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Summary How are the representations of different subfields of biology, as well as the phenomena represented by them, related to one another? For instance, are ecological or developmental phenomena emergent from molecular processes, or are they ultimately reducible to them? This entry includes work aiming to answer these and related questions.
Key works Kitcher's early piece, "1953 and all that," (Kitcher 1984) on the relationship between classical and molecular genetics is very influential, as is Sober's The Nature of Selection (Sober 1984). On the relationship between developmental biology and molecular biology and evolution, see Rosenberg 2006.
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  1. Lluís Barceló-Coblijn (2013). Biology: A Newcomer in Linguistics. [REVIEW] Biological Theory 7 (3):281-284.
  2. H. Clark Barrett, Stephen Stich & Stephen Laurence (2012). Should the Study of Homo Sapiens Be Part of Cognitive Science? Topics in Cognitive Science 4 (3):379-386.
    Beller, Bender, and Medin argue that a reconciliation between anthropology and cognitive science seems unlikely. We disagree. In our view, Beller et al.’s view of the scope of what anthropology can offer cognitive science is too narrow. In focusing on anthropology’s role in elucidating cultural particulars, they downplay the fact that anthropology can reveal both variation and universals in human cognition, and is in a unique position to do so relative to the other subfields of cognitive science. Indeed, without cross-cultural (...)
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  3. Ann-Sophie Barwich & Alba Amilburu (2011). Bridging Disciplines? An Inquiry on the Future of Natural Kinds in Philosophy and the Life Sciences. Biological Theory 6 (2):187-190.
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  4. Lindsay Bashford & Peter Knox (1986). Membrane‐Mediated Cytotoxicity: From Biophysics to Medicine. Bioessays 5 (3):134-135.
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  5. L. G. M. Baas Becking & E. F. Drion (1936). On the Origin of Frequency Distributions in Biology. Acta Biotheoretica 1 (3).
  6. Mark A. Bedau (2013). Weak Emergence Drives the Science, Epistemology, and Metaphysics of Synthetic Biology. Biological Theory 8 (4):334-345.
    Top-down synthetic biology makes partly synthetic cells by redesigning simple natural forms of life, and bottom-up synthetic biology aims to make fully synthetic cells using only entirely nonliving components. Within synthetic biology the notions of complexity and emergence are quite controversial, but the imprecision of key notions makes the discussion inconclusive. I employ a precise notion of weak emergent property, which is a robust characteristic of the behavior of complex bottom-up causal webs, where a complex causal web is one that (...)
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  7. Réjane Bernier (1983). Laws in Biology. Acta Biotheoretica 32 (4).
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  8. Stephan Blatti (2012). A New Argument for Animalism. Analysis 72 (4):685-690.
    The view known as animalism asserts that we are human animals—that each of us is an instance of the Homo sapiens species. The standard argument for this view is known as the thinking animal argument . But this argument has recently come under attack. So, here, a new argument for animalism is introduced. The animal ancestors argument illustrates how the case for animalism can be seen to piggyback on the credibility of evolutionary theory. Two objections are then considered and answered.
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  9. Steven J. Blumenthal (1984). New Insights Into the Origin of Biological Chirality. Bioessays 1 (6):258-260.
  10. Niels Bohr (1958/1987). Essays 1932-1957 on Atomic Physics and Human Knowledge. Ox Bow Press.
    Introduction -- Light and life -- Biology and atomic physics -- Natural philosophy and human cultures -- Discussion with Einstein on epistemological problems in atomic physics -- Unity of knowledge -- Atoms and human knowledge -- Physical science and the problem of life.
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  11. Giovanni Boniolo (2013). On Molecular Mechanisms and Contexts of Physical Explanation. Biological Theory 7 (3):256-265.
    In this article, two issues regarding mechanisms are discussed. The first concerns the relationships between “mechanism description” and “mechanism explanation.” It is proposed that it is rather plausible to think of them as two distinct epistemic acts. The second deals with the different molecular biology explanatory contexts, and it is shown that some of them require physics and its laws.
