-one relationship between genes and traits (characteristics) and ignoring, purposefully or not, the known associations between DNA and the environment, epigenetic inheritance and the role of non-coding DNA, including RNAs. We may be seeing an instance where the older metaphors cannot be extended to these new relations. No mention of these concepts is made within the standards, although they are dated by molecular biology standards. But continued use may not allow these newer concepts to be understood and incorporated into an individual‘s conceptions of the actual role of DNA in cell function.

We can begin to see how deeply ingrained these metaphors are in talking about the role and structural characteristics of DNA and genes that it appears in

117

National Science Standards. How these spatial metaphors affect later conceptual development of gene expression requires investigation.

Definitions of Heredity

Herbert Spencer (1866, p. 254) wrote in Principles of Biology on the concept of heredity that ―[W]e must conclude that the likeness of any organism to either parent, is conveyed by the special tendencies of the physiological units derived from that parent‖ and that ―sperm-cells and germ-cells are essentially nothing more than vehicles, in which are contained small groups of the physiological units in a fit sate for obeying their proclivity towards the structural arrangement of the species they belong to.‖

August Weismann (1889, p. 71) stated that ―[H]eredity is the process which renders possible that persistence of organic beings throughout successive generations…‖ and further that ‖[T]he word heredity in its common acceptation, means that property of an organism by which its particular nature is transmitted to its descendants. From an eagle‘s egg an eagle of the same species developes; and not only are the characteristics of species transmitted to the following generation, but even the individual peculiarities. The offspring resemble their parents among animals as well as men.‖

Waddington (1939, p. 29) presents the following argument justifying the search for the physical basis of inheritance: ―Since we can easily find examples of an animal inheriting, say, the colour of its eyes from its father; and since there are no eyes in the sperm, which is the only connection between the two individuals, it is clear that

118 the eye colour must be represented in the sperm by something else which is responsible for passing on the father‘s characteristic to his son. We must therefore draw the distinction between the characters of an adult individual and the representation of those characters which are present in the germ cells and passed onto the next generation.‖

These definitions of heredity were developed during early investigations into aspects of heredity. Heredity itself is a metaphor comparing what offspring receive from parents during reproduction to inheritance of material goods from parents

(usually father) to offspring. These ideas about passing characteristics to offspring are used today in the gene-P conceptualization of DNA. We should not be surprised to see descriptions of the role of DNA using the metaphors in the studies framed as inheriting characteristics even though biologists are aware of the molecular basis of inheritance; old metaphors die hard.

119

CHAPTER 5: STUDY 1

In this Study, students were asked to write what they thought each of nine commonly used metaphors mean to them; the results of four are presented here: computer program, carrier of information, code, and language.

DNA is a Computer Program

We know from molecular biology that organisms not only have something ‗like‘ a computer program, they actually do have a program. But saying that does not, of itself, help me to understand how to make a mouse. Sydney Brenner, in Judson, p. 194

Student responses were coded for the action/interactional strategies presented for the metaphor DNA IS A COMPUTER PROGRAM; these strategies were the concepts.

The consequences of these strategies were also determined. The action/interactional strategies that described aspects of computer program development and use are presented as Figure 11. Concepts that refer to aspects of programs were grouped to make up Sub-categories.

One hundred thirteen students agreed to participate in the Study. Of those 113 students, 93 provided an explanation of the metaphor, 3 did not agree with the contention that DNA IS A COMPUTER PROGRAM and provided an explanation why they did not agree, 6 students did not provide an explanation indicating that ―they did not

120 know how DNA is like a computer program‖ or simply responding ―don‘t know‖, and

1 student did not know how DNA is like a computer program but ventured a guess.

Figure 11. Categories, sub-categories and concepts from students‘ action/interactional strategies developed from responses to DNA IS A COMPUTER PROGRAM.

From the 93 responses, eight sub-categories were developed from students‘ action/interactional strategy concepts; these were further grouped to Categories that captured four aspects of computer programs: writing programs, downloading or

121 installing programs, execution or running the program, and output or the results of running a program.

Category: Write

The category ‗Write‘ was made up of sub-categories of the action/ interactional strategy concepts and consequences that altogether describe the similarity of DNA to a computer program in that both refer to some aspect of writing a program that included what the program is made up of, features of programs, who does the programming, what the program contains and the program itself results. I will describe each of the sub-categories related to writing computer programs and DNA. A summary of the concepts and consequences of those strategies is shown in Figure 12.

Sub-category: Structure, Composition (of a Program)

Twenty-six students wrote that DNA IS A COMPUTER PROGRAM because of similarities in the composition of a computer program and DNA. The sub-category

‗Structure, Composition of‘ included the action/interactional strategy concepts

‗Codes‘, ‗Contains information/details/functions‘, ‗Molecules‘, and ‗Combinations.‘

Code

Fifteen of twenty-six responses that included ‗codes‘ or ‗code‘ as the action/interactional strategy for DNA as a computer program made up the concept

‗Codes.‘ The verbs used varied and included ―contains‖, ―has‖, ―uses‖, and ―is‖. One student used ―code‖ as verb: ―it codes.‖ There were three aspects that ‗code‘ was used: first, structure of a code indicated by the phrases ‗code is‟ or „coding is‟ in

122

Figure 12. Sub-categories, concepts and consequences that made up the category ‗Write‘ in the DNA IS A COMPUTER PROGRAM responses. Sub-categories are shown in shades of blue. Concepts that formed each sub-category are shown in a concentric arc adjacent to the sub-category wedge. Consequences of the concepts are in the arc outside of the concept arc.

123 which some sort of symbolic representation is used to represent a function; secondly, the function of a code in the sense of „codes for‟ a cell function; and thirdly, function as a cipher, a cryptic function, so that the code needs to be decoded for some action to be taken.

The ‗structure‘ aspect of code was developed from responses such as ―made up of genetic codes ATGC that must be used together to create the gene‖, ―has specific lines of coding makes [DNA] what they are‘, ――its [sic] a code that your body uses to operate. Like the matrix of 0s and 1s in a computer‖, and ―It is in its own programming language, acts like a computer program since programs follow the code, and the code is the DNA.‖

For the cell function aspect of code, students wrote: ―DNA uses genetic codes‖, ―is like code tells a piece of software how to run, when a certain prompt is received what commands to follow‖, ―contains coding for cell function‖, ―is a series of codes to run other functions of your body and ―writes codes for functions‖, ―has a code that tells its different parts how to work smoothly as a whole‖, ―uses codes to create an organism‖, ―are internal codes that reveal an outward appearance on a person‖, and ―is the code for your existance [sic].‖

The cipher, cryptic function of code was developed from responses such as

―contains code that can be deciphered by the cell to carry out certain functions…has set of codes for cell functioning.‖

Contains

124

Five responses included a reference to ‗contains‘ or ‗has‘. Not surprisingly, the focus was on the container ‗DNA‘ (container locative) due to the metaphor‘s focus on DNA. What did DNA ‗contain‘? DNA contained information, specific details, a set of functions, and specific programs. Students wrote: ―it contains the information that needs to be followed in order to make the body work‖, and ―it basically contains all the information needed to create all parts of the cell. It also acts as a long term storage for information‖, and indicating a bit of uncertainty in the response a student wrote that DNA ―Contains specific [programs] for specific functions and identification?‖

Molecules

Four students identified the composition of DNA as a code by making reference to molecules or the form that the molecules take, such as sequence. ―DNA is a mash-up of base pairs like binary code is a mash-up of 1‘s and 0‘s, but they code for something much greater‖, ―different programs do different things for a computer. different [sic] strands of dna [sic] do different things for the body‖, ―I can see DNA represented as a computer program, because each character or amino acid leads to a certain formula/code or protein strand‖ (this student added, ―But this is confusing and overly complicated‖), and ―an organism has many DNA sequences that form complex components.‖

Combination

‗Combination‘ included responses for which the combination that makes up the structure is important for both DNA and a computer program and included

125 responses such as ―each character… when combined you have the total function‖ and

―its [sic] very intertwined with a lot of information to really combine to make us up.‖

Sub-category: Features

This sub-category was developed to include action-interactional strategy concepts of computer programs that focused on aspects of a computer program, how parts are related to one another, how they are organized and for what it is that they are used. Twenty responses related one of these ‗Feature‘ aspects.

Complexity

‗Complexity‘ was used in eight responses. One aspect was that computer programs and DNA was made up of many different components and that was what made it complex. One student included a very detailed explanation and wrote, ―A computer program is very complex with many different components inside. From outside it looks like one object. Same with DNA, an organism has many DNA sequences that form complex components on the inside but from the outside, it looks like one organism.‖ In addition to complexity, the student also related a complex inside but looks like one organism from the outside. No one else mentioned this aspect of inner structure versus outer structure. Other students were more concise in their responses: ―DNA is a computer program, because like a computer program,

DNA is complex‖, ―DNA is like a computer program because it is very complex and includes many intricate parts‖, ―DNA is like a computer program because it is complicated and very complex‖,

126

In addition to the multiplicity of components that makes computer programs complex, these components must work together for the program (or DNA) to work properly. A student wrote: ―The language of a computer program is very complex,[sic] much like a program DNA is very complex. All of its complex parts must work together for it to work correctly. Once these parts are in place they connects [sic] and work together to make one.‖ This response includes aspects of

‗Complexity‘ and ‗Relationship between parts.‘

Relationship between parts

Three responses, in addition to the one just quoted indicated that there is a relationship between parts that were important to the functioning of a computer program and DNA; only one response indicated what the ―parts‘ were: ―DNA is like a computer program in the way that the individual ―wires‖ come together in the right way in order for the computer to work.‖ Responses where the identity of the ―parts‖ was not explicitly stated included ―DNA is like a computer program because a computer program has many parts that work together to make the whole work better.

DNA has parts that come together to make DNA work as effectively as it does.‖

Organized

―Computer programs are very informative, organized, and LONG, much like

DNA‖ (emphasis original); ―in order for a computer to run efficient [sic], everything must be in tact just like DNA‖; ―everything is written but in a strict pattern that is necessary for everything to work‖; ―I believe DNA is like a computer program because one of these programs is very exact and runs like a well-oiled machine just as

127

DNA has to be very exact to translate for the genes it needs to.‖ ―A computer program is very intrinsic [sic, intricate], detailed, and a vital part to a computer. DNA is also very detailed and without it, an organism cannot run, like a computer.‖ These explanations describe the computer program –like features of DNA as detailed, very exact, organized, and in a strict pattern with the consequence that an efficient operation results.

Actions Using

Features of a program also included ‗Actions Using‘ the program that included being copied and stored. ―DNA is like a computer program because it can be copied and even stored in other media with no loss of information.‖ ―DNA is like a computer program because it stores and presents the information that is needed by the ribosomes to build the different proteins. This is similar to computer programs because they save all your information on the hard drive that you can retrieve at different times to accomplish tasks.‖ The consequences of the storage of information were that information will not be lost and the information is available to build proteins

(accomplish a task).

Sub-category: Programmer

In a very interesting interpretation of the computer program metaphor, seven responses indicated that DNA was a programmer programming the way the body works, cells and genes, or itself. ―DNA programs cells and genes to act in a certain way in order to develop functional life. DNA programs different aspects of the body, creating the code for our lives.‖ ―DNA is like a computer program because it

128 sequences itself, like a computer program does, in order to relay information to the gene and to the rest of the body that can read a gene.‖ ―It programs how we function.‖

―Computer programs are based on numeral codes of 0 and 1 and the combination of these two numbers form distinct software and programs. DNA works similarly and it programs itself to form a human software.‖ ―DNA is like a computer program because it programs the way our body works.‖ DNA, as programmer, programs cells, genes, itself or a function such as the way the body works. The consequences of the programming were for functional life to develop, to relay information, how we function or how our body works.

Sub-category: Programmed

Six responses mentioned that DNA was programmed to perform a certain function but the ‗programmer‘ was not identified. Explanations in this vein included:

―It is programmed to always do the same thing. Nothing can change the program‖ (I will have more to say about this response in the Discussion); ―DNA is like a computer program in that computer programs are programmed with a series of functions that serve a purpose. With DNA, the nucleic acids are the functions that tells [sic] the program, DNA, what it is supposed to do. For this example, the nucleic acids would determine what the DNA is supposed to do and what genes it would carry.‖; ―it‘s programmed for certain development‖; ―it is programmed to contain all the information about your body‖; ―DNA is programmed for each of us like programs are programmed for computers.‖

Category: Download/Install

129

The second feature encountered with computer programs is that they need to be downloaded and installed into a computer to be used. Responses such as ―It has genes programmed into cells to dictate what they should do‖ and ―code entered into the body allows it to run the whole body‖, ―A computer program asks you to take different steps before you can install a computer program‖, ―DNA is a compouter [sic] program because it needs to load itself and install itself for it to work‖, with one student focusing on the time factor it takes to accomplish downloading and installation when it was explained that ―like a computer program, different options are available and it takes time to download or upload many if the processes‖ and, in a creative interpretation of the metaphor, parents install their DNA into their children: ―A computer program is downloaded to the computer and makes up the computers way of working as DNA is given from the parents genetic make-up and installed into their children and programs the way the body works‖ convey this download/install feature of program use. There were five responses that focused on this feature and the consequences of the download and install feature were that the body or cells worked.

Downloaded and installed programs allow the computer or person or cell to work.

Figure 13 shows the summary of this category.

130

Figure 13.DNA IS A COMPUTER PROGRAM action/interactional strategy concepts and the consequences of those strategies that formed the categories ‗Download/Install‘ and ‗Run/Execute‘.

Category: Execution/How Executed

Sixteen responses focused on the ‗Execution‘ feature of computer programs when explaining how DNA was a computer program. Three action/interactional strategy concepts and their consequences were developed from those responses that focused on running the program in a sequential order of steps, features of execution and similarity to an operating system. These concepts and the consequences are summarized in Figure 13.

Sequential Order of Steps

131

This concept was developed from explanations that focused the requirement that a computer program needs to be run described by students using language such as

‗run‘, ‗carried out‘ or ‗read‘. Most often, the ‗computer‘ that ran, carried out or read the program was not identified by the student. Responses that were used to develop the action/interactional strategy concept of ‗Sequential Order of Steps‘ included those responses that most clearly stated that programs are carried out in different steps:

―DNA is like [sic] a computer program in that there are different steps you have to take in order to get to where you want to be‖, ―DNA is like a computer program because it has different steps in order to get the living organism to function properly‖,

―It is a set of instructions that are followed through in a progressional [sic] manner to achieve a certain desired output‖ to simply stating that DNA is read or run by the body or part of a body seen in explanations such as ―DNA is a computer program because it runs on your body and tells your body how to work and acts like a computer, sending messages to a cell‖ and ―It is read sort of like binary code only with letters.‖There was one student who gave similarity relations between computers and programs and a cell and identified the computer: ―It is like a computer program in that the cell acts as the computer. The cell reads the DNA and performs accordingly, just as a computer would.‖

‗Features of‘ Execution were noted by several students who wrote of the efficiency-like nature when DNA and programs are run stating ―DNA is like a computer program because it runs efficiently but at times there may be glitches‖, ―A computer program maps out a system to run that program, similar to DNA‖

132

Several students compared DNA to a computer program in the feature of a operating system. One student explained the metaphor as ―DNA is a computer program because it runs the operating system of the cell.‖

Category: Output

The final feature of a computer program that was used to explain the metaphor was ‗Output‘, that is, what the final result of the program or DNA would be which we will designate as the ‗Functions.‘ This category was developed from action/interactional strategy concepts from 26 responses that were categorized as

Output including ―Tasks or What gets done‘, the appearance of the organism, designated as ‗Looks‘, and that the final result was the ‗Whole.‘ Additionally, students explained that the final result of the DNA program was to ‗Give or Carry

Out‘ some process, and lastly that the organism ‗Runs‘ because of the program that is present in the organism. These action/interactional strategy concepts and their consequences that make up the category Output, Sub-category Functions is shown in

Figure 14.

Output: Tasks/What gets done

One of the features of a computer program and DNA was that discussed was that both perform tasks or functions, including construction of molecules, providing an outline for development, or telling other things what to do as their raison d‘être. These features can be seen in responses such as ―DNA tells other things what to do.

Computer programs have things encoded in them like DNA and tells other things what

133

Figure 14. Summary of the action/interactional strategy concepts and the consequences of those strategies for the category Output, Sub-category Functions developed from student responses to the DNA IS A COMPUTER PROGRAM metaphor. to do in order for the program to work‖, ―DNA is the blueprint, the ―program‖ behind the construction of proteins in a cell as well as RNA molecules‖, ―DNA is a computer program because it is developed to do a certain function just like each portion of DNA is‖, ―DNA is like a computer program because computer programs are designed specifically to serve a function and DNA is like that too‖, ―It does a specific job‖,

―The functions within DNA get operated just as functions are operated in a program‖,

―DNA‘s function is to provide the genetic code and overall outline for how cells

134 develop and where‖, and ―DNA is like a computer program in that it has a specific job to perform, and does this by assigning various tasks.‖

Output: Looks

―A computer program and DNA are both internal devices that have external appearances whether on the computer screen or on a person.‖ ―DNA is a computer program because they both work in a way that what composes them is different from what the user or individual actually sees. Writing one thing in DNA or a computer program will lead to a different outcome for its appearance.‖ ―It dictates how the person forms.‖

Output: Whole

―A computer program helps set up something important like Microsoft Office on a computer. DNA helps create different parts of a living organism in hopes to allow it to grow and prosper, much like a computer program can help strengthen a computer‘s overall use.‖ ―DNA helps our bodies operate in different ways also with restrictions such as recessive and dominant traits.‖

Gives/Carry Out

―DNA gives the genetic information of a person like a computer program can do.‖ ―DNA has specific details in the way its [sic] made so carry out the function of your body to create height, eye color, etc.‖ ―Allows people to have an identity and function.‖ ―A computer program can help you determine things about a computer, just like DNA can help you determine things about a person.‖ ―Tells us what to do.‖

―Computer programs give instructions to the computer. DNA gives instructions to the

135 cell.‖ ―A computer program carries out a certain function, some have different functions. Just like DNA does.‖ ―It carries out designated tasks that were created by an outside force.‖

Runs

The category ‗Runs‘ was developed from strategies that indicated that DNA as a computer program makes the body ‗run.‘ ―Because it makes the body system run.‖ ―It runs how the person is.‖

Discussion of Study 1

Several students gave explanations as to why DNA is not a computer program.

One student wrote that ―I don‘t relate DNA to a computer program. For me, I envision a computer program as taking specific inputs, and through some process, transforming them into an output. I don‘t relate this to DNA as I do not associate specific inputs with the operation of DNA.‖ This student focused on the ‗Execution‘ aspect of computer program function. This is counter to the student who wrote that ―is like code tells a piece of software how to run, when a certain prompt is received what commands to follow.‖ With the first student, we encounter an example where inputs are not seen as applicable to the function of DNA but for the second, inputs are what allow commands to be followed. However, work starting with Jacob, Monod, and

Pardee in the 1950s on gene regulation- transcription regulation and also post- transcriptional regulation- that continues to this day has clearly demonstrated that

DNA is subject to inputs from within the organism and from the environment for its role in function within a cell.

136

Is it the metaphor itself that hinders the student from accepting that DNA can be regulated, that there are ―inputs it responds to‖? And what role does the interpretation of this metaphor play in the students‘ conception of how living things respond to their environment? How do they do it? Does DNA and regulated gene expression not play a role?I posit that metaphor does play a role in how students understand DNA and further that student understanding of the base of the metaphor affects how the metaphor will be interpreted; incorrect understanding of the base will lead to incorrect understanding of DNA. This is a plausible hypothesis. Supporting this contention, there was the student who wrote: ―DNA has a code that tells its different parts how to work smoothly as a whole, they must coexist so the body as a whole can run smoothly. This way when the program is told to do something, it can do it with ease. DNA is the same way.‖ The feature of computer program that was used in metaphor interpretation included that programs receive ‗input‘ – ―when the program is told to do something‖. This ‗regulatory, respond to input‘ function of

DNA and computer programs needs to be stressed if one is both using the computer program metaphor or some related version, such as software, and are talking about gene regulation.

This is a common thema in biology, one of the agreed upon properties of living things: organisms respond to their environment. DNA does play a role but the relationship of DNA to the environment and why proteins are made when they are is not commonly discussed with non-majors. We instead focus on a one-way ―flow of information‖ concept starting with DNA and ending with a protein, in essence, the

137

Central Dogma but there is no ―input‘ in the opposite direction; ‗nothing‘ seems to be

‗talking‘ to DNA.

My thesis that these metaphors were developed early in the history of gene expression research before gene regulation was fully understood, or accepted for that matter -even Francois Jacob had to convince Monod that regulation was possible (lead to the origin of the ―genes switched on/off‖ metaphor). And that metaphors promote thinking about a target (in this case DNA) in a specific way, and this may make it more challenging to construct propositions to the new concepts because you have framed an existing concept a specific way (due to the metaphor used) that does not allow say gene regulation ideas to be added to the idea of DNA as a master, not responding to input, ―molecular communication‖ from both inside and outside of the cell. Is the root of what we call ‗misconceptions‘ and/or difficulty learning new concepts related to pre-existing schemata related to metaphor interpretation?

There was an interesting relationship between computer, including some confusion of what the ‗computer‘ exactly is composed of, computer program and operating systems including the features of each. For example, when writing about the relationship between the computer and a computer program, one student wrote that ―A computer program sets up a system that is followed in order to make the computer work‖ or another who said that ―DNA programs cells and genes to act in a certain way in order to develop a functional life. This is much like a computer program telling a computer how to act in order to reach the end that is desired.‖In a related vein, ―DNA is like a computer program because it allows people to have an identity and function

138 like a computer programs [sic] allows a computer to function.‖ I am reminded of

Pavlov‘s use of the factory metaphor to understand the structure and functioning of the digestive process in mammals. Pavlov worked with a conception of a factory as a well-organized, functioning place contrary to the factories of the times that were quite the opposite (Todes, 2002). Pavlov‘s conception was not founded on any concrete experience of a factory but by his admiration for Western Industrialism and construction of how factories must operate to achieve the progress they have demonstrated. These students‘ conceptions of the relationship between computer, program and operating systems is superficial and incomplete and, although additional questioning of the students would be necessary, it would be interesting to determine exactly the basis for their understanding of computers and programs and operating systems. Is it Pavlovian, as first reading would seem to indicate?

In a bit of confusion with the computer program metaphor and how DNA is a program, a student wrote, ―I don‘t really understand how DNA is like a computer program. I think DNA is more like an operating system.‖ Here, confusion about the structure and function is not enhanced through the use of the metaphor but further the metaphor may actually interfere with further conceptual understanding of DNA. A different student had a different conception of what the operating system was- the cell- when it was written that ―DNA is a computer program because it runs the operating system of the cell.‖ There is inkling of the relationship between DNA and the cell and for lack of an ―on‖ after ―runs‖, that is a completely different conception of the

139 identity of the operating system compared to the student who identified DNA as the operating system.

About computer programs and DNA as a program, one student wrote: ―It is programmed to always do the same thing. Nothing can change the program.‖

Computer programs, and DNA, can be changed: computer programs by patches and updates and DNA through various types of mutations- point mutations, insertions, deletions, mobile elements (transposons). This fact is important to the understanding of the development of variation within a species and speciation that is part of the molecular basis of evolution by natural selection; one proposed mechanism of evolution (natural selection) involves variation due to random mutation and selection based on these differences.

Students who described DNA as being programmed did not specifically mention a ‗programmer.‘ This may lead to negative analogy of a sentient, willful, entity doing the programming of DNA. Current theories of the origin of DNA include the RNA World hypothesis, the viral origin of DNA in both prokaryotic and eukaryotic cells including the work of Forterre (2006) and Villarreal & DeFilippis

(2000) and the role of hydrothermal vents on the ocean floors (Martin et. al., 2008); none of these includes a sentient programmer.

DNA IS A LANGUAGE

One hundred twelve students provided interpretations of the metaphor DNA IS

A LANGUAGE; thirteen gave more than one action/interactional strategy. All

140 interpretations were coded for action/interactional strategies for the analogy between

DNA and language to form concepts of related strategies. Similar concepts were grouped to form a category. The concepts were further described by the consequences of the action/interactional strategies. After this coding, eight categories were developed from action/interactional strategy concepts: Internal Dialogue,

Uses/Aspects of Language, Private Language, Order, Know Language to Understand,

Translate, Code, and Purpose. These eight categories with the concepts that were used to form each category are summarized in pie chart as Figure 15 (p.142). Categories are depicted as the colored wedges; concepts used to form each category are shown adjacent to the category wedge. I will explain the formation of each category and how the action/interactional strategy concepts were developed from student responses.

Consequences of the strategies will also be summarized.

Category: Internal Dialogue

One interesting theme began to present itself as I began to group strategies from 36 responses together, that of communication. This was not unexpected since communication is a main function of language and would be readily available for similarity relations when interpreting the metaphor, but was unexpected since that was not the feature used by Crick and early molecular biologists when they developed and began to use the metaphor. Related ideas included DNA speaking to, DNA Telling

141

Figure 15. Compilation of the categories, action/interactional strategy concepts and their consequences that formed those categories developed from student explanations of the metaphor DNA IS A LANGUAGE. and Instructing and information were provided. I next looked at the strategies I had classified as Communication that included those explanations that specifically used the verb communicate, or noun communication to see if there were any interesting features of communication that might provide insight into how students used communicate. There were interesting uses of communicate as a result of that further reading and DNA‘s role in communication. DNA was described as a participant in communication as in DNA communicates with (Figure 16). DNA was a participant in

142 communication with an organism, cells, the body, body parts or through genes to organism parts. The consequence of this communication was that the interlocutor

Figure 16. Internal Dialogue Category formed from action/interactional strategy concepts from student interpretations of the DNA IS A LANGUAGE metaphor. obtained information about their structure, function, how to act, what to do, when to reproduce, to maintain health, and how they should be constructed.

DNA was also described as the medium of communication used by molecules and cells. In this sense, DNA was functioning as a language. The consequence of the

143 communication using the DNA language was so cells could work together to construct a larger being. DNA was the language DNA used to communicate with RNA.

A final strategy of communication was the intent or purpose of the communication was an important feature. The one consequence for the purpose of communication was to store information.

Due to the observation that the communication DNA used for dialogue was with structures or molecules that DNA was inside of and DNA was used as a medium of communication between cells or molecules, I re-named the Communicate concept as ‗Communicate Between/Within.‘ The action/interactional strategies of twenty-two responses formed this concept.

Two concepts related to communication were developed from strategies from

12 explanations that explained DNA‘s language relationship in terms of speaking or telling. At first, these two may seem to be part of the ‗Communicate Between/Within‘ concept. However, to communicate seems to be vaguer than to Speak and most especially to Tell which indicates a unidirectional, almost monologue version of communication. Similar in conception to DNA as a participant in communication,

DNA Speaks to Cells and the Body and as a consequence of speaking to the body, the make-up of the body is known and the body forms appropriately. DNA was also seen as a medium of the speaking between cells. Tell and Instruct was what DNA does to parts of the cell or to organisms the consequence of the telling to both was structure and function.

144

Lastly, the Internal Dialogue was done for a purpose to provide information to cells about their functions and processes was developed from 3 explanations.

It must be noted that in none of the explanations that were used to develop the concepts was the communication, speaking or telling bi-directional in nature; only the sub-concept in which DNA was described to be a language used by cells to communicate could the communication be interpreted as bi-directional.

Category: Uses/Aspects of language

Uses or aspects of language was developed from action/interactional strategies concepts that conveyed why language is used and aspects of language including what forms of language exist and their complexity (Figure 17, p. 146). Twenty-three explanations of the metaphor discussed one of these features of language.

How Language is Used includes action/interactional strategies where DNA and language are spoken, written, read, studies, interpreted, can be learned and that all organisms can speak. The consequences of these uses of DNA as language were that cells follow commands, because it can be interpreted so that we can understand traits in organisms or how a living thing is comprised and organisms can speak it.

Additionally, DNA is like a language because it follows rules and has proper techniques plus there must be a transmitter and receiver of language. A consequence of the rules for structure of language and what occurs between a receiver/transmitter for students was the difficulty for interpretation and to be able to understand the language.

145

Figure 17. Uses/Aspects of Language Category formed from action/interactional strategy concepts from student interpretations of the DNA IS A LANGUAGE metaphor.

DNA as a language has meaning and cells know the meaning of the sequences of DNA, DNA stands for something and can be understood. Additionally, languages, including DNA, contain or stores information and send a message as a consequence organisms can carry out processes. And lastly, languages are complex and difficult to learn.

Category: Private Language

The category name ‗Private Language‘ is derived from the linguistic phenomenon where a language is developed and used by two or very few individuals

146 because they are the only ones who know the language. Twenty-two responses were used to develop concepts that define this category. Two concepts were developed from action/interactional strategies that can be interpreted to mean that DNA is a rare and unique type of language (see Figure 18, p. 148). ‗Individual Differences‘ indicated the uniqueness of DNA to an individual taking private language to the extreme of a single individual. Students wrote that ―different for each person‖, ―just like people have different DNA‖, ―organism learns language, only that person with that DNA can understand‖, ―talk to body in own individual language‖, ―has it‘s [sic] own meaning each person is different and each person has their own way of talking‖, and ―made for your own body.‖ ‗DNA is Unique‘ in the sense that DNA is different for every person or organism and it is that difference in DNA that consequently leads to the differences we see between individuals as expressed in statements such as ―DNA is different‖, ―is very specific‖, and ―different from the next.‖ A third strategy, ‗Different Languages

Exist Just Like People Have Different DNA‘ compares the observations that there are thousands of different languages in the world and as different people speak different languages there is different DNA. Students wrote ―every language is different just like everyones [sic] DNA is different‖, ―different among cultures‖, ―is its own language‖, ― only certain combination‘s [sic] can make up a certain individual kind of language‖, and ―just like people have different DNA.‖ Students who conceptualized

DNA as a language in this manner did not elaborate on the consequences of these action/interactional strategies.

147

Figure 18. Action/interactional strategies that were used to develop the category Private Language from student explanations of the metaphor DNA IS A LANGUAGE.

