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  1. Knowledge‐Making Distinctions in Synthetic Biology.Maureen A. O'Malley, Alexander Powell, Jonathan F. Davies & Jane Calvert - 2008 - Bioessays 30 (1):57-65.
  2. From Theory to Data: Representing Neurons in the 1940s. [REVIEW]Tara H. Abraham - 2003 - Biology and Philosophy 18 (3):415-426.
    Recent literature on the role of pictorial representation in the life sciences has focused on the relationship between detailed representations of empirical data and more abstract, formal representations of theory. The standard argument is that in both a historical and epistemic sense, this relationship is a directional one: beginning with raw, unmediated images and moving towards diagrams that are more interpreted and more theoretically rich. Using the neural network diagrams of Warren McCulloch and Walter Pitts as a case study, I (...)
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  3. Theory of Evolution and Historical Explanation in Biology.Keyvan Alasti - forthcoming - Philosophical Investigations.
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  4. Los límites del reduccionismo molecular.Armando Aranda-Anzaldo - 1994 - Ciencia y Desarrollo 20 (116):18-25.
    Existen inconsistencias fundamentales entre el paradigma de la biología molecular y el paradigma de la física contemporánea y, por lo tanto, el marco conceptual vigente en la biología molecular resulta insuficiente para abordar las cuestiones del origen y desarrollo de la forma y organización biológicas.
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  5. The Probabilistic Character of Evolutionary Explanations.A. Ariew - 1998 - Biology and Philosophy 13 (2):245-253.
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  6. Ernst Mayr's 'Ultimate/Proximate' Distinction Reconsidered and Reconstructed.André Ariew - 2003 - Biology and Philosophy 18 (4):553-565.
    It's been 41 years since the publication of Ernst Mayr's Cause and Effect in Biology wherein Mayr most clearly develops his version of the influential distinction between ultimate and proximate causes in biology. In critically assessing Mayr's essay I uncover false statements and red-herrings about biological explanation. Nevertheless, I argue to uphold an analogue of the ultimate/proximate distinction as it refers to two different kinds of explanations, one dynamical the other statistical.
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  7. Practice Oriented Controversies and Borrowed Epistemic Support in Current Evolutionary Biology. The Case of Phylogeography.Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva - 2015 - Perspectives on Science 23 (3):310-334.
    Philosophical treatments of scientific controversies usually focus on theory, excluding important practice related aspects. However, scientists in conflict often appeal to extra-theoretical and extra-empirical elements. To understand better the role that non-empirical elements play in scientific controversies, we introduce the notion of borrowed epistemic credibility, illustrating our proposal with a recent controversy in a field of evolutionary biology known as phylogeography. Our analysis shows how scientific controversies that spring from disagreements about methodological issues potentially involve deeperdebates regarding whatconstitutes good science, (...)
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  8. The Ontology of Organisms: Mechanistic Modules or Patterned Processes?Christopher J. Austin - 2016 - Biology and Philosophy 31 (5):639-662.
    Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...)
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  9. Adaptation and Novelty: Teleological Explanations in Evolutionary Biology.Francisco J. Ayala - 1999 - History and Philosophy of the Life Sciences 21 (1):3 - 33.
    Knives, birds' wings, and mountain slopes are used for certain purposes: cutting, flying, and climbing. A bird's wings have in common with knives that they have been 'designed' for the purpose they serve, which purpose accounts for their existence, whereas mountain slopes have come about by geological processes independently of their uses for climbing. A bird's wings differ from a knife in that they have not been designed or produced by any conscious agent; rather, the wings, like the slopes, are (...)
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  10. Teleological Explanations Versus Teleology.Francisco J. Ayala - 1998 - History and Philosophy of the Life Sciences 20 (1):41 - 50.
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  11. The Cement of Medical Thought. Evolutionary Emergence and Downward Causation.Giovanni Felice Azzone - 1998 - History and Philosophy of the Life Sciences 20 (2):163 - 187.
    The aetio-pathogenetic sequences and the physio-pathological patterns of diabetes, emphysema, cholera, circulatory shock and thrombosis have been analysed with respect to an evolutionary interpretation. The diseases, although reflecting alterations of processes that can always be described in physico-chemical language, occur only at the level of biological systems which reflects the decodification of genomic project: the teleonomic projects that have been developed during evolution. The concepts of evolutionary emergence and of downward causation have been used to discuss the relationship between the (...)
