About this topic
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. The Umwelt of Uexküll and Merleau-Ponty.Agustin Ostachuk - 2013 - Ludus Vitalis 21 (39):45-65.
    The organism against its environment. The organism against other organisms, competing and struggling for life. Antagonism and confrontment as the only possible relation in nature. The tendency to anthropomorphize nature and explain it using concepts and facts from the human sphere. A stroll through the worlds of Uexküll and Merleau-Ponty in the search of alternative knowledge that allow us to understand relation from another point of view. A counterpoint and identification of common tonalities between the research programs from both thinkers (...)
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  2. Life: the Center of our Existence.Agustin Ostachuk - 2018 - Ludus Vitalis 26 (50):257-260.
    Life is the center of our existence. One would be tempted to say that first of all we live. However, our existence does not seem to pass in that modality. The exacerbated materialism in which our existence takes place, displaces life from the center of the scene. Our society is organized around production, consumerism, exploitation, efficiency, trade and propaganda. That is to say, our existence seems to have economy as the center of organization of our activities. The struggle of this (...)
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  3. Unifying the Essential Concepts of Biological Networks: Biological Insights and Philosophical Foundations.Daniel Kostic, Claus Hilgetag & Marc Tittgemeyer - forthcoming - Philosophical Transactions of the Royal Society B: Biological Sciences.
    Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the definition, motivation (...)
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  4. Levels of Organization in the Biological Sciences.Daniel Stephen Brooks, James DiFrisco & William C. Wimsatt (eds.) - forthcoming - MIT Press.
    The subject of this edited volume is the idea of levels of organization: roughly, the idea that the natural world is segregated into part-whole relationships of increasing spatiotemporal scale and complexity. The book comprises a collection of essays that raise the idea of levels into its own topic of analysis. Owing to the wide prominence of the idea of levels, the scope of the volume is aimed at theoreticians, philosophers, and practicing researchers of all stripes in the life sciences. The (...)
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  5. A New Look at ‘Levels of Organization’ in Biology.Daniel S. Brooks - forthcoming - Erkenntnis 2019:1-26.
    Despite its pervasiveness, the concept of ‘levels of organization’ has received relatively little attention in its own right. I propose here an emerging approach that posits ‘levels’ as a fragmentary concept situated within an interest-relative matrix of operational usage within scientific practice. To this end I propose one important component of meaning, namely the epistemic goal motivating the term’s usage, which recovers a remarkably conserved and sufficiently unifying significance attributable to ‘levels’ across different instances of usage. This epistemic goal, to (...)
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  6. Making Sense of Downward Causation in Manipulationism. Illustrations From Cancer Research.Christophe Malaterre - 2011 - History and Philosophy of the Life Sciences 4 (33):537-562.
    Many researchers consider cancer to have molecular causes, namely mutated genes that result in abnormal cell proliferation (e.g. Weinberg 1998); yet for others, the causes of cancer are to be found not at the molecular level but at the tissue level and carcinogenesis would consist in a disrupted tissue organization with downward causation effects on cells and cellular components (e.g. Sonnenschein & Soto 2008). In this contribution, I ponder how to make sense of such downward causation claims. Adopting a manipulationist (...)
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  7. Beeing & Time: Kiss of Chemoreception & the Bug in Dasein's Mouth.Virgil W. Brower - 2014 - In Laurence Talairach-Vielmas & Marie Bouchet (eds.), Insects in Literature & the Arts. Brussels, Belgium: pp. 197-217.
    "Brower explores the way philosophers were inspired by entomological social systems and communication to reflect on human psyche, social behavior, community organization, communication, and inter-individual relationships. His essay rehearses the swarms of insects embedded in contemporary philosophy and literary theory, not only showing how many of the major concepts (or philosophemes) in continental philosophy – sexuality, politics, thinking, time, interdependence, and language – draw lessons from the world of insects, but also illustrating again how the insect world spurred human reflection.".
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  8. The Origin of Species by Means of Mathematical Modelling.Nikolai Bessonov, Natalia Reinberg, Malay Banerjee & Vitaly Volpert - 2018 - Acta Biotheoretica 66 (4):333-344.
    Darwin described biological species as groups of morphologically similar individuals. These groups of individuals can split into several subgroups due to natural selection, resulting in the emergence of new species. Some species can stay stable without the appearance of a new species, some others can disappear or evolve. Some of these evolutionary patterns were described in our previous works independently of each other. In this work we have developed a single model which allows us to reproduce the principal patterns in (...)
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  9. The Significance of Levels of Organization for Scientific Research: A Heuristic Approach.Daniel S. Brooks & Markus I. Eronen - 2018 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 68:34-41.