Category: Order

For seventeen responses students conceptualized DNA as a language by using the syntax feature of languages-words and sentences- and the order of the structural components, nucleotides, and how they are arranged. The action/interactional strategy concept ―Arrange‖ focused on the arrangement of components or how they are put together as was stated by students as ―DNA is like a language because it has parts that can be arranged in certain ways that mean different things‖,

‗Sequence‘ was a concept of Order that focused on the sequential, linear pattern of nucleotides, bases, genes, or amino acids. This feature of languages was the aspect that Crick stressed when comparing DNA to a language. This was clearly communicated by one student: ―DNA is a language because the nucleic acids can be seen as words in a language, and when words (nucleic acids) come together they form

148 a sentence, and the sentence represents language.‖ Other students wrote ―DNA is like a language because the combination of four bases create [sic] different results. Its

[sic] often used a coding sequence too.‖, ―DNA is like a language because it contains bases, A, G, C and T that when combined and replicated often create messages‖,

―DNA has set Nucleic acids much like a language has set letters. These nucleic acids are set up in a certain order to create certain proteins, much like the words of a sentence are organized to create meaning,‖ ―DNA is based on a four letter alphabet

(A, C, T, G) and these letters form codons or words that instructs genes to structure in a certain pattern‖, ―DNA has own special ―code‖. Every code on DNA stands for a character in language. All the code are [sic] arranged in a particular sequence which means unique information.‖‖has a specific set of letters and numbers‖, ―it uses sequences of amino acids to code for a protein‖, and ―it has parts that go in a certain order just like in language where there is a specific order in which sentence parts must be arranged.‖ One response contained both ‗Order‘ concepts: ―DNA is basically a language. DNA is built up of nucleotides, just like other languages are built of letters and words. [Sequence concept] In language, components have to be put together correctly or the final message will not make sense. In DNA, if all the components are not correctly put together then the final message will not make sense and there will be mutations in the living organism. [Arrangement concept]‖ These concepts and the consequences of those concepts are summarized in Figure19, page 150.

The consequences of sequence and arrangement concepts ranged from the proximate and very specific molecules of protein to the ultimate and vague features of

149

―certain patterns‖, ―cellular information for different traits‖, ―traits‖, ―create messages‖, and ―functions.‖

Figure 19. Action/interactional strategy concepts and their consequences that define the category ‗Order‘ for the interpretation of the metaphor DNA IS A LANGUAGE.

Category: Know Language to Understand

Twelve responses focused on the feature of language that because there are many different languages and not everyone knows and can understand every language.

As a result, to understand a language, you have to understand it. Three action/interactional strategy concepts were developed: ‗Some do but others do not‖,

‗Need specialists‘, and Personal language.‘ Figure 20 (p.152) shows these concepts and the consequences of those strategies.

The concept ‗Some know but others do not‘ was developed from student responses that indicated that in order to understand a language you have to know it.

Examples such as ―not all can be read/understood‖, ―some understand it, some don‘t‖,

150

―have to know both languages‖, ―everyone doesn‘t understand it if they haven‘t studied the language and become affluent [sic] in it‖, ―cells know exactly what the meaning of each sequence are. This information comes fluently to the cells, just like

English comes to a native-English speaker‖, and ―people have to know both languages in order for their [sic] to be communication just like DNA‖, ―it is like a language because without knowing what the language is, you don‘t know what it is saying. Its like when you go to a foreign country and talk to someone who‘s [sic] language you do not know. It all sounds like jibberish.‖

The concept ‗Need specialists‘ focuses on the observation that some languages are so specialized that only a few, well-trained individuals can read and understand them, one students wrote ―it can be understood by only scientists and other professionals that really know what everything means.‖ Two students‘ interpretations and emotions about the aptness of the metaphor were at odds with each other. One student who clearly indicated that the meaning of the metaphor was no apparent but attempted an interpretation anyway wrote ―don‘t quite understand how

DNA is a language. I guess DNA speaks different languages through data that we human [sic] would not understand if not scientists.‖ The other wrote ―It is very specific and informative. It can only be read by a few qualified individuals.

The concept ‗Personal language‘ talks about shared communication based on a common language. For instance, a student related that ―DNA is like a language because it can only communicate with its own kind. If this were not the case cross breeding would be possible with any number of animals, but since it is only a small

151 number of very genetically similar species can be cross bread [sic].‖ For this student, this personal communication allows for cross breeding between genetically-related animals; genetically-related is similar to sharing a common language. One response has elements of all three concepts: ―DNA is like a language because not everybody can speak it. However those that can know it in great detail and can share their knowledge with other people that know about DNA.‖

Figure 20. Action/interactional strategy concepts and consequences of the Categories ―Know language to understand‘, ‗Translate‘, ‗Code‘, and ‗Purpose.‘

The consequences of knowing a language was that of understand information,

―knowing what everything means‖, and communication can only occur between genetically-similar organisms.

152

Category: Translate

A consequence of the multitude of languages is the need to translate from one language to another and that a ‗translator‘ is necessary to accomplish the translation.

Twelve students focused on this feature of languages when explaining the similarity of

DNA and language. Students wrote ―DNA can “tell” us what’s the secret of heredity when we translate its language to ours‖, ―it is read and translated for a specific reason‖, ―DNA can be translated‖, ―DNA, like a language, stands for something and needs to be translated in a way so people can understand it. DNA is translated through outward appearance based on what it is made up of internally‖, and from a student who clearly felt the metaphor was apt wrote ―DNA is definitely like a language. It is a language that can be translated (into RNA, then protein), and a language that can be communicated (outwardly, by eye color, skin color, height, etc.).”

There is a need for someone or something to do translating. ―It needs to be translated by different things in order to be understood‖ does not identify a specific translator only the need for one and ―it translates the genetic code into polypeptide bonds‖ infers that the translator is DNA, that is, DNA translates itself; DNA as translator.

Category: Code

Five students described DNA as a language by drawing upon the code-like features of DNA. Two aspects of a code were used: DNA as‘ a code‘ and ‗Actions with codes‘ including encoding and decoding. As a code, students wrote ―DNA codes

153 for specific traits‖, ―it is a language of genetic codes‖, ―it has a code‖, and ―DNA has own special ―code‖. Every code on DNA stands for a character in language. All the code are arranged in a particular sequence which means unique information.‖

‗Actions using codes‘ compared the need for translation of one language to another with codes which are decoded or encoded to a different form. ―DNA is like a language because like a foreign language it can be decoded into our native language to make sense and convey a message.‖ ―It is encrypted and hard to decipher‖ focused on both aspects of code, encoding and decoding.

Category: Purpose

Three responses related that DNA is a language because languages have a purpose; this highlights the pragmatic aspect of language. As a language, DNA is used ―to make proteins‖, body parts can understand their roles and ―genes create body parts.‖

Syntax, Semantics, Pragmatics

There are three aspects of language use acknowledged by linguists; they are syntax, semantics and pragmatics. Syntax language use includes sentences and words and the arrangement of these to create well-formed sentences in language. Semantic language use entails the understanding, message, information, meaning and implications and includes conceptual semantics which deals with the meaning of a word, phrase, sentence or text and lexical semantics which studies word meanings and word relations. Pragmatics studies language use and the contexts in which it is used.

154

The categories of action/interactional strategies for DNA IS A LANGUAGE were classified as either pragmatic, semantic or syntax. Sixty percent of the responses were classified as pragmatic and included the categories ‗Internal Dialogue‘, ‗Uses/Aspects of Language‘, ‗Translate‘, ‗Code‘, and ‗Purpose‘. Twenty-six percent of responses were classified as semantic uses of language and included the categories ‗Know

Language to Understand‘ and ‗Private Language.‘ Table 1 summarizes the classification. A syntax aspect of language was used by 13% of students to explain how DNA is a language as reflected by the category ‗Order.

Aspect of Action/Interactional Strategy Percent of Language Concepts Category Responses Pragmatic 60.4 Internal Dialogue 27.5 Uses/Aspects 17.6 Translate 9.2 Code 3.8 Purpose 2.3 Semantic 25.9 Private Language 16.8 Know Language to 9.1 Understand Syntax 13 Order 13

Table 1. Classification of DNA IS A LANGUAGE Categories into pragmatic, semantic or syntax aspects of language and pervasiveness of those aspects.

DNA IS A CARRIER OF INFORMATION

The dominant idea in molecular biology is that DNA carries information encoded in the form of specific sequences of nucleotides which determines the amino acid sequence of proteins. Sydney Brenner, Cold Spring Harbor Symposium, 1961

155

The conceptual metaphor that explains DNA as a carrier of information is, like code and language, one of the older metaphors used by molecular biologists and is related to them conceptually through information Theory. Information, according to

(Shapiro, 2009), is the conceptual metaphor through which scientists should continue to frame their hypotheses and theories about DNA function. As such, an understanding of how students understand this foundational conceptual metaphor, not only because it helped form the conceptual foundation of models and as a source for neologisms related to DNA function in the past, but because of its predicted continued use in the future.

When analyzing students‘ responses to the information carrier metaphor, I needed to account for their understanding of both base concepts: carry and information. Both can have multiple meanings and the choice of meaning can affect understanding of DNA function. Both carry and information had very specific uses when the metaphor was used by molecular biologists beginning in the late 1940s and

1950s. As was mentioned, Crick made it a point to state specifically what he meant when he used information.

Carry, as a verb, can have two distinct meanings: hold or contain and transfer, as to move from one place to another. Carry had the hold or contain meaning in mid-

20th century molecular biology. Information referred to the order of bases of DNA used in the synthesis of a protein. I had these definitions in mind when coding responses.

156

How did students explain „Information‟?

I had initially began the analysis of responses by looking for ―what information is/ about‖ because, from the initial few responses it did not seem like the specifics of information was only about the structure of DNA but also included the ultimate use of the information either by a mutlicellular organism or a cell. So I initially had two concepts: information ―Is‖ a molecule or a code and information is

―About‖ some ultimate use.

I needed to further define each of these two concepts. So I went through each response and determined what ―is‖ and ―about‖ described. In doing so, these further refinements were the concepts and ‗Is‘ and ‗About‘ were categories. As a result of this further coding, the Information category ‗Is‘ was defined by 6 concepts: Codes,

Structure of DNA, Genes, Genetic Information, Message and Data.

1. Information as ‗Genes‟ concept was used in 12 responses. Eleven specifically used only genes and one more used genes and traits.

2. Information carried was related to the „Structure of DNA‟ in 10 responses. Of these 10, 7 responses specifically mentioned some aspect of the molecular composition of DNA, mentioning bases, nucleotides, base pairs, deoxyribonucleotides, and nucleic acids. Students wrote:―nucleotides contain the information‖, ―carries nucleic acids‖, ―4 bases A, T, C and G are that information‖, ―the way it‘s made forms a double helix‖, and ―base pairs make codons that code for different things about your body.‖ Three students additionally explained that, in addition to the molecular composition, the sequence of DNA was important aspect of the Information carried by

157

DNA. They wrote that DNA is ―composed by different arrangeing [sic] of many deoxyribonucleotides that stands for different information‖, ―has 4 different combinations with the 4 amino acids‖, and ―is a series of nucleic acids.‖

3. In 10 responses, the information carried was „Codes‟. Six responses simply stated codes, 4 elaborated a bit more on the code: one said it was ―complex coding‖ and three stated that it was a ―genetic‖ code.

4. Seven students said that the information was ―genetic‖ information.

5. Three explanations identified information as a message.

6. Two responses identified the information as data.

The information concept ‗About‘ was developed further as to what the ultimate use was. Again, similar to the reasoning with ‗Is‘, I wanted to determine what the students thought the ultimate use was. Nine students said that the information was about the makeup of a person (3 used) or the general ―genetic‖ makeup. Eight students explained that the information was about cells, including cell function, cell form, and a general ―cell information.‖ Six students said that the information was about molecules, either proteins or molecules without being specific about their identity. Six students explained that the information was about appearance including ―traits‖ (3 used), ―appearance‖ without further elaboration about what appearance means, ―outward appearance‖, and ―shape and make of the human body.‖ Five talked about function including ―body functions‖, ―body to successfully function‖, ―define functions of parts of the body‖, and Functions of an organism.‖ Four students described information about both appearance and

158

Figure 21. Results of coding for concepts of DNA IS A CARRIER OF INFORMATION metaphor for explanation of ‗Information‘ including the consequences of those concepts. ‗About‘ and ‗Is‘ in the central circle are the categories of what information was. The pie chart portion are the concepts that formed the two categories. Wedge sizes reflect % of responses that used that concept. Consequences of each concept shown outside of the concept.

function when they wrote ―personality, feelings, physical attributes‖, ―traits and body function‖, ―look and function‖, and ―look like and physical health.‖ Explanations that

159 stated that the information was ―about a person‖, ―give human identity‖, ―identifies you‖, ―who you are‖, ―my information‖ and ―about your body‖ were used to develop the concept Give Specific Identity; eight responses described that information was about giving individuals their identity. The information carried was about what an offspring was ―going to be‖, to ―create an offspring‖ or ―create a human‖ for three students. Three responses indicated that the information was about characteristics of

―living organism‖ with one student describing the characteristics as ―personality, physical attributes.‖ Lastly, one student explained that information was used in

―development and throughout life.‖

Of the 97 responses that explained what information was that DNA carried,

44 used ‗Is‘ and 53 used an ‗About‘ description. Information carried ‗Is‘ codes, genes, and molecular structure of DNA and is ‗About‘ cells, makeup, identity of a person, molecules appearance and function.

How did students explain „Carry‟?

Students used both meanings of carry, contain/hold and transfer. There were

102 responses to this metaphor. The majority, fifty-seven, or 55.9%, explained carry in the hold or contain sense of carry specifically using one of four verbs: has, hold, stores, or contain. Thirty-four, or 33.3%, explained carry as a transfer from one place to another with no consensus as to either the original place or the final place of transfer. Eleven, or 10.8 %, explained carry using both definitions of carry. For purposes of analysis, the responses in that used both will be put into separate carry and transfer categories.

160

The transfers were explained as follows with number of responses using that meaning in the parentheses:

Transfer was throughout the body (7)

DNA  Proteins - Gene expression (7)

Intercellular – Cell  Cell (6)

Heredity: Parent  child (6)

Intracellular (5)

o A  B (2)

Not specified (1)

Mode of Transfer Throughout the Intracellular Heredity Gene Intercellular Not Totals Body Expression Specified Is Code Genetic Series Genetic 7(21%) Data code of informati Genes nucleic on acids Data (struct ure of DNA) About Characteris Cell (2) Gives Protein Gives 15 (44 tics Gives specific s (4) specific %) Gives specific identity identity specific identity Offspring identity Molecul Appearan es ces Functio (Traits) ns Not 4 2 2 1 1 1 12 (35 Specifi %) ed n= 9 7 6 6 5 1 34 % (out 26.5 % 20.6 % 17.6 % 17.6 % 14.7 % 2.9 % of 34)

Table 2. Category ‗Transfer‘, Sub-category Modes of transfer analysis of what ‗Information‘ is transferred by DNA.

I further wanted to know what was transferred in each of these modes. For this I needed to combine the results of the ‗Information‘ coding with the ‗Transfer‘ analysis. The results of this combined analysis are presented in Table 2.

161

The students who used ‗Carry‘ in the sense of hold or contain used both categories of the meaning of ‗Information‘, Is and About. Sixty-eight responses, 57 that used only hold or contain and 11 that used both meanings of carry- hold/contain and transfer- were coded for the use of Information, that is, what DNA held or contained. Thirty-five responses characterized the information DNA held/contained as ‗Is‘ molecules, genes or code. Thirty-three responses explained that the

Information DNA held/carried was about some aspect of the living thing that held/contained the DNA. Table 3 summarizes the number of responses for each aspect of Information.

Meaning of Specific aspect Number of Information Responses Is Genes 9 Genetic 6 information Message 3 Structure of DNA 9 Code 7 About Makeup 9 Cell 5 Proteins 5 Appearance 3 Both (Appearance 4 + Function) Function 3 Offspring 2 Characteristics 1 Development/Life 1 Table 3. Summary of the number of responses for each aspect of information.

The meaning of ‗Information‘ in the ‗Is‘ or ‗About‘ concepts developed classified according to the meaning of Carry used in the explanation and shown in

Table 4. 162

Carry Meaning of Hold/Contain Transfer Information Is 36 7 Genes 11 1 Structure of 9 1 DNA Code 7 2 Genetic Info 6 1 Message 3 0 Data 0 2 About 33 15 Makeup 9 0 Appearance 3 1 Proteins 5 4 Both 4 0 Function 3 1 Offspring 2 1 Characteristics 1 1 1 0 Development/Life Specific Identity 0 4 Cell 5 2 Molecules 0 1

Table 4. The number of responses given for the meaning of information for responses that used the two meanings of carry, hold/contain and transfer.

DNA IS A CODE

The origin of the code is very close to the origin of life. Francis Crick, in Judson, p. 191

Erwin Schrodinger first used the code metaphor in 1941 making it one of the oldest analogies in molecular biology. It was proposed to explain what features the hereditary material would have to have in order for it to perform the functions on heredity. As such, when the structure of DNA was published in 1953, the code metaphor was extended to DNA. Because of the pervasiveness of the code metaphor 163 in modern molecular biology theory and terminology, how students understand this metaphor is of the utmost importance.

Code for Form

Decipher/ Decode

Figure 22. Action/interactional strategy concepts and the categories developed from them for interpretations of the metaphor DNA IS A CODE.

One-hundred six students provided interpretations of the DNA IS A CODE metaphor. Concepts developed from action/interactional strategies used by students were combined to form six different categories. The six categories and the concepts that define them are shown in Figure 22 (previous page). I will discuss how each

164 category was developed including action/interactional strategy concepts combined to define each one.

Category: Form

The category ‗Form‘ was developed from 6 concepts developed from action/interactional strategies provided by students to explain how DNA is a code and included ‗Specific order‘, ‗Uniqueness/Individual‘, ‗Composition‘, ‗Composition and

Order‘, ‗Makeup‘, and ‗Complex.‘ These six concepts focus on the composition, which molecules compose DNA, the Sequence, which is the specific order of those components, the complexity of both codes and DNA, codes and DNA need to be deciphered/decoded to another, understandable form, what is encoded in the code/DNA, the communication function of codes , and the final goal or plan for the code (Figure 23).

Fifty-five responses used some aspect of ‗Form‘ in their explanations of the code metaphor. Of those 55, 14 students discussed the order and sequence features, 10 focused on the composition of DNA including nucleotides, bases and non-specific molecules, 7 combined the composition and the importance of a specific order of the molecules as the similarity between codes and DNA. The composition mentioned included molecules accurate to the structure of DNA-bases, nucleotides, acronyms for the nucleotides A, T, G, C, base pairs- and components that are not structural components of DNA-amino acids and 4 proteins. Students wrote ―uses base pairs to

165

Figure 23. Action/interactional strategy concepts for the category ‗Form.‘ hold information at the genetic level‖ and ―DNA is made up of G, C, T, and A—and looks like a written out code‖,

Sequence was important as was demonstrated by the responses ―put together in the right order‖, ―put together in different combinations‖, ―certain order‖, ―specific way to be written‖, ―a specific sequence is a specific code‖, ―specific genetic sequence‖, and ―have sequence.‖ Students wrote ―DNA is a code because it uses the four bases to create a set of linked pairs to create proteins‖, and ―they both have a certain sequence that tells what the final outcome is.‖

166

Molecules in a particular order was determined from responses such as ―uses sequence of amino acids‖, ―specific order of nucleotides‖, ―is a combination of nucleotides‖, ―DNA is like a code because of the sequencing of the components, the specific sequence makes up a specific code that then determines the outcome of the gene and that makes the gene individual from each other‖, ―different order of deoxyribonucleotides on the DNA stands for different code‖, ―DNA is like a code because it is a chain of base pairs and each base pair encodes for another base pair to match up with it‖, and ―is sequence of bases.‖ One student provided the features of a code and how they map to similar features of DNA: ―A code is like a system of numbers, letters or symbols that represent a larger meaning. DNA is made up of four proteins that can be put together in many different combinations to create different things that your body needs.‖

Three students explained the DNA code components in terms of genes. They wrote that there were ―different variations of genes‖, ―combination of genes‖, and different genes.‖

The concept ‗Uniqueness/Individual‘ focused on the feature that codes are different from each other when they wrote ―not all the same‖, ―different from any other code‖, ―is unique‘, ―are special/unique/different‖, ―is extremely unique‖, ―is individualistic‖, and ―no code is the same.‖

‗Makes up‘ explained that DNA is made up of that were not specific molecules. Students wrote ―is made up of genotypes‖, ―is made up of smaller parts‖, and ―DNA is a code that we are made up of different things and we are all different.‖

167

Category: Decipher/Decode

This concept focuses on the part of the process in which one form of information is converted to a different form of information (Figure 24). Codes use letters, numbers, and symbols in a particular sequence to stand for information. Using a key, these letters, numbers and symbols are converted to a readable form; known as decoding or deciphering. Twenty responses focused on this feature of codes. They discussed what is done and how it is done. ‗What is done‘ responses used transcribe, translate, decode, decipher or analyze to emphasize the conversion that is done to a form of the code to get it to a usable form. Students wrote that ―I see code as a sequence of alphanumeric digits that are aligned in some manner which makes some sort of sense when aligned with some sort of decoding mechanism‖, ―it can only be deciphered and read by certain means and under certain conditions‖, and ―you can find out a lot from cracking a code. The same applies for DNA. When analyzing DNA, you can learn a lot about a person and his or her traits.‖ In a response that hits the intent of the code metaphor as used starting in the early 1950s, the student wrote

―DNA is like a code because it needs to be deciphered by the cell, mainly by ribosomes using RNA, to create certain proteins.‖ And an example of how decipher means figuring out, a student wrote ―DNA can decipher the mystery of characteristic that various [sic] by people. It can explain why some people have brown hair and why some have blonde.‖

‗How is done‖ simply explained that ―It cannot be read by everything, only certain things that are supposed to read it‖, ―it is read and translated into a specific

168 function‖, ―can be read just like a code can be read‖, ―it has to be read by different parts of your body‖, and ―DNA is like a code because by analyzing it you can determine how it will manifest into a whole, Like cracking a code allows you to learn the whole message, analyzing DNA allows you to determine someone’s features.‖

One student used the sequence and composition concept with reading in the response to DNA is like a code ―Because it is complex and encrypted. It is the sequence of bases that tell what a gene is for, but the same four bases over and over again make up the gene, so reading DNA isn‘t like reading a set of instructions.‖

Figure 24. Action/Interactional strategy concepts for the category Decipher/Decode.

Several students likened the gene expression process of transcription and translation to the decoding process. ―DNA is like a code because it has to because it undergoes the process of translation and transcription similar to ―cracking a code‖ and

―DNA is like a code because they can be translated into understandable descriptions.‖

Category: Code For 169

Fifteen students described the similarity between DNA and a code using the phrase ―codes for‘ or ―is a code of‖ sometimes with an expressed specific end structure or a function as in ―It codes for something‖, ―it codes for the function of the cell‖, ―is a code for protein‖, ―it is a code of letters‖, ―it is a code of genes‖, ―it codes to make up your body‖, and ―it codes for all the little things need to make an unique individual.

Category: What is encoded

This concept was the main focus for 7 students. Four stated that codes, and

DNA, hold secrets and 2 stated that they contain information. Students wrote ―it also holds secrets‖, ―it is secretive and unknown‖, ―holds information at the genetic level‖, and ―has a set of information.‖

Category: Communication

The main feature used for the comparison between DNA and a code was as a means of communication as was determined from the responses ―gives directions‖,

―gives characteristics‖, and ―gives specific instructions.‖ A purpose of communication is an understanding of the means of communication as in ―is understood by cells.‖

Category: Teleonomic

Mayr (1982) described the tendency of explanations about living things to have a final purpose as teleonomic. There were several instances where the main feature used in the comparison between DNA and a code is that both provide a final, known and planned final product. Responses to that effect included ―is a laid out

170 plan‖, ―DNA causes life to act and look in certain ways‖, and ―used to create a finished product.‖

Figure 25. Action/Interactional strategy concepts that formed the Categories codes for, What is encoded, Communication and Teleonomic.

Regardless of the action/interactional strategy of code used to describe DNA,

44% (n=37) of the explanations provided a structure/ function for components of an organism consequence of the strategy: 20 provided a structural consequence, 10 a functional consequence and 7 provided both structure and function as a consequence.

Structural consequences included the identity of the component including the molecules protein and RNA (7), but most often the identity of the component was not provided only vague references such as ―body composition‖, ―your body‖, ―explains different traits‖, ―makes you who you are‖, ―components‖, ―creates parts of cells‖,

171 create body things needed‖, ―certain characteristics to become an individual.‖

Function consequences included ―how your body grows‖, ―cells to function properly‖,

―function of an organism‖, ―function are unique from each other‖, and ―perform.‖

Responses such as ―how we act and look‖ provided references to both structure (look) and function (act).

Twenty-four percent (n= 25) of explanations provided consequences that result in the organism as a whole including responses such as ―organism‖, ―human being‖, ―living organism‖, unique individual‖, ―everyone‖, the whole‖, ―cells told how to make a human or organism‖ or ―be stable in place‖, and ―to understand the organism or body.‖ Information can be ―held‘, ―organized‖ understood‖, be related to specific people‖, ―relayed‖, and ‖specified‖ according to 17 % (n=14) students.

Additional non-structure/function outcomes (8.4 %, n=7) included that it was

‖something complex‖ and ―hard to decipher‖, ―tells what genes are for‖, ―gives answers‖, and ―can know how patients are sick.‖ And, what we will call

Characteristics of a Code, Not Otherwise Specified consequences (7.2 %, n=6) included ―is for security‖ or ―is a form of security‖, is something complex‖, ―is flawed if altered‖, and ―takes a long time to decode.‖

172

CHAPTER 6: CONCLUSIONS FOR STUDY 1

With the molecular picture of the gene it is no longer inconceivable that the miniature code should precisely correspond with a highly complicated and specified plan of development and should somehow contain the means to put it into operation. Erwin Schrödinger, What is Life?, p. 62

It is necessary to know the exact number and sequence of the genes, how they interact, what they do. We have to know the program, and know it in machine language which is molecular biology. Sydney Brenner, in Judson, p. 194

It is like a code. If you are given one set of letters you can write down the others. Now we believe that D.N.A. is a code. That is, the order of the bases (the letters) makes one gene different from another gene (just as one page of print is different from another. Francis Crick, 1953

It follows that in a long molecule many different permutations are possible, and it therefore seems likely that the precise sequence of the bases is the code which carries genetical information. J.D. Watson & FHC Crick, Nature, 1953

So there was a certain resistance to simple ideas like three nucleotides coding an amino acid. Francis Crick, in Judson, p. 240

On Information and Language

Crick (in Judson, p. 179) explained his use of both the information –note his use of the metaphor CARRY - and the language metaphors as ―The most basic idea is that biological information is mainly carried by the sequence of side groups on the regular backbone of a macromolecule. The genetic information is not conveyed and

173 expressed by a large number of intricate symbols – it is not in Chinese- but in two very simple as it were alphabetic languages. Genetically, the information is carried by nucleic acid, in the sequence of bases; but many such sequences can be translated into the other language- amino acid sequences of proteins- by special pieces of biochemical machinery.‖ Seven features about information, carriers of information and language that were used to form positive analogy to DNA are to be found in this quote:

1. Biological-genetic information is ‗carried by‘ nucleic acids with carry in the sense

of hold/contain not transfer from one place to another.

2. The sequence of side groups of a macromolecule ‗carries‘ the biological-genetic

information. It can be inferred that he is speaking of both DNA and proteins as

carriers of information: genetically by DNA but the ‗information‘ can be

‗translated‘ into protein ‗language.‘

3. Genetic information is ―conveyed and expressed‖ in an alphabet language, not a

symbolic language like Chinese.

4. The alphabet languages are simple.

5. There are two alphabet languages involved: nucleic acid bases and amino acids

of proteins.

6. One language, the sequence of bases, can be ‗translated‘ into the other language

‗amino acid sequence of proteins.‘

7. Special ―biochemical machinery‖ carries out the ‗translation.‘

174

Student responses focused on four aspects of information: DNA is a ―storer‖ of information in the have or holds sense (1 above); how the information gets used to determine either structure, function or both; what the information is about if the structure is the sequence of amino acids then number 2 above, but students also said the information is about traits, appearance, functions, a cell or a person; how the information is stored, as a sequence of nucleotides, number 2 above for sequence and

5 above for alphabet languages involved, but codes, messages and data were also identified as information.

How many interpretations reflected the accepted use in gene expression?

As was discussed before, scientific metaphors, unlike common metaphors, were developed for utility in model development, to guide research, aid in interpretation of data, and serve as a conceptual foundation for a new domain; like a standard usage. As such, when used in discussions of models, as technical terms, and to set a conceptual foundation, they are not open to free interpretation. I wanted to know how students interpreted the common gene expression metaphors. From experience, I expected that students generally either do not understand the metaphors to even attempt an interpretation – even if they say DNA is a code, they do not know what that means- or do not use the standard usage, but had no empirical evidence to support this observation.

How many students did not offer an interpretation of each metaphor? For

DNA IS A CODE, 4 students offered no interpretation, for DNA IS A LANGUAGE, 8, for

175

DNA IS A COMPUTER PROGRAM,7, and DNA IS A CARRIER OF INFORMATION, 3. Most stated some form of ―I don‘t know‖ or ―I have no idea.‖

How many students used the standard usage for their interpretations? Seven percent of responses to DNA IS A LANGUAGE focused on the sequence of bases

(Category Order, Concept Sequence) and 12 percent discussed translation as an aspect of language (Category Translate, Concepts To translate and Translator). The translation aspect of language is preserved in the technical term ―Translation.‖ Fifteen responses (14%) to DNA IS A CODE focused on sequence of nucleotide bases, bases, or

A,T,G,C. For DNA IS A CARRIER OF INFORMATION, the information is again the order of bases of DNA that is used to synthesize a specific order of amino acids. Ten responses, 10 %, said that information was the structure of DNA in terms of bases, base pairs, or deoxyribonucleotides. ―Carry‖ is the have or holds meaning, not transfer or move from one location to another; 56% of responses used this meaning.

Of the 10 students using the standard information usage, 9 used the contain meaning of carry.

Uses of Code- Beyond Schrödinger and Crick

There were twelve distinct meanings of code used by students.

