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  1. When One Model is Not Enough: Combining Epistemic Tools in Systems Biology.Sara Green - 2013 - Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2):170-180.
    In recent years, the philosophical focus of the modeling literature has shifted from descriptions of general properties of models to an interest in different model functions. It has been argued that the diversity of models and their correspondingly different epistemic goals are important for developing intelligible scientific theories. However, more knowledge is needed on how a combination of different epistemic means can generate and stabilize new entities in science. This paper will draw on Rheinberger’s practice-oriented account of knowledge production. The (...)
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  • Interdisciplinary Lessons for the Teaching of Biology From the Practice of Evo-Devo.Alan C. Love - 2013 - Science & Education 22 (2):255-278.
    Evolutionary developmental biology (Evo-devo) is a vibrant area of contemporary life science that should be (and is) increasingly incorporated into teaching curricula. Although the inclusion of this content is important for biological pedagogy at multiple levels of instruction, there are also philosophical lessons that can be drawn from the scientific practices found in Evo-devo. One feature of particular significance is the interdisciplinary nature of Evo-devo investigations and their resulting explanations. Instead of a single disciplinary approach being the most explanatory or (...)
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  • Interdisciplinary Lessons for the Teaching of Biology From the Practice of Evo-Devo.Alan C. Love - 2013 - Science & Education 22 (2):255–278.
    Evolutionary developmental biology (Evo-devo) is a vibrant area of contemporary life science that should be (and is) increasingly incorporated into teaching curricula. Although the inclusion of this content is important for biological pedagogy at multiple levels of instruction, there are also philosophical lessons that can be drawn from the scientific practices found in Evo-devo. One feature of particular significance is the interdisciplinary nature of Evo-devo investigations and their resulting explanations. Instead of a single disciplinary approach being the most explanatory or (...)
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  • The Phenomena of Homology.Paul Edmund Griffiths - 2007 - Biology and Philosophy 22 (5):643-658.
    Philosophical discussions of biological classification have failed to recognise the central role of homology in the classification of biological parts and processes. One reason for this is a misunderstanding of the relationship between judgments of homology and the core explanatory theories of biology. The textbook characterisation of homology as identity by descent is commonly regarded as a definition. I suggest instead that it is one of several attempts to explain the phenomena of homology. Twenty years ago the ‘new experimentalist’ movement (...)
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  • Part-Whole Science.Rasmus Winther - 2011 - Synthese 178 (3):397-427.
    A scientific explanatory project, part-whole explanation, and a kind of science, part-whole science are premised on identifying, investigating, and using parts and wholes. In the biological sciences, mechanistic, structuralist, and historical explanations are part-whole explanations. Each expresses different norms, explananda, and aims. Each is associated with a distinct partitioning frame for abstracting kinds of parts. These three explanatory projects can be complemented in order to provide an integrative vision of the whole system, as is shown for a detailed case study: (...)
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  • The Mind, the Lab, and the Field: Three Kinds of Populations in Scientific Practice.Rasmus Grønfeldt Winther, Ryan Giordano, Michael D. Edge & Rasmus Nielsen - 2015 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 52:12-21.
    Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R.A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the notion (...)
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  • Prediction in Selectionist Evolutionary Theory.Rasmus Grønfeldt Winther - 2009 - Philosophy of Science 76 (5):889-901.
    Selectionist evolutionary theory has often been faulted for not making novel predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli, and the origin of eukaryotic cells through endosymbiosis.
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  • Recent Work in The Philosophy of Biology.Christopher J. Austin - 2017 - Analysis 77 (2):anx032.
    The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...)
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  • Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation.Ingo Brigandt - 2013 - Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):477-492.
    The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...)
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  • In What Sense Does ‘Nothing Make Sense Except in the Light of Evolution’?Paul Edmund Griffiths - 2009 - Acta Biotheoretica 57 (1-2):11-32.
    Dobzhansky argued that biology only makes sense if life on earth has a shared history. But his dictum is often reinterpreted to mean that biology only makes sense in the light of adaptation. Some philosophers of science have argued in this spirit that all work in ‘proximal’ biosciences such as anatomy, physiology and molecular biology must be framed, at least implicitly, by the selection histories of the organisms under study. Others have denied this and have proposed non-evolutionary ways in which (...)
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  • Modelling with Words: Narrative and Natural Selection.Dominic K. Dimech - 2017 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 62:20-24.
    I argue that verbal models should be included in a philosophical account of the scientific practice of modelling. Weisberg (2013) has directly opposed this thesis on the grounds that verbal structures, if they are used in science, only merely describe models. I look at examples from Darwin's On the Origin of Species (1859) of verbally constructed narratives that I claim model the general phenomenon of evolution by natural selection. In each of the cases I look at, a particular scenario is (...)
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  • Typology Reconfigured: From the Metaphysics of Essentialism to the Epistemology of Representation.Alan C. Love - 2009 - Acta Biotheoretica 57 (1-2):51-75.
    The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...)
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  • Explanation in Biology: Reduction, Pluralism, and Explanatory Aims.Ingo Brigandt - 2011 - Science & Education 22 (1):69-91.
    This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...)