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  12. Causal Explanation Beyond the Gene: Manipulation and Causality in Epigenetics.Jan Baedke - 2012 - Theoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 27 (2):153-174.
    This paper deals with the interrelationship between causal explanation and methodology in a relatively young discipline in biology: epigenetics. Based on cases from molecular and ecological epigenetics, I show that James Woodward’s interventionist account of causation captures essential features about how epigeneticists using highly diverse methods, i.e. laboratory experiments and purely observational studies, think about causal explanation. I argue that interventionism thus qualifies as a useful unifying explanatory approach when it comes to cross-methodological research efforts: It can act as a (...)
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  13. Levels of Research in the Biological Sciences.Orville T. Bailey - 1945 - Philosophy of Science 12 (1):1-7.
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  14. Orgons Andbiolons in Theoretical Biology: Phenomenological Analysis and Quantum Analogies.Francis Bailly, Françoise Gaill & Rémy Mosseri - 1993 - Acta Biotheoretica 41 (1-2):3-11.
    In this paper we define two types of formal biological entities corresponding to biological levels of organization, thebiolons and theorgons, the properties of which are phenomenologically analyzed and discussed.We examine then, in a rather speculative manner, how some characteristics of these entities may suggest analogies between properties of biological systems and some special features of quantum systems.
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  15. Occam's Razor in Science: A Case Study From Biogeography.A. Baker - 2007 - Biology and Philosophy 22 (2):193-215.
  16. 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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  17. Entangled Life: Organism and Environment in the Biological and Social Sciences.Gillian Barker, Eric Desjardins & Trevor Pearce (eds.) - 2014 - Springer.
    Despite the burgeoning interest in new and more complex accounts of the organism-environment dyad by biologists and philosophers, little attention has been paid in the resulting discussions to the history of these ideas and to their deployment in disciplines outside biology—especially in the social sciences. Even in biology and philosophy, there is a lack of detailed conceptual models of the organism-environment relationship. This volume is designed to fill these lacunae by providing the first multidisciplinary discussion of the topic of organism-environment (...)
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  18. Biological Explanations, Realism, Ontology, and Categories.Matthew Barker - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):617-622.
  19. Asking Questions in Biology: A Guide to Hypothesis Testing, Experimental Design and Presentation in Practical Work and Research Projects.C. J. Barnard - 2011 - Pearson.
  20. A Web of Controversies: Complexity in the Burgess Shale Debate. [REVIEW]Christian Baron - 2011 - Journal of the History of Biology 44 (4):745 - 780.
    Using the Burgess Shale controversies as a case-study, this paper argues that controversies within different domains may interact as to create a situation of "complicated intricacies," where the practicing scientist has to navigate through a context of multiple thought collectives. To some extent each of these collectives has its own dynamic complete with fairly negotiated standards for investigation and explanation, theoretical background assumptions and certain peculiarities of practice. But the intellectual development in one of these collectives may "spill over" having (...)
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  21. Are All Bases Covered?Louise Barrett & S. Peter Henzi - 2002 - Behavioral and Brain Sciences 25 (4):506-507.
    In addition to ensuring that appropriate standards of evidence are employed when attempting to identify adaptations, researchers should investigate all nonevolutionary factors that could potentially explain their results. Evolutionary analyses may be undermined by alternative, non-evolutionary explanations either because not all relevant information is included in an evolutionary analysis, or because inappropriate methods incapable of detecting an adaptation are employed.
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  22. Towards an Ecological View of Immunity. [REVIEW]Swiatczak Bartlomiej - forthcoming - Studies in History and Philosophy of Science Part A.
    The immune system does not just fight pathogens but also engages in interactions with beneficial microbes and non-immune cells of the body to harmonize their behavior by means of cytokines, antibodies and effector cells (Dinarello, 2007; Moticka, 2015, pp. 217e226, 261e267). However, the importance of these “housekeeping” functions has not been fully appreciated (Cohen, 2000). In his new book Immunity: The Evolution of an Idea Alfred I. Tauber traces the history of fundamental ideas in immunology and refers to recent advances (...)
