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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. 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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  6. Francisco J. Ayala (1998). Teleological Explanations Versus Teleology. History and Philosophy of the Life Sciences 20 (1):41 - 50.
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  7. Jonathan B. L. Bard (2008). Waddington's Legacy to Developmental and Theoretical Biology. Biological Theory 3 (3):188-197.
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  8. Gillian Barker, Eric Desjardins & Trevor Pearce (eds.) (2014). Entangled Life: Organism and Environment in the Biological and Social Sciences. Springer.
  9. 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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  10. 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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  11. Michael Baumgartner & Alexander Gebharter (forthcoming). Constitutive Relevance, Mutual Manipulability, and Fat-Handedness. British Journal for the Philosophy of Science.
    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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. Fred L. Bookstein (2009). Measurement, Explanation, and Biology: Lessons From a Long Century. Biological Theory 4 (1):6-20.
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  18. Stephen Boulter (2012). Contrastive Explanations in Evolutionary Biology. Ratio 25 (4):425-441.
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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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.
  24. 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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  25. Jack G. Chamberlain (1998). Editorial Comment: More on Scientific Reasoning. Bioessays 20 (4):355-355.
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  26. 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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  27. Christopher Clarke (forthcoming). Multi-Level Selection and the Explanatory Value of Mathematical Decompositions. British Journal for the Philosophy of Science.
    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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. Michel Delsol & Janine Flatin (1991). Qu'est-Ce Qu'une Grande Theorie Biologique? Acta Biotheoretica 39 (3-4).
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  34. 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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  35. Eric Desjardins (2011). Reflections on Path Dependence and Irreversibility: Lessons From Evolutionary Biology. Philosophy of Science 78 (5):724-738.
  36. 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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  37. 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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  38. Jan Doroszewski & Andrzej Delegacz (1988). Model Structure of a Fragment of Biological Knowledge (Cell Motility). Acta Biotheoretica 37 (3-4).
    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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  39. P. Dullemeijer (1972). Explanation in Morphology. Acta Biotheoretica 21 (3-4).
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  40. 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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  41. Mehmet Elgin (2010). Mathematical Models, Explanation, Laws, and Evolutionary Biology. History and Philosophy of the Life Sciences 32 (4).
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  42. 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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  43. 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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  44. Melinda Fagan (2012). Waddington Redux: Models and Explanation in Stem Cell and Systems Biology. Biology and Philosophy 27 (2):179-213.
    Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington’s landscape to triangulate between stem cell and systems approaches. This simple abstract model represents (...)
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  45. Peter Fazekas & Gergely Kertész (2011). Causation at Different Levels: Tracking the Commitments of Mechanistic Explanations. Biology and Philosophy 26 (3):365-383.
    This paper tracks the commitments of mechanistic explanations focusing on the relation between activities at different levels. It is pointed out that the mechanistic approach is inherently committed to identifying causal connections at higher levels with causal connections at lower levels. For the mechanistic approach to succeed a mechanism as a whole must do the very same thing what its parts organised in a particular way do. The mechanistic approach must also utilise bridge principles connecting different causal terms of different (...)
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  46. Mark Fedyk (2014). How (Not) to Bring Psychology and Biology Together. Philosophical Studies 1:1-19.
    Evolutionary psychologists often try to “bring together” biology and psychology by making predictions about what specific psychological mechanisms exist from theories about what patterns of behaviour would have been adaptive in the EEA for humans. This paper shows that one of the deepest methodological generalities in evolutionary biology—that proximate explanations and ultimate explanations stand in a many-to-many relation—entails that this inferential strategy is unsound. Ultimate explanations almost never entail the truth of any particular proximate hypothesis. But of course it does (...)
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  47. Carla Fehr, Sex and Explanatory Pluralism: Is It a Case of Causal Mechanism Versus Unifying Theories of Explanation?
    There is more than one explanation for the evolution of sexual reproduction. This paper investigates the possibility that this pluralism exists because these different explanations rely on intuitions provided by different philosophical theories of explanation, namely unifying views and causal mechanical views. I conclude that this is not the case.
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  48. John R. S. Fincham (2000). More on Popper and Biology: The Utility of Induction. Bioessays 22 (7):684-684.
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  49. Patrick Forber (2009). Spandrels and a Pervasive Problem of Evidence. Biology and Philosophy 24 (2):247-266.
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  50. L. R. Franklin-Hall, The Emperor's New Mechanisms.
    This paper argues that the increasingly dominant new mechanistic approach to scientific explanation, as developed to date, does not shed new light on explanatory practice. First, I systematize the explanatory account, one according to which explanations are mechanistic models that satisfy three desiderata: 1) they must represent causal relations, 2) describe the proper parts, and 3) depict the system at the right ‘level.’ Then I argue that even the most promising attempts to flesh out these constraints have fallen far short. (...)
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