Forms and Functions : Life-Anatomy Or Physiology?
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Designing Biological Systems
Downloaded from genesdev.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Designing biological systems David A. Drubin,1 Jeffrey C. Way,2 and Pamela A. Silver1,3 1Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; 2EMD Lexigen Research Center, Billerica, Massachusetts 01821, USA The design of artificial biological systems and the under- chemical systems that mimic living systems, especially standing of their natural counterparts are key objectives in regard to replication and Darwinian selection. This of the emerging discipline of synthetic biology. Toward review will primarily focus on accomplishments of the both ends, research in synthetic biology has primarily first strategy; however, readers are referred to several fine focused on the construction of simple devices, such as reviews on the generation of artificial, life-emulating transcription-based oscillators and switches. Construc- systems (Szostak et al. 2001; Benner 2003; Benner and tion of such devices should provide us with insight on Sismour 2005). the design of natural systems, indicating whether our According to the synthetic biology paradigm, a syn- understanding is complete or whether there are still gaps thetically programmed cell should be composed of many in our knowledge. Construction of simple biological sys- subsystems that operate successfully as a result of ex- tems may also lay the groundwork for the construction tensive characterization and educated design. System of more complex systems that have practical utility. To construction is the product of iterative cycles of com- realize its full potential, biological systems design bor- puter modeling, biological assembly, and testing. In this rows from the allied fields of protein design and meta- way, much from the field of systems biology can be ap- bolic engineering. -
The NEURONS and NEURAL SYSTEM: a 21St CENTURY PARADIGM
The NEURONS and NEURAL SYSTEM: a 21st CENTURY PARADIGM This material is excerpted from the full β-version of the text. The final printed version will be more concise due to further editing and economical constraints. A Table of Contents and an index are located at the end of this paper. A few citations have yet to be defined and are indicated by “xxx.” James T. Fulton Neural Concepts [email protected] July 19, 2015 Copyright 2011 James T. Fulton 2 Neurons & the Nervous System 4 The Architectures of Neural Systems1 [xxx review cogn computation paper and incorporate into this chapter ] [xxx expand section 4.4.4 as a key area of importance ] [xxx Text and semantics needs a lot of work ] Don’t believe everything you think. Anonymous bumper sticker You must not fool yourself, and you are the easiest person to fool Richard Feynman I am never content until I have constructed a model of what I am studying. If I succeed in making one, I understand; otherwise, I do not. William Thomson (Lord Kelvin) It is the models that tell us whether we understand a process and where the uncertainties remain. Bridgeman, 2000 4.1 Background [xxx chapter is a hodge-podge at this time 29 Aug 11 ] The animal kingdom shares a common neurological architecture that is ramified in a specific species in accordance with its station in the phylogenic tree and the ecological domain. This ramification includes not only replication of existing features but further augmentation of the system using new and/or modified features. -
The Device Approach to Emergent Properties
arXiv:1801.05452, Version 3 Asking Biological Questions of Physical Systems: the Device Approach to Emergent Properties Bob Eisenberg Department of Applied Mathematics Illinois Institute of Technology USA Department of Physiology and Biophysics Rush University USA [email protected] January 17, 2018 9/23/2021 9:14 AM Abstract Life occurs in concentrated ‘Ringer Solutions’ derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology from those in the physical chemistry he knew. Biology is inherited. Information is passed by handfuls of atoms in the genetic code. A few atoms in the proteins built from the code change macroscopic function. Indeed, a few atoms often control biological function in the same sense that a gas pedal controls the speed of a car. Biological questions then are most productive when they are asked in the context of evolution. What function does a system perform? How is the system built to perform that function? What forces are used to perform that function? How are the modules that perform functions connected to make the machinery of life. Physiologists have shown that much of life is a nested hierarchy of devices, one on top of another, linking atomic ions in concentrated solutions to current flow through proteins, current flow to voltage signals, voltage signals to changes in current flow, all connected to make a regenerative system that allows electrical action potentials to move meters, under the control of a few atoms. -