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  23. Normative Characterization in Biological and Cognitive Explanations.Mark Bauer - 2015 - Theoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 30 (2):271-286.
    Normative characterization is a commonplace feature of biological and cognitive explanation. Such language seems to commit the biological and cognitive sciences to the existence of natural norms, but it is also difficult to understand how such normativity fits into a natural world of physical causes and forces. I propose to map normativity onto systems stabilized by counteractive constraints. Such a mapping, I believe, can explain normativity’s causal-explanatory role in biological and cognitive inquiry. The common approach in the literature is to (...)
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  24. Normative Characterization in Empirical Explanation.Mark Bauer - 2015 - Theoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 30 (2):271.
    Normative characterization is a commonplace feature of biological and cognitive explanation. Such language seems to commit the biological and cognitive sciences to the existence of natural norms, but it is also difficult to understand how such normativity fits into a natural world of physical causes and forces. I propose to map normativity onto systems stabilized by counteractive constraints. Such a mapping, I believe, can explain normativity's causal-explanatory role in biological and cognitive inquiry. The common approach in the literature is to (...)
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  25. Constitutive Relevance, Mutual Manipulability, and Fat-Handedness.Michael Baumgartner & Alexander Gebharter - 2016 - British Journal for the Philosophy of Science 67 (3):731-756.
    The first part of this paper argues that if Craver’s ([2007a], [2007b]) popular mutual manipulability account (MM) of mechanistic constitution is embedded within Woodward’s ([2003]) interventionist theory of causation--for which it is explicitly designed--it either undermines the mechanistic research paradigm by entailing that there do not exist relationships of constitutive relevance or it gives rise to the unwanted consequence that constitution is a form of causation. The second part shows how Woodward’s theory can be adapted in such a way that (...)
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  26. Mapping the Continuum of Research Strategies.Matthew Baxendale - forthcoming - Synthese:1-23.
    Contemporary philosophy of science has seen a growing trend towards a focus on scientific practice over the epistemic outputs that such practices produce. This practice-oriented approach has yielded a clearer understanding of how reductive research strategies play a central role in contemporary scientific inquiry. In parallel, a growing body of work has sought to explore the role of non-reductive, or systems-level, research strategies. As a result, the relationship between reductive and non-reductive scientific practices is becoming of increased importance. In this (...)
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  27. Why Do Biologists Argue Like They Do?John Beatty - 1997 - Philosophy of Science 64 (4):443.
    "Theoretical pluralism" obtains when there are good evidential reasons for accommodating multiple theories of the same domain. Issues of "relative significance" often arise in connection with the investigation of such domains. In this paper, I describe and give examples of theoretical pluralism and relative significance issues. Then I explain why theoretical pluralism so often obtains in biology--and why issues of relative significance arise--in terms of evolutionary contingencies and the paucity or lack of laws of biology. Finally, I turn from explanation (...)
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  28. Mechanism and Biological Explanation.William Bechtel - 2011 - Philosophy of Science 78 (4):533-557.
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  29. Generalization and Discovery by Assuming Conserved Mechanisms: Cross‐Species Research on Circadian Oscillators.William Bechtel - 2009 - Philosophy of Science 76 (5):762-773.
    In many domains of biology, explanation takes the form of characterizing the mechanism responsible for a particular phenomenon in a specific biological system. How are such explanations generalized? One important strategy assumes conservation of mechanisms through evolutionary descent. But conservation is seldom complete. In the case discussed, the central mechanism for circadian rhythms in animals was first identified in Drosophila and then extended to mammals. Scientists' working assumption that the clock mechanisms would be conserved both yielded important generalizations and served (...)
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  30. Reduction, Integration, and the Unity of Science: Natural, Behavioral, and Social Sciences and the Humanities.William P. Bechtel & Andrew Hamilton - 2007 - In T. Kuipers (ed.), Philosophy of Science: Focal Issues (Volume 1 of the Handbook of the Philosophy of Science). Elsevier.
    1. A Historical Look at Unity 2. Field Guide to Modern Concepts of Reduction and Unity 3. Kitcher's Revisionist Account of Unification 4. Critics of Unity 5. Integration Instead of Unity 6. Reduction via Mechanisms 7. Case Studies in Reduction and Unification across the Disciplines.