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  12. Robert N. Brandon (1984). Grene on Mechanism and Reductionism: More Than Just a Side Issue. PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1984:345 - 353.
    In this paper the common association between ontological reductionism and a methodological position called 'Mechanism' is discussed. Three major points are argued for: (1) Mechanism is not to be identified with reductionism in any of its forms; in fact, mechanism leads to a non-reductionist ontology. (2) Biological methodology is thoroughly mechanistic. (3) Mechanism is compatible with at least one form of teleology. Along the way the nature and value of scientific explanations, some recent controversies in biology and why reductionism has (...)
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  13. Jack Chamberlain (2001). A Biologist Looks at the Study of Consciousness. Bioessays 23 (3):297-298.
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  14. Mark Colyvan, The Undeniable Effectiveness of Mathematics in the Special Sciences.
    In many of the special sciences, mathematical models are used to provide information about specified target systems. For instance, population models are used in ecology to make predictions about the abundance of real populations of particular organisms. The status of mathematical models, though, is unclear and their use is hotly contested by some practitioners. A common objection levelled against the use of these models is that they ignore all the known, causally-relevant details of the often complex target systems. Indeed, the (...)
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  15. Michael M. Cox (1993). Problems and Paradigms: Relating Biochemistry to Biology: How the Recombinational Repair Function of RecA Protein is Manifested in its Molecular Properties. Bioessays 15 (9):617-623.
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  16. Angela N. H. Creager (1996). Wendell Stanley's Dream of a Free-Standing Biochemistry Department at the University of California, Berkeley. Journal of the History of Biology 29 (3):331 - 360.
    Scientists and historians have often presumed that the divide between biochemistry and molecular biology is fundamentally epistemological.100 The historiography of molecular biology as promulgated by Max Delbrück's phage disciples similarly emphasizes inherent differences between the archaic tradition of biochemistry and the approach of phage geneticists, the ur molecular biologists. A historical analysis of the development of both disciplines at Berkeley mitigates against accepting predestined differences, and underscores the similarities between the postwar development of biochemistry and the emergence of molecular biology (...)
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  17. Soraya De Chadarevian (1996). Sequences, Conformation, Information: Biochemists and Molecular Biologists in the 1950s. [REVIEW] Journal of the History of Biology 29 (3):361-386.
  18. Frans B. M. de Waal (2004). Monkey Business and Business Ethics. The Ruffin Series of the Society for Business Ethics 2004:7-41.
    To what degree has biology influenced and shaped the development of moral systems? One way to determine the extent to which human moral systems might be the product of natural selection is to explore behaviour in other species that is analogous and perhaps homologous to our own. Many non-human primates, for example, have similar methods to humans for resolving, managing, and preventing conflicts of interests within their groups. Such methods, which include reciprocity and food sharing, reconciliation, consolation, conflict intervention, and (...)
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  19. Thomas Durt (2010). Experimental Proposal for Testing the Emergence of Environment Induced (EIN) Classical Selection Rules with Biological Systems. Studia Logica 95 (1/2):259 - 277.
    According to the so-called Quantum Darwinist approach, the emergence of "classical islands" from a quantum background is assumed to obey a (selection) principle of maximal information. We illustrate this idea by considering the coupling of two oscillators (modes). As our approach suggests that the classical limit could have emerged throughout a long and progressive Evolution mechanism, it is likely that primitive living organisms behave in a "more quantum", "less classical" way than more evolved ones. This brings us to seriously consider (...)
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  20. Henryk Eisenberg (1988). Biophysics — Theme and Variation: 9th International Biophysics Congress Jerusalem, Israel, 24–29 August 1987. Bioessays 9 (1):34-35.
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  21. Niles Eldredge (1987). A Thermodynamic Perspective on Evolution. Evolution as Entropy. By Daniel R. Brooks and E. O. Wiley. 1986. University of Chicago Press Pp. 335. $19.95. [REVIEW] Bioessays 6 (5):239-240.
