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  1. Federico Abascal & Rafael Zardoya (2012). LRRC8 Proteins Share a Common Ancestor with Pannexins, and May Form Hexameric Channels Involved in Cell‐Cell Communication. Bioessays 34 (7):551-560.
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  2. Aare Abroi & Julian Gough (2011). Are Viruses a Source of New Protein Folds for Organisms?–Virosphere Structure Space and Evolution. Bioessays 33 (8):626-635.
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  3. Douglas Allchin (2002). To Err and Win a Nobel Prize: Paul Boyer, ATP Synthase and the Emergence of Bioenergetics. [REVIEW] Journal of the History of Biology 35 (1):149 - 172.
    Paul Boyer shared a Nobel Prize in 1997 for his work on the mechanism of ATP synthase. His earlier work, though (which contributed indirectly to his triumph), included major errors, both experimental and theoretical. Two benchmark cases offer insight into how scientists err and how they deal with error. Boyer's work also parallels and illustrates the emergence of bioenergetics in the second half of the twentieth century, rivaling achievements in evolution and molecular biology.
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  4. Stefan Artmann (2004). Four Principles of Evolutionary Pragmatics in Jacob's Philosophy of Modern Biology. Axiomathes 14 (4):381-395.
    The French molecular biologist François Jacob outlined a theory of evolution as tinkering. From a methodological point of view, his approach can be seen as a biologic specification of the relation between laws, describing coherently the dynamics of a system, and contingent boundary conditions on this dynamics. From a semiotic perspective, tinkering is a pragmatic concept well-known from the information-theoretic anthropology of Claude Lévi-Strauss. In idealized contrast to an engineer, the tinkerer has to accept the concrete restrictions on his material (...)
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  5. Tudor Baetu (2012). Filling in the Mechanistic Details: Two-Variable Experiments as Tests for Constitutive Relevance. [REVIEW] European Journal for Philosophy of Science 2 (3):337-353.
    This paper provides an account of the experimental conditions required for establishing whether correlating or causally relevant factors are constitutive components of a mechanism connecting input (start) and output (finish) conditions. I argue that two-variable experiments, where both the initial conditions and a component postulated by the mechanism are simultaneously manipulated on an independent basis, are usually required in order to differentiate between correlating or causally relevant factors and constitutively relevant ones. Based on a typical research project molecular biology, a (...)
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  6. Tudor M. Baetu (2011). A Defense of Syntax-Based Gene Concepts in Postgenomics: Genes as Modular Subroutines in the Master Genomic Program. Philosophy of Science 78 (5):712-723.
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  7. Majid Bani-Yaghoub & David E. Amundsen (2008). Study and Simulation of Reaction–Diffusion Systems Affected by Interacting Signaling Pathways. Acta Biotheoretica 56 (4).
    Possible effects of interaction (cross-talk) between signaling pathways is studied in a system of Reaction–Diffusion (RD) equations. Furthermore, the relevance of spontaneous neurite symmetry breaking and Turing instability has been examined through numerical simulations. The interaction between Retinoic Acid (RA) and Notch signaling pathways is considered as a perturbation to RD system of axon-forming potential for N2a neuroblastoma cells. The present work suggests that large increases to the level of RA–Notch interaction can possibly have substantial impacts on neurite outgrowth and (...)
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  8. Ancha Baranova (2012). The More the Merrier: The Pannexin Family Just Got a New Branch (Comment on DOI 10.1002/Bies. 201100173). Bioessays 34 (7):530-531.
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  9. Marcello Barbieri (2003). The Organic Codes: An Introduction to Semantic Biology. Cambridge University Press.
    The genetic code appeared on Earth with the first cells. The codes of cultural evolution arrived almost four billion years later. These are the only codes that are recognized by modern biology. In this book, however, Marcello Barbieri explains that there are many more organic codes in nature, and their appearance not only took place throughout the history of life but marked the major steps of that history. A code establishes a correspondence between two independent 'worlds', and the codemaker is (...)
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  10. Nils Aall Barricelli (1956). A “Chromosomic” Recombination Theory for Multiplicity Reactivation in Phages. Acta Biotheoretica 11 (3-4).
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  11. Jordan Bartol (forthcoming). Biochemical Kinds. British Journal for the Philosophy of Science.
    Chemical kinds (e.g. gold) are generally treated as having timelessly fixed identities. Biological kinds (e.g. goldfinches) are generally treated as evolved and/or evolving entities. So what kind of kind is a biochemical kind? This paper defends the thesis that biochemical molecules are clustered chemical kinds, some of which–namely, evolutionarily conserved units–are also biological kinds.On this thesis, a number of difficulties that have recently occupied philosophers concerned with proteins and kinds are shown to be resolved or dissolved.
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  12. M. Bayram, J. P. Bennett & M. C. Dewar (1993). Using Computer Algebra to Determine Rate Constants in Biochemistry. Acta Biotheoretica 41 (1-2).