1. Order of bases

2. Order of bases related to the order of amino acids

3. Order of bases carries genetic information

4. Unique- different sequences give different genes

5. Needs to be solved or figured out what genes are for

176

6. What is being said

7. Order of genes

8. Purpose- for a person, individual, organism

9. Form of safety, security

10. Unique- no two are the same

11. Sequence makes the codes different

12. Has, gives directions or information

There were 4 meanings of decode:

1. mRNA  amino acid sequence (Crick‘s original use)

2. determine the sequence of nucleotides of DNA

3. determine traits of an organism

4. person, individual, organism

Mixed Metaphors: Language and Code

Fourteen students used some aspect of ‗code‘ to explain how DNA IS A LANGUAGE and thirteen students used some aspect of language to explain how DNA IS A CODE.

Examples of code used to explain language included:

encoded: ―DNA codes for specific traits, but base pairs don‘t read, B-L-U-E-E-

Y-E-S, but instead their own language‖, ―DNA is like a language because it uses

sequences of amino acids to code for a protein‖

decoded: ―DNA is like a language because like a foreign language it can be

decoded into our native language‖,

177

communication: ―Dna [sic] is like a language because it communicates with the

rest of the body to makeup the genetic code of a person‖

is a code: ―It translates the genetic code into polypeptide bonds‖ and ―DNA has

own special ―code.‖ Every code on DNA stands for a character in language. All

the codes are arranged in a particular sequence.‖

Examples of language used to explain code included translation and is read: translation- ―needs to be translated into genetic code characteristics‖, ―can be translated into understandable descriptions―; is read - is very detailed and gives specific instructions that cannot be read by everything can only be read by certain things‖, ―genes of DNA of an organism can be read to understand the organism as a whole‖; translation and read- ―is read and translated into parts, RNA and proteins‖ and ―is read and translated into specefic [sic] function.‖

Using Metaphor Interpretation to understand how students are thinking about the role of DNA

One of the features of other-generated metaphors is that they are subject to multiple interpretation; the students did not disappoint. As was mentioned, most interpretations of the metaphors offered by students were not the standard usage.

However, that does not mean that somehow they are ‗wrong‖ as would be a possible interpretation of the results using the ―deficit model‖ of science education- students are somehow deficient in an aspect of a domain and we must somehow make up for the deficit. This would be a mistake. The explanations offered by students give us insight into their conceptualization of DNA and its role in a living thing. DNA as a

178 participant in communication with cell parts or other molecules or carrying information about how cells should function correctly are conceptually on track with how biologists talk about intracellular and intercellular signaling. What needs to be addressed is the role DNA plays in this communication not that some form of ―cellular communication‖ occurs. This may indicate a gap in curriculum more than a misconception on the part of students. Again, this bears further study.

What we need to understand next is how they constructed these schemata, what role did metaphor play in this construction, and how could the use of these metaphors during instruction and in instructional materials be improved?

Additionally, if presented with the standard usage, with a focus on key features used in positive analogy, would understanding of DNA structure and function change? Are these alternative metaphor interpretations actually alternative conceptions? Do they reflect alternative conceptions or did they have a hand in constructing them? Given our discussion of the role of these metaphors in biological molecules and terminology, these questions bear further study.

Utility of Metaphor to understanding DNA structure and function

The purpose of using metaphor, analogy and simile, in fact any type of comparison between what you already know (the base)and something you are trying to understand (the target), is to see relations between features of the two, the base and the target, thereby constructing knowledge of the target. Other-generated metaphors which include the theory-constitutive metaphors explored during this study are challenging to hearers or readers of the metaphor in several ways.

179

The first challenge is in identifying the statement as a metaphor in need of an interpretation versus seeing it as an instance of a category, known as a Categorical

Assertion. The statements may be interpreted metaphorically. Students would need to find similarities, features for comparison. According to Black, this can occur when a metaphor is used. Discerning this difference can be particularly difficult for well- established scientific metaphors like DNA is a code, DNA is a computer program,

DNA carries information and DNA is a language. DNA may be categorized as a type of language, type of code and is a computer program and is a type of information found ―in‖ DNA when reading these statements. Depending on personal experience and DNA schema constructed to date, some students may interpret the statements as categorizations even though they are told they are metaphors and should be interpreted as such. When providing an interpretation of the DNA IS A CODE metaphor, a student wrote: ―DNA is a code. This analogy is not helpful to me because it is trying to separate two things that should not be separated. DNA is a type of code. They are not similar, they are the same.‖ This student sees DNA as an instance of the category

‗code‘ – ―DNA is a type of code‖, not as separate target DNA and base concept code where a ground (positive analogy) needs to be found (―is trying to separate two things that should not be separated‖). The code metaphor from Schrödinger to Crick had an analogical use. The Life of Metaphor Theory predicts that as the metaphor is used, the link between the base and target is lost and the result is a technical term- DNA code or genetic code. This interpretation can be useful to understand this student‘s response.

180

Another student stated that ―DNA is definitely like a language.‖ There is a recognition that the statement is metaphorical and a comparison can be made. The student further explained, ―It is a language that can be translated (into RNA, then protein), and a language that can be communicated (outwardly, by eye color, skin color, height, etc.).‖ The structure of the interpretation, with properties of DNA used in the similarity relationship with language in parentheses), indicates that the student has retained the metaphorical nature of the statement ‗DNA is a language.‘

Second, which features should be used in the interpretation or, using Hesse‘s terminology, the features to be used for positive analogy, rather than features that are not appropriate for similarity relations, that is, the negative analogy; neutral analogy is to be explored and confusion may arise as to whether they are appropriate for similarity relations or not. One student, when attempting to provide an interpretation of the DNA IS A CODE metaphor encountered this conundrum. According to the response, ―I feel a little fuzzy on this one too. The term ―code‖ can mean a million different things. Perhaps like a pin code.‖ This student is confused (―a little fuzzy‖) because of many features (―a million different things‖) that are possible for comparison are available. A possible relation is offered that of a pin code and an explanation is provided: ―This goes along with being specific and having to have everything lined up just right.‖ Another student, for the DNA IS A LANGUAGE metaphor, wrote: ―I don‘t understand how DNA is a language. It would seem the same as a message to me.‖

181

This also occurred for the DNA IS A CARRIER OF INFORMATION interpretations when determining which meaning of ―carry‖ should be used in the interpretation.

Students used three different meanings of carry and one student succinctly put the problem of which meaning of carry should be used: ―I feel a tad confused about this.

By carrier of information, do you mean like specifically how does it carry information in and out of the mitochondria? Or by comparison, how is DNA like, for example, a mail carrier? In that case, it is a vital part of getting messages from point A to point

B.‖ This response can be used as an example of why context of interpretation is important. Simply using a metaphor without elaborating on why it being used can open the door to confusion.

Third, if a metaphor was never encountered before, is a novel metaphor and if the metaphor base and target seem not to be relatable, it is an obscure metaphor.

According to Glucksberg (2003), an attempt to interpret a metaphor should occur even if it was never encountered before; humans have no choice but to interpret metaphor,

―it is mandatory and automatic‖ (p. 93). They will even offer an interpretation for obscure metaphors. I encountered a response from a student who implied that the DNA

IS A LANGUAGE metaphor was both novel and obscure. ―I don‘t see how DNA is a language at all [obscure] and this is the first time I have ever read/heard this [novel].‖

The student offered no explanation for the metaphor; counter to Gluckberg‘s assertion that ―people can usually find some interpretation that makes sense‖ (2003, p. 95).

There was another student who did not classify DNA as a language, the DNA IS

A LANGUAGE metaphor, yet offered a plausible interpretation: ―DNA to me is not like

182 a language but I can see how they can use this metaphor. DNA can tell the organism how to learn and gives the organism the way to learn a different language and only that person with their DNA can understand that language.‖ This example supports

Glucksberg‘s contention; a sensible interpretation was offered. This is also a cautionary tale for us that the intent of a scientific metaphor in clarifying an aspect of gene expression and the role of DNA in that process may not be obvious to the hearer or reader and further that as humans we will attempt an interpretation that most likely will not be the one the originator of the metaphor had in mind.

Fourth, does the metaphor help in furthering understanding of the target?

According to one student, who was very open about the aptness of the code metaphor, wrote ―It‘s hard to imagine that something as small and simple as chromosomes could be so essential in determining what we are, but because they act as a code it‘s easier to understand.‖ This explanation of aptness is fascinating for several reasons. One deals with the student‘s changing ontological stance about size and function as a result of the metaphor: small things can influence an organism (―what we are‖). Second, the student uses a feature of a code and applies it to a biological phenomenon that was challenging that lead to an increased understanding of chromosomes and their role in what it is that determines ―what we are.‖ In conceptual change language, there was a dissatisfaction with how ―small chromosomes‖ can influence ―what we are.‖ An intelligible metaphor allowed a comparison to be made between a familiar base concept, a code, that was understandable and a phenomenon of chromosome structure and function. The constructed understanding is plausible to the student who attributes

183 the conceptualization using code features to the use of the metaphor. Posner et. al.,

(1982) suggested the utilization of metaphor in conceptual change; this was a nice instance results of that utilization.

However, for another student the metaphors did not aid in conceptual understanding: ―frankly these metaphors don‘t [sic] help and they make it worse.‖

DNA as “Doer”

Three of the bases of the metaphors in this study are human constructions, namely, language, code, and computer program. The positive analogy to these base concepts was on specific structural features of the base concept: letters of a particular alphabet form words that form sentences, a series of letters stands for a word, and a series of codes are run to produce an outcome. There were instances when students interpreted the metaphor so that DNA actually did or carried out functions of these bases that require either a human or machine to carry them out. For example, ―code gives specific instructions‖ (Code metaphor), ―DNA allows access to certain functions when needed or necessary‖ (Code metaphor), ―DNA sets the plan for the cells to follow‖ (Code metaphor), ―DNA gives directions to create an organism‖ (Language metaphor), ―DNA communicates to the body how a being is‖ (Language metaphor),

―DNA must tell all the other parts of the cell their function and it instructs them on all aspects of their self‖ (Language metaphor), ―It translates the genetic code into polypeptide bonds‖ (Code metaphor), ―tells other things what to do‖ (Code metaphor), and ―it programs itself to form human software (Computer program metaphor).‖

184

This phenomenon was most clearly seen in the category ‗Internal Dialogue‘ developed from action/interactional strategy concepts of interpretations of DNA IS A

LANGUAGE from both Study 1 and Study 2 and those students who conceptualized

DNA as a carrier of information in the sense of ‗Transfer‘ from one place to another.

The conceptualization of DNA was as a participant in communication, speaking, telling and instructing molecules, cells, the body, parts of the body or organism what to do or what structures to form.

As a ―carrier of information‖ from one place to another, students wrote ―It transfers information between the different components of living things, so it is fact a carrier of information‖, ―DNA carries information to cells‖, ―sends data all throughout the organism‖, ―DNA is like a mailman/mailwoman who takes letters (information) to different areas‖, ―it can transport information for a cell‖, and ―it carries information all throughout your body.‖ DNA is conceptualized as actively moving information, not holding or containing information (―holds the information necessary for the cell‖ in the sense of a container and information is the contents) nor somehow being made up of or composed of something (―DNA is composed of many deoxyribonucleotides, the different arrangeing [sic] of which stands for different information‖); all three interpretations of carry are acceptable meanings of ―carry‖. The last meaning, being made up of something, is the sense used by biologists when they say ―carry information.‖ Of the 57 responses that used the ―contain/hold‖ meaning of ―carry‖, 10 used the ―being composed of‖ aspect. The first two meanings transfer and container,

DNA is doing something.

185

The use of the active tense could be in the context of interpreting a feature of

DNA metaphorically; students can know that DNA does not ―give‖, ―set plans‖, or

―tell‖ literally but does so metaphorically. However, these metaphors can be interpreted in the passive tense for example ―It needs to be translated by different things in order to be understood.‖ The question, which cannot be answered by this study, is whether students do literally think that DNA ―does‖ anything-which it doesn‘t- or if they are thinking DNA is a ―doer‖ only in the metaphorical sense. This is an important question that needs to be researched further. That DNA does not do anything but is a molecule that is acted upon by other molecules is an important foundation concept to understanding DNA function.

Students are not the only ones who have DNA ―doing‖ something. Biologists say that ―DNA copies itself‖ when they describe DNA replication or that DNA is self- replicating or that ―DNA makes protein‖ are common jargon phrases used by biologists not only in their conversations with each other but in communication with non-biologists, including students. As Lewontin points out ―First, DNA is not self- reproducing; second, it makes nothing; and third, organisms are not determined by it.

DNA is a dead molecule, among the most nonreactive, chemically inert molecules in the living world‖ (2001, p. 141). We must be tighter with the language chosen to explain the role of DNA in order to have it more accurately reflect our knowledge of the role of DNA in the cellular functioning.

The use of the active tense could also be explained as a feature of the English language. Boroditsky (2011) argues that ―English speakers tend to phrase things in

186 terms of people doing things, preferring transitive constructions‖ and further that

―nonagentitive language sounds evasive in English‖ (p. 64).

Mis-facts in Metaphor Interpretation

Another interesting observation in students‘ interpretations of metaphors is their use of scientific terms used improperly, particularly the building blocks of DNA and proteins, nucleotides and amino acids. I will refer to these as mis-facts instead of misconceptions due to the inexperience of the students in the domain of biology and limited understanding of the relationship between molecular structure of amino acids and nucleotides, structure of the nucleic acids DNA and RNA and of proteins, and how these structures are related to function. For example, ―DNA is a code by how it is made up of 4 proteins‖ (Code), ―it is a series of nucleic acids‖ (Carrier), and ―DNA has four different combinations with the four amino acids it has‖ (Carrier). One student, in offering an explanation of the ‗carrier‘ metaphor wrote ―Actually RNA is the carrier of information, not DNA. It‘s RNA because RNA can make exact replicas of itself.‖ The conception of a carrier of information was the ability to make replicas of itself, not the standard usage of to be composed of a specific sequence of nucleotides. In that case, both DNA and RNA technically are ―carriers of information.‖ Also, copies of RNA are not made from RNA in eukaryotic or prokaryotic cells, only in RNA viruses. RNAs are ―made from‖ DNA using enzymes to carry out the task. What is the relationship between the mis-fact and metaphor interpretation? What effect on conceptual understanding of the metaphor does the mis- fact have? This is another question that should be studied further.

187

Determinism

Biological determinism holds that it is DNA (and genes) that determine all aspects of the organism. That one need only know the DNA sequence of a gene and one will know every structure and feature of an organism. This ontology has its physical manifestation in a new field of endeavor within molecular biology, called synthetic biology. Craig Venter, microbiologist and Human Genome Project leader, is at the forefront of this field that seeks, at its most extreme, to design a living organism from scratch starting with its DNA. In May of 2010, his research group has succeeded in engineering a strain of the bacterium Mycoplasma that has its DNA designed by humans. Venter is very fond of calling DNA the ―software of life‖; write the program for how you want the cell to work, insert the program, you get the organism to do what you want it to do.

DNA as the sole arbiter of final form was observed in students‘ responses.

One need only look at the consequences of concepts developed from interpretations of the four metaphors to see this. A few examples of student responses to each of the four metaphors will highlight the point: ―DNA is a carrier of information in that it contains the genes that develop in organism. All the information you would use to describe an organism is brought about by DNA.‖ (Carrier of Information); ―DNA programs cells and genes to act in a certain way in order to develop functional life. This is much like a computer program telling the computer how to act to reach the end that is desired.

DNA programs different aspects of the body, creating the code for our lives.‖

(Computer program); ―DNA has specific details in the way its [sic] made so carry out

188 the function of your body to create your height, eye color, etc.‖ (Computer program);

―carries the code of what each of us is.‖ (Computer program); ―DNA is the code that makes up the genes that make an organism function the way to does.‖; ―DNA is like a code in some ways because if you can break down the code of any person you can find out what they will look like or who they will be just from their DNA.‖; ―a code of many different genes that make you who you are.‖; ―DNA is like a code because DNA gives directions to create an organism.‖; ―DNA is like a language because it must tell all of the other parts of the cell their function and it instructs them on all aspects of their self.‖; and ―It speaks the language of instruction. It tells a cell when to perform certain functions and when to develop certain aspects of itself.‖

These examples highlight the determinism attributed to DNA: all you need to know about is DNA and you will know everything about a person- yes notice, the examples focus on humans, not other animals or organisms from the remaining five kingdoms (Bacteria, Archaea, Protista, Fungi, Plants). The focus on humans was consistent in the responses if mention of a particular living thing was provided.

Several points need to be made: first, as was previously mentioned, we are aware of the fact that DNA is not the sole determinant of phenotypes and traits. Epigenetics, chromosome territories, external environment, and extended genotypes (role of bacteria in development and function) all play a role in gene expression, phenotype and traits. Is this a case of metaphorical interpretive license or does it indicate an ontological perspective based on the master molecule conceptual metaphor or an example of essentialism? Do these metaphors reinforce an already constructed view

189 of DNA or aid in the development of the view? Its pervasiveness in the interpretations of these students suggests that these are questions that deserve further attention.

Whether you conceptualize DNA as master or one of the players in cellular function affects decisions related to our physical and mental health and our response to the physical and mental health of others, and actions taken by others (is there a gene for aggression or a propensity to steal or to take risks) and whether we feel they are

―responsible‖ for their actions or ―it‘s in their genes‖, you know ―boys will be boys‖ and gene-related explanations proffered for why females are not in science and engineering.

190

CHAPTER 7: STUDY 2

In this study students were asked to define the target of the metaphors, DNA, and the bases of the metaphors including blueprint, recipe, script, plan, computer program, information, message and bar code. The analysis of the responses to

Language and Code will be discussed here.

Analysis of responses to the base concept Language

Analysis of the student-generated definitions of Language proceeded first by identifying the action/interactional strategies and consequences in each response. As each response was coded, a possible concept that reflected the strategy was developed and named. These concept assignments and concept names were tentative and many changed as additional responses were coded. The final concepts and the nine categories they formed were as follows:

1. Category: Intent/Purpose included the concepts Communicate, Share

information, Self-expression, encode/decode, and understand.

2. Category: Different Languages Exist included the sub-category Living

which included the concepts Human and Animal, and the sub-category

Non-living that included the concepts Computer, DNA, Math, Science and

non-specified.

3. Category: Forms included the concepts Sounds, Visual, verbal, Written,

191

Gestures, Non-Verbal and Message.

4. Category: Method included the concepts Intercultural, Interpersonal,

Between (Non-Human or Non-specified) Things, Between Living Things.

5. Category Specific or Used by included the concepts Scientists, Cultures,

Geographic and sub-concepts of Geographic, Region and Countries.

6. Category: Who Does included the concepts Molecular, Organisms, Human and

Animal.

7. Category: Must Know Language To included the concepts Speak It,

Translate, and Understand.

8. Category: Composition included the concepts Syntax (including Specific

Sequence), Thoughts, Meaning, Symbols, Words, Sounds, Code-Like and

Letters.

9. Category: Aspects included the concepts Makes Civilization Possible,

Evolved or Changed Over Time, Standardized, Complex, Unique and Shapes

How See World.

Categories included both the structural and functional aspects of language.

Composition and Forms reflect the structural aspects of language: it is made up of symbols or letters that can be in the form of words in a particular order that give meaning and these can be visual, written, gestures, verbal, or sounds. These are the syntax and semantics of language. Intent/Purpose, Different Languages Exist, Method,

Used By, Who Does, Must Know to, and Aspects reflect the functional aspects of language. These are the pragmatics of language. Focus was on the functional,

192 pragmatic aspects of language rather than on the structure, syntax and semantics, of language.

Category: Intent/Purpose

The concept ‗Communicate‘ was formed from the action/interactional strategies that specifically used the words ‗communicate‘ or ‗communication.‘

Typical responses included: ―is a way of communicating‖, ―people use to communicate‖, ―is something used to communicate‖, ―is how we communicate‖, ―is needed to communicate‖, ―the essential tool of communication for humans‖, and ―way of verbal communication.‖

The concept ‗Understand‘ was formed from responses that stated that language is used to either have someone understand you or for people to understand each other.

Responses that were used to form this concept included: ―what you use to have someone understand you‖, ―how populations interact with and understand each other‖,

―enables us to understand the needs and desires of others‖ and ―so that we can understand each other.‖

The concept ‗Self-Expression‘ was formed to include responses that indicated that language was a medium whereby personal thoughts and feelings are expressed.

Responses included: ―system for communicating ideas and feelings‖, ―way of telling about events, things or storytelling‖, and ―helps people express thoughts and opinions.‖

193

The concept ‗Share Information‘ included responses that specifically indicated that sharing information was a purpose of language and included responses such as,

―to share information with others‖ and ―share information.‖

The concept ‗Encode/Decode‘ specifically used those terms as ―a system for encoding or decoding information.‖

Category: Different Languages Exist

The concepts developed to form this category included any reference to types of languages that may be used or exist. Responses were grouped to form two Sub- categories, ‗Living‘ and ‗Non-Living.‘ The sub-category ‗Living‘ included references to languages used by humans or other living organisms, specifically animals and the sub-category ‗Non-Living‘ included references to languages developed by humans but which students did not specifically state were human languages including computer, math and scientific and DNA as an example of a language. Examples of responses that made up the ‗Living Human‘ concept included: ―comes in many different forms‖,

―are many defferent [sic] languages‖ and ―certain groups of people use different languages.‖ Examples of types of languages that are ‗Non-living‘ included: ―DNA language‖, ―Programming language C++ and java and html‖ and‖ are many different languages from spoken language to math.‖

Category: Forms

This category was developed from concepts derived from action/ interactional strategies that provided information about the specific form in which the language is used including how it is physically presented. Concepts included ―Sounds‖, ―Visual‘,

194

‗Verbal‘, ‗Written‘, ‗Gestures‖ and ‗Non-verbal not specified.‘ ‗Gestures‘ formed a separate concept from ‗Visual‘ because there are forms of visual representation of language that do not involve gestures. Student responses included: ―it‘s how people talk, or write or any other form of visual communication‖, ―using sounds, gestures, sings [sic], or marks‖, ―can be spoken or signed‖, ―is a system of written symbols‖ ,

―using our own voices or writing it down‖ and ―is a form of verbal communication.‖

Category: Method

This category was based on the observation that language was used between two or more living things, whether they are human or non-human. Concepts developed that form the ―Method‘ category included language used between cultures,

‗Intercultural‘, between two or more humans, ‗Interpersonal‘, between living things that are not human, ‗Between (Non-Human, Non-Living, or not specified) Things‘ and between living things, ―Between Living). Examples of responses that formed the concept ‗Intercultural‘ included: ―is how people communicate culture to culture‖ and

―is a way of communicating with your culture or even other cultures.‖ The concept

‗Interpersonal‘ was formed from ideas including: ―is the way people communicate with each other‖, ―is what human beings use to communicate with each other‖, ―is something used to communicate to other individuals‖, ―is used in the way we communicate with each other‖ and ―is the primary tool we all use to communicate with each other.‖ The concept ‗Between Things‘ included ―is a means of communication from one thing to another‖, ―way of communication between two

195

Self-Expression Makes Civilization Possible

Figure 26. Concept map developed from responses to define the base concept ―language.‖ Categories are in blue boxes and action/interactional strategy concepts used to form the category are shown in the black boxes.

196 things‖ and ―is a form of communication used to send messages from transmitter to receiver.‖ Lastly, the concept ‗Between Living‘ included ideas such as ―is a common code used by two like beings in order to communicate between each other‖, is what other animals use to communicate with each other‖ and ―is a means of communicating with another organism.‖

What was noticed when developing the concepts was that students provided rich descriptions of the term Language so that their action/interactional strategies comprised more than one concept in more than one category. In order to be able to discern what relationships existed between concepts for any one student and additionally to get an overall ‗feel‘ for what the group as a whole stated about

Language, a concept map for the group‘s categories and concepts was developed

(Figure 26).

A drawback, in my view, to qualitative methodology is the lack of visual representation techniques with which one could see the action/interactional strategies of each category and the relationships between categories. This is particularly important as the number of concepts increases due to the diversity of strategies drawn from responses. Also, keeping my intended audience in mind – scientists who teach undergraduates- and their preferred way of representing and visualizing data analysis,

I needed to develop a means to visualize my analysis both for clarity of theory development that I could use and a way to facilitate communication of my analysis to colleagues not trained in qualitative research methodology (and who, quite frankly, are skeptical of contributions to be made by this methodology).

197

What may contribute to this lack of visualization of and between categories may be that very few samples are used for any one study whereas I chose to use a larger sample in order to get an idea of as many of the possible ways students could interpret the metaphors as could be thought of by a class. I wanted to get an idea of how the metaphors were being interpreted, how the students were conceptualizing both base and targets of the metaphor then what were they coming up with as an interpretation.

I looked to education to provide insights for possible graphic organizers. To visualize categories, concepts and the action/interactional strategies that were used to form the concepts, I chose to use a concept map, but with structural and conceptual modifications. This map differed in several respects from the original concept map design of Novak (1984). First, the map is for a group, not just a single person; it is a compilation of 96 individual concept maps. Second, there are no hierarchical relationships to the map. Categories and their component concepts are arranged around the periphery of the map and order has no interpretive value. Thirdly, there are no propositions linking concepts. If present these would be represented as a word or short phrase written on a line linking two concepts indicating the relationship between the two concepts.

The map retains several features of the original concept map design. Firstly, lines linking concepts are directional arrows indicating the relationship between concepts. For example, an arrow is drawn from the concept ‗Human‘ of the category

‗Who Does‘ to the concept ‗Communicate‘ of the Category ‗Intent/Purpose‘ indicating

198 that ‗Humans‘ ‗Communicate‘ indicating that Language is what humans use to communicate. Secondly, the intent of concept maps is to visually represent how a person, or in this case people, conceptualizes a domain that includes relationships between concepts. The group map does accomplish this goal.

Information that can be determined from this map that cannot be gained easily from an individual map or from an assembly of individual maps is how a group - students in a classroom- thinks about a domain. From the group map, not only

Intent/Purpose

Communicate

20 Interpersonal 32

5 Other 48 Concepts Method Standardized Between Understand Things Visual, Verbal, Human written

Who Does

Figure 27. Most prevalent links from the Language group concept map. Squares indicate Category names and ovals represent concept names. Numbers on the arrows indicate the number of individual responses that indicated that conceptual relationship.

199 prevailing pattern of associations can easily be determined but which concepts are not prevalent. Plus, if you wish, any individual student‘s links can be viewed.

Focusing on the links between concepts on the concept map shows most links were between three of the nine categories: Intent/Purpose, Who Does and Method.

Between these three categories, most links were between four concepts:

Intent/Purpose, Communicate; Who Does, Human; Method, Interpersonal and

Between (non-human, not specified) Things. Looking at the definitions of language,

75 of 96 responses referred to ‗Communication‘ or to ‗Communicate‘; that is 78% of individual responses. It is not surprising to see these links as the most prevalent.

Figure 27 depicts the most prevalent conceptual links.

Analysis of the Target of the metaphors: DNA

On initial reading of responses to ‗tell me what you know about DNA‘, I noticed that students used metaphors to describe both the structure and function of

DNA. The first metaphor I decided to look for was ‗Double Helix‘, a term used by

Watson and Crick (1953) to describe the structure of the DNA molecule and used by scientists and non-scientists alike. Additionally, I looked at all responses, whether they used Double Helix or not, for further structural descriptions of DNA using the names of the molecules that make up DNA; use of a molecular referent need not be dependent on use of the term ‗Double Helix.‘ DNA is composed of two antiparallel strands of deoxyribonucleotides. Deoxyribonucleotides, or simply shortened to nucleotides, are made up of three smaller molecules: deoxyribose sugar, a phosphate molecule and one of four nitrogen-containing bases, adenine, guanine, cytosine, and

200 thymine. The four bases are usually referred to by the first letter of the name; when in writing, either in capital letters or lowercase letters. I accepted as molecules any reference to the names of bases, the term nucleotide or the letter abbreviations for the four bases.

The use of any of these molecular referents to DNA structure were not the only molecular referent noted. Due to the relationship of DNA to protein synthesis, it is possible that the building blocks units of proteins, amino acids, may be included in responses. Any referent to DNA being composed of proteins or amino acids was included as a structural referent. These would be mis-facts about the molecular structural composition of DNA, but since they are noted by students, they were counted as molecular composition. Any molecular referent not anticipated was also included as a molecular structural referent regardless of the accuracy of the referent to extant knowledge of DNA structure.

Double Helix Used No Double Helix No ≥1 No ≥ 1 Metaphor Metaphors Metaphor Metaphors Used Used Total 12 28 18 38

# Discussed 7 13 4 8 Structure using molecules

% of Total 58 46 22 21 Discussing Structure

Table 5. Coding of DNA definition responses: the use of Double Helix

I then developed concepts based on the metaphors used. The metaphors could either be structural or functional uses. It must be noted that not all responses used 201 metaphorical descriptions of DNA structure or function. A summary of the use of

Double Helix and whether additional metaphors were used is shown in Table 5.

Double Helix Use

Forty of 96 responses used the term ‗Double Helix‘ or a related metaphor; 37 used the term ‗Double Helix‘, one used ―like a curvy ladder‖, one used ―twisted ladder‖, and one used ―like a corkscrew.‖ The last three clearly noted the helical nature of the molecule and were included with ‗Double Helix‘ responses.

Structure in terms of Molecules

Thirty-two of 96 responses included a structural referent in terms of molecules when defining DNA; 15 of these were factually accurate descriptions. These included:

―has ATGC bases‖, ―contains A, T, G, C‖, ―is consisted of [sic] GATC‖, ―sequence of bases‖, and ―is a double helix structure made of nucleotides.‖ One response included accurate information and mis-facts stating, ―nucleic acid make-up DNA and

RNA, base sugar and phosphate, AC paired hydrogen bond, GT paired Hydrogen bond‖. All information is accurate with the exception of the base pairing: A base pairs with T, not A with C, and G base pairs with C, not with T. This was included as a correct response.

Seventeen molecular structural-containing responses included inaccurate information about the structural components of DNA. Five said DNA was made up of proteins, 3 said amino acids, 5 said nucleic acids, and 3 said genes. DNA, along with

RNA, is classified as a category of molecules called nucleic acids, but they are not made up of nucleic acids. Genes, also known as coding regions, by any of a variety of

202 accepted definitions, are specific sequences of nucleotides at a specific location along a DNA molecule that are transcribed and translated to a polypeptide – and more recently extended to include transcription to functional RNAs- but DNA is not made up of genes, per se. There are non-gene sections of DNA known as non-coding sequences. In fact, most of DNA sequence is non-coding.

We can break down the data of Figure 28 further to reveal patterns among the uses of Double Helix, structural references and metaphor usage.