    The concept of 'levels of organization' has come under fire recently as being useless for scientific and philosophical purposes. In this paper, we show that 'levels' is actually a remarkably resilient and constructive conceptual tool that can be, and in fact is, used for a variety of purposes. To this effect, we articulate an account of the importance of the levels concept seen in light of its status as a major organizing concept of biology. We argue that the usefulness of (...)
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  10. Note on the Individuation of Biological Traits.Mihnea D. I. Capraru - 2018 - Journal of Philosophy 115 (4):215-221.
    Bence Nanay has argued that we must abandon the etiological theory of teleological function because this theory explains functions and functional categories in a circular manner. Paul Griffiths argued earlier that we should retain the etiological theory and instead prevent the circularity by making etiologies independent of functional categories. Karen Neander and Alex Rosenberg reply to Nanay similarly, and argue that we should analyze functions in terms of natural selection acting not on functional categories, but merely on lineages. Nanay replies (...)
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  11. Error Management, Reliability and Cognitive Evolution.Bengt Autzen - 2017 - Biology and Philosophy 32 (6):935-950.
    The paper offers a partial vindication of Sterelny’s view on the role of error rates and reliability in his theory of decoupled representation based on modelling techniques borrowed from the biological literature on evolution in stochastic environments. In the case of a tight link between tracking states and behaviour, I argue that in its full generality Sterelny’s account instantiates the base-rate fallacy. With regard to non-tightly linked behaviour, I show that Sterelny’s account can be vindicated subject to an adequate evolutionary (...)
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  12. On Interdisciplinary and Such.Leigh M. Van Valen - 1996 - Biology and Philosophy 11 (2):255-257.
  13. An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...)
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  14. Mechanistic Levels, Reduction, and Emergence.Mark Povich & Carl F. Craver - forthcoming - In Stuart Glennan & Phyllis McKay Illari (eds.), The Routledge Handbook of Mechanisms and Mechanical Philosophy. Routledge.
    We sketch the mechanistic approach to levels, contrast it with other senses of “level,” and explore some of its metaphysical implications. This perspective allows us to articulate what it means for things to be at different levels, to distinguish mechanistic levels from realization relations, and to describe the structure of multilevel explanations, the evidence by which they are evaluated, and the scientific unity that results from them. This approach is not intended to solve all metaphysical problems surrounding physicalism. Yet it (...)
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  15. Is a Unified Science of the Mind-Brain Possible? A Review of Patricia Smith Churchland, "Neurophilosophy: Toward a Unified Science of the Mind/Brain". [REVIEW]John Bishop - 1988 - Biology and Philosophy 3 (3):375.
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  16. Explanation: A Mechanist Alternative.William Bechtel & Adele Abrahamsen - 2005 - Studies in History and Philosophy of Biological and Biomedical Sciences 36 (2):421-441.
    Explanations in the life sciences frequently involve presenting a model of the mechanism taken to be responsible for a given phenomenon. Such explanations depart in numerous ways from nomological explanations commonly presented in philosophy of science. This paper focuses on three sorts of differences. First, scientists who develop mechanistic explanations are not limited to linguistic representations and logical inference; they frequently employ diagrams to characterize mechanisms and simulations to reason about them. Thus, the epistemic resources for presenting mechanistic explanations are (...)
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  17. On Margitay’s Notion of Reduction by Definition.Gergely Kertész - 2012 - Tradition and Discovery 39 (2):16-21.
    In a recent article “From Epistemology to Ontology,” Tihamer Margitay argues, in addition to other things, that the ontological arguments Polanyi provided for his ontological realism with respect to the levels of reality are insufficient. Although Margitay shows this correctly in the case of arguments from boundary conditions, his arguments are not that convincing against the unidentifyability thesis, the thesis that entity kinds on higher levels cannot be identified with descriptions given on lower levels. I argue that here Polányi relies (...)
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  18. The Hedgehog, the Fox, and Reductionism in Biology. [REVIEW]A. C. Love - 2007 - Evolution 61:2736–2738.
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  19. Transcending the Emergence/Reduction Distinction: The Case of Biology.Rom Harré - 2005 - Royal Institute of Philosophy Supplement 56:1-2.
    The groups of problems that fall under the titles ‘reduction’ and ‘emergence’ appear at the boundaries of seemingly independent and well-established scientific disciplines, such as chemistry and biology, biology and psychology, biology and political theory, and so on. They arise in this way.
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  20. SMT and TOFT: Why and How They Are Opposite and Incompatible Paradigms.Mariano Bizzarri & Alessandra Cucina - 2016 - Acta Biotheoretica 64 (3):221-239.
    The Somatic Mutation Theory has been challenged on its fundamentals by the Tissue Organization Field Theory of Carcinogenesis. However, a recent publication has questioned whether TOFT could be a valid alternative theory of carcinogenesis to that presented by SMT. Herein we critically review arguments supporting the irreducible opposition between the two theoretical approaches by highlighting differences regarding the philosophical, methodological and experimental approaches on which they respectively rely. We conclude that SMT has not explained carcinogenesis due to severe epistemological and (...)