  22. Claus Emmeche, Causal Processes, Semiosis, and Consciousness.
    The evolutionary emergence of biological processes in organisms with inner, qualitative aspects has not been explained in any sufficient way by neurobiology, nor by the traditional neo-Darwinian paradigm — natural selection would appear to work just as well on insentient zombies (with the right behavioral input-output relations) as on real sentient animals. In consciousness studies one talks about the ‘hard problem’ of qualia. In this paper I sketch a set of principles about sign action, causality and emergent evolution. On the (...)
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  23. Claus Emmeche (2001). Does a Robot Have an Umwelt? Reflections on the Qualitative Biosemiotics of Jakob von Uexküll. Semiotica 2001 (134):653-693.
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  24. B. Fantini (1999). [Embryology,'Chemical Geography'of the Cell and Synthesis Between Morphology and Chemistry (1930-1950)]. History and Philosophy of the Life Sciences 22 (3):353-380.
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  25. Maciej Giertych (2001). Rola informacji w funkcjonowaniu przyrody w kontekście sporu o ewolucję. Filozofia Nauki 2.
    Biological reality does not consist of chemistry and physics of organism alone. It also includes their information content. This information regulates developmental and reproductive processes. Its quantity is finite. We observe mixing of information (mating patterns, reduction division, hybridisation, genetic engineering), its loss (species extinction, reduction of genetic diversity in domestication, isolation, inbreeding) and increase of useless or injurious information (duplications, neutral and harmful mutations, genetic load). On the other hand we do not observe new useful biological information arising (positive (...)
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  26. Stanford Goldman (1973). The Mechanics of Individuality in Nature. II. Barriers, Cells, and Individuality. Foundations of Physics 3 (2):203-228.
    The cell theory of Schleiden and Schwann is generalized to the effect that throughout the natural world, in physics, biology, and sociopsychology, there is a widespread phenomenon of the existence of organized cells, whose organization is usually protected by barriers. These barriers exist not only in space, but in time and even in other domains. These barriers typically not only protect the organization within the cell from external disturbance, but they actively participate in reducing the internal disorganization. It appears that (...)
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  27. Attila Grandpierre & Menas Kafatos (2012). Biological Autonomy. Philosophy Study 2 (9):631-649.
    We argue that genuine biological autonomy, or described at human level as free will, requires taking into account quantum vacuum processes in the context of biological teleology. One faces at least three basic problems of genuine biological autonomy: (1) if biological autonomy is not physical, where does it come from? (2) Is there a room for biological causes? And (3) how to obtain a workable model of biological teleology? It is shown here that the solution of all these three problems (...)
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  28. Karen L. Hollis (2000). Strategies for Integrating Biological Theory, Control Systems Theory, and Pavlovian Conditioning. Behavioral and Brain Sciences 23 (2):258-259.
    To make possible the integration proposed by Domjan et al., psychologists first need to close the research gap between behavioral ecology and the study of Pavlovian conditioning. I suggest two strategies, namely, to adopt more behavioral ecological approaches to social behavior or to co-opt problems already addressed by behavioral ecologists that are especially well suited to the study of Pavlovian conditioning.
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  29. Ernest H. Hutten (1960). Physics and Biology. British Journal for the Philosophy of Science 11 (42):101-108.
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  30. Ulrich Krohs & Mark A. Bedau (2013). Interdisciplinary Interconnections in Synthetic Biology. Biological Theory 8 (4):313-317.
  31. Anand Kumar & Barry Smith (2004). Biomedical Informatics and Granularity. Comparative and Functional Genomics 5:501-508.
    An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).
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  32. Peter Leadlay (1992). Biochemistry with a Human faceBiochemistry (1991). By Mary K. Campbell. Saunders College Publishing, Philadelphia. 622pp. $43. [REVIEW] Bioessays 14 (1):69-70.