1. Students were less likely to discuss structure in terms of molecules if they did not include the metaphor DOUBLE HELIX. Twenty of 32 responses that discussed structure did use DOUBLE HELIX; 12 of 32 did not use DOUBLE HELIX.

2. Of the 32 who discussed structure, 28 used metaphors: 20 used DOUBLE HELIX with 13 of the 20 using one or more additional metaphors; 8 did not use DOUBLE HELIX but did use one or more metaphors; 4 used no metaphors at all. Sixty-four of 96 students did not discuss structure at all.

3. Of the 17 responses that included inaccurate molecular information, 10 used the metaphor DOUBLE HELIX: 5 of the 10 said proteins or amino acids make up DNA, 4 said DNA is made up of nucleic acids, and 1 said genes.

4. Of the 15 responses that included accurate information about molecules and structure, 10 used DOUBLE HELIX.

5. Using the metaphor DOUBLE HELIX does not imply that the user knows what molecules comprise the helix: 10 of 20 students who used DOUBLE HELIX provided accurate information, 10 of 20 provided inaccurate information.

203

Figure 28. Comparison of metaphor use and reference to the structure of DNA between students who used the metaphor Double Helix and those that did not. Numbers refer to the number of responses (96 total) making up each category.

Metaphors used in DNA Responses

In addition to DOUBLE HELIX, students used several additional metaphors when explaining DNA; the metaphors used included: CONTAIN/CARRY/HOLD, CODE,

INFORMATION, INSTRUCTIONS, BLUEPRINT, BUILDING BLOCK, COPY, TRAVEL, MAP, TELL,

MAKE and STORE. Sixty-nine responses included metaphors other than DOUBLE HELIX:

25 used one metaphor, 27 used 2 metaphors, 11 used 3 metaphors and 5 used 4 or 5 metaphors. Figure 29 and Figure 30 show concept maps showing the metaphors used by students and the interrelationships between concepts. Also included on the concept maps are the responses that described the structure of DNA and whether the information, as previously discussed, was accurate.

204

Figure 29 (p.206) shows the concept map for responses that used double helix in addition to other metaphors. Forty of the responses used DOUBLE HELIX with 28 of these responses using one or more additional metaphors in addition to DOUBLE HELIX.

Fifteen responses used CARRY, 7 used INFORMATION, 2 used INSTRUCTIONS, 15 used

CODE, 4 used BUILDING BLOCKS, and 2 used BLUEPRINT. Ten of 28 responses used 1 additional metaphor, 10 used 2 metaphors, 6 used 3 metaphors and 2 used 4 or 5 metaphors. These are noted by color coding on the figure.

Also shown are the relationships between metaphors and concepts.

BLUEPRINT, MAP, BUILDING BLOCK, and TELLS were not linked to any other metaphor or concept and are depicted on the periphery of the concept map to reflect this fact.

Most links were between CONTAIN, CODE, and DOUBLE HELIX. So were 17 of 20 responses where structure was discussed.

As for what DNA ‗contains‘, two metaphors were common ‗contents‘:

CODE(9) and INFORMATION (5).Additional ‗contents‘ included proteins, chromosomes, genes (2), genetic makeup, genetic identity, INSTRUCTIONS. The focus was on DNA as a ‗container‘ rather than on the ‗contents‘; container locative rather than content locative (Pinker, 2007).

Figure 30 (p.207) is the concept map for the 41 responses that did not use double helix to describe DNA but that used metaphors to describe DNA. Again, these were the explanations that were not likely to discuss structure in terms of molecules; 8 of 41 responses did so. These responses are noted by orange boxes on the Figure. Six of the 8 responses are associated with use of the metaphor CODE.

205

Figure 29. Concept map showing the relationship between responses to define DNA that contain the metaphor ‗Double Helix‘ with additional metaphors. Circles and arrows shown in green are metaphors used whether ‗Double Helix‘ was mentioned or not. Each box indicates a single student‘s response. The color of the boxes indicates the number of metaphors that student used. Yellow indicates one metaphors used; black, 2 used; red, 3 used; blue, 4 or 5. Orange fill indicates reference to structure. Cross-hatch orange indicates a reference to structure that is incorrect.

206

Figure 30. Concept map showing the relationship between responses to define DNA that used at least one metaphor but did not contain the metaphor ‗Double Helix.‘ Circles and arrows shown in green are metaphors used whether ‗Double Helix‘ was mentioned or not. Each box indicates a single student‘s response. The color of the boxes indicates the number of metaphors that student used. Yellow indicates one metaphors used; black, 2 used; red, 3 used; blue, 4 or 5. Orange fill indicates reference to structure.

207

Twenty-two of 41 responses used CARRY with the ‗contents‘ being other metaphors used, INSTRUCTIONS (4), BLUEPRINT (1), INFORMATION (10), CODE (2) and the concepts ―polymers‖, ―genetic material‖, ―traits‖, ―everything about ourselves‖,

―genes‖, and ―chromosomes.‖ Two students wrote that DNA was the ‗contents‘ and the cell was the ‗container‘ as in ―every cells contains DNA‖.

CODE was used by 13 students with three meanings. One was in the sense of

‗DNA CONTAINS a genetic CODE‘ (2), ‗DNA is a (set of)CODE‘ or in the sense of ‗codes for‘ (5) in responses that relate ―a code that carries instructions for cells and is also responsible for what we look like and how our mind functions and all of our senses‖ and ―it is a code that shows us what we look like‖, ‗DNA is encoded‘ (with code) (2) such as ―DNA is coded by genes‖ and DNA is the genetic CODE (4).

INFORMATION was the ‗contents‘ of the DNA ‗container‘ as well as being the object of some action either by DNA or some other structure. As the ‗contents‘, students wrote the following about INFORMATION: ―DNA holds the information that determines the genetic makeup of an organism‖, ―DNA is a nucleic acid that contains the information necessary for a functioning organism to grow and survive‖, and

―Within it‘s [sic] chemicals it holds the information that forms an organism because it holds the information for the task of a cell.‖ As an object of action, one student wrote, ―DNA is a strand of information that comes out of a cell and gets read.‖

When DOUBLE HELIX is not used, students discussed the functional aspects of

DNA mostly in terms of INFORMATION, CODES and as a CONTAINER. Although these

208 three metaphorical concepts were used in the DOUBLE HELIX responses, the number of responses using them was less than when DOUBLE HELIX was not used.

The concept ‗genes‘ is also important when understanding the structure and function of DNA. I was interested in the relationship between genes and DNA for those who included genes in their responses. Ten students mentioned ‗genes‘. There were four categories for their responses. First, is CARRIES: ―carries your genes‖ and

‗contains genes.‖ Second, DNA is made up of genes: ―‖is made up of genes‖ and

―‖which is made of genes.‖ Third, is the opposite sense of the second, genes make up

DNA, as in the response, ―that make up our DNA.‖ Fourth, DNA makes genes:

‖makes genes‖ and ―double-helix strand of code for our genes.‖

Analysis of the responses to the base concept Code

When developing concepts for the responses to CODE, I had used the action/interactional strategy and consequences of the actions method employed previously. However, in determining a way of organizing and making sense out of the concepts in addition to getting a sense of students‘ understanding of codes, I decided to organize the concepts and categories within the framework of how a code works using information about the overall process of code use (Kahn, 1963). This was the sense of code used by the molecular biologists that developed the CODE metaphor although there are additional meanings to the word ‗code‘ such as a set of rules for behavior.

Although there are many different types of codes, the general process includes the following steps: first, you (known as the sender) start with the information, known

209 as the plaintext that you wish to send to another individual (known as the receiver).

Second, the plaintext is converted to an encoded or encrypted form, known as the ciphertext, during the process of encoding or encryption. Encryption requires the use of a key. A key is used to assign a sequence of letters, numbers or other symbols to either individual letters or numbers or to entire words or phrases of the plaintext. The key must be known to both the sender and receiver. Third, the ciphertext is transmitted to the receiver. Fourth, the receiver, using the key, decodes or decrypts the ciphertext to obtain the original plaintext. The process is shown graphically in

Figure 31.

Ciphertext Plaintext Encode/ Encrypt Ciphertext Transmit Decode/ Plaintext Decipher

Key Key

Sender Receiver

Figure 31. The general process of encoding and decoding a plaintext message including processes performed by both the sender and receiver. The plaintext used by the sender is the same as that is the result of decoding by the receiver. The key used during encoding and decoding is the same.

The portion of the process used by molecular biologists is on the receiver end; the coded plaintext is DNA and the plaintext is an amino acid sequence. An additional use of the process is to assign the function of the original plaintext to DNA and the coded plaintext to mRNA. This is not technically correct as the plaintext from the sender and after decoding by the receiver is the same but a sequence of deoxyribonucleotides (DNA) is not the same as a sequence of amino acids. One 210 would need to bring in the various theories of the early earth to address the sender side of the process. These theories attempt to explain the origins of proteins and nucleic acids, DNA and RNA, with the RNA World hypothesis arguing that it was RNA not

DNA that was the first nucleic acid. But, this also leaves the door open for Intelligent

Design and Creationists to bring in a designer or creator of the code. The sender side of the process is part of the negative analogy to code; there is neither direct similarity

(attributes) nor causal relations (relational).

The categories and constituent concepts were overlaid on this basic coding process. It must be noted that the coding process is made up of both structural features

(similarity relations, attributes) of what makes up the code itself and functional features (causal relations, relational) that involve the conversion process of plaintext to code and vice versa and transmission of the coded plaintext. Categories and concepts developed from student responses were matched to steps of the coding processes when such parallels could be drawn.

Categories and their constituent concepts where parallels could be drawn included the categories ‗One Form to Another‘ and ‗Attributes of a Code.‘ The subcategories ‗Form‘ and ‗Features of a Code‘ made up the category ‗Attributes of a

Code.‘

The category ―One Form to Another‘ included descriptions, features, and meanings that involve the taking, reading, decoding, encoding of information or code form one form to a different form and the means by which this is accomplished using a key to the code. The concept ―Break Code/Decode‘ included responses such as

211

―have to break a code‖, ―allow it to be broken‖, ―something that needs to be decoded‖,

―can be deciphered‖, and ―understood by whoever/whatever is supposed to be decoding it.‖ There were also responses that did not use the term decode or decipher but used language that indicated that a code by itself is not of use but must be interpreted. The most common verbs used were ―read‖ and ―interpret‖ as in ―gets read‖, something that is interpreted‖ and ―systematic way of interpreting information.‖

Encrypt or encode were used by a few students who wrote, ―is an encryption of a message‖ and ―changes one form of communication into a different form.‖ One student used genetic code as a specific example and wrote, ―genetic code which incripts [sic] what the person is genetically.‖

Several students indicated that a code is ‗Something That Stands for

Something Else‘, the code was a ‗Message‘ and a ‗Key‘ was needed to convert the information or message or to unlock something. The concept ‗Stands for Something

Else‘ was developed from action/interactional strategies that specifically stated that a code ―stands for something else‖, is ―something that stands for something else‖, or used a specific example such as ―codes for specific gene sequences.‖

There were two aspects to ‗Key‘ used by students; I called them

‗Cryptographic‘ and ‗Non-Cryptographic‘. A ‗Cryptographic Key‘ would be used in the coding/decoding process of a plaintext message/information and included such explanations as ―something needed to convert a piece of information‖, ―information deciphered if you have the correct means of doing so‖, and ―a series of letters or numbers that allude to a table or set of instructions.‖ A ‗Key‘ in the ‗Non-

212

Cryptographic‘ sense included responses that allude to something needed to lock or unlock safes or other things locked with a code. Explanations included ―is what you must know to unlock something‖, ―something you would need to get into something else‖, ―to lock something important‖ or ―used to open safes.‖

This category and its constituent concepts describe the coding process and are shown in Figure 32 in relationship to the overall coding process.

The category ‗Attributes of a Code‘ was developed from two sub-categories,

‗Form‘ and ‗Features of a Code.‘ One of these two sub-categories also nicely overlaid onto the coding process, namely, ‗Form.‘ ‗Form‘ included features of the code itself including what it is composed of, ‗Composition‘, that order or sequence of the components was important and accuracy matters. ‗Composition‘ included references to what made up a code such as ―binary numbers‖, ―symbols‖, ―letters and numbers‖,

―characters‖, ‗‖sounds‖, and ―special words‖ but also specific references to the composition of DNA including ―A, T, C, G‖, ―there are four bases Adenine, Guanine,

Cytosine, and Thymine‖, and ―code in our DNA on two separate strands match up with letters A, T, G, C, D, P.‖

To get a better idea where in the coding process the action/interactional strategies that formed the concepts ‗composition‘ and ‗specific order‘ were referring, especially when taking into account the DNA and non-DNA references, the

‗Composition‘ and ‗Specific Order/Sequence‘ concepts were further denoted as either

‗Encode‘ or ‗Decode.‘ Action/interactional strategies that made any reference to

213

Figure 32. Define code responses that related to the process of encoding, transmittance and decoding. Blue squares indicate categories formed from concepts (shown by red circles). Square with black dots indicate coding concepts not mentioned by students.

214

Figure 33. Responses to Code showing action/interactional strategy concepts (red) and the categories formed from those concepts (blue).

215 composition of a code in terms of letters, numbers, or symbols and ‗Specific

Order/Sequence‘ of the letters, numbers or symbols in a specific combination were classified as part of the encoding process regardless of whether a specific mention of encoding/encryption was made were further classified as ‗Encode.‘ Strategies that made reference to DNA composition in terms of bases and/or the specific order of these bases being important plus any reference to composition in terms of letters, numbers, or symbols with or without mention of sequence as part of the decoding process were classified as ‗Decode.‘ This classification strategy was based on the previous argument that DNA transcription and translation positive analogy similarity and causal relations are aspects of the decoding process. These concepts are shown in

Figure 32.

Although these categories of action/interactional strategies are conceptually aspects of the coding process that are used to interpret the CODE metaphor, students included additional features of ‗code‘ in their responses. Figure 33 presents all of the categories and concepts with the details of the ‗Form‘ and ‗Sequence‘ concepts removed.

The Attributes category had a second sub-category: ‗Features of a Code.‘

‗Features‘ included aspects of the code itself unrelated to composition or sequence.

‗Features‘ included the concept ‗Complex‘ as ―complex‖ and ―more complicated than normal.‖ Codes are a ‘Shortcut‘, stated as a ―shortcut way‖ and ―abbreviated way‖,

‗Organized‘, stated as ―organized information‖, ―Store Information in genes‖, and are

216

‗Original/Unique‘ such as ―are different for specific locks‖ and ―each organism has an original code in their DNA.‖

The category ‗Uses of a Code‘ related the purpose of using a code neither related to any aspects of composition or sequence nor to aspects of the code categorized as

‗Features‘. Twenty-four of 96 responses included features that relate to the purpose for using a code. Three main concepts relating to purpose were developed from the action/interactional strategies. One is that codes are used to ‗Transport or Transmit

Information.‘ Responses that relate this feature included, ―transport information‖,

―method to transport information‖, used to send information‖, and ―information read by RDA [sic] transported out of the nucleolus to make proteins.‖ This concept is a feature of the coding process. Nine responses made reference to the exclusivity of codes in communication in the sense that some people know the code and others do not. The concept ‗Exclusive, Some Know‘ was developed from action/interactional strategies such as, ―not known by all‖, ―usually meant for a specific person or group‖,

―used to prevent outsiders in‖, ―not everyone knows what it is‖, ―two parties can communicate without outside parties knowing‖, and ―people that know the code understand the message.‖ Lastly, the purpose of codes is to keep information secret.

The concept ‗Secret‘ included explanations such as, ―to keep things secret‖, ―a way of hiding something‖, ―something that we use that can be confidential‖, and ―make a message more discreet [sic].‖

The action/interactional strategies that formed the concepts of the category

‗Communication‘ was developed as a separate category instead of including them in

217

‗Features of a Code‘ or in ‗Uses‘ because of earlier analyses from Study 1 and Study

5, developing own metaphors, the category ‗Communication‘ was used often across uses of ‗code‘. Since its common usage would indicate its importance to students, it remains a separate category in this study as well.

Concepts developed that are aspects of code as a ‗Communication‘ included that it is a ‗Type of Language‘, is a ‗Way to‘ communicate, it is a ‗Form of Written,

Non-Spoken‘ or is a ‗Form of Spoken‘ communication and lastly is a method of

‗Intracellular‘ communication. For ‗Type of Language,‘ students wrote that codes are

―a type of language,‖ ―some sort of language‖, is a form of language‖, and ―computer language.‖ ―A form of communication‖, ―something you use to communicate‖, and

―way of communicating‖ are the concept ‗Way to.‘

―A non-spoken‖ and ―system of writing‖ are ‗Form of Written, Non-Spoken‘ and

―system of speaking‖ is ‗Form of Spoken.‘ And ―what the DNA tells the cells to do‘ is ‗Intracellular Communication.‘

Finally, there was the feature of a code, but unlike most code references to codes as symbols in a specific order that are used for communication between individuals that not all can understand without a key or in the sense of code to a lock, a third aspect of code is as a set of standards of human behavior. The ‗Standards‘ category included aspects such as ―are a set of standards/code of conduct‖ and

―highway rules, regulations, honor code, building code.‖ The category also included references to codes as a set of instructions or rules and included responses such as ―set

218 of instructions‖, set of rules‖ and ‗is a rule that must be followed.‖ These features of a code would not be used in interpreting the DNA IS A CODE metaphor.

Analysis of responses to the meaning of the metaphor DNA IS A LANGUAGE

Student responses were read to determine the action/interactional strategy and consequences of those strategies. Strategies were grouped into concepts according to coherent meanings of the responses. Consequences were grouped with the action/interactional strategy and organized according to coherent meaning. The concepts for the Strategies were grouped to form a Category that reflected similarity of meaning so that a category can be defined by the action/interactional strategy concepts and consequences of those strategies. A summary of the categories, concepts and consequences for student responses to DNA IS A LANGUAGE are shown as a pie chart in

Figure ##. Fractions of the pie represent the percentage of total responses that contained those strategies and consequences. The names of categories are shown as the colored wedges of the figure; percentage of the wedge indicates the percent of responses that used the category. Concepts used to form each category are shown within the concentric circle near the category they were used to form. The percent of the arc of the circle indicates the percent of responses that used that concept; the larger the arc, the more responses that used that concept. I will discuss each category and how it was developed. I will explain the formation of each category separately by discussing the concepts from the action/interactional strategies. In addition to each concept, I will discuss the consequences of the concepts. I will remove the

219 appropriate wedge from the figure and add the consequences for each strategy concept.

How is DNA a like a Language? Communication

The most common feature (positive analogy or ground) of language that was transferred to DNA was communication. Forty-three or 45% of students used this feature when explaining how DNA was like a language. This feature was prominent in the development of the Category ‗Internal Dialogue.‘

Category: Internal Dialogue

The category ‗Internal Dialogue‘ was developed from action/interactional strategies that related some form of communication occurring either with DNA in dialogue with another molecule or cellular structure or as a medium of communication between cells or between body parts. These strategies personify DNA as a participant in communication or as a physical medium of the process of communication.

Concepts developed from action/interactional responses are shown in Figure 34.

The concept ‗Communicate Between/Within‘ was developed from action/interactional strategies that related DNA as either a participant in communication, as a medium for communication in which DNA functions as a language, or where meaning is imparted due to DNA communication Figure 35.

220

Figure 34. Pie Chart for Categories and Concepts from Action/interactional strategies of DNA IS A LANGUAGE RESPONSES.

Responses that described DNA as a participant in communication could further be separated based on what DNA was communicating with (phrases in parentheses are those used on Figure 35: DNA to the organism (DNA → Organism),

DNA to cells (DNA→ Cells), DNA to the body (DNA → Body), and DNA to molecules including DNA to itself (DNA → DNA) and DNA to RNA and RNA to

DNA (DNA ↔ RNA).

From students‘ explanations, it was assumed that the communication of DNA to cells, organisms and molecules was within the same organism. Examples of

221

Figure 35 Action/Interactional Strategy concepts and their consequences for the category Internal Dialogue developed from responses to the metaphor DNA IS A LANGUAGE.

222 student‘s action/interactional strategies for communicate between and within with

DNA as a participant and, when given, the consequences of that communication

(italicized) are:

‗DNA to the organism‘ included statements such as ―DNA communicates with the rest of the organism how each part is made up witout [sic] the DNA the organism would not know how to function properly‖, ―DNA ultimately wants to communicate to an organism everything it needs to know to survive‖ and ―it communicates with the organism to work together to allow organism to live and function‖;

‗DNA to cells‘ included responses like ―communicates to the rest of the cell what to do‖, ―it is an ongoing commentary by the DNA to instruct cells on their function‖,

―body‘s way of communicating to other body parts how to run properly‖, and ―it communicates function by interacting with other parts of the cell‖;

‗DNA to the body‘ included ―it communicates to the body what to do‖ and ―must have a language that body [sic] can recognize and interpret if it could not communicate correctly nothing would get accomplished‖;

‗DNA to DNA‘ included statements such as ―it communicates to other DNA‖ and

―all DNA sort of speaks the same language so that all DNA can understand and communicate with one another‖;

‗DNA to RNA‘ included responses such as ―DNA and RNA can easily interact between each other, RNA can interpret DNA coding to be used by other systems in the cell‖ and ―it is an expression for other genetic materials to communicate within the cell.‖

223

DNA was also seen as a language, that is, as a medium of communication. The language DNA was used for cells to communicate with each other (Intercellular (Cell

→ Cell), for communication within an individual cell (Intracellular (Cell)), for parts of the body to communicate with each other (Interbody), and the way the body communicates with the code (Body → Code). Examples of student‘s action/interactional strategies for communicate between and within with DNA as a medium for communication, that is, functions as a language and, when given, the consequences of that communication (italicized) are:

‗Intercellular (cell to cell)‘ communications was stated as ―is used to communicate, way cells communicate through transferring information‖,

―communicates between all cells what they are to do in creation of a living organism‖ and ―is used by cells to communicate instructions to each other‖, and ―DNA is the way cells communicate to get information from one place to another”;

‗Intracellular (cell)‘ within a cell communication included responses such as

―allows cells to communicate and share information connects functions of the cell and allows it to interpret meaning of what it needs to do‖, ―it is an expression for other genetic materials to communicate within the cell‖; ―is how cells and genes speak to one another‖

‗Body to the code‘ included ―is how our body and code communicate‖;

‗Inter-body part‘ is communication between parts of the same body. One response was particularly clear about the role of DNA as a language used for communication between parts of a body: ―is a way of communication between two parties. DNA is

224 the way different parts of the body communicate.‖ Additional responses included

―body‘s way of communicating to other parts how to run properly.‖

DNA was seen as a language as telling and giving instructions. This concept was communication between DNA and organisms and cells but unlike the ‗Communicate

Between/Within‘ concept, this was communication with a specific purpose rather than a vague communication. Examples of student‘s action/interactional strategies for ‗Tell and Instruct‘ and, when given, the consequences of that communication (italicized) are

DNA to:

‗Cell‘ and included responses such as ―tell each cell how many times to reproduce and what they are to form‖, ―it tells the cells what to do and what to make‖, ―is a way to tell the cell how to act‖,

‗Organism‘ as in the response ―it communicates the necessary ideas and processes to develop an organism‖; ‗Body‘ such as the responses ―tells the body what to do.‖

DNA also ‗Speaks‘ to the body (DNA → Body) and allows for communication between cells and genes. Students wrote: ―is a way of verbal communication from one part of the body to another‖ and ―it talks to our body.‖

DNA was seen as facilitating communication between body parts and cells.

Students wrote the following:‖it helps different parts of the body communicate‖, ―all the other parts of the cell need DNA to communicate and work together‖, and

―communicates so transcription and other functions run smoothly.‖

225

Finally, DNA was seen to ‗Provide Information‘ as when students wrote,‖ [it] communicates a message of genetic makeup of an organism‖ and ―it informs and communicates.‖

Category: Uses/Aspects

There were 35 action/Interactional strategies that reflected the ‗Uses‘ or

‗Aspects‘ of language. ‗Uses‘ included the concepts of ‗Type of Communication‘,

―Needed for Correct Communication‘, ‗is ‗Always the Same‘, ‗Evolves‘ and ‗Make‘ which indicated that language exists for a specific purpose to make a final product,

‗Standardized Common Language‘ and ‗Controls.‘ ‗Aspects‘ of DNA AS A LANGUAGE included that ‗Different Languages Exist‘ and that there are different forms of

Language, that is, ‗How Language is Used‘ in communication. Figure 36 shows the

‗Uses/Aspects‘ category with the concepts and the consequences of those concepts for the uses and aspects of DNA IS A LANGUAGE. I will further discuss the development of each concept from student responses.

The ‗Aspect‘ ‗How Language is Used‘ was considered to be the forms language can take when it used is for communication and included strategies such as

―it says things‖, ―has to be read and understood by something else to make sense and do anything”, ―it can be read‖, ―allows them to be read‖, ―is an expression‖,

―describes what a being is made of‖, ―is a language spoken by our bodies‖, and ―it speaks the same message.‖

The consequences of these actions/ interactional strategies describe information about the final, ultimate result of the speaking, reading, and saying

226 including that we ―building life‖, knowing ―information about an organism‖ or

―everything about cell function‖, and ―describe the makeup of a being.‖ Additional ideas were determined from these consequences that included ―speaking DNA language‖ and speaking ―through different genetic makeups [sic].‖

Figure 36. Uses/Aspects of language category and the action/interactional strategy concepts used to form the category.

‗Different Languages Exist‘ action/interactional strategies related that DNA is a type of language, but since there was no consensus among students who stated the type of language DNA was, the concept indicates that DNA can be many different types of languages. To give some examples: ―there are many different kinds and variations‖, ―is a biological language‖, ―it‘s like a language of the cells‖, ‖is the 227 language of life‖ and ―is the language of the body.‖ An interesting explanation indicated that, in a sense, the DNA language can be learned by humans for a purpose:

―DNA is kind of like the language of science when creating organisms.‖ As an interesting point, students who described DNA as a type of language did not provide statements about the consequences of the type of language; the explanations were matter-of-fact statements- DNA is.

The ‗Uses‘ concepts of ‗Uses/Aspects‘ included the ways in which language is used or what occurs when language is used. DNA was described as carrying, containing or holding information in the generic sense of information or a specific type of information. Students wrote that ―DNA contains a message of information sent throughout to make sure everyone is doing what they are supposed to be‖ and

―each part of the DNA chain has important information about the organism.‖ As a carrier of information as in it ―carries informationa [sic] for the cell‖ and ―because it carries information and lets you know who you are and how you are different.‖

Another function of language was to relay information: ―is a system in which it can relay information from one thing to another.‖ When the consequences of actions were stated, they were for proper functioning of cells, that organisms know what to do, or is what you are.

Additional ‗Uses‘ of DNA as a language was that it is a ‗Standardized,

Common Language‘ used by the body in that it ―sets the standards/common understanding for everything it unites everything in your body‖ and ―it must have a language that the body can recognize and interpret, a common language must be

228 understood to pass on information properly.‖ Also, ―it is a type of communication‖, that without this common language ―it [the body] could not communicate correctly with DNA then nothing would get accomplished‖ and, in a bit of idiosyncratic interpretation of language, one student wrote that DNA is like a language because ―it is always the same‖ while another wrote that ―there are so many different types of

DNA that are all particular to a specific cell and organism‖ and that ―all DNA evolved from common and original DNA and can be traced back.‖ This change over time, evolution, was a fascinating aspect of languages to use for similarity relations to DNA and one that was unique in all responses to DNA IS A LANGUAGE both in this study (96 students) and of the 113 students explaining this metaphor as part of Study 1.

Category: Private Language

The category name ‗Private Language‘ is derived from the linguistic phenomenon where a language is developed and used by two or very few individuals because they are the only ones who know the language. Two concepts were developed from action/interactional strategies that can be interpreted to mean that

DNA is a rare and unique type of language. ‗Individual Differences‘ indicated the uniqueness of DNA to an individual taking private language to the extreme of a single individual. Students wrote that ―it is different for everyone and is spoken with our features‖ and that ―DNA communicates with the person in a way that only that person can “understand”.”‗DNA is Unique‘ in the sense that DNA is different for every person or organism and it is that difference in DNA that consequently leads to the differences we see between individuals as expressed in statements such as DNA

229

―speaks in a specific way based on our genes, or our influences in life‖, ―there are so many different types of DNA that are all particular to a specific cell and organism‖,

―DNA creates specific codes that allow humans to be unique and express themselves in their own way‖ and ―is its own specific thing that when variated [sic] forms different creatures instead of different words.‖ Private language highlights the aspect of DNA that individuals have unique DNA and this leads to the individual differences

Figure 37. Action/Interactional strategy concepts and Private language, know language to, code, order and translate categories for DNA IS A LANGUAGE.

230 between the DNA that we see distinct individuals with different traits and characteristics that can be used for identification purposes. These concepts and consequences are shown in Figure 37 (p. 230).

Two concepts formed the category ‗Know Language to‘: ‗Some do but others do not‘ and ‗Need Specialists.‘ Some do but others do not was developed from action/interactional strategies including ―[I]n order to know about DNA and how to read and interpret whats [sic] on it you need to know the language and meaning of words and terms and everything about it‖, ―humans can’t understand it and talk to individual cells , so therefore it has it‘s [sic] own kind of language to communicate among one another‖, and ―it is readable at the cellular or nuclear level, its information is jibberish [sic] outside that.‖ The last student, to highlight the need to know the language and knowing it is necessary to communicate wrote, ―(theoretically- we are now-in the last 2 decades or so, are starting to translate the language into something understandable to use).‖ And from a student who prefaced the response with ―I dont

[sic] really see DNA as a language‖ comes the explanation ―RNA can interpret DNA coding to be used by other systems in the cell‖; the cell ‗Needs a Specialist‘ that

‗knows‘ the DNA coding in order for it to be used.

Category: Code

‗Code‘ included the action/interactional strategies that explained the metaphor in any way as a code including the structural aspects of a code, its composition or sequence, called ‗A Code‘ , and the process aspects of code including encoding or decoding, called ‗Action Using.‘ ‗A Code‘ included ―codes for different proteins to

231

RNA‖ and ―it is given in code form‖, ‗Action Using‘ included ―we are now able to read DNA code and see exactly which parts of the DNA strand performs it’s [sic] specific function‖, with overlap of concepts in explanations such as ―is full of encryptions we can decode to understand people, plants, animals.”

