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  1. Tara H. Abraham (2003). From Theory to Data: Representing Neurons in the 1940s. [REVIEW] 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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  2. Plutynski Anya (2005). Parsimony and the Fisher–Wright Debate. Biology and Philosophy 20 (4):697-713.
    In the past five years, there have been a series of papers in the journal Evolution debating the relative significance of two theories of evolution, a neo-Fisherian and a neo-Wrightian theory, where the neo-Fisherians make explicit appeal to parsimony. My aim in this paper is to determine how we can make sense of such an appeal. One interpretation of parsimony takes it that a theory that contains fewer entities or processes, (however we demarcate these) is more parsimonious. On the account (...)
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  3. A. Ariew (1998). The Probabilistic Character of Evolutionary Explanations. Biology and Philosophy 13:245-253.
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  4. André Ariew (2003). Ernst Mayr's 'Ultimate/Proximate' Distinction Reconsidered and Reconstructed. 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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  5. Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva (2015). Practice Oriented Controversies and Borrowed Epistemic Support in Current Evolutionary Biology. The Case of Phylogeography. 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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  6. Francisco J. Ayala (1999). Adaptation and Novelty: Teleological Explanations in Evolutionary Biology. 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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  7. Francisco J. Ayala (1998). Teleological Explanations Versus Teleology. History and Philosophy of the Life Sciences 20 (1):41 - 50.
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  8. Jonathan B. L. Bard (2008). Waddington's Legacy to Developmental and Theoretical Biology. Biological Theory 3 (3):188-197.
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  9. Gillian Barker, Eric Desjardins & Trevor Pearce (eds.) (2014). Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer.
  10. Matthew J. Barker (2013). Biological Explanations, Realism, Ontology, and Categories (Reviewing J. Dupré, Processes of Life: Essays in the Philosophy of Biology). Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):617-622.
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  11. Christian Baron (2011). A Web of Controversies: Complexity in the Burgess Shale Debate. [REVIEW] 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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  12. Louise Barrett & S. Peter Henzi (2002). Are All Bases Covered? 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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  13. Michael Baumgartner & Alexander Gebharter (forthcoming). Constitutive Relevance, Mutual Manipulability, and Fat-Handedness. British Journal for the Philosophy of Science:axv003.
    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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  14. William Bechtel (2011). Mechanism and Biological Explanation. Philosophy of Science 78 (4):533-557.
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  15. William Bechtel (2009). Generalization and Discovery by Assuming Conserved Mechanisms: Cross‐Species Research on Circadian Oscillators. 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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  16. William P. Bechtel & Andrew Hamilton (2007). Reduction, Integration, and the Unity of Science: Natural, Behavioral, and Social Sciences and the Humanities. 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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  17. Réjane Bernier (1983). Laws in Biology. 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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  18. Jonathan Birch (2014). Hamilton's Rule and Its Discontents. 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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  19. Jonathan Birch (2012). Robust Processes and Teleological Language. 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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  20. Alexander Bird (2006). Selection and Explanation. In , Rethinking Explanation. Springer. 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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  21. Fred L. Bookstein (2009). Measurement, Explanation, and Biology: Lessons From a Long Century. Biological Theory 4 (1):6-20.
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  22. Stephen Boulter (2012). Contrastive Explanations in Evolutionary Biology. 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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  23. Ingo Brigandt (2013). Explanation in Biology: Reduction, Pluralism, and Explanatory Aims. Science and 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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  24. Ingo Brigandt (2013). Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation. 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 (as the analysis of a whole in terms of its structural parts and their qualitative interactions) have (...)
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  25. Ingo Brigandt & Alan C. Love (2012). Conceptualizing Evolutionary Novelty: Moving Beyond Definitional Debates. 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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  26. Henry C. Byerly & Richard E. Michod (1991). Fitness and Evolutionary Explanation. [REVIEW] Biology and Philosophy 6 (1):45-53.
    Recent philosophical discussions have failed to clarify the roles of the concept fitness in evolutionary theory. Neither the propensity interpretation of fitness nor the construal of fitness as a primitive theoretical term succeed in explicating the empirical content and explanatory power of the theory of natural selection. By appealing to the structure of simple mathematical models of natural selection, we separate out different contrasts which have tended to confuse discussions of fitness: the distinction between what fitness is defined as versus (...)
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  27. Brett Calcott (2013). Why How and Why Aren't Enough: More Problems with Mayr's Proximate-Ultimate Distinction. Biology and Philosophy 28 (5):767-780.
    Like Laland et al., I think Mayr’s distinction is problematic, but I identify a further problem with it. I argue that Mayr’s distinction is a false dichotomy, and obscures an important question about evolutionary change. I show how this question, once revealed, sheds light on some debates in evo-devo that Laland et al.’s analysis cannot, and suggest that it provides a different view about how future integration between biological disciplines might proceed.