(12) United States Patent (10) Patent No.: US 7.923,221 B1 Cabilly Et Al
US007.923221B1 (12) United States Patent (10) Patent No.: US 7.923,221 B1 Cabilly et al. (45) Date of Patent: *Apr. 12, 2011 (54) METHODS OF MAKING ANTIBODY HEAVY 4,512.922 A 4, 1985 Jones et al. AND LIGHT CHAINS HAVING SPECIFICITY 4,518,584 A 5, 1985 Mark 4,565,785 A 1/1986 Gilbert et al. FORADESIRED ANTIGEN 4,599,197 A 7, 1986 Wetzel 4,634,665 A 1/1987 Axel et al. (75) Inventors: Shmuel Cabilly, Monrovia, CA (US); 4,642,334 A 2f1987 Moore et al. Herbert L. Heyneker, Burlingame, CA 4,668,629 A 5/1987 Kaplan 4,704,362 A 11/1987 Itakura et al. (US); William E. Holmes, Pacifica, CA 4,713,339 A 12/1987 Levinson et al. (US); Arthur D. Riggs, LaVerne, CA 4,766,075 A 8, 1988 Goeddeletal. (US); Ronald B. Wetzel, San Francisco, 4,792.447 A 12/1988 Uhr et al. CA (US) 4,816,397 A * 3/1989 Boss et al. ...................... 435/68 4,816,567 A 3/1989 Cabilly et al. (73) Assignees: Genentech, Inc, South San Francisco, 4,965,196 A 10, 1990 Levinson et al. 5,081,235 A 1/1992 Shively et al. CA (US); City of Hope, Duarte, CA 5,098,833. A 3/1992 Lasky et al. (US) 5,116,964 A 5/1992 Capon et al. 5,137,721 A 8, 1992 Dallas (*) Notice: Subject to any disclaimer, the term of this 5,149,636 A 9, 1992 Axel et al. patent is extended or adjusted under 35 5,179,017 A 1/1993 Axel et al. -
How the Techniques of Molecular Biology Are Developed from Natural Systems
How the techniques of molecular biology are developed from natural systems Isobel Ronai [email protected] School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia. Abstract A striking characteristic of the highly successful techniques in molecular biology is that they are derived from natural systems. RNA interference (RNAi), for example, utilises a mechanism that evolved in eukaryotes to destroy foreign nucleic acid. Other examples include restriction enzymes, the polymerase chain reaction, green fluorescent protein and CRISPR-Cas. I propose that biologists exploit natural molecular mechanisms for their effectors’ (protein or nucleic acid) activity and biological specificity (protein or nucleic acid can cause precise reactions). I also show that the developmental trajectory of novel techniques in molecular biology, such as RNAi, is four characteristic phases. The first phase is discovery of a biological phenomenon, typically as curiosity driven research. The second is identification of the mechanism’s trigger(s), the effector and biological specificity. The third is the application of the technique. The final phase is the maturation and refinement of the molecular biology technique. The development of new molecular biology techniques from nature is crucial for biological research. These techniques transform scientific knowledge and generate new knowledge. Keywords: mechanism; experiment; specificity; scientific practice; PCR; GFP. 1 Introduction Molecular biology is principally concerned with explaining the complex molecular phenomena underlying living processes by identifying the mechanisms that produce such processes (Tabery et al. 2015). In order to access the causal structure of molecular mechanisms it is generally necessary to manipulate the components of the mechanism and to observe the resulting effects with sophisticated molecular techniques. -
Were Ancestral Proteins Less Specific?
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.27.120261; this version posted May 30, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Were ancestral proteins less specific? 1 1,2,3 1,2* Lucas C. Wheeler and Michael J. Harms 2 1. Institute of Molecular Biology, University of Oregon, Eugene OR 97403 3 2. Department of Chemistry and Biochemistry, University of Oregon, Eugene OR 97403 4 3. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder 5 CO 80309 6 7 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.27.120261; this version posted May 30, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract 8 Some have hypothesized that ancestral proteins were, on average, less specific than their 9 descendants. If true, this would provide a universal axis along which to organize protein 10 evolution and suggests that reconstructed ancestral proteins may be uniquely powerful tools 11 for protein engineering. Ancestral sequence reconstruction studies are one line of evidence 12 used to support this hypothesis. Previously, we performed such a study, investigating the 13 evolution of peptide binding specificity for the paralogs S100A5 and S100A6. -
Systems Biology and Its Relevance to Alcohol Research