Category: Order

Action/Interactional strategies that related to the sequence, variation or arrangement of components of DNA made up the category ‗Order.‘ ―Its nucleotides are codes that can be read‖, ―each part of the DNA chain‖, and ―its information follows rules by having a specific form and syntax‖ relate ‗Sequence‘ information; ―it has patterns that can be read and deciphered‘ indicates ‗Arrangement.‘ Consequences of ‗Sequence‘ strategies allow it to be read and used as well as giving information about organisms while different creatures result for ‗Change.‘

Category: Translate

There were only two responses that drew upon the translation feature of languages. This category could easily have been included within ‗Know Language to‘ category, but it is an important feature of language that it deserves special attention specifically since it is this aspect of language from which was drawn a major term in gene expression- Translation- the process of the synthesis of an amino acid chain

(polypeptide) using messenger RNA (mRNA).

The two intrepid students hit upon two features of translation: ―you have to know how to translate it‖ (concept ‗Know How‘) and ―starting to translate the language into something understandable to us.‖ Neither of these two ideas is in the

232

spirit of the ‗Translation‘ used to explain gene expression: systematic conversion of

one language (nucleic acid) to another language (protein).

Analysis of the responses to the meaning of the metaphor DNA IS A CODE

Action/interactional strategies from interpretations of DNA IS A CODE were

developed to form concepts reflecting a feature of code used to conceptualize DNA.

Similar concepts were combined to form categories. Six categories were formed:

‗Form‘, ‗Decipher‘, ‗Information‘, ―Codes for‘, ―Communication‘, ‗and ‗Types of.‘

Figure 38 visually represents these categories and the concepts that formed them. I

Figure 38. Categories and action/interactional strategy concepts that form them from the responses to the DNA IS A CODE metaphor. 233 will discuss how each category was developed from concepts derived from action/interactional strategies.

Figure 39. The category ‗Form‘ developed from action/interactional strategies from the explanations of DNA IS A CODE.

Category: Form (Made up of)

234

The category ‗Form‘ includes action/interactional strategy concepts that related that DNA was like a code because of similarities between the compositional units and arrangement of code and the similarity to the components from which DNA is composed. The action/interactional concepts and consequences of those are shown in Figure 39.

The concept ‗Composition‘ was developed from action/interactional strategies that explained DNA as a code due to the component feature of a code and similarity to the composition of DNA. Student responses discussing composition for how DNA is a code included ―it is made up of differnt [sic] ‗numbers‘ and ‗letters‘‖ (note the single quotes around numbers and letters indicating that this students recognizes the metaphorical nature of the comparison), ―it uses symbols to stand for certain things and must be decoded to determine [the certain things]‖, ―it is a code of four bases,

Thymine, Adenine, Cytosine, and Guanine‖, ―because different alleles code for actual traits‖, and ―it is made up of different bases which are codes for different kinds of proteins.‖

The concept ‗Specific Order‘ includes the feature that order is an important similarity between DNA and codes but did not specify what was in an order.

Explanations of order included ―because it too is basically a large combination when its combination is translated it has a very specific goal‖, ―it is a specific pattern‖, and

―because there is a certain way the DNA has to line up just like theres [sic] a certain pattern in order to unlock a code.‖

235

Then there were explanations that combined the concepts to provide the explanation that components were in a specific arrangement to form the concept

‗Composition and Order.‘ ―Both contain numbers or letters that are in a special order that give instructions on what to do‖, ―it‘s a special link of symbols that stand for something else‖, and ―DNA comes in the form of the four letters A, T, G, C all arranged in special orders‖ express the idea that both components in a specific order is an important feature of both DNA and codes.

The next idea was that different codes exist. This is related to the observation that people have different DNA; that similarity gave the concept ‗Different Code,

Different DNA, Different People.‘ Students wrote: ―every code is different just like

DNA‖; ―it is specific to every organism. A person‘s DNA can be used to identify them so in a sense DNA can be used like a code to “unlock’ a person’s identity‖, and

―because each organism‘s DNA is different it is how we recognize an organism. Just like we can identify items by a code [sic].‖

The final concept of ‗Form‘ is that of encryption. That DNA is encrypted as in

―DNA is encrypted with instructions that are very code like‖ and ―DNA is highly encripted [sic] just as codes are highly encripted so only people or things in the cell highly trained to understand that code can figure it out.‖

Category: Decipher

The category ‗Decipher‘ was formed from action/interactional strategies related to the transformation of DNA and codes form one form to another with or without a stated purpose for the transformation and with or without the need of some

236 type of specialist who does the transformation indicating that codes and by extension

DNA cannot be transformed into a useable form by anything or anyone. These features were developed into the concepts for decipher called ‗Need Specialists to

Transform‘ and ‗Transform‘ that was made up of two sub-concepts- ‗Decode for a

Purpose‘ and ‗Act of Deciphering.‘ These concepts, along with consequences of the strategies, are shown visually in Figure 40 (p. 239).

The ‗specialists‘ were indicated by phrases that indicated only a few or highly trained, or if you have the means; they made up the ‗Need Specialists to Transform‘ concept were either a human who did the deciphering or was a component of an organism such as body parts, cells, molecules including RNA and proteins or simply a non-descript receiver or a combination of these entities; sometimes the decipherer was left unidentified.

Mixed human specialists and components of an organism were indicated by explanations such as ―people or things in the cell trained to understand that code can figure it out.‖

Components of an organism included ―specialized characters communicating together ...only few other parts of the body can read‖ and ―it can only be read by certain cells.‖

Receiver, used in a general sense and unidentified, was found in the explanation

―it can be read and understood by the receiver.‖

Unnamed decipherers were interpreted from strategies such as ―can only be read by other entities specific to cell creation‖, ―can only be read by those with appropriate

237 information to understand the code‖, and ―the DNA can not [sic] be read easily by the bystander just like a code cannot be easily cracked.‖ ‗Receiver‘ was not used as part of this group of specialists because receiver and what does deciphering are mutually exclusive; the receiver does not do the deciphering.

The concept ‗Transform‘ was developed from strategies that discussed the deciphering feature of the coding process: that a plaintext was converted to a cipher text and a cipher text to plaintext. Although students did not use these technical terms, the general idea of a conversion of one form to another was evident in eleven responses.

‗Decode with a Purpose‘ was developed from action/interactional strategies that explained DNA as Code-like because, similarly to a code, DNA must be deciphered or decoded on some way so that a specific goal can be accomplished; the consequences of the action ‗decode.‘ ‗Decode‘ was determined to be actions including ―translated‖, ―transcribed‖, ―interpreted‖ or ―cracked.‖ In some responses, the decoder was named. The decoder could be:

the cell as indicated in the response ―the cell can interpret and therefore accomplish selected tasks and retrieve vital information‖;

molecules, such as ―it is interpreted by proteins and RNA so they know what specific function they need to take‖ – the molecules are RNA and proteins, ―DNA has to be interpreted from a set of instructions. RNA reads and copies DNA then carries it out to be transcribed used to link amino acids into specific chains of proteins‖ – the molecule here is RNA;

238

although not indicated, the decoder here would seem to involve a human due to the explanation ―A persons [sic] DNA is a code that can be cracked to identify an individual.‖

Figure 40. Concepts that made up the Category Decipher with the consequences of the actions/interactions of DNA as a code.

239

Some responses did not name the decoder: ―when its combination is translated it has a very specific goal‖ and ―coded information that needs to be transcribed before it can be used.‖

The consequence of the ‗transformation‘ was, in most cases, vague. Taking all strategies into account, whether the decoder was identified or not, the consequences of decoding were either vague, such as ―specific goals‖, ―determine certain things‖,

‖retrieve information‖, ―accomplish certain tasks‖, or in one case very specific ―used to link amino acids to specific chain of proteins‖ or a specific component plus a vague component, ―proteins and RNA [specific] know specific functions [vague].

The ‗Act of Deciphering‘ included strategies that indicated that the transformation from one form to another was a common feature between codes and

DNA. Student responses included reference to a decoder such as ―it is like a message that has to be interpreted by the body of the organism‖ or no decoder was indicated as in explanations such as ―because it has to be broken up into pieces to be properly translated‖ and ―has to be decifered [sic]‖; these strategies did not have stated consequences.

Category: Information

I had action/interactional strategies of DNA as a code that included reference to the information function of codes as a feature of DNA as well. Fifteen responses included as reference to information with DNA either as a carrier of information, that

DNA gives or tells instructions or lastly specifically what the information is that DNA has. Figure 41 shows a summary of the Category ‗Information‘ with the

240 action/interactional strategy concepts and consequences that were used to develop the category.

‗Contains‘ was developed from any reference to containing and included

―contains‖, ―has‖, ―holds‖, or ―carries‖ (as in contain, not in the sense of transport from one place to another). DNA ―has information‖, ―holds all of your information‖,

―hold secret information that is very important‖, and with a consequence of carrying information ―because it carries information that is necessary for the function of its host.‖

Figure 41. Category Information was developed from the action/interactional strategies contains, tell/give and information identified. Consequences are depicted as the outermost information. 241

The ‗Information‘ was identified as being in coded form, was a message, or was (a set of) instructions; consequences were not always identified. So, we have ―it‘s coded information that needs to be transcribed before it can be used‖, ―it is a message on how to shape a certain organism‖ and ―has instructions for making proteins.‖

Lastly, DNA was described as giving or telling information, similar to the conception of DNA speaking to cells or the body (category Internal Dialogue) that was discussed for how DNA was a language. The recipient of information was mentioned once in the response ―each part of DNA that is paired with another part tells us information about the genetic makeup.” For the remaining explanations, DNA was seen as the ‗giver‘ with no named recipient: ―DNA provides instructions for how a living thing is to be created‖ and ―both contain numbers or letters that are in special order that give instructions on what to do.‖ The identity of the information itself was vague. In the end what was told about was the ‗genetic makeup‘, ‗how to create a living thing‘ or ‗what to do.‘

Category: Codes for

Codes for provided information about what the code was used for, that is, pragmatic aspects of a code. These included what the final product of the code would be or how the code was used to get the final product that did not involve deciphering.

A summary of the category is shown in Figure 42.

242

Figure 42. Category Codes for developed from action/interactional strategy concepts from interpretations of DNA IS A CODE. Consequences of concepts are shown as the outermost information.

The final product of the code was either genes, the body, traits or molecules:

Genes: ―It makes up our genes‖ and ―DNA is a code for genes‖,

Body: ―is a code for the body‖ and ―DNA codes for everything in your body‖, ultimately to DNA as ―the code for all life‖,

Traits: ―the sections of dna [sic] code for specific fine details‖, DNA ―codes‖ the organism for the characteristics it is genetically designed to have‖, and ―it is a code of what traits we will receive‖,

Molecules: ―codes for RNA And [sic] proteins‖ and ―for our molecular makeup.‖ 243

In addition to the final product, what DNA can ‗code for‘ was related to construction as when students wrote ―it contains a certain code in it that can be used to reproduce results in the same thing over and over again‖, ―it‘s the code used when making a living thing‖ and ―is a code for the building blocks of life.‖

What is ‗coded for‘ as the final product was seen as the consequence of the action strategy of coding and ranged from the small and not directly visible (molecules and genes) to the visible (body and traits). The role of the code in construction was either to consistently get reproducible things or a living thing.

Category: Communication

Communication describes the Code-like feature of DNA is to communicate with or to relay some function or final message to a destination. A summary of the concepts that were used to describe the communication feature of DNA as a code is shown in Figure 43.

The concept ‗Gives‘ was developed to communicate the transfer feature of

DNA as a code. ‗Gives‘ included ―they both give you a secret thing that you need‖,

―DNA sends messages to other parts of the body in the most efficient way possible‖, and ―it has a certain message that it delivers.‖

‗Tell‘, similar to the meaning of ‗Tells‘ for DNA IS A LANGUAGE, is communication with a directive function as in ‗tell what to do‘ unidirectional communication versus a more casual type of give-and-take dialogue. What was ‗told‘ was either ―you‖ or a ―cell.‖ DNA ―tells you what to do‖, ―tells you what one will end up like‖, and ―telling cell what to do.‖

244

Figure 43. Categories Communication and Types of. And concepts developed from interpretations to DNA IS A CODE. Consequences of those concepts are shown as the outermost information.

Codes, including the metaphorical relationship to DNA, were seen to be made up of a language and the feature of language used in the interpretation of the metaphor was the purpose of the language as a medium of communication between

DNA and either cells, as in ―is a language for the cells of how they merge, grow, develop, ect [sic]‖ or nondescript communication with a specific goal as in ―it is a language that communicates how to build an organism.‖

‗Describes‘ explained the final goal of the describing but not to what or whom the description is given or how the description was used. We read ―DNA describes what a being is made of‖, DNA describes the structure of a ―being‘, and ―it describes what

245 something is‖; I am not certain what the ―something‖ is referring to specifically among all living things nor what ―is‖ means-whether structure, function, or both.

And lastly, DNA is a code because it is a ‗Medium of‘ communication. This is similar in conceptualization to language as a medium of communication with the exception that the word language or other reference to what constituted the ‗medium‘ was never explained. Students wrote, ―it is used for cells and stuff to communicate‖ without a consequence of the communication or what was communicated but included that cells use it in their communication (but not if it was intracellular or intercellular communication) and ―it is used to communicate a function‖ does provide the identity of what was communicated, but not to what.

246

CHAPTER 8: CONCLUSIONS FOR STUDY 2

The purpose of Study two was two-fold: to determine which features of the target and base were used in the interpretation of the metaphor and secondly, to determine if having students think about both the base and target of a metaphor before presenting them with the metaphor would result in interpretations conceptually different than students who had not been presented with an opportunity to think about the target and base.

To address the first purpose, students were asked to write everything they know about the target for the metaphors, DNA, and two bases, code and language.

Then, they were asked to provide an interpretation of two metaphors, DNA IS A CODE and DNA IS A LANGUAGE. Action/interactional strategies were determined for each student‘s response to form concepts; related concepts were combined to form a category. These action/interactional strategy concepts and categories were used to develop three separate class concept maps, one for each of the two bases and the target. Additionally, to determine the pervasiveness of concepts and categories for each base and the target, the number of the student who used a particular proposition

(2 linked concepts) was put onto the line linking the two concepts. Without this last

247 step, one would not know which propositions were more common and which propositions were unique to an individual or to a few individuals.

Eighty-one of 96 students described either the structure, function or both of the target, DNA, using one or more metaphors such as carry, code, information, blueprint, building blocks, read, tell, transfer or copy. Of the 81, half described DNA structure as a double helix, the term first used by Watson and Crick in 1953. Of the 41 students who did not use double helix, only 8 discussed the structure of DNA in terms of molecules. Of the 40 who used double helix, half talked about the double helix in terms of the molecules that made up the double helix; half provided incorrect molecules such as amino acids, nucleic acids, or proteins. Using the term double helix to describe DNA does not necessarily mean that the person knows the molecular structure of DNA. Further questioning is required when a student described DNA as a double helix.

Students who did not use double helix were most likely to talk about the structure of DNA in conjunction with the metaphor ―code‘ and did not talk about structure if they discussed DNA carrying information, instructions, or a blueprint, genes, polymers, and genetic material. With the exception of code, most non-double helix explanations were about the function of DNA. Overall, whether double helix was used or not, the additional metaphors and links between the metaphors were similar.

The base ―language‖ was described by the majority of students as a means of interpersonal communication developed and used by humans of different cultures and

248 geographic locations; the function of language. There was less of a focus on the structural aspects of language (syntax and semantics) such as it is made up of words and symbols that have meaning and can be visual, verbal written or gestures; fewer focused on translation. These translation, ‗Composition‘ and ‗Form‘ features of language are what are used by biologists when they speak of the language-like features of DNA. So it is not surprising that when asked to interpret the metaphor DNA IS A

LANGUAGE, 89% used some aspect of interpersonal communication for their interpretation. The remaining 11 % used the structural features, code and order and the translation of one language to another. The features they described as characteristic of language are what they used to interpret the language metaphor.

The base ―code‖ was described by students by focusing on the composition of codes and the order of those components. Twenty-four students described the composition in terms of letters, numbers, symbols, or characters. Interestingly, 16 described the composition and order of components using DNA as an example. A quarter of the students talked about the ‗Uses of a code‘ to transmit information, to keep information secret, and that not everyone knows the code. Seventeen responses described codes a means of communication. A few responses focused on the need for a key to encode and decode the information, that codes can be standards of behavior, rules and instructions that must be followed, and that codes are complex, organized, and unique and are used to store information.

Which features of code did students use to interpret DNA IS A CODE? What is the relationship between the features of a code that students described when asked to

249 define ‗code‘ and which features they used to interpret the metaphor DNA IS A CODE?

To visualize the features chosen to make the comparison, I had taken the categories and concepts developed from the DNA IS A CODE coding and highlighted them on

Figure 44 that showed how their concepts fit into the sequence of sending a plaintext to a receiver. Features used in the metaphor explanations are underlined in yellow and are shown as Figure 44.

Figure 44. Features of code used by students to interpret the metaphor DNA IS A CODE. Categories (blue box), concepts (red ovals) and sub-concepts (black ovals) underlined with yellow are the features used to interpret the code metaphor.

As with ―language‖, the pervasiveness of concepts used in the definition of code was transferred to DNA when students interpreter the metaphor, with a few

250 exceptions. The composition and sequence were mentioned in a quarter of responses, communication in 13% of responses, and Information in 15 % of responses. What was surprising was that 22 responses focused on decipher whereas only 14 definitions mentioned that feature. The interesting feature that transferred to DNA was the rules and standards concept.

Code as an example of a communication system that can be represented according to Information Theory

Information and communication seems to be a likely conceptual framework for interpreting the role of DNA within the cell (Shapiro, 2009). It would be interesting to see where student conceptualizations of DNA as a code fit into information as a system of communication. Using the concepts of Information

Theory, with code as an example of information transfer within a communication

Figure 45. Code is used as an example of information transfer within a communication system. Steps in communication derived from Information Theory are shown in boxes. Concepts from students‘ responses are written below each step in information transfer.

251 system, we can assign student conceptualizations of DNA as a code onto this framework (Figure45, based on Quastler, 1958, p. 35).

The source, DNA, was given to students but additional aspects of information transfer were derived from their responses. Students focused on the encoding and decoding aspects of information transfer; the message as gene, letters, symbols, bases, alleles, strands of code, strands of messages, or specific order, the decoder was identified as a specialist with decoding carried out for a purpose, the message after decoding is a protein with a final destination of genes, the body, traits or molecules.

Interpretation of language and code as types of communication of information within an organism can be based on Information Theory; aspects of both can be explained by

Information Theory. As we can see from students‘ identification of the ―message‖ and

―destination‖, they are not clear about the message that is sent from DNA and what is the destination. If using information theory to explain DNA as a carrier and how

‗information‖ is transferred from DNA, the message and destination will need to be made explicit.

252

CHAPTER 9: CONCLUSIONS FOR STUDY 1 AND STUDY 2

I wanted to know if the features used by students in their interpretations of metaphors would be different whether they thought about the base and target before being presented with the metaphor (Study 2) versus if they were only asked to interpret the metaphor Study 1).

When comparing the language categories and the action/interactional strategy concepts and consequences used to describe them for both studies (Figure 46), the categories are nearly identical, except for the category ‗Purpose‘ in Study 1 which was not developed from responses of Study 2. What is different is the pervasiveness of the categories developed from interpretations. Internal Dialogue is the most common conception of how DNA is a language for both studies, but slightly more common for

Study 2 when both the target DNA and base ―language‖ were presented for consideration before students interpreted the metaphor. Another interesting similarity between the two groups is that the concepts used to form the category are identical with ‗Communicate Between/Within‘ the most used action/interactional strategy used to describe how DNA is a language. DNA as a participant in this communication with the organism, cells, body, or molecules was again similar.

253

―Uses and Aspects‖ of language is more commonly used by students in Study

2, but the concepts used to form the category were different. ‗How language is used‘ was the most common concept in both studies; that‘s where the similarity ends. That

DNA functions as a ‗Private Language‘ understood by one or a few organisms was used in nearly twice as many responses in Study 1 than Study 2. ‗Order‘, the main feature used for the formation of the language metaphor was used by three times as many students in Study 1 than in Study 2.

A B

Figure 46. Comparison of Categories and action/interactional strategy concepts for the metaphor DNA IS A LANGUAGE A: Study 1, B: Study 2.

While the categories of concepts used to explain DNA‘s similarity to a code do not vary much between the two groups, the pervasiveness of use is different. The main feature of ‗Order‘ was used less in Study 2 when students wrote about language first; they focused mainly on interpersonal communication.

When comparing the code categories and the action/interactional strategy concepts and consequences used to describe them for both of the studies (Figure 47),

254 the Categories ―Form‖, ―Decipher‖, ―Code for‖, and ―Communication‖ are the same for both studies. Similar to the pattern seen with ―language‖, the pervasiveness of use is different. ―Form‖, which is the concepts composition of the code/DNA, the order of the components, is unique DNA for individuals, is similar for both studies, but was more widely used by Study 1 participants than those of Study 2. ―Decipher‖ is the second most used concept for both studies with nearly identical use by both groups.

―Codes for‖ is also nearly identical in use including what is coded for. Codes and

DNA are used for ‗Communication‘ is more common for Study 2 than Study 1 participants; ―Rules and Standards‖ as a definition of code is not a feature of codes chosen by students in Study 1.

A B

Figure 47. Comparison of Categories and action/interactional strategy concepts for the metaphor DNA IS A CODE A:Study 1, B: Study 2.

255

The features of codes in use by biologists for the standard code metaphor are part of the interpretation of the metaphor of students who do not define the base and target before interpreting the code metaphor.

Both of these results are opposite from what I thought would happen. My initial rationale for the study was that if students did not have the features of codes and language as part of their conceptual ecology, then that might be a reason why they may not provide standard-use interpretations of the metaphor. It seems that affording students the opportunity to reflect on the features of the base and target does not insure that they will develop a working interpretation of the metaphor for use in a discussion of gene expression and the role of DNA in that event.

I would suggest, however, that for a base such as language that students are very familiar with, asking for the meaning before a discussion of the use of language in models and terms of gene expression would allow the instructor to point out the features for positive analogy that should be used in the interpretation and those of negative analogy that are not valid for use in interpretation. This would also be useful strategy for bases that are less familiar, such as code, where-at least according to this study- students provided more features and more used the features that are useful in the code metaphor interpretation. It is also possible that, although metaphors are useful to help us learn about unfamiliar target concepts, the myriad of features that could be useful in interpretation hinders students from knowing exactly which features should be transferred to the target. Scientific metaphors have different uses than common, ordinary metaphors such as ―life is a journey‖ where multiple interpretations

256 aid in exploring all possibilities of life when conceptualized as a journey. Scientific metaphors form the foundation of conceptual understanding of a domain. Guided usage of the metaphor is a logical way to proceed in using them to their maximum effectiveness. That is not to say that additional meanings could not be explored.

Finding out why at student views DNA as communicating with cells or telling molecules where to go would be intriguing and aid in our understanding as teachers as to how knowledge is constructed. What is known is this: if allowed to think about these metaphors on their own, interesting interpretations will be formulated. What role do these interpretations play in overall conceptual understanding of DNA? As

Ortony (1975) pointed out with how much we can assume about the student‘s knowledge of a topic, ―If he makes an incorrect judgement [sic] in this respect a situation may arise in which his addressee cannot construct an appropriate distinctive set of characteristics because he doesn‘t know enough about the topic to reduce tension-reducing ones. There can be two consequences. He may simply fail to grasp the metaphor and recognize his failure, or worse, he may attribute inappropriate characteristics to the topic and go away misled‖ (p. 51). We must insure that consequence two does not happen.

257

CHAPTER 10: STUDY 3

Bases Used by Students in their Own Metaphors

A third group of students (n=113) was asked to provide their own metaphor for six targets, DNA, RNA, Protein, Ribosomes, Transcription and Translation and then asked to provide an explanation for their choice. This removed the potential problems encountered when trying to interpret other-generated metaphors and provided the opportunity to see examples of novel metaphors. A potential problem would be the lack of understanding of the target to find bases that have features similar to both target and base.

To help them formulate the metaphor, students were given the form, using

DNA as the example, DNA is like ______because ______. Not all students provided a base and explanation: DNA (n=111), RNA (n=107), Proteins

(n=107), Ribosome (n=108), Transcription (n=107) and Translation (n=106). Student responses have two components, the base they provide and the explanation of why they chose the base. Bases for each target will be assigned to categories, and then each category will be defined by the action/interactional strategy and consequences of those strategies. A complete list of bases provided by students for each target is found in Appendix B.

258

The categories developed from bases and the percent of bases in a specific category are summarized in Table 6. These are the common concepts across the six targets. Percents do not add up to 100, the difference being accounted for by concepts unique to a particular target. These unique categories will also be discussed for each target.

Base Category Targeta DNA Transcription RNA Translation Proteins Ribosome Language 16 14 13 19 0 5.5 Copy 0 43 8.4 0 0 0 Code 9 3.7 1.9 19 0 0 Computer 7 2.8 8.4 0 0 < 1 Blueprint 26 0 5.5 0 0 0 Construction/Factory 0 3.7 1.9 14 31 55 Manufacturing 0 3.7 1.9 28 38 58 Machines 0 0 0 14 6.5 3 Human 2.7 7.5 12 26.5 27 15 Activity/Profession Messenger < 1 < 1 20 0 0 0 aNumbers are percent of total responses for a target that were classified in a specific category for the bases of the metaphors.

Table 6. Percent of base concept categories for the six targets DNA, Transcription, RNA, Translation, Proteins and Ribosomes for Study 3 shared across the 6 target concepts

Transcription

Transcription was compared to concepts that reflected the copying aspect stressed for the transcription process. Forty percent of responses proposed bases for a process, copy, copying, scanning, and cloning. Related to the copying process is what does the copying and included bases such as copying machine, Xerox machine, photocopy machine, copier, copy machine, and scanner.

259

The Language category was developed from bases that included three aspects of language: first, writing as a mechanistic process of hand copying, or recording information highlighting a ‗sameness‘ and fidelity to the original indicated in base concepts that included ―scribe‖ , ―transcribing‖, and ―writing‖; secondly, Translator a mechanistic process that focuses on a conversion or change from one form to another as in ‗DNA into RNA‖ with the bases ―translator‖ and ―personal translator‖ used; thirdly, Translation as a process of conversion with the purpose of understanding, essentially, the purpose of the mechanistic process that included the base concept

―translating a language.‖

The remainder of the base concepts focused on six additional concepts

DNA/RNA structure, Information of some sort, copying, work in steps, and telling.

The structure of DNA and/or RNA and what physically occurs to them during the process of transcription that included the bases ―zipper‖, ―string cheese‖, ―twizzler‘, and ―teeth impression.‖ Information in some form such as human-made objects such as ―homework‖, ―a color wheel‖, and ―script‖, human activities such as ―drafting‖ and

―transferring money‖, machines such as ―a calculator‖ and ―computer.‖ To change, alter or transform included bases such as Machines ―microwave‖, religious including

―creator‖ and ―Jesus‖, human activities including ―Play piano‖ and ―drawing a portrait‖, and the biological process ―DNA Replication.‖ Copying was done by a computer‘s ―floppy disc drive‖, a human in ―multiplying‖ and a ―mime‖, and occurs in biological processes including ―mitosis‖ and living things ―twins‖ and ―fraternal twin‖

260

Base Concepts Action Machines Human Religio Human Biological Tot ‘Focus’ Made us Activities Processe al s DNA/RNA String 4 structure cheese Teeth impressio n Zipper twizzler Information Calculator Script Mailman 20 of some Computer Homewor Typing sort k Drafting Color Transfer wheel money Code/puz Author a zle (3) manual Writing (5) Scribe Secret agent Change Microwav Creat Play DNA 15 Alter e or piano Transform Jesus Disguise Replicati Draw on portrait Replicati (2) on Economy Translate d (5) Translati on Copy/Copy Floppy replica Multiplyin Mitosis 59 ing a copy disc drive g Twins Copy Mime fraternal Machine Copying twin (25) (14) cloning Scanner Transcrib (4) (3) ing photocopy Cheating ing Creating Work in Assembly 2 Steps line Cooking Telling Telling 1 Total. 33 11 2 47 9 10 6

Table 7. Categories from Transcription base concepts from all responses. Totals are given for both the concepts and action.

261

are copies as well as human-made objects that are ―relicas.‖ Working in steps was accomplished on an ―assembly line‖ and during ―cooking.‖

Categories of the base concepts were combined for all responses with a focus on the action/interactional strategy that was the focus for each. This analysis is shown in Table 7 (p. 261).

Translation

Translation was conceptualized analogically as aspects of language, codes and code breaking, manufacturing and human activities or professions; these formed the main categories of bases chosen by students.

Language was a focus of twenty base concepts that focused on the use of a

―translator‖ or ―interpreter‖ as one who causes change from one form to another, communication to relate information such as ―phone calls‖, and ―dictionary.‖

Codes and code breaking/decoding also focused on a change or conversion form one form to another and included the base concepts ―decrypting a code‖,

―decoding program‖, ―decoding‖, ―a decoder‖, ―a decoding chart‖, and ―decipher a language.‖ What was converted included molecules mRNA and RNA, DNA that were converted to molecules, amino acids and proteins. Additionally, it was not molecules but ―messages‖, ―programs‖, ―genetic information‖, ―genetic code‖ and ―complex code‖ that were converted to ―understandable form‖, ―message‖, ―information‖ and

―meaning.‖

Twenty-eight of the base concepts focused on some aspect of manufacturing including the process of construction or building and the machines that carry out a 262 manufacturing process. Translation is a term for the process of protein synthesis: mRNA is ―read‖ by a ribosome and correct amino acids are brought to the ribosome by tRNA and the amino acids are bonded together, one-at-a-time. Comparing this process to manufacturing was to be expected. Bases of this category included

―assembly line‖ analogous to the one-a-a-time manner that amino acids are bonded together, ―a machine‖, ―What happens at a factory‖, ―production‖, ―Building construction‖, ―meat processing plant‖, ―production system‖, ―legos‖, and ―a factory system.‖

Human objects were compared to translation with a focus on two functions of machines: what was capable of performing a conversion process as well as what was converted and what it was converted into and some machines are used to move materials or information from one place to another. Machines are capable of taking something in one form and converting/making/specifying to something new and different from the original. Fourteen bases chosen included the ―converting‖ function of machines such as carried out by ―typewriter‖, ―oven‖, ―equation builder‖, ―printing press‖, ―Xerox machine‖, ‖calculator‖, and the ―move‖ function accomplished by

‖fax machine‖, ―flash drive‖, and ―cell phone.‖

Human activities and professions focused on the action performed not on the consequences of the action and included ―crossing guard‖, ―surgery‖, ―economy‖,

―reporter‖, ―reading sheet music‖, ―teaching‖, ―security guard‖, ―cooking‖,

―mailman‖, ―reading‖, ―manager‖, ―read a map‖, and ―give gift.‖ The actions performed included direct, read, deliver, bring, make, and create.

