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  1. The Origins of Order: Self Organization and Selection in Evolution.Stuart A. Kauffman - 1993 - Oxford University Press.
    Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays an (...)
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  • (1 other version)Epistemische Konkurrenz zwischen Entwicklungsbiologie und Genetik um 1900: Traditionen, Begriffe, Kausalität. [REVIEW]Robert Meunier - 2016 - NTM Zeitschrift für Geschichte der Wissenschaften, Technik und Medizin 24 (2):141-167.
    Der Artikel führt den Begriff der epistemischen Konkurrenz ein. Im Gegensatz zu „wissenschaftliche Kontroverse“ beschreibt er eine Situation, in der sich zwei Forschungsfelder gegenseitig als mit demselben Bereich von Phänomen befasst wahrnehmen, wobei ihre methodischen Ansätze und theoretischen Erklärungen jedoch so unterschiedlich sind, dass ein offener Konflikt über die Wahrheit oder Falschheit bestimmter Aussagen oder die Genauigkeit in der Anwendung einer Methode nicht stattfindet. Nichtsdestotrotz streben beide Parteien danach, die maßgebliche Erklärung der entsprechenden Phänomene anzubieten. Indem die erweiterte Gemeinschaft der (...)
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  • Countering Kauffman with Connectionism: Two Views of Gene Regulation and the Fundamental Nature of Ontogeny.Roger Sansom - 2008 - British Journal for the Philosophy of Science 59 (2):169-200.
    Understanding the operation and evolution of gene regulation networks is critical to understanding ontogeny and evolution. According to Stuart Kauffman's view, (1) each cell type cycles through its own repeated pattern of gene expression, (2) the order of ontogeny is dependent on these cycles being short, and (3) evolution is possible because these cycles mutate gradually. This view of gene regulation reflects Kauffman's view that ontogeny is fundamentally the process of cells repeating cycles of activity. I criticize Kauffman's view of (...)
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  • Explanation: a mechanist alternative.William Bechtel & Adele Abrahamsen - 2005 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 36 (2):421-441.
    Explanations in the life sciences frequently involve presenting a model of the mechanism taken to be responsible for a given phenomenon. Such explanations depart in numerous ways from nomological explanations commonly presented in philosophy of science. This paper focuses on three sorts of differences. First, scientists who develop mechanistic explanations are not limited to linguistic representations and logical inference; they frequently employ diagrams to characterize mechanisms and simulations to reason about them. Thus, the epistemic resources for presenting mechanistic explanations are (...)
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  • Salmon's Paper.Henry E. Kyburg - 1965 - Philosophy of Science 32 (2):147-151.
    First, a comment on a pessimistic note: Salmon says we can't be sure there is any such thing as inductive inference: in demanding that some explanations have the form of correct inductive inferences, “we may be laying down a requirement which cannot be fulfilled.” To doubt that we can fulfill that requirement is to doubt that we can formalize inductive logic. It may be true, but why begin the fight by throwing in the sponge? It is also true that there (...)
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  • When integration fails: Prokaryote phylogeny and the tree of life.Maureen A. O’Malley - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4a):551-562.
    Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...)
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  • Repertoires: A post-Kuhnian perspective on scientific change and collaborative research.Rachel A. Ankeny & Sabina Leonelli - 2016 - Studies in History and Philosophy of Science Part A 60:18-28.
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  • The Metaphysical Foundations of Modern Physical Science.H. R. Smart & Edwin Arthur Burtt - 1926 - Philosophical Review 35 (6):589.
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  • The Architecture of Complexity.Herbert A. Simon - 1962 - Proceedings of the American Philosophical Society 106.
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  • (1 other version)Objectivity.Lorraine Daston & Peter Galison - 2007 - Cambridge, Mass.: Zone Books. Edited by Peter Galison.
    Objectivity has a history, and it is full of surprises. In Objectivity, Lorraine Daston and Peter Galison chart the emergence of objectivity in the mid-nineteenth-century sciences--and show how the concept differs from its alternatives, truth-to-nature and trained judgment. This is a story of lofty epistemic ideals fused with workaday practices in the making of scientific images. From the eighteenth through the early twenty-first centuries, the images that reveal the deepest commitments of the empirical sciences--from anatomy to crystallography--are those featured in (...)
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  • (1 other version)Calculating life? Duelling discourses in interdisciplinary systems biology.Jane Calvert & Joan H. Fujimura - 2011 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 42 (2):155-163.
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  • (1 other version)Interdisciplinary reflections: The case of physics and biology.Wilson C. K. Poon - 2011 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 42 (2):115-118.
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  • From molecules to systems: the importance of looking both ways.Alexander Powell & John Dupré - 2009 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 40 (1):54-64.