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  28. Brett Calcott (2013). Why the Proximate–Ultimate Distinction Is Misleading, and Why It Matters for Understanding the Evolution of Cooperation. In Kim Sterelny, Richard Joyce, Brett Calcott & Ben Fraser (eds.), Cooperation and its Evolution. MIT Press. 249.
  29. Brett Calcott (2009). Lineage Explanations: Explaining How Biological Mechanisms Change. British Journal for the Philosophy of Science 60 (1):51-78.
    This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, for though it is widely accepted (...)
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  30. Jack G. Chamberlain (1998). Editorial Comment: More on Scientific Reasoning. Bioessays 20 (4):355-355.
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  31. Ken Cheng (2001). Generalization and Tinbergen's Four Whys. Behavioral and Brain Sciences 24 (4):660-661.
    Shepard's exponential law provides a functional explanation of generalization. The account complements the more common mechanistic models. The elegant and powerful analyses answer one of Tinbergen's (1963) four whys of behavior: a benefit conferred on the animal by generalizing in this way. A complete account might address evolutionary and developmental questions in addition to mechanistic and functional ones. [Shepard].
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  32. Christopher Clarke (forthcoming). Multi-Level Selection and the Explanatory Value of Mathematical Decompositions. British Journal for the Philosophy of Science:axv008.
    Do multi-level selection explanations of the evolution of social traits deepen the understanding provided by single-level explanations? Central to the former is a mathematical theorem, the multi-level Price decomposition. I build a framework through which to understand the explanatory role of such non-empirical decompositions in scientific practice. Applying this general framework to the present case places two tasks on the agenda. The first task is to distinguish the various ways of suppressing within-collective variation in fitness, and moreover to evaluate their (...)
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  33. Christine Clavien & Michel Chapuisat (2013). Altruism Across Disciplines: One Word, Multiple Meanings. Biology and Philosophy 28 (1):125-140.
    Altruism is a deep and complex phenomenon that is analysed by scholars of various disciplines, including psychology, philosophy, biology, evolutionary anthropology and experimental economics. Much confusion arises in current literature because the term altruism covers variable concepts and processes across disciplines. Here we investigate the sense given to altruism when used in different fields and argumentative contexts. We argue that four distinct but related concepts need to be distinguished: (a) psychological altruism , the genuine motivation to improve others’ interests and (...)
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  34. Gregory Cooper (1996). Theoretical Modeling and Biological Laws. Philosophy of Science 63 (3):35.
    Recent controversy over the existence of biological laws raises questions about the cognitive aims of theoretical modeling in that science. If there are no laws for successful theoretical models to approximate, then what is it that successful theories do? One response is to regard theoretical models as tools. But this instrumental reading cannot accommodate the explanatory role that theories are supposed to play. Yet accommodating the explanatory function, as articulated by Brandon and Sober for example, seems to involve us once (...)
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  35. Gregory Cooper (1990). The Explanatory Tools of Theoretical Population Biology. PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1990:165 - 178.
    What is the role (or roles) of mathematical theory in ecology and evolutionary biology? How does the construction of such theory advance our understanding? The lack of clear answers to this pair of questions has been a source of controversy both within the sciences themselves, and in the philosophical discussions of these sciences as well. In an attempt to shed some light on these issues, I look at what some biologists have had to say on the matter and at some (...)
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  36. Gregory Cooper (1988). Fitness and Explanation. PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1988:207 - 215.
    Although consensus appears to be on the horizon, the foundations of the theory of natural selection remain a matter of controversy. This paper looks at two recent challenges to the emerging "received view" of this theory. It argues that different views of the nature of scientific explanation are playing a pivotal role in the debates. Do explanations in biology fit the covering-law paradigm? What are the explanatory laws of biology like? Until agreement is reached on these fundamental questions, there is (...)
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  37. A. Brito Da Cunha (1991). Commentary on the Paper by HC Byerly and RE Michod,“Fitness and Evolutionary Explanation”. Biology and Philosophy 6 (1):23-27.
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  38. James L. Dannemiller (2002). Lack of Evidentiary Criteria for Exaptations? Behavioral and Brain Sciences 25 (4):512-513.
    Andrews et al. criticize Gould and colleagues for (1) failing to provide evidentiary criteria for accepting exaptationist alternatives to adaptationist explanations, and (2) seeing exaptations and spandrels as being far more frequent than adaptations in the evolutionary history of modern humans. I argue that the first of these criticisms is wrong, and the second reflects a bias for the classical version of Darwinian evolutionary theory, which Gould was trying to expand by proposing concepts like exaptation and spandrels.
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  39. Michel Delsol & Janine Flatin (1991). Qu'est-Ce Qu'une Grande Theorie Biologique? Acta Biotheoretica 39 (3-4):363-373.
