A Biochemical Mechanism for Nonrandom Mutations and Evolution
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Thinking About Evolutionary Mechanisms: Natural Selection
Studies in History and Philosophy of Biological and Biomedical Sciences Stud. Hist. Phil. Biol. & Biomed. Sci. 36 (2005) 327–347 www.elsevier.com/locate/shpsc Thinking about evolutionary mechanisms: natural selection Robert A. Skipper Jr. a, Roberta L. Millstein b a Department of Philosophy, ML 0374, University of Cincinnati, Cincinnati, OH 45221-0374, USA b Department of Philosophy, California State University, East Bay, CA 94542-3042, USA Abstract This paper explores whether natural selection, a putative evolutionary mechanism, and a main one at that, can be characterized on either of the two dominant conceptions of mecha- nism, due to Glennan and the team of Machamer, Darden, and Craver, that constitute the Ônew mechanistic philosophyÕ. The results of the analysis are that neither of the dominant con- ceptions of mechanism adequately captures natural selection. Nevertheless, the new mechanis- tic philosophy possesses the resources for an understanding of natural selection under the rubric. Ó 2005 Elsevier Ltd. All rights reserved. Keywords: Mechanism; Natural selection; Evolution 1. Introduction This paper explores whether natural selection—a putative evolutionary mecha- nism, and a main one at that—can be adequately characterized under the rubric of the Ônew mechanistic philosophyÕ. What we call the new mechanistic philosophy is comprised of two dominant conceptions of mechanism, one due to Glennan E-mail addresses: [email protected] (R.A. Skipper Jr.), [email protected] (R.L. Millstein). 1369-8486/$ - see front matter Ó 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.shpsc.2005.03.006 328 R.A. Skipper Jr., R.L. Millstein / Stud. -
Behavioral Responses of Zooplankton to Predation
BULLETIN OF MARINE SCIENCE, 43(3): 530-550, 1988 BEHAVIORAL RESPONSES OF ZOOPLANKTON TO PREDATION M. D. Ohman ABSTRACT Many behavioral traits of zooplankton reduce the probability of successful consumption by predators, Prey behavioral responses act at different points of a predation sequence, altering the probability of a predator's success at encounter, attack, capture or ingestion. Avoidance behavior (through spatial refuges, diel activity cycles, seasonal diapause, locomotory behavior) minimizes encounter rates with predators. Escape responses (through active motility, passive evasion, aggregation, bioluminescence) diminish rates of attack or successful capture. Defense responses (through chemical means, induced morphology) decrease the probability of suc- cessful ingestion by predators. Behavioral responses of individuals also alter the dynamics of populations. Future efforts to predict the growth of prey and predator populations will require greater attention to avoidance, escape and defense behavior. Prey activities such as occupation of spatial refuges, aggregation responses, or avoidance responses that vary ac- cording to the behavioral state of predators can alter the outcome of population interactions, introducing stability into prey-predator oscillations. In variable environments, variance in behavioral traits can "spread the risk" (den Boer, 1968) of local extinction. At present the extent of variability of prey and predator behavior, as well as the relative contributions of genotypic variance and of phenotypic plasticity, -
Molecular and Cellular Signaling
Martin Beckerman Molecular and Cellular Signaling With 227 Figures AIP PRESS 4(2) Springer Contents Series Preface Preface vii Guide to Acronyms xxv 1. Introduction 1 1.1 Prokaryotes and Eukaryotes 1 1.2 The Cytoskeleton and Extracellular Matrix 2 1.3 Core Cellular Functions in Organelles 3 1.4 Metabolic Processes in Mitochondria and Chloroplasts 4 1.5 Cellular DNA to Chromatin 5 1.6 Protein Activities in the Endoplasmic Reticulum and Golgi Apparatus 6 1.7 Digestion and Recycling of Macromolecules 8 1.8 Genomes of Bacteria Reveal Importance of Signaling 9 1.9 Organization and Signaling of Eukaryotic Cell 10 1.10 Fixed Infrastructure and the Control Layer 12 1.11 Eukaryotic Gene and Protein Regulation 13 1.12 Signaling Malfunction Central to Human Disease 15 1.13 Organization of Text 16 2. The Control Layer 21 2.1 Eukaryotic Chromosomes Are Built from Nucleosomes 22 2.2 The Highly Organized Interphase Nucleus 23 2.3 Covalent Bonds Define the Primary Structure of a Protein 26 2.4 Hydrogen Bonds Shape the Secondary Structure . 27 2.5 Structural Motifs and Domain Folds: Semi-Independent Protein Modules 29 xi xü Contents 2.6 Arrangement of Protein Secondary Structure Elements and Chain Topology 29 2.7 Tertiary Structure of a Protein: Motifs and Domains 30 2.8 Quaternary Structure: The Arrangement of Subunits 32 2.9 Many Signaling Proteins Undergo Covalent Modifications 33 2.10 Anchors Enable Proteins to Attach to Membranes 34 2.11 Glycosylation Produces Mature Glycoproteins 36 2.12 Proteolytic Processing Is Widely Used in Signaling 36 2.13 Reversible Addition and Removal of Phosphoryl Groups 37 2.14 Reversible Addition and Removal of Methyl and Acetyl Groups 38 2.15 Reversible Addition and Removal of SUMO Groups 39 2.16 Post-Translational Modifications to Histones . -
Mechanism and Biological Explanation*