263

DNA

DNA was compared mostly to a blueprint (26% of responses), some aspect of language (16%), a code (9%) and a computer (7%). These bases focus on the function of DNA not the structure. Blueprint was identified as such or with a qualifier in four responses: ―the blueprint of life‖, ―blueprints for building‖, ―blueprint for the body‖, and ―genetic blueprint.‖ Code was identified as ―a code‖ or as a type of code such as

―a secret code‖, ―a necessary code‖ and ―a special code.‖

Computer-related bases used included ―a disk‖, ―a database‖, ―a computer chip‖, ―a memory drive‖, ―blank disk‖, ―flashdrive‖, and ―a computer hard drive.‖

These bases focus on the information-storage function of DNA.

DNA was seen as instructions or directions that can be found in maps or books.

This feature was in bases such as ―instruction booklet‖, ―directions‖, ―set of directions‖, ―an instruction manual‖, ―instructions‖, ―set of instructions‖, ―an instruction booklet‖, ―city map‖, ―treasure map‖, ―cookbook‖, and ―recipe.‖ This feature also includes a list of materials needed and how to use them.

DNA was compared to a hierarchy, the head or boss, the one in charge in eight bases such as ―a brain‖, ―nucleus‖, and ―a boss.‖

The structure of DNA was the focus of base concepts such as ―a double helix‖,

―ladder‖, and ―a spiral staircase‖ that highlight the overall shape of a DNA molecule and bases such as ―a train‖, ―charm bracelet‖, and ―rope of genes‖ that highlight that

DNA is made up of a linear arrangement of building block units, a monomer called a nucleotide that are bonded together to form the larger polymer called DNA. Puzzle‖

264 that ―has pieces that fit together‖ and ―has to be complete and inexact order‖ also focus on the structure of DNA though not the overall shape or linear arrangement.

Several bases focused on a fact about DNA: the exact order of nucleotides for organism‘s DNA is not the same for any two organisms of the same species and can be used to identify especially one person from another. Bases that reflect this uniqueness included ―snowflakes‖ –‗no two are alike‘, ―a tattoo‖, ―an ID‖, ―a birthmark‖, ―a password‖, and ―an identifier.‖

RNA

Many of the same categories of base concepts developed for DNA were used by students to describe RNA with the addition of copy, messenger and human activities that focused on work or positions as an intermediary. RNA has many roles in gene expression; many continue to be elucidated in the present. The most well- known function as a copy of DNA that is used to synthesize proteins by a ribosome- this is the Central Dogma‘s focus on RNA. However, additional RNAs perform functions integral to protein synthesis including tRNA that ‗transfers‘ (the ‗t‘ of tRNA) amino acids to ribosomes and rRNA that, along with proteins, make up a ribosome and actually performs the bond-forming between amino acids. Regulatory

RNAs are also important though would be less known to non-science majors. I did not give the identity of the RNA so as to allow for the possibility that these many types of RNA could be identified; this was not the case. Messenger RNA was the

RNA for which analogies were formed.

265

Messenger was the base concept used most often used by students with 20% of responses using the concept of a messenger either using the bases ―messenger‖ or messenger man.‖ Additional bases with a messenger or delivery aspect included

―messenger pigeon‖, ―carrier‖, ―and ―mailman.‖

Human activities or persons were used by 12% of students and included

―operator‖, ―intermediary‖, ―mom‖, ―middle child‖, ―fraternal twin‖, and ―copy cat.‖

Aspects of language were also the basis for comparison including books, syntax, semantics, and translator. Books and manual bases included ―instruction manual dictates the building of proteins‖, ―text that is read‖, ―for Dummies book is the same instructions the DNA carries but in a language ribosomes can understand‖,

―book with words only on one side‖, ―and textbook allows students (ribosomes) to succeed (to create a protein.‖ Features of syntax included, ―letters‖, and ―single line on a page.‖ Semantics included ―sentence can be rearranged and mean the same thing‖, ―translator‖, and ―summary of DNA that says the same thing but in different words.‖

Copy (8.4% of responses) indicated the noun as in ‗a copy‘, not copy the verb as in the process of producing a copy. Bases used included ―copy‖, ―photocopy‖,

―copy of a recipe‖, ―copy of DNA‖, and ―copy of the blueprint.‖ Use of copy indicates an exact copy.

Information storage was the aspect of computers used by students (7.5% of responses). ―Memory‖, ―info on a floppy disk‖, ―memory card‖, and ―information

266 going onto a blank disk‖ reflect this information storage feature of RNA. Two students used ―printer‖ because it ―copies print material on to other things.‖

Blueprint or technical drawing was used by 6 students who also used blueprint for DNA; consistent use of the blueprint metaphor was demonstrated by these 6 students plus one more from the ―copy‖ category who described RNA as a ―copy of the blueprint.‖ All seven used blueprint for DNA, but only one used blueprint for

RNA, five used the bases ―a different blueprint‖, ―DNA just different‖, ―copies of blueprint‖, and ―a second blueprint‖ and one student used ―drawing‖ but the idea is of a technical drawing from the explanation ―is between the blueprint and the final product.‖

Scientific terms were used as the base by 22 students (20.6%). Half made a comparison to DNA citing a similarity in structure such as ―is half of dana [sic]‖, ―has one less strand but looks exactly alike‖, ―contains nucleotides‖, ―is basically the same, except single stranded‖ and function such as ―stores and transmits hereditary information‖, ―contains the same information‖, and performs a similar function.‖

Additional base concepts used were ―enzyme‖ because it ―builds protein‖, ―caffeine‖,

―snake‖ because contains a long strand of nucleotide units‖, ―thalamus‖ because it

―has a specific function‖, ―rabbits‖ because ―it multiplies quickly.‖

Additional bases focused on the structure of RNA. ―Puzzle pieces‖,

―corkscrew‖, and ―a train‖ because it ―is a part of DNA‖, is ―single strainded [sic]‖, and ―has a train of nucleotides‖ respectively. A ―foundation‖ because it ―holds‘, and

―conveyor belt‖ because it picks which genes are expressed.‖ The conveyor belt is the

267 only explanation that comes close to an RNA that is not mRNA, namely, ncRNA or non-coding RNAs that are involved in gene regulation- which ones are expressed.

Proteins

One-hundred seven students provided a response for this target. Base concepts for the protein analogy addressed both the structure of proteins and the function of proteins. Categories that focused on the structure of proteins in the sense of taking small components and putting them together were ‗toys‘ and ‗objects.‘

‗Toys‘ included ―the game barrel of monkeys‖, ―toyboat kit‖, ―clay‖, ―Legos‖,

―orgami‖, ―necklaces‖, ―blocks‖, ―the game Wordle‖, and ―necklace of beads.‖ The

―toyboat kit‖ and one ―Lego‖ response indicated that directions were needed to put the components together correctly.

Objects were used to make a comparison to structure included ―doors‖ because they ―have channels that allow only certain things to go in and out‖, ―a chain‖ because ―are made of amino acids linked by bonds‖, ―ribbon‖ because they ―have that shape‖- this could be a reference to the representation of proteins‘ secondary and tertiary structure where a particular folding pattern called an α-helix is shown as a coiled ribbon.‖ The other objects are used to point out functions of proteins such as

―keys‖ because they ―unlock certain functions‖, ―special treats‖ because they ―provide much needed things for the cell‖, ―file full of information‖ because they ―provide information to other cell structures‖, ―directions‖ because they ―tell what should go where‖, and ―telephones‖ because they ―send messages.‖

268

Construction/Manufacture/Business concepts were used by 33 students to focus on the structure and functions of proteins. The base concept ―building blocks‖ had two aspects used by students: proteins as building blocks of more complex structures such as tissue, muscle, cells, ―useful parts of cells‖, ―combine to make other things‖, and ―build things in your body‖ and proteins are broken down to get back the building blocks and are used to build bigger things‖ with an analogy made to Legos.

This aspect is different from how building block was used for the other two molecules,

DNA and RNA for which building block referred to the monomers combined to make the larger polymer. The base ―a house‘s foundation‖ is used conceptually the same as

―building blocks‖: ―are the basic structures of the body like muscle, skin and bones.‖

As part of the same Construction category, proteins carry out ―activities‖ and

―tasks‖ of the cells, ―determine things that go on in a cell‖, ―help body function properly‖, and ―help build cells‖ were the explanations for the base concepts ―work- horse‖, ―workers‖, ―CEOs‖, ―customers to a business‖, ―the labor‖, ―worker ants‖,

―managers‖, ―construction workers‖, ―builders‖, and ―robot workers.‖

The category of base concepts ‗Machines‘ also focuses on the function

(actions) of proteins as a basis for comparison. ―Motors move and act‖, ―buses‖ because they ―are transporter molecules‖, and ―a car‖ because it is made up of different parts that work together.‖ An interesting base concept was ―alarm system.‖

The features of this base used to form the similarity relations to proteins was that proteins very often work in concert with each other, with different proteins arriving

269 and leaving a complex in a particular order. The student wrote: ―needs to have a specific code in order to work correctly or be turned on or off.‖

Human activities formed a category of base concepts that again focused on the functions that proteins perform in a cell. Of the base each chose, students wrote:

―little messangers [sic]‖ because ―they tell the body what to do‖, ―nosey neighbors‖ because are involved in almost every process in the cell‖, ―a leader‖ because they

―hold it all together and take part in every process‖, ―servants‖ because they ―carry out any duty that their master (RNA + DNA) tells them to do‖, ―mothers‖ because they

―keep the cells running smoothyly [sic] directing them on what they can and cannot do‖, all the employees in a hospital‖ because ―they are all necessary and all take care of you in different ways as have different jobs‖, and ―an actor‖ because they ―perform whichever tasks necessary [sic] and they are modified.‖

Lastly, seventeen students offered base concepts related to human body and human needs; the focus again is on the important functions performed.

―Water‖ is ―necessary for your body to live‖, ―salt‖ was used to focus on the fact that which proteins are present in a cell determines that cell‘s function when it was written that proteins ―bring certain functions in the cells like salt brings out certain tastes in food‖, ―oxygen is needed to sustain life‖, ―nutrients supply much needed things throughout the cell‖, and ―vegetables are needed for humans to function.‖

Ribosomes

Ribosomes are the cell structures that carry out protein synthesis, using mRNA and insuring correct tRNAs are positioned to ensure the correct order of amino

270 acids for a specific polypeptide chain, Biologists have used the machine/ construction metaphor consistently since the 1950s to describe the function of ribosomes. It was not surprising to see that 58% of students used a manufacturing related base concept for their analogy. Although manufacturing/ construction base concepts were used for comparisons to Translation and proteins, the numbers of students using a manufacturing/construction analogy here was nearly double for proteins and double the number who used it for translation. Also, the focus here was on the manufacture of proteins with the ribosome seen as ―a factory‖ by 22 or 58 students, that is, where the protein synthesis takes place. Similar to this were bases that included

―construction site‖ and ―work site.‖ Sixteen saw the ribosome as a machine, or what does the manufacturing of proteins using the base concepts ―machine‖ (15) and ―robot maker machines.‖ Three focused on the step-by-step process of manufacturing and used the base concept ―assembly line.‖ Nine students focused on the ribosome as a worker, the one who carries out or does the manufacturing of proteins. The base concepts they used were ―factory workers‖, ―a construction worker‖, ―working ants‖,

―a workhorse‖, ―a little worker‖, ―a factory worker‖, ―worker bee‖, and ―workers.‖

Human related activities was the next most used category of base concepts; fifteen percent of responses. There are several features that are the foci of a comparison between human activity and the ribosome.

Deliver or transports from base concepts that included: ―messenger‖ and ―a mailman‖;

Reads information from the base concept ―a brain‖ ;

271

Makes from the base concepts ―a crafty person‖ (as in does arts and crafts not devious), ―a chef‖, ―a candy maker‖, ―a middle man‖, ―a kid who takes Lego packs and makes them into usable proteins from amino acids‖;

Creates such as ―an inventor.‖

Objects developed by humans were also used as base concepts but there were no common action/interactional strategies to tie them together. ―A washing machine converts stored genetic information into protein molecules like a washing machine converts dirty dry clothes in to clean wet ones‖, ―a microwave prepares DNA and proteins for the body‖, ―a phone line connects two things so info can be transferred‖,

―tape reader reads or translates codons‖ (this one goes back to the 1950s when Crick said, ―Once you get the idea that the ribosome was a reading head, then the whole world changed.‖). The two bases that are the most conceptually similar were ―a cooking pot is the site of protein production‖ and ―kitchen is where proteins are made.‖

One of the oldest conceptual metaphors for DNA and gene expression is

‗Language‘ specifically DNA has ‗words‘ that make ‗sentences.‘ If this conceptual metaphor is extended across transcription and translation, then ―reading‖ is expected as a base concept for the ribosome which has been conceptualized as ‗reading‘ mRNA. Students wrote: ―a reader reads the message from rna‖, ―someone who reads the instructions grabs a messenger RNA, studies it, then follows how its amino acids are arranged to create the correct protein‖, and ―when you read a book allows you to see information in a figurative sense.‖

272

Action/Interactional Strategies for Base concept Categories

I next developed action/interactional strategy concepts and identified the consequences of those strategies for the 7 base concept categories previously developed; these categories were shared by at least two targets.

Language

Language-related base concepts were used for comparison to 5 of the 6 targets; there were none for Proteins. For language base concepts, DNA contains/holds letters, information, instructions, recipe or ingredients with the result of ―the development of organisms‖, ―build and run your body‖, ―replicate cells‖,

―build the cell‖, ―proteins‖, ―cell function‖, and ―make new cells‖. RNA contains/holds information and instructions for the building of protein; a ribosome uses compiled information. DNA provides instructions, a code or information and

RNA provides information.

Transcription, RNA converts the molecules DNA and RNA or a form of something to proteins or increase comprehension, Translation converts DNA molecules, one form of something or comprehension to RNA, an understandable form including by the cell, Translation converts molecule RNA to proteins, one form of something, comprehension, message and information to molecules, a sequence of amino acids, proteins, and a polypeptide chain.

Transcription and RNA create molecules such as different amino acid sequences, RNA is a copy of DNA, RNA and Translation builds a molecule, protein,

273 and Translation reads DNA or RNA and a ribosome reads directions, ―the message from rna‖ to ―make protein‖ or ―the correct protein.‖

Copy

Transcription and RNA are involved in copying, including copy, replicate and duplicate, molecules or less often, information. ―DNA is copied into RNA‖ forming exact copies of the DNA molecule as the result of the copying process. Transcription creates or makes the molecule RNA which is a copy of DNA. Transcription transfers information though neither the identity of the information nor the final destination of the information transfer was identified.

Code

Features of code, encoding and decoding were used to explain DNA,

Transcription, RNA, and Translation. As a code, DNA contains/holds information for ―cell function‖ and the genetic makeup, gives instructions for ―what traits to show for a person‘s body‖, and defines traits is used to create ―us.‖ Transcription contains information, puts together an order or sequence and codes molecules. RNA relays genetic information. Translation gives meaning, converts-including decode- information, message or molecules produces proteins, usable proteins or a polypeptide chain, reveals a message, and codes molecules.

Blueprint

DNA and RNA were compared to a blueprint. As a blueprint, DNA instructs the building of the organism; is a design for ―our entire makeup‖ including for the

―body‘s structure‖ and for ―functions and outcomes‖;contains/ holds information for

274

―cellular design‖, ‖the body‖, ―the design for life‖, ―for building cells‖, and ―for cell function‖, instructions ―for the body‖ and ―to construct other cell components‖, and codes ―for building your body‖ and ―for life to exist‖, and design ―for life.‖ Also,

DNA is a code for everything in the body, maps out the genome and systems, builds the individual, shows the makeup of cells, and tells the body what to do and how to look.

RNA as a blueprint holds/contains the genetic material, codes molecules, structure of molecules and is an intermediary “between blueprints and final product.‖

Computer

Computer-related features were used for three targets, DNA, Transcription, and RNA. DNA is similar to components of a computer because it holds/contains information, saves/stores information for later use, and determines cell function.

RNA holds/contains information, stores/saves data, converts information, and transfers information ―to a code.‖Transcription writes/copies information and holds/contains information.

Manufacturing is Construction/Factory plus machines

Students provided base manufacturing concepts for all targets except DNA.

Ribosomes are similar to manufacturing because they work in steps to produce the molecule protein, are like laborers because they build and do tasks to produce proteins from amino acids, they instruct or send plans to molecules but mostly were seen to construct/ make molecules of protein from amino acids and tissues and cells.

275

Proteins work in steps to produce molecules, make up tissues and cells, act as laborers to do tasks and manage, communicate a message, construct/make tissues and cells, produce a final function or molecule, and move/transfer.

Translation works in steps to produce proteins in an efficient manner, is involved in the copying or molecules and information, creates molecules, instructs/sends molecules or information to start the construction of proteins, construct/make protein, convert molecules to a usable form, decodes mRNA to produce proteins and move/transfer information.

RNA sends molecules and transcription works in steps to produce a strand of

RNA, copies DNA, writes plans for the organism and uses raw products (DNA) to create RNA.

Human Activity and Professions

Human related activities were used most for translation, proteins and ribosomes, but base concepts were provided for all six targets. Transcription was conceptualized as writing mRNA from DNA. Creating/making produced growth for

DNA, transcription produced a replica, translation and proteins produced molecules and a ribosome produced molecules. Moving/Transfer of messages, information, genes, or molecules from one position to another occurs for DNA, Translation,

Proteins, and Ribosomes. Transcription and RNA copy molecules. Translation is involved with instructing/directing molecules and cells what to do or what to become. RNA is an intermediary to assist with cell functions. Translation, RNA, and ribosomes read recipes, molecules, information and a plan. Translation, along with

276 ribosomes, converts mRNA to proteins. Proteins are involved in maintenance of cells and life.

277

CHAPTER 11: CONCLUSION STUDY 3 OWN METAPHORS

The purpose of Study 3 was for students to provide their own base for comparison to each of six target concepts of gene expression. Although there were bases students used that were already in use, such as code, blueprint, language, most were unique. ―Worker ants‖ for ribosomes, ―primary sector of the economy‖ for transcription, ―Reading sheet music‖ for translation and ―a paper globe‖ for proteins were examples of novel base usage. The only target for which novel metaphors were not common was DNA. Conceptually, if code, blueprint, recipe, program or code were not specifically used, some related concept was used. Examples include ―flash drive‘, ―computer chip‖, ―a memory drive‖, and ―a computer hard drive‖ express information storage, a use of the computer metaphor. DNA, of all the targets used in this study, is by far the one that gets the most attention both in classrooms and in the media. It is, as Lakoff would say, an ―iconic metaphor.‖ It is the base for the concepts students expressed in this study, such as determinism as in phrase such as

―it‘s in our corporate DNA, we have to do that‖ that I overheard at a Panera when two executives were discussion why they had to act a certain way to a proposal presented to them. Almost has that ―set of rules or standards‖ meaning that students used for code.

278

The remaining targets are only likely to be encountered in a classroom and are less influenced by popular interpretations and indeed they were conceptualized in a similar way despite different base concepts that were used. Ribosomes are like machines used in the construction of proteins whether you envision them as ―workers‖ or a ―machine‖, the action/interactional strategy was the same. RNA is a messenger or a copy and transcription is copying whether by ―scanner‖, ―Xerox machine‖, or

―cheating.‖ Standard interpretation applies here.

Base concepts chosen were Basic-Level Categories

I looked at the base concepts to determine whether they were at the superordinate, basic or subordinate level of classification. Mervis & Rosch (1981 in

Lakoff & Johnson, 1999, pp. 27-28) identified basic-level categories as having four conditions:

Condition 1: It is the highest level at which a single mental image can represent an entire category.

Condition 2: It is the highest level at which category members have similarly perceived shapes.

Condition 3: It is the highest level at which a person uses similar motor actions for interacting with category members.

Condition 4: It is the level at which mist of our knowledge is organized.

The basic level category is where ―we interact with the world‖ and ―it the source of our most stable knowledge‖ (Lakoff & Johnson, 1999, p. 29). The superordinate level is more general than the basic-level and the sub-ordinate category is more specific

279 than the basic-level providing a specific instance of the basic level. It was expected that the base concepts chosen by students to form the analogies would be at the basic- level. Appendix B lists all of the base concepts provided by students for each of the six targets. When a base was provided, it was at the basic level: computer chip, mailman, conveyor belt, fingerprint, snowflake, tattoo, pyramids, calculator, fax machine and car were offered, not things that carry out calculations, ways to deliver things from one place to another, means of identification, solid forms of compounds that are different from each other, somatic ornamentation, large, stone structures, devices to transmit information over distances, or vehicles; these are superordinate categories for the basic level concepts. Nor did they use Intel Core 2 Duo™ processor, US Postal service letter carrier, double loop whorls versus tented arches, the great pyramid of Kufu, TI=85, or Nissan X-Terra 4X4; these are at the subordinate level.

Were base concepts consistent across the six targets?

An important question to consider when trying to understand a complex process such as gene expression is whether a consistent conceptual structure would make it easier to understand the process? For example, if the ‗language‘ metaphor is used to understand the structure and function of DNA, would understanding of RNA, transcription, protein, translation and proteins be facilitated if language features were used to explain the role of each in gene expression? Or, would it not matter if consistent conceptual metaphor was used for these concepts of gene expression? We have been introduced to many of the common conceptual metaphors used for gene

280 expression. Does the number of conceptual metaphors interfere with conceptual understanding?

To begin to answer this question, I wanted to determine if students used a consistent conceptual metaphor for each molecule, organelle and process associated with gene expression. Referring to Appendix B, a consistent conceptual metaphor was used by 10 students (out of 112); they are highlighted in yellow. Construction was the most common concept used by 7 of the 10 students. Molecules and cooking were the other concepts used. Seventeen used 3 consistent concepts but not all six. These are shown in blue.

Copying and the Copy: Focus is on?

Copies, making and creating are an action/interactional strategy involved in transcription. Transcription was described as a process of copying and also, since copying must be done by something or someone, the process transcription was conceptualized as a machine that does copying such as a copy machine or scanner.

For the process, there are physical entities present in a cell to carry out this copying, namely, DNA and an enzyme called RNA Polymerase; RNAs are the result of this copying process. The focus each strategy, copies, making or creating, depends on whether the process or a machine was the base concept.

Transcription as the strategy ―copies‖ as a process, such as ―copying a code‖,

―copying a sentence‖ or ―process of copying‖ focused on what is copied, that is, the

DNA. Copy machine also focused on what is copied, DNA. Copy Machines described as ―Makes‖ focuses on what is copied, the DNA, as in ―copy machines

281 make a copy of DNA.‖ But used as ―making a copy‘, the focus is on RNA, the copy.

When the action/interactional strategy ―creates‖ is used to describe the meaning of the analogy, whether as a process or by a copy machine, the focus is on the copy, RNA.

When base concepts formed the category ‗copy‘, the action/interactional strategies ―made‖, ―used‘, ―copies‖ or ―is copied‖ used focused on what is copied,

DNA because RNA is a copy of DNA.

Transcription and Translations interpreted using the Source-Path-Goal Schema

The source-path-goal (SPG) schema is a spatial relations concept (Lakoff &

Johnson, 1999, pp. 32-34) in which a figure, called a trajector, moves from a source to a goal either of which can be considered the landmark depending on which is the focus of the movement: to profiles the goal and the landmark of relative motion whereas from profiles the source and identifies it as the landmark relative to motion. Both transcription and translation can be conceptualized using this schema. We can use this schema to begin to understand explanations such as ―for transcription information moves from DNA to RNA.‖ ―Information‖ is the trajectory with two landmarks: the source DNA and the goal RNA. The trajector was also identified as instructions or message, as in the explanation for the base ‗making copies‘ for transcription metaphor

TRANSCRIPTION IS LIKE MAKING COPIES because it ―is like when a message is send [sic] from the computer to the copier and the information is transferred.‖ In this explanation, ―message‖ and ―information‖ are the trajectors, ―computer‖ is the source landmark and ―copier‖ is the goal. Explained a different way but with the same underlying causal structure, ―DNA translates the data to RNA‖ or TRANSCRIPTION IS

282

LIKE TRANSFER MONEY because it takes DNA info to RNA.‖ The second explanation is interesting because transcription is conceptualized as the trajectory as well as information (―info‖) with the landmark as the goal RNA (―to RNA‖).

In a combination of ‗States are Places‘ and the Source-Path-Goal schema, is the following explanation of ―Translation is like decrypting a code‖: ―takes a complex form of code and decrypts it to an understandable form.‖ Complex and understandable are states of understanding not physical places, yet they are conceptualized as places: state of complex form and state of understandable form.

Translation is the trajector taking another trajectory, the code, from state of complex form to state of understandable form.

The ‗Machines‘ category of bases used for translation metaphors were conceptualized by students as being capable of taking something in one form or from one place and converting/making/moving it – action/interactional strategies- to something new, different or at a different place than the original- consequences. For example, Translation was described by a student as ―sending that copy to the workers‖; copy is the trajector and the workers are the goal. Translation is like a ―fax machine because it receives information and copies it‖ and another student used the same base but with the explanation ―takes information and passes it on.‖ The first explanation is receiving a fax and the second is sending a fax. ―Information‖ is the trajector in both explanations and ―fax machine‖ is the goal in the first explanation and the source in the first. Another example translation is like a ―car because it moves things from place to place.‖

283

The base ―messenger‖ provided for RNA analogies was conceptualized as the trajector in explanations such as ―carries information from ribosomes‖, ―carries information to the ribosomes‖, sends messages from the DNA‖, carries genetic information from one place to another‖, ―carries information from DNA to the ribosomes‖, ―carries information out of the nucleus and transfers it elsewhere‖, and

―sends messages to the cytoplasm.‖ In all of these examples, information is a trajectory and there was directionality for each ―transport‖, whether ―carry‖ or ―send‖ was used. The source was identified as either DNA or the nucleus as indicated by use of the from profile. The goal was identified as cytoplasm, ribosomes or organism as was indicated by use of the ―to” profile. One explanation identified the entire source- path-goal: ―carries information from DNA to the ribosomes, ‖Use of the base ―mail carriers‖ communicated the same conceptual structure in responses such as RNA is like ―a mail carrier because it carries information from the nucleus to cytoplasm like a mailman would carry information from one location to the next.‖ This student‘s explanation not only provided the complete schema but provided the similarity relations between source, goal, and trajector for RNA and the mail carrier.

Also for translation, ―mailman‘ was used to convey this conceptualization. For example, translation is like a ―mailman because he brings info from one place to another.‖ This base is interesting for another reason: translation is a process, not an entity. The conceptualization here is a PROCESS AS A PERSON performing a similar function. I have not come across this conceptual metaphor before and that propose it is used in these analogies.

284

According to Lakoff & Johnson (1999, p. 33), the source-path-goal schema has the following elements:

1. A trajector that moves

2. A source location (the starting point)

3. A goal, that is, an intended destination of the trajectory

4. A route from the source to the goal

5. The actual trajectory of motion

6. The position of the trajector at any given time

7. The direction of the trajectory at any given time

8. The final destination of the trajector

Except for elements 5, 6, and 7, the remaining elements of the SPG schema were described by the students.

Object performs the function

An additional conceptualization was observed for molecules such as DNA and

RNA that were conceptualized as non-kinetic objects- not unexpected- but these non- kinetic objects performed a function: object performing a function for which the object is usually used by a human. Examples of this conceptualization included DNA is a ―blueprint because it instructs how to build the organism‖ where DNA is engaging in instructing the building of an organism, in a sense, the blueprint is the builder.

Additional examples included ―tells your body essentially all what it will be composed of characteristic wise‖, ―literally is responsible for the making of every individual‖, and ―tells you what everything is going to do and look like.‖ In all of these examples,

285

DNA is conceptualized anthropomorphically as instructing, telling, and making and further, as a blueprint, the blueprint is conceptualized as an instructor, teller and maker; features which it does not possess.

Process is represented as a physical object

Transcription and translation are both processes, the terms serve to draw attention to a specific set of chemical reactions that are part of the overall process of protein synthesis. It is interesting that several students provided base concepts of a physical object for a process. For transcription, examples included machines such as copy machines, scanners, and Xerox machines. For translation examples included

Causing is Making

Lakoff & Johnson (1999) discuss a minor causation metaphor they call

―causing is making‖ and describe it as ―[W]hen you make something, you apply a direct force to an object, changing it to a new kind of object with a new significance.

For example, ―He made lead into gold‖‖ (pp. 208-209). There were several instances of the ―causation is making‖ causation metaphor in student explanations for transcription included for the base ―Translating Languages‖ the student explained that it ―takes one thing and turns it into another understandable and useful form‖, for the base ―Translator‖ was the explanation ―‖recodes RNA into DNA‖ and ―DNA being converted into RNA‖ and for the base ―Replication‖ was the explanation ―creates another form in a sequence of DNA.‖

286

CHAPTER 12: GENERAL CONCLUSIONS

I would like to conclude this work by discussing the credibility of qualitative research and this work, suggestions for further research both as a continuation of the current project with the aim towards a theory of metaphor interpretation and its contribution to conceptual understanding of gene expression and lines of research that are a logical extension of the work begun here, suggestions to teachers who discuss

DNA and gene expression in their courses, the uses of information by students and by biologists and suggestions for discussion of ―information‖ as it related to DNA and gene expression. I also suggest a possible reason for the determinism noted as consequences of the actions of DNA with a discussion of the concept of dimension in biological explanation and as an extension dimensionality of metaphors.

Credibility of Qualitative Research, Grounded Theory, and this study

Qualitative research has its own set of standards for judging the ―reliability‖ and ―validity‖ of a project. Generally, these terms are not used because of comparisons to standards of quantitative research. According to Freeman et al.(2007), quality research in science education should include attention to: ―a thorough description of design and methods in reports‖; ―adequate demonstration of the relationship of claims to data, at a minimum, sufficient data are cited in reports to

287 support each claim‖; consideration of the strengths and limitations of the study‖ (p.