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  31. Complex Biological Mechanisms: Cyclic, Oscillatory, and Autonomous.William Bechtel & Adele Abrahamsen - unknown
    The mechanistic perspective has dominated biological disciplines such as biochemistry, physiology, cell and molecular biology, and neuroscience, especially during the 20th century. The primary strategy is reductionist: organisms are to be decomposed into component parts and operations at multiple levels. Researchers adopting this perspective have generated an enormous body of information about the mechanisms of life at scales ranging from the whole organism down to genetic and other molecular operations.
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  32. Thinking Dynamically About Biological Mechanisms: Networks of Coupled Oscillators. [REVIEW]William Bechtel & Adele A. Abrahamsen - 2013 - Foundations of Science 18 (4):707-723.
    Explaining the complex dynamics exhibited in many biological mechanisms requires extending the recent philosophical treatment of mechanisms that emphasizes sequences of operations. To understand how nonsequentially organized mechanisms will behave, scientists often advance what we call dynamic mechanistic explanations. These begin with a decomposition of the mechanism into component parts and operations, using a variety of laboratory-based strategies. Crucially, the mechanism is then recomposed by means of computational models in which variables or terms in differential equations correspond to properties of (...)
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  33. Weak Emergence Drives the Science, Epistemology, and Metaphysics of Synthetic Biology.Mark A. Bedau - 2013 - 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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  34. Laws in Biology.Réjane Bernier - 1983 - Acta Biotheoretica 32 (4):265-288.
    In the first part of my analysis, I wish briefly to clarify the different modes of relation found in the living being, and point out the multiplicity of disciplines in which biologists use (explicitly or implicitly) the notion of laws. In the second part, I shall analyse the notion of universal laws in biology and examine successively: (1) accidental generalizations; (2) non-causal biological correlations; (3) the meaning of 'necessity' in these correlations; and (4) causal connections. Finally, in the third part, (...)
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  35. On the Structure of Biological Explanations: Beyond Functional Ascriptions in Cancer Research.Marta Bertolaso - 2013 - Epistemologia 36 (1):112-130.
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  36. Hamilton's Rule and Its Discontents.Jonathan Birch - 2014 - British Journal for the Philosophy of Science 65 (2):381-411.
    In an incendiary 2010 Nature article, M. A. Nowak, C. E. Tarnita, and E. O. Wilson present a savage critique of the best-known and most widely used framework for the study of social evolution, W. D. Hamilton’s theory of kin selection. More than a hundred biologists have since rallied to the theory’s defence, but Nowak et al. maintain that their arguments ‘stand unrefuted’. Here I consider the most contentious claim Nowak et al. defend: that Hamilton’s rule, the core explanatory principle (...)
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  37. Robust Processes and Teleological Language.Jonathan Birch - 2013 - European Journal for Philosophy of Science 3 (3):299-312.
    I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” optimize some (...)
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  38. Selection and Explanation.Alexander Bird - 2006 - In Rethinking Explanation. Springer. pp. 131--136.
    Selection explanations explain some non-accidental generalizations in virtue of a selection process. Such explanations are not particulaizable - they do not transfer as explanations of the instances of such generalizations. This is unlike many explanations in the physical sciences, where the explanation of the general fact also provides an explanation of its instances (i.e. standard D-N explanations). Are selection explanations (e.g. in biology) therefore a different kind of explanation? I argue that to understand this issue, we need to see that (...)
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  39. A Contextualized Approach to Biological Explanation.Giovanni Boniolo - 2005 - Philosophy 80 (2):219-247.
    In the paper, starting from a slightly modified version of van Fraassen's pragmatic approach to explanation, I will propose a pragmatical meta-model for the different biological explanatory models. That is, I will offer a pragmatic point of view to rule different explanatory models in function of the biological context from which the given biologist explains.
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  40. Measurement, Explanation, and Biology: Lessons From a Long Century.Fred L. Bookstein - 2009 - Biological Theory 4 (1):6-20.
    It is far from obvious that outside of highly specialized domains such as commercial agriculture, the methodology of biometrics—quantitative comparisons over groups of organisms—should be of any use in today’s bioinformatically informed biological sciences. The methods in our biometric textbooks, such as regressions and principal components analysis, make assumptions of homogeneity that are incompatible with current understandings of the origins of developmental or evolutionary data in historically contingent processes, processes that might have come out otherwise; the appropriate statistical methods are (...)