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  21. Bodily Parts in the Structure-Function Dialectic.Ingo Brigandt - 2017 - In Scott Lidgard & Lynn K. Nyhart (eds.), Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives. Chicago: University of Chicago Press. pp. 249–274.
    Understanding the organization of an organism by individuating meaningful parts and accounting for organismal properties by studying the interaction of bodily parts is a central practice in many areas of biology. While structures are obvious bodily parts and structure and function have often been seen as antagonistic principles in the study of organismal organization, my tenet is that structures and functions are on a par. I articulate a notion of function (functions as activities), according to which functions are bodily parts (...)
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  22. Programming the Emergence in Morphogenetically Architected Complex Systems.Angélique Stéphanou & Nicolas Glade - 2015 - Acta Biotheoretica 63 (3):295-308.
    Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems. While taking the emergence of properties seriously, the notion of MACS enables at the same time the design of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the self-organized systems studied in the field (...)
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  23. Relations Among Fields: Mendelian, Cytological and Molecular Mechanisms.Lindley Darden - 2005 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 36 (2):349-371.
    Philosophers have proposed various kinds of relations between Mendelian genetics and molecular biology: reduction, replacement, explanatory extension. This paper argues that the two fields are best characterized as investigating different, serially integrated, hereditary mechanisms. The mechanisms operate at different times and contain different working entities. The working entities of the mechanisms of Mendelian heredity are chromosomes, whose movements serve to segregate alleles and independently assort genes in different linkage groups. The working entities of numerous mechanisms of molecular biology are larger (...)
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  24. Interlevel Relations and Manipulative Causality.Gero Schwenk - 2006 - Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 37 (1):99-110.
    The topic of this article is the analysis of the relations between different levels of reality. The core argument is based on considerations of both an epistemology of action and manipulative causality as a criterion of object identity. The argumentation is extended towards the concepts of self-organization and self-regulation. Finally, several views on reduction and the problems of emergence and complexity are discussed.
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  25. Simulation informatique et pluriformalisation des objets composites.Franck Varenne - 2009 - Philosophia Scientae 13:135-154.
    A recent evolution of computer simulations has led to the emergence of complex computer simulations. In particular, the need to formalize composite objects (those objects that are composed of other objects) has led to what the author suggests calling pluriformalizations, i.e. formalizations that are based on distinct sub-models which are expressed in a variety of heterogeneous symbolic languages. With the help of four case-studies, he shows that such pluriformalizations enable to formalize distinctly but simultaneously either different aspects or different parts (...)
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  26. Unifying Biology: The Evolutionary Synthesis and Evolutionary Biology.V. B. Smocovitis - 1992 - Journal of the History of Biology 25 (1):1-65.
  27. Wendell Stanley's Dream of a Free-Standing Biochemistry Department at the University of California, Berkeley.Angela N. H. Creager - 1996 - 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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  28. Conceptualizing Evolutionary Novelty: Moving Beyond Definitional Debates.Ingo Brigandt & Alan C. Love - 2012 - Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 318:417-427.
    According to many biologists, explaining the evolution of morphological novelty and behavioral innovation are central endeavors in contemporary evolutionary biology. These endeavors are inherently multidisciplinary but also have involved a high degree of controversy. One key source of controversy is the definitional diversity associated with the concept of evolutionary novelty, which can lead to contradictory claims (a novel trait according to one definition is not a novel trait according to another). We argue that this diversity should be interpreted in light (...)
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  29. Multilevel Research Strategies and Biological Systems.Maureen A. O'Malley, Ingo Brigandt, Alan C. Love, John W. Crawford, Jack A. Gilbert, Rob Knight, Sandra D. Mitchell & Forest Rohwer - 2014 - Philosophy of Science 81 (5):811-828.
    Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.
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  30. Toolbox Murders: Putting Genes in Their Epigenetic and Ecological Contexts: P. Griffiths and K. Stotz: Genetics and Philosophy: An Introduction. [REVIEW]Thomas Pradeu - 2016 - Biology and Philosophy 31 (1):125-142.
    Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what (...)
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  31. Structured System in Chemistry: Comparison with Mechanics and Biology. [REVIEW]Giovanni Villani - 2014 - Foundations of Chemistry 16 (2):107-123.
    The fundamental concept of structured chemical system has been introduced and analysed in this paper. This concept, as in biology but not in physics, is very important in chemistry. In fact, the main chemical concepts (molecule and compound) have been identified as systemic concepts and their use in chemical explanation can only be justified in this approach. The fundamental concept of “environment” has been considered and then the system concept in mechanics, chemistry and biology. The differences and the analogies between (...)