Commentary: Systems Biology and Its Relevance to Alcohol Research Q. Max Guo, Ph.D., and Sam Zakhari, Ph.D. Systems biology, a new scientific discipline, aims to study the behavior of a biological organization or process in order to understand the function of a dynamic system. This commentary will put into perspective topics discussed in this issue of Alcohol Research & Health, provide insight into why alcohol-induced disorders exemplify the kinds of conditions for which a systems biological approach would be fruitful, and discuss the opportunities and challenges facing alcohol researchers. KEY WORDS: Alcohol-induced disorders; alcohol research; biomedical research; systems biology; biological systems; mathematical modeling; genomics; epigenomics; transcriptomics; metabolomics; proteomics ntil recently, most biologists’ emerging discipline that deals with, Alcohol Research & Health intend to efforts have been devoted to and takes advantage of, these enormous address. In this commentary, we will Ureducing complex biological amounts of data. Although scientists try to put the topics discussed in this systems to the properties of individual and engineers have applied the concept issue into perspective, provide views molecules. However, with the com of an integrated systemic approach for on the significance of systems biology pleted sequencing of the genomes of years, systems biology has only emerged as a new, distinct discipline to study 1 High-throughput genomics is the study of the structure humans, mice, rats, and many other and function of an organism’s complete genetic content, organisms, technological advances in complex biological systems in the past or genome, using technology that analyzes a large num the fields of high-throughput genomics1 several years. -
Communication Theory in Biological Systems
SUMMARY CDI TYPE I: A Communications Theory Approach to Morphogenesis and Architecture Maintenance The assertion that biological systems are communication networks would draw no rebuke from biologists – the terms signaling, communication, and network are deeply embedded parts of the biology parlance. However, the more profound meanings of information and communication are often overlooked when considering biological systems. Information can be quantified, its flow can be measured and tight bounds exist for its representation and conveyance between transmitters and receivers in a variety of settings. Furthermore, communications theory is about efficient com- munication where energy is at a premium – as is often the case in organisms. But perhaps most important, information theory allows mechanism-blind bounds on decisions and information flow. That is, the physics of a system allows determination of limits that any method of information description, delivery or processing must obey. Thus, rigorous application of communication theory to complex multi-cellular biological sys- tems seems both attractive and obvious as an organizing principle – a way to tease order from the myriad engineering solutions that comprise biological systems. Likewise, study of biological systems – engineering solutions evolved over eons – might yield new communication and com- putation theory. Yet so far, a communications-theoretic approach to multi-cellular biology has received scant, if any, attention. We therefore propose to explore this interdisciplinary intellectual -
Species Delimitation in Sea Anemones (Anthozoa: Actiniaria): from Traditional Taxonomy to Integrative Approaches
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 10 November 2019 doi:10.20944/preprints201911.0118.v1 Paper presented at the 2nd Latin American Symposium of Cnidarians (XVIII COLACMAR) Species delimitation in sea anemones (Anthozoa: Actiniaria): From traditional taxonomy to integrative approaches Carlos A. Spano1, Cristian B. Canales-Aguirre2,3, Selim S. Musleh3,4, Vreni Häussermann5,6, Daniel Gomez-Uchida3,4 1 Ecotecnos S. A., Limache 3405, Of 31, Edificio Reitz, Viña del Mar, Chile 2 Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue km. 6, Puerto Montt, Chile 3 Genomics in Ecology, Evolution, and Conservation Laboratory, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, P.O. Box 160-C, Concepción, Chile. 4 Nucleo Milenio de Salmonidos Invasores (INVASAL), Concepción, Chile 5 Huinay Scientific Field Station, P.O. Box 462, Puerto Montt, Chile 6 Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Avda. Brasil 2950, Valparaíso, Chile Abstract The present review provides an in-depth look into the complex topic of delimiting species in sea anemones. For most part of history this has been based on a small number of variable anatomic traits, many of which are used indistinctly across multiple taxonomic ranks. Early attempts to classify this group succeeded to comprise much of the diversity known to date, yet numerous taxa were mostly characterized by the lack of features rather than synapomorphies. Of the total number of species names within Actiniaria, about 77% are currently considered valid and more than half of them have several synonyms. Besides the nominal problem caused by large intraspecific variations and ambiguously described characters, genetic studies show that morphological convergences are also widespread among molecular phylogenies. -