Mechanism and Biological Explanation* William Bechtel†‡ This article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insuf- ficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with com- plex dynamics requires coordinating research directed at decomposing mechanisms into parts (entities) and operations (activities) with research using computational models to recompose mechanisms and determine their dynamic behavior. This coordinated endeavor yields dynamic mechanistic explanations. 1. Introduction. Within biology (and the life sciences more generally), there is a long tradition of explaining a phenomenon by describing the mechanism responsible for it. A perusal of biology journals and textbooks yields many mentions of mechanisms but few of laws. Philosophers of *Received October 2010; revised January 2011. †To contact the author, please write to: Department of Philosophy, University of Cali- fornia, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0119; e-mail: bill@mechanism .ucsd.edu. ‡I thank Adele Abrahamsen, Colin Allen, Carl Craver, Lindley Darden, William Wim- satt; audiences at Duke University, Indiana University, University of the Basque Coun- try, University of California, Irvine, University of Chicago, University of Groningen; and referees for this journal for many helpful comments and suggestions. This article’s title is not original; it previously appeared as the title of a 1972 article in Philosophy of Science by Francisco Varela and Humberto Maturana. -
ARISTOTLE's TELEOLOGY and Uexk1tll's THEORY of LIVING NATURE
ARISTOTLE'S TELEOLOGY AND UEXK1tLL'S THEORY OF LIVING NATURE THE purpose of this paper is to draw attention to a similarity between an ancient and a modern theory of living nature. There is no need to present the Aristotelian doctrine in full detail. I must rather apologize for repeating much that is well known. My endeavour is to offer it for comparison, and, incidentally, to clear it from misrepre- sentation. Uexkiill's theory, on the other hand, is little known, and what is given here is an insufficient outline of it. I do not maintain that either doctrine is right. I am fully aware that the problem of the essence of living nature by no means admits of an easy solution.' In offering for consideration the comparison contained in this paper I would go no farther than owning my belief that the two authors here discussed, both thinkers who combine an intensely philosophical outlook with a wide biological experience, are worth the attention not only of the historian of science and philosophy, but also of the student of philosophical biology. One of the various meanings which dv'at bears for Aristotle is that of a cause. In the second book of his Physics, as is well known, he investigates the philosophical character of that cause. The result is what we are accustomed to call his teleology. He maintains that not only rpoalpacr~sbut also dv'c is rTwvEIEKL r'tov alrlwv.2 This teaching has exercised a deep influence, especially throughout the Middle Ages. It has subsequently been discarded, especially since modern science established its mechanistic outlook on nature, which is strictly opposed to teleological explana- tions. -
GENE REGULATION Differences Between Prokaryotes & Eukaryotes
GENE REGULATION Differences between prokaryotes & eukaryotes Gene function Description of Prokaryotic Chromosome and E.coli Review Differences between Prokaryotic & Eukaryotic Chromosomes Four differences Eukaryotic Chromosomes Form Length in single human chromosome Length in single diploid cell Proteins beside histones Proportion of DNA that codes for protein in prokaryotes eukaryotes humans Regulation of Gene Expression in Prokaryotes Terms promoter structural gene operator operon regulator repressor corepressor inducer The lac operon - Background E.coli behavior presence of lactose and absence of lactose behavior of mutants outcome of mutants The Lac operon Regulates production of b-galactosidase http://www.sumanasinc.com/webcontent/animations/content/lacoperon.html The trp operon Regulates the production of the enzyme for tryptophan synthesis http://bcs.whfreeman.com/thelifewire/content/chp13/1302002.html General Summary During transcription, RNA remains briefly bound to the DNA template Structural genes coding for polypeptides with related functions often occur in sequence Two kinds of regulatory control positive & negative General Summary Regulatory efficiency is increased because mRNA is translated into protein immediately and broken down rapidly. 75 different operons comprising 260 structural genes in E.coli Gene Regulation in Eukaryotes some regulation occurs because as little as one % of DNA is expressed Gene Expression and Differentiation Characteristic proteins are produced at different stages of differentiation producing cells with their own characteristic structure and function. Therefore not all genes are expressed at the same time As differentiation proceeds, some genes are permanently “turned” off. Example - different types of hemoglobin are produced during development and in adults. DNA is expressed at a precise time and sequence in time. -
What Makes the Lac-Pathway Switch: Identifying the Fluctuations That Trigger Phenotype Switching in Gene Regulatory Systems