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  • On Mechanistic Reasoning in Unexpected Places: The Case of Population Genetics.Lucas J. Matthews - 2017 - Biology and Philosophy 32 (6):999-1018.
    A strong case has been made for the role and value of mechanistic reasoning in process-oriented sciences, such as molecular biology and neuroscience. This paper shifts focus to assess the role of mechanistic reasoning in an area where it is neither obvious nor expected: population genetics. Population geneticists abstract away from the causal-mechanical details of individual organisms and, instead, use mathematics to describe population-level, statistical phenomena. This paper, first, develops a framework for the identification of mechanistic reasoning where it is (...)
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  • Interweaving Categories: Styles, Paradigms, and Models.Rasmus Grønfeldt Winther - 2012 - Studies in History and Philosophy of Science Part A 43 (4):628-639.
    Analytical categories of scientific cultures have typically been used both exclusively and universally. For instance, when styles of scientific research are employed in attempts to understand and narrate science, styles alone are usually employed. This article is a thought experiment in interweaving categories. What would happen if rather than employ a single category, we instead investigated several categories simultaneously? What would we learn about the practices and theories, the agents and materials, and the political-technological impact of science if we analyzed (...)
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  • Organisms and Organization.Marvalee H. Wake - 2008 - Biological Theory 3 (3):213-223.
    Organisms are organized both internally and externally. The centrality of the organism in examination of the hierarchy of biological organization and the kinds of “emergent properties” that develop from study of organization at one level relative to other levels are my themes. That centrality has not often been implicit in discussion of unifying concepts, even evolution. Few general or unifying principles integrate information derived from various levels of biological organization. However, as the genetic toolbox and other new techniques are now (...)
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  • Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity.Rasmus Grønfeldt Winther - 2009 - Acta Biotheoretica 57 (1-2):129-162.
    The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...)
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  • Development and Mechanistic Explanation.Fabrizzio Mc Manus - 2012 - Studies in History and Philosophy of Science Part C 43 (2):532-541.
  • Development and Mechanistic Explanation.Fabrizzio Mc Manus - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (2):532-541.
  • Pluralism in Evolutionary Controversies: Styles and Averaging Strategies in Hierarchical Selection Theories.Rasmus Grønfeldt Winther, Michael J. Wade & Christopher C. Dimond - 2013 - Biology and Philosophy 28 (6):957-979.
    Two controversies exist regarding the appropriate characterization of hierarchical and adaptive evolution in natural populations. In biology, there is the Wright-Fisher controversy over the relative roles of random genetic drift, natural selection, population structure, and interdemic selection in adaptive evolution begun by Sewall Wright and Ronald Aylmer Fisher. There is also the Units of Selection debate, spanning both the biological and the philosophical literature and including the impassioned group-selection debate. Why do these two discourses exist separately, and interact relatively little? (...)
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  • Waddington’s Legacy to Developmental and Theoretical Biology.Jonathan B. L. Bard - 2008 - Biological Theory 3 (3):188-197.
    Conrad Hal Waddington was a British developmental biologist who mainly worked in Cambridge and Edinburgh, but spent the late 1930s with Morgan in California learning about Drosophila. He was the first person to realize that development depended on the then unknown activities of genes, and he needed an appropriate model organism. His major experimental contributions were to show how mutation analysis could be used to investigate developmental mechanisms in Drosophila, and to explore how developmental mutation could drive evolution, his other (...)
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  • Rational Disagreements in Phylogenetics.Fabrizzio Guerrero Mc Manus - 2009 - Acta Biotheoretica 57 (1-2):99-127.
    This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and (...)
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  • Laws of Biology, Laws of Nature: Problems and (Dis)Solutions.Andrew Hamilton - 2007 - Philosophy Compass 2 (3):592–610.
    This article serves as an introduction to the laws-of-biology debate. After introducing the main issues in an introductory section, arguments for and against laws of biology are canvassed in Section 2. In Section 3, the debate is placed in wider epistemological context by engaging a group of scholars who have shifted the focus away from the question of whether there are laws of biology and toward offering good accounts of explanation(s) in the biological sciences. Section 4 introduces two relatively new (...)
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  • Homology Thinking.Marc Ereshefsky - 2012 - Biology and Philosophy 27 (3):381-400.
    This paper explores an important type of biological explanation called ‘homology thinking.’ Homology thinking explains the properties of a homologue by citing the history of a homologue. Homology thinking is significant in several ways. First, it offers more detailed explanations of biological phenomena than corresponding analogy explanations. Second, it provides an important explanation of character similarity and difference. Third, homology thinking offers a promising account of multiple realizability in biology.
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  • From Humanized Mice to Human Disease: Guiding Extrapolation From Model to Target.Monika Piotrowska - 2013 - Biology and Philosophy 28 (3):439-455.
    Extrapolation from a well-understood base population to a less-understood target population can fail if the base and target populations are not sufficiently similar. Differences between laboratory mice and humans, for example, can hinder extrapolation in medical research. Mice that carry a partial or complete human physiological system, known as humanized mice, are supposed to make extrapolation more reliable by simulating a variety of human diseases. But what justifies our belief that these mice are similar enough to their human counterparts to (...)
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