    Although molecular biology has meant different things at different times, the term is often associated with a tendency to view cellular causation as conforming to simple linear schemas in which macro-scale effects are specified by micro-scale structures. The early achievements of molecular biologists were important for the formation of such an outlook, one to which the discovery of recombinant DNA techniques, and a number of other findings, gave new life even after the complexity of genotype–phenotype
    relations had become apparent. Against this (...)
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  • (1 other version)What Is a Mechanism? A Counterfactual Account.James Woodward - 2002 - Philosophy of Science 69 (S3):S366-S377.
    This paper presents a counterfactual account of what a mechanism is. Mechanisms consist of parts, the behavior of which conforms to generalizations that are invariant under interventions, and which are modular in the sense that it is possible in principle to change the behavior of one part independently of the others. Each of these features can be captured by the truth of certain counterfactuals.
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  • Making Sense of Life.Evelyn Fox Keller - 2002 - Cambridge: Harvard University Press.
    What do biologists want? If, unlike their counterparts in physics, biologists are generally wary of a grand, overarching theory, at what kinds of explanation do biologists aim? A history of the diverse and changing nature of biological explanation in a particularly charged field, "Making Sense of Life" draws our attention to the temporal, disciplinary, and cultural components of what biologists mean, and what they understand, when they propose to explain life.
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  • Science as a Process: An Evolutionary Account of the Social and Conceptual Development of Science.David L. Hull - 1988 - University of Chicago Press.
    "Legend is overdue for replacement, and an adequate replacement must attend to the process of science as carefully as Hull has done. I share his vision of a serious account of the social and intellectual dynamics of science that will avoid both the rosy blur of Legend and the facile charms of relativism.... Because of [Hull's] deep concern with the ways in which research is actually done, Science as a Process begins an important project in the study of science. It (...)
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  • Discovering Complexity: Decomposition and Localization as Strategies in Scientific Research.William Bechtel & Robert C. Richardson - 2010 - Princeton.
    An analysis of two heuristic strategies for the development of mechanistic models, illustrated with historical examples from the life sciences. In Discovering Complexity, William Bechtel and Robert Richardson examine two heuristics that guided the development of mechanistic models in the life sciences: decomposition and localization. Drawing on historical cases from disciplines including cell biology, cognitive neuroscience, and genetics, they identify a number of "choice points" that life scientists confront in developing mechanistic explanations and show how different choices result in divergent (...)
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  • Toward a History of Epistemic Things: Synthesizing Proteins in the Test Tube.Hans-Jörg Rheinberger - 1997 - Stanford University Press.
    In this powerful work of conceptual and analytical originality, the author argues for the primacy of the material arrangements of the laboratory in the dynamics of modern molecular biology. In a post-Kuhnian move away from the hegemony of theory, he develops a new epistemology of experimentation in which research is treated as a process for producing epistemic things. A central concern of the book is the basic question of how novelty is generated in the empirical sciences. In addressing this question, (...)
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  • Discovering Complexity.William Bechtel, Robert C. Richardson & Scott A. Kleiner - 1996 - History and Philosophy of the Life Sciences 18 (3):363-382.
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  • Molecular Models of Life: Philosophical Papers on Molecular Biology.Sahotra Sarkar - 2004 - Bradford.
    Despite the transformation in biological practice and theory brought about by discoveries in molecular biology, until recently philosophy of biology continued to focus on evolutionary biology. When the Human Genome Project got underway in the late 1980s and early 1990s, philosophers of biology -- unlike historians and social scientists -- had little to add to the debate. In this landmark collection of essays, Sahotra Sarkar broadens the scope of current discussions of the philosophy of biology, viewing molecular biology as a (...)
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  • Towards philosophical foundations of Systems Biology: introduction.Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff - 2007 - In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Boston: Elsevier.
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  • (1 other version)More about metaphor.Max Black - 1977 - Dialectica 31 (3‐4):431-457.
    An elaboration and defense of the “interaction view of metaphor” introduced in the author's earlier study, “Metaphor” . Special attention is paid to the explication of the metaphors used in the earlier account.The topics discussed include: selection of the “targets” of the theory; classification of metaphors; how metaphorical statements work; relations between metaphors and similes; metaphorical thought; criteria of recognition; the “creative” aspects of metaphors; the ontological status of metaphors.Metaphors are found to be more closely connected with background models than (...)
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  • Scientific Change.Hanne Andersen & Brian Hepburn - 2013 - Internet Encyclopedia of Philosophy.
    Scientific Change How do scientific theories, concepts and methods change over time? Answers to this question have historical parts and philosophical parts. There can be descriptive accounts of the recorded differences over time of particular theories, concepts, and methods—what might be called the shape of scientific change. Many stories of scientific change attempt to give […].