Introduction: the Powers of Association
Copyrighted Material CHAPTER ONE Introduction: The Powers of Association In the summer of 2000, as the rainy season started, I made my way to the poor Dakar suburb of Th iaroye to meet a family with multiple cases of sickle cell anemia. Th ere were no paved sidewalks and my shoes sank in the mud when I jumped off the rusty minibus in a line of other hurried passengers. Stray sewer water bubbled from an opening in the street, creating small puddles of grey that were now being abluted by the downpour. Mr. Seck, the man I had come to see, had his niece keep watch for me, “the American from the hospital.” She surveyed me like sport as I divided my attention between the faulty gutters and locating the house. When we entered the compound, Seck welcomed me with a hard handshake. Th e whole family joined around, every one extending an arm, to introduce themselves with the familiarity and cheer an American usually reserves for a loved one. Doctors in town had recently diagnosed two of Seck’s children, ages eight and twelve, with HbSC sickle cell anemia, a less serious, heterozygous form of the more common homozygous HbSS disease. Both forms of the illness pro duce the hallmark symptom of this hemoglobin disorder: the vascular pain of arterial vessels clogged with sticky, damaged red blood cells, commonly called “the sickle cell crisis.” Th e children were prescribed folic acid for fi ft een days a month and Doliprane, the local name of acetaminophen, for pain when needed. -
The Bioanalysis Glossary
November 2014 Bioanalysis Vol. 6 No. 16 Suppl. 1 The Bioanalysis Glossary Brought to you by PUSHING THE LIMITS IN SENSITIVITY Exceedingly sensitive. Sharply focused. THE 6500 SERIES WITH IONDRIVE™ TECHNOLOGY See what couldn’t be seen. Until now. The new AB SCIEX 6500 LC/MS/MS series with multi-component IonDrive™ technology is the world’s most sensitive triple quadrupole, improving sensitivity up to 10X and detector dynamic range by 20X over the best selling high performance triple quad – with no compromise in mass range. Unique QTRAP® linear ion trap technology and optional SelexION™ differential ion mobility technology help enhance data quality and improve throughput while reducing the need for sample preparation. When merged with the Eksigent ekspert™ microLC 200 system, the functionally stackable design reduces lab space by 100%, while minimizing maintenance costs and reducing mobile phase costs by up to 95%. The new AB SCIEX 6500 Series. It’s the farsighted successor to a long line of leading AB SCIEX mass spec systems. Explore visionary sensitivity at www.absciex.com/6500-CEN © 2012 AB SCIEX. For Research Use Only. Not for use in diagnostic procedures. The trademarks mentioned herein are the property of AB SCIEX Pte. Ltd. or their respective owners. The Bioanalysis Glossary Contents The Bioanalysis Glossary November 2014 Bioanalysis Vol. 6 No. 16 Suppl. 1 Brought to you by Bioanalysis and Bioanalysis Zone S5 FOREWORD S6 SCOPE S7 TERMS & DEFINITIONS S84 INDEX S89 COMPANY PROFILES Publishing information ISBN PDF: 978-1-910420-53-2 ISBN ePub: 978-1-910420-53-9 ISBN print: 978-1-910420-54-6 Publication history First edition published November 2014 S3 Bioanalysis (2014) 6(16) Suppl. -
The Biological Person
03-Hutchison P&E-45383.qxd 8/14/2007 6:22 PM Page 79 CHAPTER 3 THE BIOLOGICAL PERSON Stephen French Gilson Key Ideas 81 Case Study 3.1: Cheryl’s Brain Injury 82 Case Study 3.2: A Diabetes Diagnosis for Bess 82 Case Study 3.3: Melissa’s HIV Diagnosis 83 Case Study 3.4: Lifestyle Changes for Thomas 83 Case Study 3.5: Max’s Postpolio Syndrome 84 Case Study 3.6: Juan and Belinda’s Reproductive Health 84 An Integrative Approach for Understanding the Intersection of Interior Biological Health and Illness and Exterior Environment Factors 85 A Look at Six Systems 88 Nervous System 88 Endocrine System 93 Immune System 96 Cardiovascular System 100 Musculoskeletal System 103 Reproductive System 107 79 03-Hutchison P&E-45383.qxd 8/14/2007 6:22 PM Page 80 80 THE MULTIPLE DIMENSIONS OF PERSON Exterior Socioeconomic Environment/Interior Health Environment 112 Implications for Social Work Practice 114 Key Terms 115 Active Learning 115 Web Resources 115 03-Hutchison P&E-45383.qxd 8/14/2007 6:22 PM Page 81 Chapter 3 The Biological Person 81 What do social workers need to know about the interior environment of human biology? How does knowledge of biology contribute to important roles that social workers play in individual and community health and illness? KEY IDEAS As you read this chapter, take note of these central ideas: 1. Although there are a variety of ways that we can think about our bodies, the approach proposed here locates understandings of the body within theories of environments, in this case, the interior environment.