    In earlier work we have described how computer algebra may be used to derive composite rate laws for complete systems of equations, using the mathematical technique of Gröbner Bases (Bennett, Davenport and Sauro, 1988). Such composite rate laws may then be fitted to experimental data to yield estimates of kinetic parameters.Recently we have been investigating the practical application of this methodology to the estimation of kinetic parameters for the closed two enzyme system of aspartate aminotransferase (AAT) and malate dehydrogenase (MDH) (...)
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  13. Mary C. Beckerle (1997). Zyxin: Zinc Fingers at Sites of Cell Adhesion. Bioessays 19 (11):949-957.
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  14. Martin J. Bishop (1985). Software Club: Software for Molecular Biology. IV. Power Where It is Needed: Workstations and Networks. Bioessays 2 (5):218-221.
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  15. Martin J. Bishop (1984). Software Club: Software for Molecular Biology. II. Restriction Mapping and DNA Sequencing Programs. Bioessays 1 (2):75-77.
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  16. Francisco Javier Serrano Bosquet (2009). Linus Pauling : Molecular Disease and the Oorigins [Sic] of Molecular Biology. In González Recio & José Luis (eds.), Philosophical Essays on Physics and Biology. G. Olms.
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  17. Terence A. Brown & Keri A. Brown (1994). Ancient DNA: Using Molecular Biology to Explore the Past. Bioessays 16 (10):719-726.
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  18. Richard M. Burian (1996). "The Tools of the Discipline: Biochemists and Molecular Biologists": A Comment. Journal of the History of Biology 29 (3):451 - 462.
    This last result leads, rather naturally, to some concluding observations and a series of questions for further investigation. These case studies show that in all of the sites examined, the institutionalization of molecular biology as a “discipline” was primarily driven by the need to separate groups of practitioners with divergent but overlapping interests within the local context. Thus molecular biology was contingently separated from agricultural or medical biochemistry, virology, work on the physiology of nucleic acids, and so forth for contingent (...)
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  19. Werner Ceusters & Barry Smith (2010). Foundations for a Realist Ontology of Mental Disease. Journal of Biomedical Semantics 1 (10):1-23.
    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...)
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  20. Rosine Chandebois (1980). Cell Sociology and the Problem of Automation in the Development of Pluricellular Animals. Acta Biotheoretica 29 (1).
    The principles of automation (automatism and programming) in the unfolding of spatio-temporal patterns during animal development are deduced from experimental data reconsidered from the point of view of cell sociology. The developmental programme in the egg is not part of the genetic information but a part of the cytoplasmic information. Throughout development cells store extra-cellular information released by their neighbours in the form of cytoplasmic information. Successive determinations cannot be considered as successive reprogrammings of cells: each one consists of a (...)
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  21. Rosine Chandebois (1977). Cell Sociology and the Problem of Position Effect: Pattern Formation, Origin and Role of Gradients. Acta Biotheoretica 26 (4).
    The control of pattern formation and the significance of gradients is reconsidered on the basis of the concept of cell sociology (which takes into account continuous exchange of information between cells and the possibility of autonomous progression in differentiation). Not all traits of a pattern are imposed by a single prepattern, which would be an organized molecular framework or a gradient. Patterns are unfolded in steps; these are readjustments of a cell population to intrinsic and extrinsic changes in cell activities. (...)
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  22. Rosine Chandebois (1976). Cell Sociology: A Way of Reconsidering the Current Concepts of Morphogenesis. Acta Biotheoretica 25 (2-3).
  23. Philip Cohen (1985). Hormones, Second Messengers and the Reversible Phosphorylation of Proteins: An Overview. Bioessays 2 (2):63-68.
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  24. Angela N. H. Creager (2010). The Paradox of the Phage Group: Essay Review. [REVIEW] Journal of the History of Biology 43 (1):183 - 193.
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  25. Eric H. Davidson (1994). Molecular Biology of Embryonic Development: How Far Have We Come in the Last ten Years? Bioessays 16 (9):603-615.
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  26. Fordyce A. Davidson (2012). Is Cell Fusion Driven by Excitation?(Comment on DOI: 10.1002/Bies. 201100135). Bioessays 34 (4):258-258.
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  27. Soraya de Chadarevian (1999). Mapping Development or How Molecular is Molecular Biology? History and Philosophy of the Life Sciences 22 (3):381-396.
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  28. Xavier de la Cruz, Sergio Lois, Sara Sánchez‐Molina & Marian A. Martínez‐Balbás (2005). Do Protein Motifs Read the Histone Code? Bioessays 27 (2):164-175.
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  29. Alexis De Tiège, Koen Tanghe, Johan Braeckman & Yves Van de Peer (2014). From DNA- to NA-Centrism and the Conditions for Gene-Centrism Revisited. Biology and Philosophy 29 (1):55-69.
    First the ‘Weismann barrier’ and later on Francis Crick’s ‘central dogma’ of molecular biology nourished the gene-centric paradigm of life, i.e., the conception of the gene/genome as a ‘central source’ from which hereditary specificity unidirectionally flows or radiates into cellular biochemistry and development. Today, due to advances in molecular genetics and epigenetics, such as the discovery of complex post-genomic and epigenetic processes in which genes are causally integrated, many theorists argue that a gene-centric conception of the organism has become problematic. (...)