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  • Towards a processual microbial ontology.Eric Bapteste & John Dupre - 2013 - Biology and Philosophy 28 (2):379-404.
    Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...)
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  • Science as Social Knowledge: Values and Objectivity in Scientific Inquiry.Helen E. Longino - 1990 - Princeton University Press.
    This is an important book precisely because there is none other quite like it.
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  • Mathematical Modeling in Biology: Philosophy and Pragmatics.Rasmus Grønfeldt Winther - 2012 - Frontiers in Plant Evolution and Development 2012:1-3.
    Philosophy can shed light on mathematical modeling and the juxtaposition of modeling and empirical data. This paper explores three philosophical traditions of the structure of scientific theory—Syntactic, Semantic, and Pragmatic—to show that each illuminates mathematical modeling. The Pragmatic View identifies four critical functions of mathematical modeling: (1) unification of both models and data, (2) model fitting to data, (3) mechanism identification accounting for observation, and (4) prediction of future observations. Such facets are explored using a recent exchange between two groups (...)
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  • (1 other version)Interdisciplinary reflections: The case of physics and biology.Wilson C. K. Poon - 2011 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 42 (2):115-118.
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  • (1 other version)Calculating life? Duelling discourses in interdisciplinary systems biology.Jane Calvert & Joan H. Fujimura - 2011 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 42 (2):155-163.
    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by (...)
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  • (1 other version)The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.S. J. Gould & R. C. Lewontin - 1994 - In Elliott Sober (ed.), Conceptual Issues in Evolutionary Biology. The Mit Press. Bradford Books. pp. 73-90.
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  • Three Kinds of Idealization.Michael Weisberg - 2007 - Journal of Philosophy 104 (12):639-659.
    Philosophers of science increasingly recognize the importance of idealization: the intentional introduction of distortion into scientific theories. Yet this recognition has not yielded consensus about the nature of idealization. e literature of the past thirty years contains disparate characterizations and justifications, but little evidence of convergence towards a common position.
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  • (1 other version)Paradigm change in evolutionary microbiology.Maureen A. O’Malley & Yan Boucher - 2005 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 36 (1):183-208.
    Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance to this (...)
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  • The sciences of the artificial.Herbert Alexander Simon - 1969 - [Cambridge,: M.I.T. Press.
    Continuing his exploration of the organization of complexity and the science of design, this new edition of Herbert Simon's classic work on artificial ...
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  • Aspects of scientific explanation.Carl G. Hempel - 1965 - In Carl Gustav Hempel (ed.), Aspects of Scientific Explanation and Other Essays in the Philosophy of Science. New York: The Free Press. pp. 504.
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  • (4 other versions)The Structure of Scientific Revolutions.Thomas Samuel Kuhn - 1962 - Chicago: University of Chicago Press. Edited by Otto Neurath.
    A scientific community cannot practice its trade without some set of received beliefs. These beliefs form the foundation of the "educational initiation that prepares and licenses the student for professional practice". The nature of the "rigorous and rigid" preparation helps ensure that the received beliefs are firmly fixed in the student's mind. Scientists take great pains to defend the assumption that scientists know what the world is like...To this end, "normal science" will often suppress novelties which undermine its foundations. Research (...)
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  • The Disorder of Things: Metaphysical Foundations of the Disunity of Science.John Dupré - 1993 - Harvard University Press.
    With this manifesto, John Dupré systematically attacks the ideal of scientific unity by showing how its underlying assumptions are at odds with the central conclusions of science itself.
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  • Causation in biology: Stability, specificity, and the choice of levels of explanation.James Woodward - 2010 - Biology and Philosophy 25 (3):287-318.
    This paper attempts to elucidate three characteristics of causal relationships that are important in biological contexts. Stability has to do with whether a causal relationship continues to hold under changes in background conditions. Proportionality has to do with whether changes in the state of the cause “line up” in the right way with changes in the state of the effect and with whether the cause and effect are characterized in a way that contains irrelevant detail. Specificity is connected both to (...)
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  • Complexity and Organization.William C. Wimsatt - 1972 - PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1972:67-86.
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  • Rethinking Scientific Change and Theory Comparison: Stabilities, Ruptures, Incommensurabilities?Lena Soler, Howard Sankey & Paul Hoyningen-Huene (eds.) - 2008 - Springer.
    The volume is a collection of essays devoted to the analysis of scientific change and stability. It explores the balance and tension that exist between commensurability and continuity on the one hand, and incommensurability and discontinuity on the other. Moreover, it discusses some central epistemological consequences regarding the nature of scientific progress, rationality and realism. In relation to these topics, it investigates a number of new avenues, and revisits some familiar issues, with a focus on the history and philosophy of (...)