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  32. Towards Disciplinary Disintegration in Biology.Wim J. Van Der Steen - 1993 - Biology and Philosophy 8 (3):259-275.
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  33. No Levels, No Problems: Downward Causation in Neuroscience.Markus Eronen - 2013 - Philosophy of Science 80 (5):1042-1052.
    I show that the recent account of levels in neuroscience proposed by Craver and Bechtel is unsatisfactory since it fails to provide a plausible criterion for being at the same level and is incompatible with Craver and Bechtel’s account of downward causation. Furthermore, I argue that no distinct notion of levels is needed for analyzing explanations and causal issues in neuroscience: it is better to rely on more well-defined notions such as composition and scale. One outcome of this is that (...)
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  34. [Embryology,'Chemical Geography'of the Cell and Synthesis Between Morphology and Chemistry (1930-1950)].B. Fantini - 1999 - History and Philosophy of the Life Sciences 22 (3):353-380.
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  35. Organisms-Mechanisms: Stahl, Wolff, and the Case Against Reductionist Exclusion.Alfred Gierer - 1996 - Science in Context 9 (4).
    Unlike Aristotelian physics with its teleological notions, modern physics was developed exclusively in relation to the nonliving domain. This raised the question as to whether mechanics applies to organisms, and if so, to what extent. From the seventeenth century on, mechanistic ideas became prominent in biological and medical theory. Contemporary biology explains essential features of life on the basis of physical laws and processes. This does not prove, however, that the early mechanists were essentially right. In the eighteenth century, following (...)
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  36. Reductionism in Biology: An Example of Biochemistry.Mehmet Elgin - 2010 - In F. Stadler, D. Dieks, W. Gonzales, S. Hartmann, T. Uebel & M. Weber (eds.), The Present Situation in the Philosophy of Science. Springer. pp. 195--203.
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  37. 8. Reductionism in Biology.W. H. Thorpe - 1974 - In Francisco Jose Ayala & Theodosius Grigorievich Dobzhansky (eds.), Studies in the Philosophy of Biology: Reduction and Related Problems. University of California Press. pp. 109.
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  38. Implications of Physical Science.Sewall Wright - 1977 - In John B. Cobb & David Ray Griffin (eds.), Mind in Nature. University Press of America. pp. 79.
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  39. Roots: Molecular Basis of Gene Expression: Origins From the Pajama Experiment.Arthur B. Pardee - 1985 - Bioessays 2 (2):86-89.
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  40. Roots: Molecular Basis of Biological Regulation: Origins From Feedback Inhibition and Allostery.Arthur B. Pardee - 1985 - Bioessays 2 (1):37-40.
  41. 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. [REVIEW]Norman Maclean - 1986 - Bioessays 4 (3):139-140.
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  42. Biochemistry with a Human faceBiochemistry . By Mary K. Campbell. Saunders College Publishing, Philadelphia. 622pp. $43. [REVIEW]Peter Leadlay - 1992 - Bioessays 14 (1):69-70.
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  43. Where Biochemistry Meets Enginneering. Protein Purification: Design and Scale-Up of Downstream Processing . By Scott M. Wheel Wright. Hanser Publishers: Munich . 246pp. DM 129/$83/$49. [REVIEW]John M. Walker - 1992 - Bioessays 14 (10):726-726.
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  44. Problems and Paradigms: Relating Biochemistry to Biology: How the Recombinational Repair Function of RecA Protein is Manifested in its Molecular Properties.Michael M. Cox - 1993 - Bioessays 15 (9):617-623.
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  45. Basic Formal Ontology for Bioinformatics.Barry Smith, Anand Kumar & Thomas Bittner - 2005 - IFOMIS Reports.
    Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize reasoning (...)
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  46. Synthetic Biology and Synthetic Knowledge.Christophe Malaterre - 2013 - 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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  47. Innovations in Communication: Origin of Biochemical & Biophysical Research Communications.W. D. McElroy - 1985 - Bioessays 3 (2):83-83.
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  48. On the Emergence of Living Systems.Bruce H. Weber - 2009 - Biosemiotics 2 (3):343-359.
    If the problem of the origin of life is conceptualized as a process of emergence of biochemistry from proto-biochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, then the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to living systems and biosemiosis. In such a view the emergence of life, and concomitantly of natural selection and biosemiosis, (...)
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  49. On Biological Science's Distinctiveness: Final Statement From an Old Master. What Makes Biology Unique? Considerations on the Autonomy of a Scientific Discipline. (2004). Ernst Mayr. Cambridge University Press, Cambridge. (Xiv + 232 Pp.) ISBN: 0‐521‐84114‐3. [REVIEW]Adam S. Wilkins - 2006 - Bioessays 28 (9):954-956.
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  50. A Biologist Looks at the Study of Consciousness.Jack Chamberlain - 2001 - Bioessays 23 (3):297-298.
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