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  41. How Quantification Persuades When It Persuades.Fred L. Bookstein - 2009 - Biological Theory 4 (2):132-147.
    Although Harry Woolf’s great collective volume Quantification mostly overlooked biology, Thomas Kuhn’s chapter there on the role of quantitative measurement within the physical sciences maps quite well onto the forms of reasoning that actually persuade us as biologists 50 years later. Kuhn distinguished between two contexts, that of producing quantitative anomalies and that of resolving them. The implied form of reasoning is actually C. S. Peirce’s abduction or inference to the best explanation: “The surprising fact C is observed; but if (...)
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  42. Contrastive Explanations in Evolutionary Biology.Stephen Boulter - 2012 - Ratio 25 (4):425-441.
    Taxonomists in biology have traditionally been concerned to delimit and classify actual biological forms or kinds. But not all useful classification schemes are of actualised forms. This paper focuses on the need to delimit and classify non‐actual forms when offering contrastive explanations in evolutionary biology. Such a classification scheme sorts actual and non‐actual forms according to their modal status. Such a sorting has been offered by theoretical morphologists, but these efforts have paid insufficient attention to the metaphysics of modality. Contemporary (...)
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  43. Explanation of Molecular Processes Without Tracking Mechanism Operation.Ingo Brigandt - forthcoming - Philosophy of Science.
    Philosophical discussions of systems biology have enriched the notion of mechanistic explanation by pointing to the role of mathematical modeling. However, such accounts still focus on explanation in terms of tracking a mechanism's operation across time (by means of mental or computational simulation). My contention is that there are explanations of molecular systems where the explanatory understanding does not consist in tracking a mechanism's operation and productive continuity. I make this case by a discussion of bifurcation analysis in dynamical systems, (...)
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  44. Review of Reductive Explanation in the Biological Sciences by Marie Kaiser. [REVIEW]Ingo Brigandt - 2016 - Notre Dame Philosophical Reviews 201608.
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  45. Explanation in Biology: Reduction, Pluralism, and Explanatory Aims.Ingo Brigandt - 2013 - 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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  46. 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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  47. Systems Biology and Mechanistic Explanation.Ingo Brigandt, Sara Green & Maureen O'Malley - 2018 - In Stuart Glennan & Phyllis McKay Illari (eds.), The Routledge Handbook of Mechanisms and Mechanical Philosophy. New York: Routledge. pp. 362–374.
    We address the question of whether and to what extent explanatory and modelling strategies in systems biology are mechanistic. After showing how dynamic mathematical models are actually required for mechanistic explanations of complex systems, we caution readers against expecting all systems biology to be about mechanistic explanations. Instead, the aim may be to generate topological explanations that are not standardly mechanistic, or to arrive at design principles that explain system organization and behaviour in general, but not specific mechanisms. These abstraction (...)
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  48. 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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  49. The Role of Models in the Process of Epistemic Integration: The Case of the Reichardt Motion Detector.Daniel S. Brooks - 2014 - History and Philosophy of the Life Sciences 36 (1):90-113.
    Recent work on epistemic integration in the life sciences has emphasized the importance of integration in thinking about explanatory practice in science, particularly for articulating a robust alternative to reductionism and anti-reductionism. This paper analyzes the role of models in balancing the relative contributions of lower- and higher-level epistemic resources involved in this process. Integration between multiple disciplines proceeds by constructing a problem agenda (Love 2008), a set of interrelated problems that structures the problem space of a complex phenomenon that (...)
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  50. Qualitative and Quantitative Explanation of the Forms of Heat Sensitive Organs in Snakes.Tjard Cock Buning - 1985 - Acta Biotheoretica 34 (2-4).
    Heat sensitive pit organs in different species of snakes show various shapes. The relation between form characters and functions were analysed by means of two different research programs. This paper presents the methodological steps involved in these research programs. The first approach is called a qualitative explanation because it connects experimental data by means of qualitative statements in order to give a functional morphological explanation for the construction of the pits in respect to the behaviour of the snake. The second (...)
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