28).

Corbin uses the criterion of ―credibility‖ to assess qualitative research.

Credibility means ―the findings are trustworthy and believable in that they reflect participants, researchers, and the readers‘ experiences with the phenomenon but at the same time the explanation is only one of many possible plausible interpretations possible from data‖ (Corbin & Strauss, 2008, p. 301). Corbin further discusses

―quality‖ of the work produced using grounded theory; it is these criteria that should be applied to this work. I will list the criteria of quality and discuss how I have addressed each in this report.

The criteria for quality in grounded theory are ―constant comparative method of analysis, the use of concepts and their development, theoretical sampling, and saturation‖ (Corbin & Strauss, 2008, p. 303). Constant comparative analysis involves comparing incidents from one respondent to other respondents. Through the use of this method, concepts are refined and new concepts are developed. I had given several examples in the analyses of Study 1 and 2 how certain concepts were developed based on comparison of students‘ responses. For example, developing the concepts from the interpretations of ―carrier‖ from DNA IS A CARRIER OF INFORMATION, it was noticed that the initial responses used the ―contain‖ meaning of carry. Then a second meaning

―transfer‖ was used by a few students. I began to note that transfer meant from one place to another, but the places involved in transfer were different. So I further refined the ―transfer‖ concept to include these distinctions. What emerged were the

288 dimensions of ―transfer‖ that included ―heredity‖ meaning transfer from parent to offspring, ―intercellular‖ meaning information was transferred from one cell to another, ―intercellular‖ meaning transfer of information within the cell and

―molecular‖ meaning transfer of information between molecules. Comparison of meanings of ―carry‖ allowed a refinement of the meanings used by students.

The use of concepts and their development was discussed at length for all three studies. I provided a brief summary of the criteria I used to develop a concept and then cited specific examples from students‘ responses used to develop the concept.

The reader was then able to judge if the meaning of the quoted responses was consistent with the explanation of the concept. Although another researcher may use the responses to form a different concept what was important was that the logical development of concepts from data was demonstrated and was plausible. As was noted by Corbin, the explanation provided was ―only one of many plausible interpretations from the data‖ (p. 301).

The last two procedures, theoretical sampling and saturation have been met to extent because of the initial, exploratory nature of the study to this point. Let me explain. Sampling in grounded theory begins with initial data collection for which the researcher may collect data ―on a whole wide range of areas… kind of like fishing, for the researcher is hoping for something but does not know what will come out of the sea‖ (Corbin & Strauss, 2008, p. 146). For me, I did not know what interpretations of metaphors to expect and I did want to meet the criterion of grounded theory for saturation of categories, that is, ―when no new categories or relevant themes are

289 emerging‖ (p. 148). The initial sample for each study was large to ensure that as many concepts for each metaphor interpretation were obtained. As was see, there were several categories that were formed from concepts that were more commonly used by students, but we also saw categories that were formed from relatively few students‘ interpretation. At the initial stage of grounded theory, these are important to determine saturation, but as I work further with the concepts developed, they become less important to further develop.

I now have a clearer picture of possible interpretations and can begin to develop each category, and the concepts used to develop each, more fully; this is where theoretical sampling will begin to become more refined and a second facet of saturation- development of categories in terms of properties and dimensions- can proceed further. This is especially true for categories formed from relatively few responses. I have a better idea of where the research should now proceed and can begin to sample within the data collected. I discuss in the suggestion for further research some of these further theoretical samplings of the data. This discussion will put them into perspective.

Suggestions for classroom discussion of DNA and gene expression concepts

At the end of Chapter 2 I offered several suggestions for teachers who cover

DNA and gene expression in their classes. These were based on the analysis of the problem, but before data were analyzed. I would like to revisit these suggestions and determine, as I had asked, ―Do the data bear these out?‖

290

Suggestion 1. Inform students that a metaphor is being used and that they can derive understanding of some aspect of DNA or gene expression from understanding and using the metaphor. (Carroll & Mack, 1999; Gentner)

Suggestion 2. Determine how students interpret the metaphor before you use it during instruction. This will allow the instructor to determine idiosyncratic interpretations and be certain that students realize how you and science are interpreting the same metaphor. (Strike & Posner, 1992)

Suggestion 3. Determine what students know about the base of the metaphor.

Not just do you know the word, but what are the relationships and properties of the base that are available for students to make links to the target.

The results from Study 2 indicate that students use features of the base when interpreting the metaphors DNA IS A LANGUAGE and DNA IS A CODE. The most common features of language- language is a means of human interpersonal communication- were used when interpreting the ‗language‘ metaphor. Although an interesting interpretation, they are neither the features that are used when the ‗language‘ metaphor was developed nor how it is used today. The syntax aspects of language are the features used for DNA IS A LANGUAGE. And although students from Study 1 were not asked to provide a definition for language, the interpersonal communication feature of language was the most commonly used interpretation. Eliciting student definitions of the base of the metaphor the teacher plans to use will help the teacher to understand not only current understanding of the base features but also if the features that are used in metaphor interpretation are part of the features students are familiar with. If they

291 are not, these features will have to be directly mentioned and how the metaphor is interpreted using them.

Suggestion 4. Work with interpreting the metaphors. Show students how the metaphor was used and how metaphorical expressions led to our current terminology.

This is an aspect of the nature of science and one that is all too often overlooked as part of scientific thinking. Concepts developed from student interpretations of the ‗language‘ and ‗code‘ metaphors from Studies 1 and 2, and the

‗computer program‘ and ‗carrier of information‘ metaphors from Study 1 indicated that students are not likely to provide the interpretation of these metaphors that form the basis of gene expression models and terminology.

Suggestion 5. Develop advance organizers to give students experience with relevant aspects of base concepts that are used as positive analogies to the target

(Ausubel) .

Although I have no results to support the effectiveness of this strategy, the results from Studies 1 and 2 do support the conclusion that students are unlikely to use the features of the base necessary for useful interpretation of ‗language‘, ‗code‘, carrier of information‘, and ‗computer program‘ metaphors. Whether direct experience with the base features will aid in conceptual understanding of some aspect of DNA and gene expression requires additional studies.

Pervasive use of information and students‟ use of the term

There are two conceptual aspects of ‗information‘ currently used in molecular biology, the causal and semantic aspects (Sarkar, 2000). The ‗Causal‘ aspect is

292 derived from Mathematical theory that can be traced historically to the work of Claude

Shannon. Semantic information is used in sense that human thoughts contain information and is extended to DNA in the ideas that DNA sequences contain information for producing proteins and DNA sequences contain all the information for producing an organism. This perspective is best seen in the writing of Maynard Smith

(2000) wherein it is tied to evolution and is often referred to as teleosemantic information. In this perspective one reduces meaning to biological function then reduces it to natural selection (Sarkar, 2000).

In light of the results of these studies, I can suggest the following prescriptions when a teacher uses the term ‗information‘ in relation to DNA, gene expression or heredity; we must be explicit about the meaning of ‗Information‘. First, what is the information ‗stored‘ and ‗transmitted‘. If using the ‗causal‘ aspect of information, the sequence of nucleotide bases for a particular section of DNA is related to the amino acid sequence of a protein. However as I have argued, in light of current understanding of gene expression, this is not a one-to-one correspondence. So, although ‗code‘, ‗language‘, and ‗computer program‘ provide positive analogy to features of sequence is related to sequence, editing and splicing of the original

‗transcript‘ and modification of proteins means that the original DNA sequence

‗information‘ is not the final arbiter of protein amino acid sequence.

If using the teleosemantic aspect of information, that is, information is ‗about‘ function as in the expressions ―gene for‖ and ―structure of cells, body, and organs‖, the teacher needs to be stressed metaphorical nature of information used in this sense.

293

Much more than the sequence of DNA is necessary for the formation of traits. If a student stated that ―DNA is code because it codes for traits‖, the actual role of DNA will need to be addressed at this point. This strategy will also help to address the determinism determined in students‘ responses.

Secondly, the teacher needs to explain how the information is ‗stored‘ and

‗transmitted‘. These concepts were not clearly communicated by students as can be seen in Study 1 for the ‗carrier of information‘ metaphor. ‗Carry‘ was used by a little more than half of the students in the ―Is‖ concept which is conceptually the ―causal‘ aspect of information and the remainder used the ―About‖ aspect which is conceptually the ‗teleosemantic‘ aspect of information. The storage and transmission of information are two entirely different concepts that can be conflated if ―carry‖ is not explained as ―stored‖ in the sense of a sequence of nucleotide bases, plus additional processes such as chromatin structure and editing.

Thirdly, what is the final receiver of the information? If the causal Crickian

―Flow of Information‖ aspect is to be used, and you must determine this, then a flow indicates a sender and a receiver of information. What is the destination of the

‗information‘? Students‘ explanations indicated there is a receiver variously identified as cells, molecules, or body parts. If the teacher does not address the identity of a receiver of information and if s/he thinks that is an appropriate positive analogy for the metaphor, then the students will identify one.

Fourthly, there is an interrelationship between concepts of information, communication, language, and code; they all are communication, conceptually. If the

294 teacher is using any of these metaphor bases, information will most likely be a feature students will use to interpret the phenomenon. Address the meaning of information you will be using for these metaphors.

Fifthly, from Study 3 we learned that overwhelmingly protein synthesis was conceptualized as involving ‗communication‘ of information and ‗construction‘ using this information to form a finished product. Again, the teacher must identify the definition of information s/he is using for the discussion.

Sixthly, when interpreting the metaphor bases ‗Blueprint‘, ‗Plan‘, and

‗Recipe‘, students use information in the teleosemantic sense in that they conceptualize DNA as information representing a final product. Students interpret the metaphor bases ‗Code‘, ‗Language‘, ‗Information‘, and ‗Computer program‘ in one of two ways: one, relates to the form of information using the structural aspects of these bases to compare to DNA structural features and the second as the purpose of information , that is, how it is used and what uses it.

It is evident from students‘ interpretations of the gene expression metaphors that they focused on features for comparison that were not the intended use when they were developed as heuristic, rhetorical devices. This is not unexpected owing to the creative interpretations that metaphors evoke. While this may be helpful to gain insight into how students conceptualize the role of DNA, if a teacher is using the metaphor for the purpose of instructing specific aspects to gene expression and the role of DNA, these creative interpretations are not helpful for helping to establish a conceptual framework on which to build gene expression. I have a suggestion and an

295 observation derived from the results of all three studies. The suggestion is a concept I will call the ―Keystone Concept‖ that acknowledges that there are specific features that set a conceptual framework based on the language, code, and carrier metaphors.

The observation is from the consequences students had for action/interactional strategies, that DNA direct the formation, proper function, and ultimate structure and behavior of an organism. These metaphors were developed for a linear arrangement of building block of nucleic acids and proteins and that is the consequence, not two- dimensional, three-dimensional or fourth dimensional features. I will discuss a proposed reason for this misapplication.

Keystone Concept

Remember my quote from Pinker: ―As scientists come to understand the target phenomenon in greater depth and detail, they highlight the aspects of the metaphor that ought to be taken seriously and pare away the aspects that should be ignored.‖ Using this idea, taken with how metaphor is developed and used in scientific metaphors – quite different from conventional metaphor use- and considering the many interpretations of a metaphor provided by students that were not congruent with the scientific usage, I would like to propose a new concept when discussing features of the base and target concepts of scientific metaphors called the

‗Keystone Concept.‖ This is similar to the idea in ecology of a ―Keystone Species‖ and like the Keystone Species, the Keystone Concept:

296

Is pivotal to the concepts that are related to it, similar to the idea of ‗Immutable

Feature‘ of a category. If it is removed, the category ceases to exist in that without the

Keystone concept, the Concept isn‘t the concept any longer.

Like the keystone species, a Keystone Concept may be neither obvious (that is, stands out as the keystone nor understood why it is the keystone (until studied closely or removed completely).

What students deem to be the key feature may not be what is the actual key feature but identification of the key feature is based on their current available information about a category, like code, but this may not be complete (all relevant information about the category) as a result, positive, negative and neutral analogical relations may not align with how science uses the base category for a metaphor.

The definition of a Keystone Concept is made up of two parts:

1. Of all immutable features, it is the one that all other features (eg., of a code) are dependent on;

2. Used as the basis of a scientific metaphor.

How do you determine the Keystone Concept for code? It is an objective concept. That is, regardless of the individual, the keystone concept is the keystone even though the features used by any one individual during interpretation of the code metaphor may vary.

How is the Keystone Concept the same or different from the idea of feature centrality (Ahn, 1998)? It would be the key feature used in both forming and interpreting a scientific metaphor. Because there was an original positive metaphor

297

(ground) that was used during the initial conception of the metaphor, other positive analogical relations may have followed during further heuristic use and model development; the latter features that were used may or may not have a direct relationship to each other.

Using the code metaphor as an example we have the analysis shown in Figure

48:

Sequence that stands for something else and needs to be decoded to get it of bases (DNA) sequence of amino acids of Translation the key, a protein What cell genetic code structure? Keystone Concept

Figure 48. Analysis of ‗Code‘ metaphor identifying the Keystone Concept.

‗Sequence that stands for something else‘ is an example of a Keystone

Concept because without it, no other concept in gene expression model or the model itself makes sense. And contrary to the conclusions of Ahn (1998), who argues that mutable features are used when interpreting metaphors, I would argue that it is immutable features that were used when developing the code metaphor. This is an immutable central feature of ‗code‘ but also the keystone concept. It is the feature of code that must specifically be discussed when any feature of the concept ‗code‘ is used including terms derived from the theory-constitutive metaphor code. If not, features of code prominent to a student will be used to interpret the term; misconceptions may follow.

298

For DNA IS A CODE, the Keystone Concept involves the features Coded

Plaintext, Plaintext and Decode/Decipher as key to understanding how the metaphor

DNA IS A CODE was used and how ‗code‘-based terms were developed from it. These features are highlighted in Figure 49.

Figure 49. Keystone concepts used in the development and interpretation of the metaphor DNA IS A CODE.

The category developed from student responses to the code metaphor that overlaps with the Keystone Concept is the category Attributes, Sub-category Form.

Referring to Figure 48, this is a feature that students used to explain the metaphor, but additional features were used as well. And as was indicated in the Results for Study 3

299 for the definition of ‗code‘, thirty-six students used part of the keystone concept in their definition of code, twenty-four students used ‗Form‘ category concepts of composition and specific order on the encode/encrypt portion of code use.

Dimensionality in Biological Explanations

For the only logic that biologists really master is one-dimensional. As soon as a second dimension is added, not to mention a third one, biologists are no longer at ease. If molecular biology was able to develop so rapidly, this is largely because, in biology, information happens to be determined by simple linear sequences of building blocks, bases in nucleic acids and amino-acids in protein chains. Thus the genetic message, the relations between the primary structures, the logic of heredity, everything turned out to be one-dimensional. Francois Jacob, The Actual and the Possible, p. 44

John Marks (2006) comments upon Jacob‘s writings saying that ―Biology cannot explain the processes by which the linear one-dimensional sequence of the bases in the genetic material is translated into the two-dimensional cell layers, three- dimensional tissues and organs, and four-dimensional behaviors‖ (p. 92). This analysis of the limitations of linear, one-dimensional explanations in biology to explain higher dimensions of organization was evident in the students‘ interpretations of the ―code‖, ―language‖, ―computer program‖, and ―carrier of information‖ that included consequences of action concepts such as know the structure and functions of cells, body parts, the structure of an organism, and behaviors. Why might the students be using linear, one-dimensional sequences of DNA to conclude that knowing this one knows about two-, three-, and four-dimensional aspects of an organism?

If we extend the analysis one step further to the metaphorical foundations of the models developed and used by molecular biologists and to our continued focus on what I will call one-dimensional metaphors (1-D metaphors), not only do most

300 metaphors used to describe DNA structure and function turn out to be 1-D, but molecular biologists have a tendency to misapply them to describe the 2-D, 3-D and 4-

D events Marks describes above. We then present these to students and the lay public and leave them to apply, inappropriately, these metaphorical tools to understand and explain tissues, organs, and organ systems. This fact comes out in students‘ explanations in the action/interactional strategies and consequences of DNA understood in 1-D metaphors including code, language, information, blueprint, and script when ―DNA directs the body ―, ―is the way cells communicate.‖ Students took

1-D appropriate metaphors and applied them to 2-D, 3-D, and 4-D events apparent in explanations that included DNA carries information for what a person should be like, basic functions, height, and personality. Why? It‘s all they have because we, as science educators and biologists, have not given them the appropriate conceptual framework to do otherwise. It‘s no wonder they do not understand these events. As the old adage goes, when all you have is a hammer, everything looks like a nail.

When you have the hammer of 1-D gene expression metaphors, 2-D, 3-D and 4-D events look like nails.

This 1-D thinking found its ultimate expression in the Human Genome Project and other genome projects for living things: if we know the linear sequence, we know about the organism. This line of thinking was present in student explanations as well.

1-D information will not enhance explanations of basic biological functions as Biro

(2004) rightly pointed out when he wrote about the Genome Project and its underlying ontology, ―The result is that we have almost the same understanding and

301 misunderstanding of our fundamental biology as we had after the last big biological revolution in the 1960s‖ (p. 952).

We can compile the sequence of events from parent to offspring and development of the immature form to the mature form (Figure 50).

Immature  Mature Form Form Parent ♀ DNA Zygote Traits DNA  Protein Developmental DNA Structure Parent ♂ DNA Black Box Function Behavior “Heredity” “Gene Expression” 1-D metaphors of code, c1arry,-D metaphors information of , information, 1-D metaphors of code, carry, language code, carry, information, information, Appropriatelanguage language INAPPROPRIATE INAPPROPRIATE

Figure 50. Sequence of events from parent to offspring and development of the immature form to the mature form showing where the 1-D metaphors are appropriate.

To end this discussion, I quote the realization by Jacob of the limitations of these 1-D metaphors in use at the 1970s and their inability to account for organization not yet discovered; he wrote: ―Today the world is messages, codes, and information.

Tomorrow what analysis will break down our objects to reconstitute them in new space?‖ (Jacob, 1970, p. 324 quoted in Marks, 2006, p. 90).

Towards a Theory

The purpose of Grounded Theory methods is to produce ―middle range theoretical frameworks that explain the collected data‖ (Charmaz, 2000, p. 509).

However, that is not the only aim of qualitative research. As Corbin & Strauss (2008) point out qualitative research can ―vary from description, to conceptual ordering, to

302 theorizing‖ (p. 53). Theory ―denotes a set of well-developed categories (themes, concepts) that are systematically interrelated through statements of relationship to from a theoretical framework that explains some phenomenon. The cohesiveness of the theory occurs through the use of an overarching explanatory concept, one that stands above the rest. And that, taken together with the other concepts, explains the what, how, when, where, and why of something‖ (Corbin & Strauss, 2008, p. 55).

My ultimate aim is a theory to explain student understanding of gene expression metaphors, how they are different from standard scientific usage, what leads to the differences and how understanding of these metaphors influences conceptual understanding of the role of DNA and of gene expression. However, I first needed to document student interpretation of other-generated gene expression metaphors. Since I hypothesized that there is a difference I needed to determine if there was a difference in interpretation. Studies 1 and 2 aimed to do that. What was accomplished towards a theory was description of the phenomenon of student interpretation of gene expression metaphors and conceptual ordering, that is,

―organization of data into discrete categories according to their properties and dimensions, then the utilization of description to elucidate those categories‖ (Corbin &

Strauss, 2008, pp. 54-55). For each metaphor, I was able to form categories based on related action/interactional strategy concepts and their consequences developed from student interpretations of ―code‖, ―language‖, ―computer program‖, and ―carrier of information‖ metaphors. I was then able to compare these to the interpretation of the metaphors used historically to form gene expression models and terminology

303 determining that the majority of student interpretations were different from scientific usage. I was also able to determine usage of terms and conceptualizations of the role of DNA from this concept ordering; these I have discussed.

This is a precursor to theory development but it is not a theory. As Corbin &

Strauss (2008) note ―this type of analysis is a precursor to theorizing‖ (p. 55) but constructing a theory ―necessitates that an idea be explored and fully considered from many different angles and perspectives‖ (p. 56). For the work to proceed to the level of theory requires an overarching explanatory concept and be explored from different angles and perspectives. These were not achieved by these studies so a theory, at this time, is not possible.

Suggestions for further research

These studies were only the beginning steps towards developing an understanding of the role that other-generated metaphors play in conceptual understanding of gene expression. I wished to determine students‘ interpretation of these metaphors to determine if they were similar to the meaning that conceptually forms the basis of these metaphors in gene expression models. The results also provide avenues for further investigations both as logical extensions of this work and new avenues based on current findings in the domain of gene expression.

The short term work will be to work with the categories developed thus far in order to determine the relationship of a certain interpretation of DNA to overall conceptual understanding of gene expression. It is also possible to use the action/interactional strategy concepts and consequences across all metaphor

304 interpretations to determine consistency in understanding of the role of DNA in gene expression. If students conceptualize DNA as a participant in communication

(language metaphor) to communicate how a cell is to function, do they hold a similar conceptualization across the interpretations of the ―code‖, ―computer program‖, and

―carrier of information‖ metaphors? Or might the metaphor itself be contributing to an idiosyncratic conceptualization? This type of analysis will also be important to determine consistency of term usage such as information: if students interpret information as the causal aspect of ―is‖ as the structure of DNA, do they also use the same interpretation for information when interpreting ―code‖, ―language‖ and

―computer program‖? Or is a certain aspect of information more likely to be used when interpreting one or more of the metaphors compared to the others such as metaphors that lend themselves to a more structural interpretation such as code or computer program?

Determining the answers to these questions will also aid in the development of a middle range theory of metaphor interpretation for gene expression and the role of these metaphors in conceptual understanding of the domain by ―arranging the concepts into a logical, systematic explanatory scheme‖ (Corbin & Strauss, 2008, p. 56).

As far as suggestions to expand the scope of metaphor use to understanding gene expression, first, look at additional gene expression metaphors. I have only used those that have been and are currently used for the role of DNA in gene expression.

But additional molecules and processes occur that contribute to the production of the final, correctly folded protein. Metaphors for gene regulation, mRNA transcript

305 editing, translation, the role of ribosomes and chaperones to assist folding of the polypeptide chain were not part of this study. However, Study 3 asked students to provide bases and explanations for their choice of base for several of these aspects of gene expression: transcription, RNA, translation, proteins and ribosomes. Their responses should give us some insight into how firmly entrenched many of these metaphors are and also of how we might use these metaphors in classroom discussions. Transcription and ribosomes as construction, proteins as the workers of the cell, RNA as a middle man and messenger, and transcription as copying provide insights into the level of understanding students have of these complex molecules and their role in both gene expression and the cell. And although students provided bases conceptually similar to other-generated metaphors for these molecules and processes, studies to determine their interpretation of RNA, Transcription, Translation, Protein and Ribosome other-generated metaphors would provide interpretations of others comparisons and not necessarily related to their understanding of the molecules or processes. It would be interesting to determine of interpretation (and conceptual understanding) of the metaphors varies depending on whether students explain their metaphors or interpret someone else‘s even thought the bases used are similar.

We need also to determine Keystone concept(s) for the commonly-used DNA metaphors. This will allow a more focused discussion of the metaphors by providing the features that are directly used in gene expression models. If the teacher desires, negative and neutral analogy may be discussed to limit students‘ conceptual wanderings to features that are not directly related to the model or its terminology. I

306 have provided an example for DNA IS A CODE. A similar line of reasoning based on past use and current models can be done for all metaphors.

Related to this, we need to determine if the teacher guiding metaphor interpretation aids conceptual understanding. I have hypothesized that it would, but evidence to support or disprove the hypothesis is required.

We need to determine the aptness based of each metaphor based on the dimensionality of currently-used gene expression metaphors and the contribution of inappropriate metaphor use to overextension of the metaphor to other dimensions.

This idea was best seen with the consequences of action/interactional strategies for language and code metaphors for which students said that the consequences were structures and functions of cells, body parts, the body, and behaviors. These are complex structures and functions that are not determined solely by knowledge of linear sequence of nucleotides for regions of DNA, not at present the linear sequence of amino acids of a polypeptide. There is still not an adequate algorithm for determining the final 3-D shape of a protein from amino acid sequence.

There is the case of simplifying a concept so that it is accessible to a non-scientist then there is conceptually misrepresenting that simplification and in doing so presenting a view of a complex process that is reduced to the sequences of DNA. To allow the consequences of DNA as code, language, computer program and carrier of information to be these complex processes extends the metaphor beyond its functional use to incorporate negative analogy or features that are not used to describe the base.

307

Codes are used to transmit a message from a sender to a receiver using symbolic representation. Codes do not embody the contents of the message.

Also from Study 3, it was determined that 10 of 112 students used bases that were conceptually consistent across the six targets for gene expression and 17 provided bases that were consistent across 3 or 4 targets but not all six. Does it matter to conceptual understanding of gene expression if bases from the same conceptual domain, such as language, construction, communication, or cooking are consistently used? We need to determine whether conceptual metaphor consistent across gene expression will contribute to intelligibility during conceptual understanding versus mixed metaphor use that was the more common pattern determined from students‘ interpretations and also in the models and terminology of gene expression.

An interesting phenomenon that was noticed in student responses that had been discussed was that of DNA as ―do-er.‖ I developed this concept to account for action/interactional strategies for which DNA was given the role of carrying out an action and stated in the present, active tense of verbs such as ―makes‖, ―tells‖,

―communicates with‖, ―moves information from one location in a cell to another.‖ As was discussed, and argued eloquently by Lewontin, as an inert molecule, DNA does nothing. We need to determine if the conceptualization of ―DNA as Doer‖ is metaphorical or literal. It is entirely possible that because students were interpreting a metaphor, they took license to describe DNA as doing a task associated with the base of the metaphor. The anthropomorphizing is merely the result of the bases being human activities or constructions. It may also be due to English language

308 constructions. We must determine the relationship of English language constructions for actions and its contribution to ―DNA as Do-er‖ and whether students are aware that DNA does nothing and they are merely engaged in a metaphorical description.

Whichever is the case, we need to find out so that we can use proper language and/or stress the limitations of a particular metaphor so that DNA is no longer a ―do-er.‖

In the review of literature on Chapter 2, I discussed the role of the Central

Dogma of molecular biology in organizing research into the relationship between

DNA, RNA and Proteins. As written, and continues to be written, DNA is seen at the beginning of a causal chain that results in protein. In conjunction with the metaphors of the day, especially information, code, and language, DNA took on conceptual role as ―master molecule‖ responsible for everything that followed in the causal chain. We need to investigate the relationship between continued stress upon the outdated central dogma and its relationship to DNA as ―do-er‖ and ―head‖ of activities that occur in protein production, the cell, and the entire organism. Perhaps it is time to let it go especially if it interferes with understanding the nuances of gene expression.

An exploration of the role that an understanding of developmental biology would have in forming a more accurate conceptualization of DNA would provide evidence to support or refute my contention that the possible reason for students stating consequences of the action of DNA are structures and function of cells, body parts, and the entire organism. Knowledge of what does occur during development and the role DNA actually plays in development may put DNA in its proper role and not as the final and ultimate arbiter of every structure and function of an organism.

309

As part of the investigation of developmental biology and its relationship to

DNA function, we should explore metaphors used in developmental biology for dimensionality aptness and continuity with common DNA metaphors. How can understanding of the function of DNA gained from proper understanding of gene expression metaphors be transferred to understanding how development occurs?

Related to this investigation of development is the role of exosymbiosis in development and organ functioning that is, the role bacteria play in the formation of the intestinal tract and immune system and as has been recently investigated, the major role bacteria play in the development of obesity. If DNA is conceptualized as master and do-er, it may be difficult to understand (not intelligible or plausible) how bacteria may influence development and contribute to obesity.

To get a better understanding of the role that metaphor plays in conceptual understanding of gene expression, one could use in-depth qualitative interviewing with grounded theory methodology to determine the connection between metaphor interpretation and understanding of the role of DNA in a cell.

And lastly we should determine how to incorporate aspects of intercellular communication and cell regulation, such as secondary messengers, regulatory RNAs, subnuclear localization (―chromosome territories‖ and ―transcription factories‖), and epigenetic regulation that results in altered chromatin structure with role of DNA. Do current metaphors allow this as positive and neutral analogy? Are these metaphors being used by biologists apt and is there conceptual continuity with extant gene expression metaphors?

310

If biology continues to base its models and terminology on metaphors, we, as science educators, must determine how we can best present how metaphors are used by biologists and conduct studies to begin to understand how students interpret and use these metaphors in conceptual development in the domain of gene expression.

These studies are an initial attempt in this direction. Further work should include interpretations of additional theory-constitutive metaphors to determine if keystone concepts are used in interpretations; and additional studies of the same metaphors with different populations to determine if the categories and the concepts and consequence that were used to describe them are unique to the study group or are a common interpretation by non-majors. A limitation to the study is that the interpretations given by many students left me with further questions about what they may have meant.

This limitation can be overcome by the use of in-depth qualitative interviewing where follow-up questions as to meaning can be accomplished. This would also allow the

―DNA as Do-er‖ questions to be answered as either literal or metaphorical. Also, many students may not have known how much of an explanation to write because they do not know the endpoint of the explanation; this is evident in responses with no consequences given. Additional follow-up questions could elucidate whether they do not know the consequences or did not know they were important in their explanation.

This may also have been the first time students were asked to either explain an other- generated-scientific metaphor -most do not recognize the depth and breadth of metaphor use in biology- or develop their own metaphor and provide a rationale for their choice of base and how DNA, RNA, proteins are like the base.

311

It is hoped that science educators and researchers will use the results and conclusions of this research to seriously consider the role metaphors play in biological. models and terminology and conduct research to further understand the role they play in concept construction in the domain of gene expression. Scientific use of metaphors is at the same time creative and heuristic but not so open to creative interpretation that conceptual understanding, hypothesis development, and model development are led astray by negative analogy. Metaphor choice is influenced by worldview. Metaphor interpretation is equally influenced by worldview. The time has come to seriously undertake the study of how other-generated biological metaphors affect our conceptual development.

312

REFERENCES

Ahn, W. et al. (2000). Causal status as a Determinant of Feature Centrality. Cognitive Psychology, 41, 361-416.

Ahn, W. (1998). Why are different features central for natural kinds and artifacts?: the role of causal status in determining feature centrality. Cognition 69, 135-178.