What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems Prasanna M. Bhogale1y, Robin A. Sorg2y, Jan-Willem Veening2∗, Johannes Berg1∗ 1University of Cologne, Institute for Theoretical Physics, Z¨ulpicherStraße 77, 50937 K¨oln,Germany 2Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands y these authors contributed equally ∗ correspondence to [email protected] and [email protected]. Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria, fate selection in viral infection, cell cycle control, and development. Stochastic switching between different phenotypes can occur as the result of random fluctuations in molecular copy numbers of mRNA and proteins arising in transcription, translation, transport, and binding. However, which component of a pathway triggers such a transition is gen- erally not known. By linking single-cell experiments on the lactose-uptake pathway in E. coli to molecular simulations, we devise a general method to pinpoint the particular fluctuation driving phenotype switching and apply this method to the transition between the uninduced and induced states of the lac genes. We find that the transition to the induced state is not caused only by the single event of lac-repressor unbinding, but depends crucially on the time period over which the repressor remains unbound from the lac-operon. We confirm this notion in strains with a high expression level of the repressor (leading to shorter periods over which the lac-operon remains un- bound), which show a reduced switching rate. -
Functions and Mechanisms: a Perspectivalist View Carl F
Functions and Mechanisms: A Perspectivalist View Carl F. Craver.1 Washington University, St. Louis Abstract. Though the mechanical philosophy is traditionally associated with the rejection of teleological description and explanation, the theories of the contemporary physiological sciences, such as neuroscience, are replete with both functional and mechanistic descriptions. I explore the relationship between these two stances, showing how functional description contributes to the search for mechanisms. I discuss three ways that functional descriptions contribute to the explanations and mechanistic theories in contemporary neuroscience: as a way of tersely indicating an etiological explanation, as a way of framing constitutive explanations, and as a way of explaining the item by situating it within a higher-level mechanisms. This account of functional description is ineliminably perspectival in the sense that it relies ultimately on decisions by an observer about what matters or is of interest in the system that they study. 1. Introduction. In its most austere and demanding forms, the mechanical philosophy insists on a disenchanted world explicable without remainder in terms of basic causal principles. Though mechanical philosophers differ from one another about which causal principles are fundamental (size, shape, and motion for Descartes, attraction and repulsion for du Bois-Reymond, conservation of energy for Helmholz), they univocally reject explanations that appeal to vital forces and final causes. Austere views such as these are commonly associated with the idea that the mechanical world is an aimless machine, churning blindly, without its own end or purpose, and also with the apparent historical opposition between functions and mechanisms as conceptual tools for understanding the natural world.2 Contrast this historical opposition of function and mechanism with the state of play in early 21st century physiological sciences, such as neuroscience. -
I = Chpt 15. Positive and Negative Transcriptional Control at Lac BMB
BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac B M B 400 Part Four: Gene Regulation Section I = Chapter 15 POSITIVE AND NEGATIVE CONTROL SHOWN BY THE lac OPERON OF E. COLI A. Definitions and general comments 1. Operons An operon is a cluster of coordinately regulated genes. It includes structural genes (generally encoding enzymes), regulatory genes (encoding, e.g. activators or repressors) and regulatory sites (such as promoters and operators). 2. Negative versus positive control a. The type of control is defined by the response of the operon when no regulatory protein is present. b. In the case of negative control, the genes in the operon are expressed unless they are switched off by a repressor protein. Thus the operon will be turned on constitutively (the genes will be expressed) when the repressor in inactivated. c. In the case of positive control, the genes are expressed only when an active regulator protein, e.g. an activator, is present. Thus the operon will be turned off when the positive regulatory protein is absent or inactivated. Table 4.1.1. Positive vs. negative control BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac 3. Catabolic versus biosynthetic operons a. Catabolic pathways catalyze the breakdown of nutrients (the substrate for the pathway) to generate energy, or more precisely ATP, the energy currency of the cell. In the absence of the substrate, there is no reason for the catabolic enzymes to be present, and the operon encoding them is repressed. In the presence of the substrate, when the enzymes are needed, the operon is induced or de-repressed. -
Teaching Gene Regulation in the High School Classroom, AP Biology, Stefanie H