    La parution récente en français du livre de M. Denton : “Evolution. Une théorie en crise” , qui traite des theories explicatives actuelles de l'évolution, nous amine à rappeler les caracteres généraux des grandes theories biologiques et à présenter une critique sommaire du livre en question.La science West pas une simple accumulation de connaissances. Le scientifique ne doit pas se contenter de decrire et de mesurer des faits. Son but eat d'essayer de les relier et de construire des théories qui (...)
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  40. Lane DesAutels (2010). Sober and Elgin on Laws of Biology: A Critique. [REVIEW] Biology and Philosophy 25 (2):249-256.
    In this short discussion note, I discuss whether any of the generalizations made in biology should be construed as laws. Specifically, I examine a strategy offered by Elliot Sober ( 1997 ) and supported by Mehmet Elgin ( 2006 ) to reformulate certain biological generalizations so as to eliminate their contingency, thereby allowing them to count as laws. I argue that this strategy entails a conception of laws that is unacceptable on two counts: (1) Sober and Elgin’s approach allows the (...)
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  41. Eric Desjardins (2011). Reflections on Path Dependence and Irreversibility: Lessons From Evolutionary Biology. Philosophy of Science 78 (5):724-738.
  42. T. E. Dickins & R. A. Barton (2013). Reciprocal Causation and the Proximate–Ultimate Distinction. Biology and Philosophy 28 (5):747-756.
    Laland and colleagues have sought to challenge the proximate–ultimate distinction claiming that it imposes a unidirectional model of causation, is limited in its capacity to account for complex biological phenomena, and hinders progress in biology. In this article the core of their argument is critically analyzed. It is claimed that contrary to their claims Laland et al. rely upon the proximate–ultimate distinction to make their points and that their alternative conception of reciprocal causation refers to phenomena that were already accounted (...)
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  43. Mauro Dorato (2012). Mathematical Biology and the Existence of Biological Laws. In D. Dieks, S. Hartmann, T. Uebel & M. Weber (eds.), Probabilities, Laws and Structure. Springer.
    An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main aim is to (...)
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  44. Mauro Dorato (2012). Mathematical Biology and the Existence of Biological Laws. In DieksD (ed.), Probabilities, Laws and Structure. Springer.
    An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main aim is to (...)
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  45. Jan Doroszewski & Andrzej Delegacz (1988). Model Structure of a Fragment of Biological Knowledge (Cell Motility). Acta Biotheoretica 37 (3-4):237-266.
    The aim of the study is to contribute to a better understanding of some aspects of the structure of biological knowledge and to make clearer to what extent the methods of reasoning may be useful in this field when only qualitative information is available. A fragment of biological knowledge (theory of cell motility) is analysed from the logico-methodological point of view as a coherent system and the possibility of its formal representation is investigated. The analysis is based on distinguishing the (...)
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  46. P. Dullemeijer (1972). Explanation in Morphology. Acta Biotheoretica 21 (3-4):260-273.
    In biology, and particularly in morphology, various types of explanation are found,e.g. causal, teleological, historical, etc.In this article an attempt has been made to analyse the relations between the various explanations to strive for an encompassing explanatory theory.The general structure of the explanatory theories appeared to be very similar, but the terms defining the phenomena and the types of the relations within the theories differ. To obtain a unifying theory it is necessary to develop methods to connect or transform the (...)
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  47. John Dupré (2010). It is Not Possible to Reduce Biological Explanations to Explanations in Chemistry and/or Physics. In Francisco José Ayala & Robert Arp (eds.), Contemporary Debates in Philosophy of Biology. Wiley-Blackwell Pub..
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  48. Mehmet Elgin (2010). Mathematical Models, Explanation, Laws, and Evolutionary Biology. History and Philosophy of the Life Sciences 32 (4).
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  49. Mehmet Elgin (2006). There May Be Strict Empirical Laws in Biology, After All. Biology and Philosophy 21 (1):119-134.
    This paper consists of four parts. Part 1 is an introduction. Part 2 evaluates arguments for the claim that there are no strict empirical laws in biology. I argue that there are two types of arguments for this claim and they are as follows: (1) Biological properties are multiply realized and they require complex processes. For this reason, it is almost impossible to formulate strict empirical laws in biology. (2) Generalizations in biology hold contingently but laws go beyond describing contingencies, (...)
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  50. Christopher Eliot (2007). Method and Metaphysics in Clements's and Gleason's Ecological Explanations. Studies in History and Philosophy of Science Part C 38 (1):85-109.
    To generate explanatory theory, ecologists must wrestle with how to represent the extremely many, diverse causes behind phenomena in their domain. Early twentieth-century plant ecologists Frederic E. Clements and Henry A. Gleason provide a textbook example of different approaches to explaining vegetation, with Clements allegedly committed, despite abundant exceptions, to a law of vegetation, and Gleason denying the law in favor of less organized phenomena. However, examining Clements's approach to explanation reveals him not to be expressing a law, and instead (...)
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