Altshuller, G. (2007). The Innovation Algorithm: TRIZ, systematic innovation and technical creativity, 2nd ed. Worchester, MA: Technical Innovation Center, Inc.

Ansari, A. Z. (2007). Chemical crosshairs on the central dogma. Nature Chemical Biology. 3, 2-6.

Ashe, A. & Whitelaw, E. (2006). Another role for RNA: a messenger across generations. TRENDS in Genetics, 23, 8-10.

Asoko, H.M, Driver, R.H., and Scott, P.H. (1991). Teaching for conceptual change: A review of strategies. In R. Duit, F. Goldberg, and H. Niedderer (Eds.), Research in Physics Learning: Theoretical Issues and Empirical Studies (pp. 310-329). Kiel, Germany: IP.

Ausubel, D.P. (2000). The Acquisition and Retention of Meaning: A Cognitive Vew.Dordrecht: Kluwer Academic Publishers.

Brachet, J. (1960). Ribonucleic Acids and the Synthesis of Cellular Proteins. Nature, 186, 194-198.

Bateson, G. (1972). Steps to Ecology of Mind.Chandler Publishing Company.

Biro, J. C. (2004). Seven fundamental, unsolved questions in molecular biology Cooperative storage and bi-directional transfer of biological information by nucleic acids and proteins: an alternative to ―central dogma‖. Medical Hypotheses, 63, 951-962.

313

Black, M. (1993). More about metaphor. In A. Ortony (Ed.) Metaphor and Thought, 2nd Edition. pp. 19-41. Cambridge, UK: CambridgeUniversity Press.

Blasko, D.G. (1999). Only the tip of the iceberg: Who understands what about metaphor? Journal of Pragmatics, 31, 1675-1683.

Blasko, D. G., & Connine, C. M. (1993). Effects of familiarity and aptness on metaphor comprehension. Journal of Experimental Psychology: Learning, Memory and Cognititon, 19, 295-308.

Bohr, N. (1933a). Light and Life. Nature, Vol, 421-423.

Bohr, N. (1933b). Light and Life. Nature, Vol, 457-459.

Boivin, A., & Vendrely. (1947). Sur le rôle possible des deux acides nucleique dans la cellule vivante. Experientia, 3, 32-34.

Botha, M.E. (1986). Metaphorical Models and Scientific Realism. PSA, 1, 374- 383.

Bowdle, B.F & Gentner, D. (2005). The Career of Metaphor. Psychological Review, 112, 193-216.

Boyd, R. (1993). Metaphor and theory change: What is ―metaphor‖ a metaphor for? In A. Ortony (Ed.) Metaphor and Thought, 2nd Edition. pp. 481-532. Cambridge, UK: Cambridge University Press.

Bradle, M. (1998). Explanation as Metaphorical Redescription. Metaphor and Symbol, 13, 125-139.

Branson,, H. R. (1956). Information Theory and the Structure of Proteins. In Symposium on Information Theory in Biology, pp. 84-104. New York: Pergamon Press.

Brown, T.L. (2003). Making Truth: Metaphor in Science. Champaign-Urbana, IL: University of Illinois Press.

Caldwell, P.C., & Hinshelwood, C. (1950). Some Considerations on Autosynthesis in Bacteria. Journal of the Chemical Society, 3156-3159.

Campbell, P. N., & Work, T. S. (1953). Biosynthesis of Proteins. Nature, 171, 997-1001.

314

Carroll, J.M., & Mack, R.L. (1999). Metaphor, computing systems, and active learning. International Journal of Human-Computer Studies. 51, 385-403.

Center for Science, Mathematics, and Engineering Education. (1996). National Science Education Standards.

Chantrenne, H. (1963). Information in Biology. Nature, 197, 27-30.

Charmaz, K. (2000). Grounded Theory: Objectivist and Constructivist Methods. In N. K. Denzin and Y.S. Lincoln (Eds.), Handbook of Qualitative Research, 2nd Ed. (pp. 509-535). Thousand Oaks: Sage Publications, Inc.

Charteris-Black, J. (2004). Corpus approaches to critical metaphor analysis. Basingstoke, UK: Palgrave-MacMillan.

Christidou, V., Dimopoulos, K., & Koulaidas, V. (2004). Constructing social representations of science and technology: the role of metaphors in the press and popular scientific magazines. Public Understanding of Science, 13, 347- 362.

Churchill, F.B. (1974). William Johannsen and the Genotype Concept. Journal of the History of Biology, 7, 5-30.

Clark, E.V. (2003). Language and mind: Let‘s get the issues straight. In D. Gentner & S. Goldin-Meadow (eds.) Language in Mind: Advances in the study of language and thought. Cambridge, MA: MIT Press.

Commoner, B. (1968). Failure of the Watson-Crick Theory as a Chemical Explanation of Inheritance. Nature, 220, 334-340.

Consulta de Ideas Previas. Retrieved from the World Wide Web on September 12, 2008 at http://www.ideasprevias.cinstrum.unam.mx:2048/presentation.htm.

Corbin, J., & Strauss, A. (1990). Grounded Theory Research: Procedures, Canons, and Evaluative Criteria. Qualitative Sociology, 13, 3-21.

Corbin, J., & Strauss, A. (2008). Basics of Qualitative Research, 3rd Ed. Los Angeles: Sage Publications.

Crick, F.H.C. (1958). On Protein Synthesis. In Symposia of the Society for Experimental Biology, XII, The Biological Replication of Macromolecules. New York, NY: Academic Press.

315

Crick, F.H.C., Barnett, F.R.S., Brenner, S,, & Watts-Tobin, R.J. (1961). General Nature of the Genetic Code for Proteins. Nature, 192, 1227-1232.

Crick, F.H.C. (1970). Central Dogma of Molecular Biology. Nature, 227, 561- 563.

Delbrϋk, M. (1970). A Physicist‘s Renewed Look at Biology: Twenty Years Later. Science, 168, 1312-1315..

Devlin, K. (1999). Infosense: Turning Information into Knowledge. New York : W.H. Freeman.

Dounce, A. L. (1953). Duplicating Mechanism for Peptide Chain and Nucleic Acid Synthesis. Enzymologia, 15, 251-258.

Dounce, A. L. (1953). Nucleic Acids Template Hypothesis. Nature, 172, 541.

Dover, G. (1980). Ignorant DNA? Nature, 285, 618-619.

Driver, R., Asoko, H., Leach, J., Mortimer, E., & Scott, P. (1994). Constructing Scientific Knowledge in the Classroom. Educational Researcher, 23, 5-12.

Fahey, L. & Prusak, L. (1998). The Eleven Deadliest Sins of Knowledge Management. California Management Review, 40, 265-276.

Falk, R. (1995). The Manifest and the Scientific. In S. Maasen, E. Mendelsohn, & P. Weingart, eds, Biology as Society, Society as Biology: Metaphors. rlands: Klewer Academic Publishers.

Fantini, B. (2006). Of Arrows and Flows. Causality, Determination, and Specificity in the Central Dogma of Molecular Biology. History and Philosophy of the Life Sciences. 28, 567-594.

Forterre, P. (2006). The origin of viruses and their possible roles in major evolutionary transitions. Virus Research, 117, 5-16.

Freeman, M., et. al. (2007). Standards of Evidence in Qualitative Research: An Incitement to Discourse. Educational Researcher, 36, 25-32.

Fuller, S. (2003). Kuhn vs Popper.Cambridge, UK: Icon Books.

Gamow, G. (1954). Possible Relation between Deoxyribonucleic Acid and Protein Structures. Nature, 173, 318.

316

Gaster, B. (1990). Assimilation of Scientific Change: The Introduction of Molecular Genetics into Biology Textbooks. Social Studies of Science, 20, 431-454.

Gentner, D. (1988). Metaphor as Structure Mapping: The Relational Shift. Child Development, 59, 47-59.

Gentner, D., & Jeziorski, M. (1989). Historical shifts in the use of analogy in science. In B. Gholson, W.R. Shandish, R.A. Neimeyer, & A.C. Houts, eds. Psychology of science: Contributions to metascience.New York: Cambridge University Press.

Glazer, R. (1998). Measuring the Knower: Towards a Theory of Knowledge Equity. California Management Review, 40, 175-194.

Glucksberg, S. (2003). The psycholinguistics of metaphor. TRENDS in Cognitive Sciences, 7, 92-96.

Gowin, D.B. & Alvarez, M.C. (2005). The Art of Educating with V Diagrams. New York, NY: Cambridge University Press.

Grimson, A., et. al. (2008). Early origins and evolution of microRNAs and Piwi- interacting RNAs in animals. Nature, Vol. 1-6.

Hamilton, L.D. (1968). DNA: Models and Reality. Nature, 218, 633-637.

Hsu, J. (2008). The Secrets of Storytelling: Our love for telling tales reveals the workings of the mind. Scientific American Mind. August/September, 46-51.

Johannsen, W. (1911). The Genotype Conception of Heredity. The American Naturalist, 45, 129-159.

Johannsen, W. (1923). Some Remarks About Units in Heredity. Hereditas, 4, 133-141.

Judson, H.F. (1981). Reflections in the Historiography of Molecular Biology. History of Science, 19, 369-421.

Judson, H.F. (1995). The Eight Day of Creation. 25th Anniversary Edition. New York, NY: Cold Spring Harbor Press.

Jukes, T.H. (1973). Possibilities for the Evolution of the Genetic Code from a Preceding Form. Nature, 246, 22-26.

317

Judson, H.F. (2001). Talking about the genome. Nature, 409, 769.

Kahn, D. (1963). The Code Breakers. New York: Macmillan.

Lewes, G.H. (1875). Problems of Life and Mind: The Foundations of a Creed, Volume II. Boston: James R. Osgood and Company.

Lewin, B. (2008). Genes IX. Sundbury, MA: Jones and Bartlett Publishers.

Kaiser, A. et al. (2007). Increase in tracheal investment with beetle size supports hypothesis of oxygen limitation on insect gigantism. Proceedings of the National Academy of Sciences, 104, 13198-13203.

Kay, H.L. (1986). The Social Meaning of Biology. New Haven: YaleUniversity Press.

Kay, L.E. (1993). The Molecular Vision of Life: Caltech, The Rockefeller Foundation, and the Rise of the New Biology. New York: OxfordUniversity Press.

Keil, F.C. (2003a). Categorisation, causation, and the limits of understanding. Language and Cognitive Processes, 18, 663-692.

Keil, F.C. (2003b). Folkscience: course interpretations of a complex reality. TRENDS in Cognitive Sciences, 7, 368-373.

Kintsch, W., & Bowles, A.R. (2002). Metaphor Comprehension: What Makes a Metaphor Difficult to Understand? Metaphor and Symbol, 17, 249-262.

Lakoff, G. (1993). The contemporary theory of metaphor. In A. Ortony (Ed.) Metaphor and Thought, 2nd Edition. pp. 202-251. Cambridge, UK: Cambridge University Press.

Lakoff, G., & Johnson, M. (1980a). Metaphors We Live By. Chicago, IL: University of Chicago Press.

Lakoff, G., & Johnson, M. (1980b). Conceptual Metaphor in Everyday Language. The Journal of Philosophy, 77, 453-486.

Lewontin, R. (2001). It Ain’t Necessarily So: The Dream of the Human Genome and Other Illusions, 2nd Edition. New York: New York Review of Books.

Lewontin, R. (2000). The Triple Helix: gene, organism and environment. Cambridge, MA: Harvard University Press.

318

Markman, A.B., & Gentner, D. (2000). Structure mapping in the comparison process. American Journal of Psychology, 113, 501-538.

Marks, J. (2006). Molecular Biology in the Work of Deleuze and Guattari. Paragraph, 29, 81-97.

Martin, W., Baross, J., Kelley, D., & Russell, M.J. (2008). Hydrothermal vents and the origin of life. Nature Reviews Microbiology, 6, 805-814.

Martins, I. & Ogborn, J. (1997). Metaphorical Reasoning about Genetics. International Journal of Science Education, 19, 47-63.

Maynard-Smith, J. (2000). The Concept of Information in Biology. Philosophy of Science, 67, 177-194.

Mayr, E. (1982). The Growth of Biological Thought. Cambridge, MA: Belknap Press.

Michael, M. & Carter, S. (2001). The Facts About Fictions and Vice Versa: Public Understanding of Human Genetics. Science as Culture, 10, 5-32.

Misteli, T. (2011). The Inner Life of the Genome. Scientific American, 66-73, February.

Moss, L. (2003). What Genes Can’t Do. Cambridge, MA:The MIT Press.

Narby, J. (1998). The Cosmic Serpent: DNA and the Origins of Knowledge. New York: Tarcher/Putnam.

Nature. (1968). Molecular Biology Comes of Age. Nature, 219, 825-829.

Newell. A. (1973). You can’t play 20 questions with nature and win: Projective comments on the papers of this symposium. In W.G. Chase (Ed.), Visual Information processing. New York: Academic Press.

Nilsen, T.W. (2007). Mechanisms of micro-RNA-mediated gene regulation in animal cells. TRENDS in Genetics, 23, 243-249.

Norwick, S.A. (2006). The History of Metaphors of Nature. Volume II Science and Literature from Homer to Al Gore.Lewiston, NY: The Edwin Mellen Press.

Novak, J.D. & Gowin, D.B. (1984). Learning How to Learn. New York, NY:

319

Cambridge University Press.

Olby, R. (1974). DNA before Watson-Crick. Nature, 248, 782-785.

Orgel, L.E., & Crick, F.H.C. (1980). Selfish DNA: the ultimate parasite. Nature, 284, 604-607.

Orgel, L.E., Crick, F.H.C., & Sapienza, C. (1980). Selfish DNA. Nature, 288, 645-646.

Ortony, A. (1975). Why Metaphors and Necessary and Not Just Nice. Educational Theory, 25, 45-53.

Oxford English Dictionary (2008) accessed on November 6, 2008 from the World Wide Web at http://dictionary.oed.com/entrance.dtl.

Oyama, S. (2000). The Ontogeny of Information: Developmental Systems and Evolution. Durham, NC: Duke University Press.

Pauler, F.M., Koerner, M.V., & Barlow, D.P. (2007). Silencing by imprinting noncoding RNAs: is transcription the answer? TRENDS in Genetics, 27, 284-292.

Peters, T. (1978). Metaphor and the Horizon of the Unsaid. Philosophy and Phenomenological Research, 38, 355-369.

Petrie, H.G., & Oshlag, R.S. (1993). Metaphor and leaning. In A. Ortony (Ed.) Metaphor and Thought, 2nd Edition. pp. 579-609. Cambridge, UK: Cambridge University Press.

Pinker, S. (2008). Interview on In Depth. C-SPAN 2 Book TV. November 2.

Pinker, S. (2007). The Stuff of Thought: Language as a Window into Human Nature. New York, NY: Penguin Books.

Posner, G.J., Strike, K.A., Hewson, P.W. & Gertzog, W.A. (1982). Accomodation of a Scientific Conception: Towards a theory of Conceptual Change. Science Education, 66, 211-227.

Rentetzi, M. (2005). The Metaphorical Conception of Scientific Explanation: Rereading Mary Hesse. Journal for General Philosophy of Science, 36, 377- 391.

Riley, P.A. (1970). A Suggested Mechanism for DNA Transcription. Nature,

320

228, 522-525.

Rosenberg, A. (2001). How is Biological Explanation Possible? British Journal for the Philosophy of Science, 52, 735-760.

Rosenbilt, L, & Keil, F. (2002). The misunderstood limits of folk science: an illusion of explanatory depth. Cognitive Science, 26, 521-562.

Sarkar, S. (1996). Biological Information: A Skeptical Look at Some Dogmas of Molecular Biology, in S. Sarkar‘s (ed) The Philosophy and History of Molecular Biology: New Perspectives. Pp. 187-231. Dordrecht: Kluwer.

Sarkar, S. (2000). Information in Genetics and Developmental Biology: Comments on Maynard Smith. Philosophy of Science. 67, 208-213.

Shapiro, J.A. (2009). Revisiting the Central Dogma in the 21st Century. Annals of the New York Academy of Sciences, 1178, 6-28.

Shea, E. (2001). The Gene as a Rhetorical Figure: ‗Nothing But a Very Applicable Little Word‘. Science as Culture, 10, 505-529.

Silva, V.T. (2005). In the Beginning Was the Gene: The Hegemony of Genetic Thinking in Contemporary Culture. Communication Theory, 15, 100-123.

Sloman, S., Love, B., & Ahn, W. (1998). Feature Centrality and Conceptual Coherence. Cognitive Science, 22, 189-228.

Spanier, B.B. (1995). Impartial Science. Bloomington, IL: IndianaUniversity Press.

Spencer, H. (1866). The Principles of Biology, Volume 1. New York: D. Appleton and Company.

Stegman, U.E. (2005). Genetic Information as Instructional Content. Philosophy of Science. 72, 425-443.

Strasser, B.J. (2006). A World in One Dimension: Linus Pauling, Francis Crick and the Central Dogma of Molecular Biology. History and Philosophy of the Life Sciences. 28, 491-512.

Strauss, A., & Corbin, J. (1990). Basics of Qualitative Research: Grounded Theory Procedures and Techniques. Newbury Park, CA: SAGE Publications.

321

Strike, K.A., & Posner, G.J. (1992). Revisionist Theory of Conceptual Change.

Ströker, E. (1997). Science and Lifeworld: A Problem of Cultural Change. Human Studies, 20, 303-314.

Šustar, P. (2007). Crick‘s Notion of Genetic Information and the ‗Central Dogma‘ of Molecular Biology. British Journal of the Philosophy of Science. 1-12.

Sternberg, S. (2008). DNA of malaria parasite decoded. USA Today, October 9.

Thagard, P. (1990). Concepts and Conceptual Change. Synthese: Epistemology and Cognition, Part I, 82, 255-274.

Van Speybroeck, L. (2000). The Organism: A Crucial Genomic Context in Molecular Epigenetics? Theory in the Biosciences, 119, 187-208.

Villarreal, L. P. , & DeFilippis, V.R. (2000). A Hypothesis for Viruses as the Origin of Eukaryotic Replication of Proteins. Journal of Virology, 74, 7079- 7084. vonGlaserfeld, E. (1989). Cognition, construction of knowledge, and teaching. Synthese, 80, 121-140. von Krogh, G. (1998). Care in Knowledge Creation. California Management Review, 40, 133-149.

Waddington, C. H. (1939). An Introduction to Modern Genetics. London: George Allen & Unwin, Ltd.

Wagner, W. (1998). Social Representations and Beyond: Brute facts, Symbolic Coping and Domesticated Worlds. Culture & Psychology, 43, 297-329.

Wagner, W. et al. (1999). Theory and method of social representations. Asian Journal of Social Psychology, 2, 95-125.

Wagner, W., Kronberger, N., & Seifert, F. (2007). Collective symbolic coping with new technology: Knowledge, images and public discourse. British Journal of Social Psychology, 41, 323-343.

Wagner, W. (2007). Vernacular science knowledge: its role in everyday life communication. Public Understanding of Science, 16, 7-22.

Wall, R. (1962). Overlapping Genetic Codes. Nature, 193, 1268-1270.

322

Waters, C.K. (1994). Genes Made Molecular. Philosophy of Science, 61, 163- 185.

Watson, J.D., & Crick, F.H.C. (1953a). Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature, 171, 737-738.

Watson, J.D., & Crick, F.H.C. (1953b). Genetical Implications of the Structure of Deoxyribonucleic Acid. Nature, 171, 964-967.

Watson, J.D., & Crick, F.H.C. (1953a). Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature, 171, 737-738.

Watson, J.D., & Crick, F.H.C. (1953b). Genetical Implications of the Structure of Deoxyribonucleic Acid. Nature, 171, 964-967.

Watts, S., & Stenner, P. (2005). Doing Q Methodology: theory, methods and interpretation. Qualitative Research in Psychology, 2, 67-91.

Weber, M. (2006). The Central Dogma as a Thesis of Causal Specificity. History and Philosophy of the Life Sciences. 28, 595-610.

Weismann, A. (1889). Essays Upon Heredity and Kindred Biological Problems. Oxford: Clarendon Press.

Werzbicki, A. P. (2007). Modelling as a way of organizing knowledge. European Journal of Operations Research. 176, 610-635.

Wilson, R.A., & Keil, F. (1998). The Shadows and Shallows of Explanation. Minds and Machines, 8, 137-159.

Yčas, M. (1969). The Biological Code. Amsterdam: North-Holland Publishing Company.

323

APPENDIX A: METAPHORS AS PART OF MISCONCEPTIONS

324

Metaphors are shown in all capital letters.

HIGH SCHOOL Statement Chromosomes CARRY genes, that‘s important because it DEFINES what people look like, for example: eye colour, hair colour, and stuff like that. (Wood-Robinson, Lewis & Leach, 2000)

Chromosomes DECIDE what texture your skin is, what colours your eyes are going to be, the colour of your hair and stuff like that.

Genes DETERMINE who you are, what your personality is, and you get them from both your parents.

Chromosomes MAKE DNA.

DNA SURROUNDS the genes.

DNA is the ladder where everything is STORED.

Cells have different chromosomes, different genes and different GENETIC INFORMATION because they have different ROLES OR JOBS.

Cells have different functions so they would not have the same genes.

Nerve cell does more things than other cells, it has to have more chromosomes.

The GENETIC INFORMATION of a man and a woman have got to be different, because if they were the same a woman would look like a man.

Two cells would have different genes because they are of different persons, all individuals have their own INDENTITY IN GENES, LIKE A FINGERPRINT.

Sperm cells have different genes and different GENETIC INFORMATION.

GENETIC INFORMATION in the eggs has to be different, because if not you would look exactly as your brother.

Different eggs from the same female would have the same genes in them and the same GENETIC INFORMATION, unless there‘s something wrong with them, like handicappe or anything like that.

325

All male chromosomes will go into the sperm, GENETIC INFORMATION will be the same as the dad‘s.

In a fertilized egg, genes and GENETIC INFORMATION would be different because it‘s a new individual and comes from different egg and sperm.

The GENETIC INFORMATION in a fertilized egg is different from the somatic cell because the somatic cell just have one function and the fertilized cells have to say how your body is, how your body should grow.

The genetic code is a personal identification as a BAR CODE is. Hereditary information is all that is transferred from parents to offspring.

The offspring would be like the father or like the mother depending on the AMOUNT of information that each one gave.

Genes are important because they TRANSFER INFORMATION.

Genetic information is the INFORMATION THAT IS STORED, in a non-specific way or as a CODE.

Genetic information is the information which GIVES INSTRUCTION FOR THE CONTROL of the cell or for the DETERMINATION of the characteristics.

Genetic information is the INFORMATION WHICH PASSES between cells.

Genetic information is the information obtained from an organism.

ADULTS Each BUILDING BLOCK of DNA carries molecules of A, T, G and C in different combinations so they presumably give INSTRUCTIONS for growing different forms of cells. The INFORMATION that comes from the DNA is also tied into the part of the body that it going to make, so that somehow DNA MOVES in a particular way throughout the organism in order to produce cells of a particular type.

The DNA is inside the cell and it MAKES proteins. The sequence CODE which causes this is called gene.

If DNA is a series of INSTRUCTIONS then you can find out what part of DNA DELIVERS OR GIVES a certain INSTRUCTION.

The gene is the CODE that makes the protein.

326

The CODE from the man and the CODE from the partner join together to make a NEW CODE in fertilization.

DNA of a new individual that comes from the mother and the father is a whole new CODE. Because the mother has got a set of DNA and the father too, then they mix together.

DNA is a SEQUENCE OF LETTERS, if you change the sequence of letters it will actually make something different. So along its length the DNA will have like different blocks of sequence of letters.

Gene is something that CAUSES the protein inside or outside make different things, like make hair, make blood. Gene is the CODE that MAKES proteins.

DNA has the same CODE it never change, it can changes the nature of protein that it CODES depending on what it is trying to produce.

There must be something in common about all human DNA because we all finish up with the same characteristics, like fingers, hands, two legs, etc. So there must be common elements for each species.

327

APPENDIX B: A LIST OF BASE CONCEPTS PROVIDED FOR STUDY 3 BY

TARGET

328

DNA Transcription RNA Translation Proteins Ribosomes ladder puzzle an operator Spanish dictionary CEOs construction worker matching blueprint copying half of DNA components ribbon a reader a power gene translation an encoder encription supply proteins filling Sudoko "barrel of city map playing the piano campus map puzzle monkeys' me charm base-letter someone who bracelet disguise summary of DNA cracking a code toy boat kit reads wadded up a book string cheese a translator peanut butter balls factory a recipe assembly line spiral staircase a factory system motors a machine transferring house's text money a translator a crossing guard foundation construction sites a blueprint copying machine a copy a csurgery catchy song a DJ the blueprints author to all-in-one instruction manual instruction manual the builder toolkit the work site buidling a code xerox machine an enzyme legos blocks a factory process of oxygen to your blueprint copying caffein equation builder humans protein factory a raw 1 sector of 2 sector of material economy an intermediary economy goods a factory an instruction booklet copying a fraternal twin rosetta stone water factory workers a code cooking text reading work-horse factory a computer hard drive cloning a fraternal twin computer hacker salt a washing machine instructions writing memory reporter workers factory rope of genes re-writing DNA encoding buses no idea personal little a blueprint translator second blueprint typewriter messangers a microwave a set of instructions copying a messanger production a chain machines directions copy machine a messanger man printing press clay printing press a cloning of a print customers to something mailman dictionary a business construction worker

329

an instruction a "for Dummies" nosey manual paint a portrait book read sheet music neighbors an assembly a map transformation carriers production system food a computer oxygen to genomes RNA DNA proteins humans proteins a cookbook copy machine a mailman currency converter the labor a factory writing a copier a book communicating telephone a machine photocopy the game a puzzle machine a mom an interpreter Wordle an assembly line blueprint for the body copy machine a messanger a factory muscle worker ants swiss army blueprint a scanner a chef traanslator knife an assembly line a textbook scanner a mail carrier a decoder workhorses lego creation meat processing manual cloning a bus plant a leader a brain a ladder a single pronged copy machine ladder a translator are like doors a workhorse building a blueprint a copier a messanger production center blocks powerhouse a genetic blueprint a copier a messanger a decoder rubber bands a machine building binary code a color wheel a middle child construction a chain a cooking pot a blueprint cloning messangers producing keys a machine blueprints typing foundation phone calls walls plumbing genes Don't Know encoding NR gross energy program to decode a flashdrive floppy disk drive info on floppy disk floppy legos lego factory information to blank a blank disc copying disk teaching orgami factory a teacher twins snake security guard the sun a machine 2 strands that carry information RNA copy information carrier production enzymes machines a memory drive copier a printer printing a gumbo factory a brain translator messanger translator special treats a little worker a brain a translator a messanger a translator nutrients worker bee

330

a recipe teeth impression a photocopy a decoding chart a car phone line a spiral decipher a staircase cloning a clone of DNA language paper globe copy machine a special using xerox copy cat worker of using xerox lego code machine dna machine structures factory workers recipe draw a portrait a textbook cooking servants a factory blueprints a scribe a messanger a translater mothers a machine powerhouse a copier DNA a decoder controls translators a blueprint script a blueprint a synonym full of info messanger nucleus cloning labor for DNA interpreting worker ants mailmen blueprint a calculator translator a calculator catalysts powerplant a set of instructions a code a keyboard fax machine managers factory a password copying a sentence dividing food a brain an identifier a creator a carrier a converter necklaces a machine instructions single line/page of what happens at copying machine instructions factory workers a factory photocopying building a blueprint process a messanger pass on information blocks of cell a machine newly created recipe writing recipe copying/interprinting things machines inportant to code of life writings related to DNA difference us piece of rna a necessary code a replica DNA decoding children an inventor factory construction machine/assembly a blueprint copy machine copies of blueprint a puzzle workers line DNA and genetics DNA copy of DNA RNA RNA proteins a computer chip copying electricity writing wires messanger a treasure map homework a pirate the mailman lego castle a factory blueprint zipping up drawings unzippin blocks a factory an instruction construction manual copying machine letters a fax machine workers bricks kid who cheats map to GC a copy machine 1000 piece puzzle lego packs the kid

331

building a secret code a copy machine original DNA a coach blocks molecular machine

blueprint for building body DNA telling RNA DNA just different RNA reading DNA blocks a factory assorted chocolate cheating a mailman a different language people workers calcium scanner DNA a flash drive vegetables a crafty person set of building directions a code a computer giving a gift blocks a machine a puzzle mitosis DNA NR a chain a machine genes computer information language an ingredient an ingredient an ID DNA copier a messanger replication of DNA builders the pwerhouse copy of the send copy to construction a blueprint making a copy blueprint workers workers protein factory the blueprint fuel of the of life DNA replication copy of the genome NR body tape reader directions a table a puzzle piece language motors a mailman a brain a zipper a conveyor belt photosynthesis accordions a factory a boss writing work in progress a machine a mother a maid a book robot maker copy machine book w/word 1 side a manager robot workers machines bleuprint rebuilding a lego postal carrier taking apart legos lego building factory double helix don't know half of dna NR from meat a machine building a blueprint copying a different blueprint production blocks a manufacturer biolding genes copy machine messanger a mirrir blocks strainer brain replication thalamus an oven legos a machine ladder multiplying rabbits creative thinking healthy sand paper what the cookbook copy a recipe copied recipe cooking recipe is for kitchen part of building a geometry building a blueprint Jesus block principle blocks a literate person long instruction necklaces of booklet peel/pull twizzler messanger pigeon language translator beads an assembly line import for prot syn employees in bleueprint making copies reading a map a hospital a research paper

332

a tatoo a translator memory card assembly line alarm system mailman snowflakes buses fingerprint cell phones pyramids cheese buidling a code copy a code a messanger interpret a code blocks a factory a birthmark fraternal twin a cork screw surgery an actor a chef a messanger copying dna move something directions proteins blueprint copy machine electrical wiring decoding program glue read a book j NR r NR b a double helix NR straight line dna phosphates part of the cells translating building blueprints language different language decrypting a code blocks factories building a blueprint NR Dna NR blocks energy a train a copy machine jelly a mailman a building building blocks life foreign language a secret agent glasses [eye] teacher cereal a machine copying a transcribe foreign blueprints sentence copy machine language something factory the brain a mime a train a mailman muscles a candy makes a brain a copy machine you car muscles a middle man a database transcribing no idea translation no idea no idea a disk a microwave a unicycle keyboard legos oxygen blueprints for instructions for building drafting tools conversion tools a factory

333