Wofford College Digital Commons @ Wofford Arthur Vining Davis High Impact Fellows Projects High Impact Curriculum Fellows 4-30-2014 Teaching Gene Regulation in the High School Classroom, AP Biology, Stefanie H. Baker Wofford College, [email protected] Marie Fox Broome High School Leigh Smith Wofford College Follow this and additional works at: http://digitalcommons.wofford.edu/avdproject Part of the Biology Commons, and the Genetics Commons Recommended Citation Baker, Stefanie H.; Fox, Marie; and Smith, Leigh, "Teaching Gene Regulation in the High School Classroom, AP Biology," (2014). Arthur Vining Davis High Impact Fellows Projects. Paper 22. http://digitalcommons.wofford.edu/avdproject/22 This Article is brought to you for free and open access by the High Impact Curriculum Fellows at Digital Commons @ Wofford. It has been accepted for inclusion in Arthur Vining Davis High Impact Fellows Projects by an authorized administrator of Digital Commons @ Wofford. For more information, please contact [email protected]. High Impact Fellows Project Overview Project Title, Course Name, Grade Level Teaching Gene Regulation in the High School Classroom, AP Biology, Grades 9-12 Team Members Student: Leigh Smith High School Teacher: Marie Fox School: Broome High School Wofford Faculty: Dr. Stefanie Baker Department: Biology Brief Description of Project This project sought to enhance high school students’ understanding of gene regulation as taught in an Advanced Placement Biology course. We accomplished this by designing and implementing a lab module that included a pre-lab assessment, a hands-on classroom experiment, and a post-lab assessment in the form of a lab poster. Students developed lab skills while simultaneously learning about course content. -
Holy Ground: Protestant Ecotheology, Catholic Social Teaching and a New Vision of Creation As the Landed Sacred
Holy Ground: Protestant Ecotheology, Catholic Social Teaching and a New Vision of Creation as the Landed Sacred Mark I. Wallace Introduction Christianity has long been a religion that endows the natural world with sacred meaning. Everyday, material existence—food and drink, life and death, humans and animals, earth and sky—is recalled in countless rituals and stories as the primary medium through which God relates to humankind and the wider earth community. Christiani- ty’s central ritual is a group meal that remembers the saving death of Jesus by celebrating the good gifts of creation—eating bread and drink- ing wine. Its central symbol is a cross made out of wood—two pieces of lumber lashed together as the means and site of Jesus’ crucifixion. Its central belief focuses on the body—namely, that God became flesh in Jesus and thereby becomes one of us, a mortal, breathing life-form who experiences the joy and suffering of life on earth. And Christianity’s primary sacred document, the Bible, is suffused with rich, ecological imagery that stretches from the Cosmic Potter in Genesis who fashions Adam from the dust of the ground to the tree of life in Revelation that yields its fruit to all of earth’s inhabitants. Christianity, then, is a “deep green” or “earthen” religion because it binds God to the created order and thereby values the natural world as a holy place. In this essay I take up the question of Christianity’s earthen identity by way of a nature-based retrieval of the Holy Spirit as the green face of God in the world. -
Systems Biology
GENERAL ARTICLE Systems Biology Karthik Raman and Nagasuma Chandra Systems biology seeks to study biological systems as a whole, contrary to the reductionist approach that has dominated biology. Such a view of biological systems emanating from strong foundations of molecular level understanding of the individual components in terms of their form, function and Karthik Raman recently interactions is promising to transform the level at which we completed his PhD in understand biology. Systems are defined and abstracted at computational systems biology different levels, which are simulated and analysed using from IISc, Bangalore. He is different types of mathematical and computational tech- currently a postdoctoral research associate in the niques. Insights obtained from systems level studies readily Department of Biochemistry, lend to their use in several applications in biotechnology and at the University of Zurich. drug discovery, making it even more important to study His research interests include systems as a whole. the modelling of complex biological networks and the analysis of their robustness 1. Introduction and evolvability. Nagasuma Chandra obtained Biological systems are enormously complex, organised across her PhD in structural biology several levels of hierarchy. At the core of this organisation is the from the University of Bristol, genome that contains information in a digital form to make UK. She serves on the faculty thousands of different molecules and drive various biological of Bioinformatics at IISc, Bangalore. Her current processes. This genomic view of biology has been primarily research interests are in ushered in by the human genome project. The development of computational systems sequencing and other high-throughput technologies that generate biology, cell modeling and vast amounts of biological data has fuelled the development of structural bioinformatics and in applying these to address new ways of hypothesis-driven research.