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  • (1 other version)Scientific Explanation and the Causal Structure of the World.Wesley C. Salmon - 1984 - Princeton University Press.
    The philosophical theory of scientific explanation proposed here involves a radically new treatment of causality that accords with the pervasively statistical character of contemporary science. Wesley C. Salmon describes three fundamental conceptions of scientific explanation--the epistemic, modal, and ontic. He argues that the prevailing view is untenable and that the modal conception is scientifically out-dated. Significantly revising aspects of his earlier work, he defends a causal/mechanical theory that is a version of the ontic conception. Professor Salmon's theory furnishes a robust (...)
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  • Genesis and development of a scientific fact.Ludwik Fleck - 1979 - Chicago: University of Chicago Press. Edited by T. J. Trenn & R. K. Merton.
    The sociological dimension of science is studied using the discovery of the Wasserman reaction and its accidental application as a test for syphilis as a basis, ...
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  • (1 other version)An introduction to science and technology studies.Sergio Sismondo - 2004 - Malden, MA: Blackwell.
    The prehistory of science and technology studies -- The Kuhnian revolution -- Questioning functionalism in the sociology of science -- Stratification and discrimination -- The strong programme and the sociology of knowledge -- The social construction of scientific and technical realities -- Feminist epistemologies of science -- Actor-network theory -- Two questions concerning technology -- Studying laboratories -- Controversies -- Standardization and objectivity -- Rhetoric and discourse -- The unnaturalness of science and technology -- The public understanding of science -- (...)
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  • Making things happen: a theory of causal explanation.James F. Woodward - 2003 - New York: Oxford University Press.
    Woodward's long awaited book is an attempt to construct a comprehensive account of causation explanation that applies to a wide variety of causal and explanatory claims in different areas of science and everyday life. The book engages some of the relevant literature from other disciplines, as Woodward weaves together examples, counterexamples, criticisms, defenses, objections, and replies into a convincing defense of the core of his theory, which is that we can analyze causation by appeal to the notion of manipulation.
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  • Complexity: hierarchical structures and scaling in physics.R. Badii - 1997 - New York: Cambridge University Press. Edited by A. Politi.
    This is a comprehensive discussion of complexity as it arises in physical, chemical, and biological systems, as well as in mathematical models of nature. Common features of these apparently unrelated fields are emphasised and incorporated into a uniform mathematical description, with the support of a large number of detailed examples and illustrations. The quantitative study of complexity is a rapidly developing subject with special impact in the fields of physics, mathematics, information science, and biology. Because of the variety of the (...)
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  • Science in action: how to follow scientists and engineers through society.Bruno Latour - 1987 - Cambridge: Harvard University Press.
    In this book Bruno Latour brings together these different approaches to provide a lively and challenging analysis of science, demonstrating how social context..
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  • (4 other versions)The Structure of Scientific Revolutions.Thomas S. Kuhn - 1962 - Chicago, IL: University of Chicago Press. Edited by Ian Hacking.
    Thomas S. Kuhn's classic book is now available with a new index.
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  • (1 other version)Rethinking mechanistic explanation.Stuart Glennan - 2002 - Proceedings of the Philosophy of Science Association 2002 (3):S342-353.
    Philosophers of science typically associate the causal-mechanical view of scientific explanation with the work of Railton and Salmon. In this paper I shall argue that the defects of this view arise from an inadequate analysis of the concept of mechanism. I contrast Salmon's account of mechanisms in terms of the causal nexus with my own account of mechanisms, in which mechanisms are viewed as complex systems. After describing these two concepts of mechanism, I show how the complex-systems approach avoids certain (...)
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  • (1 other version)Reasoning in biological discoveries.Lindley Darden - manuscript
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  • Mechanisms and the nature of causation.Stuart S. Glennan - 1996 - Erkenntnis 44 (1):49--71.
    In this paper I offer an analysis of causation based upon a theory of mechanisms-complex systems whose internal parts interact to produce a system's external behavior. I argue that all but the fundamental laws of physics can be explained by reference to mechanisms. Mechanisms provide an epistemologically unproblematic way to explain the necessity which is often taken to distinguish laws from other generalizations. This account of necessity leads to a theory of causation according to which events are causally related when (...)
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  • Explanatory unification.Philip Kitcher - 1981 - Philosophy of Science 48 (4):507-531.
    The official model of explanation proposed by the logical empiricists, the covering law model, is subject to familiar objections. The goal of the present paper is to explore an unofficial view of explanation which logical empiricists have sometimes suggested, the view of explanation as unification. I try to show that this view can be developed so as to provide insight into major episodes in the history of science, and that it can overcome some of the most serious difficulties besetting the (...)
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  • Explanation and scientific understanding.Michael Friedman - 1974 - Journal of Philosophy 71 (1):5-19.
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