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  30. Sasadhar De (1992). Short Note on the Mechanics in the Contact Behaviour of Cells. Acta Biotheoretica 40 (4).
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  31. B. Delord (1999). Attractors and Pathological Aspects in Excitable Cells. Acta Biotheoretica 47 (3-4).
    In this article, physiological and pathological forms of excitability are studied in a two-dimensional electrical model of excitable cell endowed with a generic inward persistent conductance. Bifurcation analysis of the model is performed as a function of the maximal inward persistent conductance, the input current, or the voltage dependency of the activation function. Several discharge modes are exhibited, including: (1) a basic mode that corresponds to a resting potential and production of action potential; (2) bistability between resting potential and self-sustained (...)
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  32. Michael J. Denton, Govindasamy Kumaramanickavel & Michael Legge (2013). Cells as Irreducible Wholes: The Failure of Mechanism and the Possibility of an Organicist Revival. Biology and Philosophy 28 (1):31-52.
    According to vitalism, living organisms differ from machines and all other inanimate objects by being endowed with an indwelling immaterial directive agency, ‘vital force,’ or entelechy . While support for vitalism fell away in the late nineteenth century many biologists in the early twentieth century embraced a non vitalist philosophy variously termed organicism/holism/emergentism which aimed at replacing the actions of an immaterial spirit with what was seen as an equivalent but perfectly natural agency—the emergent autonomous activity of the whole organism. (...)
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  33. Michael R. Dietrich (1994). The Origins of the Neutral Theory of Molecular Evolution. Journal of the History of Biology 27 (1):21 - 59.
  34. Ulrike Dohrmann (1992). Losing Trk of Progress in Neurotrophic Biology. Current Topics in Microbiology and Immunology 165: Neuronal Growth Factors (1991). Edited by M. Bothwell Springer‐Verlag, Heidelberg. [REVIEW] Bioessays 14 (9):649-650.
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  35. Drö & Ariane Scher (2002). Edmund B. Wilson's the Cell and Cell Theory Between 1896 and 1925. History and Philosophy of the Life Sciences 24 (3-4):357-389.
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  36. Drö & Ariane Scher (2002). Edmund B. Wilson's the Cell and Cell Theory Between 1896 and 1925. History and Philosophy of the Life Sciences 24 (3-4):357-389.
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  37. Jeremy A. Draghi & Joshua B. Plotkin (2012). A Network of Paths Toward Innovation. Bioessays 34 (6):518-520.
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  38. Leon Dure (1985). Plant Molecular Biology Comes of Age. Bioessays 3 (4):147-148.
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  39. Marc Ereshefsky (2010). Microbiology and the Species Problem. Biology and Philosophy 25 (4):553-568.
    This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes (...)
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  40. Gillian Gass & Brian K. Hall (2007). Collectivity in Context: Modularity, Cell Sociology, and the Neural Crest. Biological Theory 2 (4):349-359.
  41. G. F. Gause (1938). The Problem of Asymmetry of Protoplasm. Acta Biotheoretica 4 (1).
  42. Stéphane Genet, Robert Costalat & Jacques Burger (2000). A Few Comments on Electrostatic Interactions in Cell Physiology. Acta Biotheoretica 48 (3-4).
    The role of fixed charges present at the surface of biological membranes is usually described by the Gouy-Chapman-Grahame theory of the electric double-layer where the Grahame equation is applied independently on each side of the membrane and where the capacitive charges (linked to the transmembrane ionic currents) are disregarded. In this article, we generalize the Gouy-Chapman-Grahame theory by taking into account both intrinsic charges (resulting from the dissociation of membrane constituents) and capacitive charges, in the density value of the membrane (...)
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  43. Pierre-Luc Germain, Emanuele Ratti & Federico Boem (2014). Junk or Functional DNA? ENCODE and the Function Controversy. Biology and Philosophy 29 (6):807-831.
    In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning (...)
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  44. Joel B. Hagen (1999). Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution. Journal of the History of Biology 32 (2):321 - 341.
    Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era.
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  45. Howard Hsueh-Hao Chiang (2009). The Laboratory Technology of Discrete Molecular Separation: The Historical Development of Gel Electrophoresis and the Material Epistemology of Biomolecular Science, 1945-1970. Journal of the History of Biology 42 (3):495-527.
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  46. Thomas J. Jentsch & Willy Günther (1997). Chloride Channels: An Emerging Molecular Picture. Bioessays 19 (2):117-126.
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  47. Laurence J. Lafleur (1941). Theoretical Biochemistry. Acta Biotheoretica 5 (4).
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  48. Ehud Lamm (2009). Conceptual and Methodological Biases in Network Models. Annals of the New York Academy of Sciences 1178:291-304.
    Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between “program” and “data”. The evolutionary significance of the dynamics of trans-generational and inter-organism regulatory networks is explored and implications are presented for understanding the evolution of (...)
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  49. Muriel Lederman & Sue A. Tolin (1993). OVATOOMB: Other Viruses and the Origins of Molecular Biology. [REVIEW] Journal of the History of Biology 26 (2):239 - 254.
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  50. Arnon Levy (2011). Information in Biology: A Fictionalist Account. Noûs 45 (4):640-657.
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