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  33. Norman Maclean (1986). DNA Methylation - Biochemistry and Biological Significance. Edited by A. Razin, H. Cedar and A. D. Riggs. Springer-Verlag, New York, 1984. Pp. 392. DM 188 (Approx. �50). [REVIEW] Bioessays 4 (3):139-140.
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  34. Christophe Malaterre (2013). Synthetic Biology and Synthetic Knowledge. Biological Theory (8):346–356.
    Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. On the basis of (...)
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  35. Padmavati Manchikanti & Tapas K. Bandopadhyay (2010). Nanomaterials and Effects on Biological Systems: Development of Effective Regulatory Norms. [REVIEW] NanoEthics 4 (1):77-83.
    Nanoscience has enabled the understanding of organisation of the atomic and molecular world. Due to the unique chemical, electronic and magnetic properties nanomaterials have wide applications in the chemical, manufacturing, medical sector etc., Single walled carbon nanotubes, buckyballs, ZnSe quantum dots, TiO 2 nanoparticle based products are nearing commercialisation. Research is on-going worldwide on suitable delivery systems for nanomaterial based drugs. Nanomaterials are highly reactive in biological systems due to the large surface area. While the benefits of nanomaterials are evident (...)
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  36. Roger D. Masters (1991). The Changing Nature of the Social Sciences. Biology and Philosophy 6 (3):377-393.
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  37. W. D. McElroy (1985). Innovations in Communication: Origin of Biochemical & Biophysical Research Communications. Bioessays 3 (2):83-83.
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  38. Joachim Metallmann (1939). Der Kampf Um Die Autonomie Des Lebens. Acta Biotheoretica 5 (1).
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  39. Margaret Morrison (1997). Physical Models and Biological Contexts. Philosophy of Science 64 (4):324.
    In addition to its obvious successes within the kinetic theory the ideal gas law and the modeling assumptions associated with it have been used to treat phenomena in domains as diverse as economics and biology. One reason for this is that it is useful to model these systems using aggregates and statistical relationships. The issue I deal with here is the way R. A. Fisher used the model of an ideal gas as a methodological device for examining the causal role (...)
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  40. Karl J. Niklas, Thomas G. Owens & Randy O. Wayne (2013). Unity and Disunity in Biology. BioScience 63 (10).
  41. E. A. Nunez (1994). Biological Identity Adaptation to Environment as a Model for Social Science. World Futures 42 (1):41-48.
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  42. Maureen A. O'Malley (2009). Making Knowledge in Synthetic Biology: Design Meets Kludge. Biological Theory 4 (4):378-389.
  43. Robert Olby (1989). From Physics to Biophysics. [REVIEW] History and Philosophy of the Life Sciences 11 (2):305 - 309.
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  44. Javier Ordóñez & Ana Rioja (2009). Space. The Size of the Universe : A Problem for Natural Philosophy. In González Recio & José Luis (eds.), Philosophical Essays on Physics and Biology. G. Olms.
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  45. Arthur B. Pardee (1985). Roots: Molecular Basis of Biological Regulation: Origins From Feedback Inhibition and Allostery. Bioessays 2 (1):37-40.
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  46. Arthur B. Pardee (1985). Roots: Molecular Basis of Gene Expression: Origins From the Pajama Experiment. Bioessays 2 (2):86-89.
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  47. Eleonore Pauwels (2013). Public Understanding of Synthetic Biology. BioScience 63 (2).
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  48. Deana D. Pennington, Gary L. Simpson, Marjorie S. McConnell, Jeanne M. Fair & Robert J. Baker (2013). Transdisciplinary Research, Transformative Learning, and Transformative Science. BioScience 63 (7):564-573.
  49. Juli Peretó & Jesús Català (2007). The Renaissance of Synthetic Biology. Biological Theory 2 (2):128-130.
  50. André Pichot (1991). Physico-Chimie, Biologie, Information Et Connaissance. Acta Biotheoretica 39 (3-4).
    This paper deals with the notion of physico-chemical distance between the living being and its environment, as the result of their separate evolution (see Solignac VI and VIII). Then, it attempts (in vain) to understand it in the theory of information.
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