18 found
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  1.  57
    Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.Sara Green, Maria Şerban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel - 2018 - Synthese 195 (4):1751-1777.
    The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from (...)
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  2. The Proximate–Ultimate Distinction and Evolutionary Developmental Biology: Causal Irrelevance Versus Explanatory Abstraction.Massimo Pigliucci & Raphael Scholl - 2015 - Biology and Philosophy 30 (5):653-670.
    Mayr’s proximate–ultimate distinction has received renewed interest in recent years. Here we discuss its role in arguments about the relevance of developmental to evolutionary biology. We show that two recent critiques of the proximate–ultimate distinction fail to explain why developmental processes in particular should be of interest to evolutionary biologists. We trace these failures to a common problem: both critiques take the proximate–ultimate distinction to neglect specific causal interactions in nature. We argue that this is implausible, and that the distinction (...)
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  3.  6
    The Philosophy of Historical Case Studies.Raphael Scholl & Tilman Sauer (eds.) - 2016 - Springer.
    This volume collects reflections on the role of philosophy in case studies in the history of science. Case studies have played a prominent role in recent history and philosophy of science. They have been used to illustrate, question, explore, or explicate philosophical points of view. Even if not explicitly so, historical narratives are always guided by philosophical background assumptions. But what happens if different philosophies lead to different narratives of the same historical episodes? Can historical case studies decide between competing (...)
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  4. Presume It Not: True Causes in the Search for the Basis of Heredity.Aaron Novick & Raphael Scholl - 2017 - British Journal for the Philosophy of Science (1):axy001.
    Kyle Stanford has recently given substance to the problem of unconceived alternatives, which challenges the reliability of inference to the best explanation (IBE) in remote domains of nature. Conjoined with the view that IBE is the central inferential tool at our disposal in investigating these domains, the problem of unconceived alternatives leads to scientific anti-realism. We argue that, at least within the biological community, scientists are now and have long been aware of the dangers of IBE. We re-analyze the nineteenth-century (...)
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  5.  87
    Causal Inference, Mechanisms, and the Semmelweis Case.Raphael Scholl - 2013 - Studies in History and Philosophy of Science Part A 44 (1):66-76.
    Semmelweis’s discovery of the cause of puerperal fever around the middle of the 19th century counts among the paradigm cases of scientific discovery. For several decades, philosophers of science have used the episode to illustrate, appraise and compare views of proper scientific methodology.Here I argue that the episode can be profitably reexamined in light of two cognate notions: causal reasoning and mechanisms. Semmelweis used several causal reasoning strategies both to support his own and to reject competing hypotheses. However, these strategies (...)
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  6.  63
    Towards a Methodology for Integrated History and Philosophy of Science.Raphael Scholl & Tim Räz - 2016 - In Tim Räz & Raphael Scholl (eds.), The Philosophy of Historical Case Studies. Springer Verlag.
  7.  64
    Modeling Causal Structures: Volterra’s Struggle and Darwin’s Success.Raphael Scholl & Tim Räz - 2013 - European Journal for Philosophy of Science 3 (1):115-132.
    The Lotka–Volterra predator-prey-model is a widely known example of model-based science. Here we reexamine Vito Volterra’s and Umberto D’Ancona’s original publications on the model, and in particular their methodological reflections. On this basis we develop several ideas pertaining to the philosophical debate on the scientific practice of modeling. First, we show that Volterra and D’Ancona chose modeling because the problem in hand could not be approached by more direct methods such as causal inference. This suggests a philosophically insightful motivation for (...)
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  8.  41
    Scenes From a Marriage: On the Confrontation Model of History and Philosophy of Science.Raphael Scholl - 2018 - Journal of the Philosophy of History 12 (2):212-238.
    According to the "confrontation model," integrated history and philosophy of science operates like an empirical science. It tests philosophical accounts of science against historical case studies much like other sciences test theory against data. However, the confrontation model's critics object that historical facts can neither support generalizations nor genuinely test philosophical theories. Here I argue that most of the model's defects trace to its usual framing in terms of two problematic accounts of empirical inference: the hypothetico-deductive method and enumerative induction. (...)
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  9.  34
    Discovery of Causal Mechanisms: Oxidative Phosphorylation and the Calvin–Benson Cycle.Raphael Scholl & Kärin Nickelsen - 2015 - History and Philosophy of the Life Sciences 37 (2):180-209.
    We investigate the context of discovery of two significant achievements of twentieth century biochemistry: the chemiosmotic mechanism of oxidative phosphorylation and the dark reaction of photosynthesis. The pursuit of these problems involved discovery strategies such as the transfer, recombination and reversal of previous causal and mechanistic knowledge in biochemistry. We study the operation and scope of these strategies by careful historical analysis, reaching a number of systematic conclusions: even basic strategies can illuminate “hard cases” of scientific discovery that go far (...)
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  10.  9
    Historical Case Studies: The “Model Organisms” of Philosophy of Science.Samuel Schindler & Raphael Scholl - forthcoming - Erkenntnis:1-20.
    Philosophers use historical case studies to support wide-ranging claims about science. This practice is often criticized as problematic. In this paper we suggest that the function of case studies can be understood and justified by analogy to a well-established practice in biology: the investigation of model organisms. We argue that inferences based on case studies are no more problematic than inferences from model organisms to larger classes of organisms in biology. We demonstrate our view in detail by reference to a (...)
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  11.  41
    Inference to the Best Explanation in the Catch-22: How Much Autonomy for Mill’s Method of Difference?Raphael Scholl - 2015 - European Journal for Philosophy of Science 5 (1):89-110.
    In his seminal Inference to the Best Explanation, Peter Lipton adopted a causal view of explanation and a broadly Millian view of how causal knowledge is obtained. This made his account vulnerable to critics who charged that Inference to the Best Explanation is merely a dressed-up version of Mill’s methods, which in the critics’ view do the real inductive work. Lipton advanced two arguments to protect Inference to the Best Explanation against this line of criticism: the problem of multiple differences (...)
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  12.  20
    Discovery of Causal Mechanisms: Oxidative Phosphorylation and the Calvin–Benson Cycle.Raphael Scholl & Kärin Nickelsen - 2015 - History and Philosophy of the Life Sciences 37 (2):180-209.
    We investigate the context of discovery of two significant achievements of twentieth century biochemistry: the chemiosmotic mechanism of oxidative phosphorylation and the dark reaction of photosynthesis. The pursuit of these problems involved discovery strategies such as the transfer, recombination and reversal of previous causal and mechanistic knowledge in biochemistry. We study the operation and scope of these strategies by careful historical analysis, reaching a number of systematic conclusions: even basic strategies can illuminate “hard cases” of scientific discovery that go far (...)
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  13.  5
    Unwarranted Assumptions: Claude Bernard and the Growth of the Vera Causa Standard.Raphael Scholl - 2020 - Studies in History and Philosophy of Science Part A 82:120-130.
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  14.  19
    Spot the Difference: Causal Contrasts in Scientific Diagrams.Raphael Scholl - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 60:77-87.
    An important function of scientific diagrams is to identify causal relationships. This commonly relies on contrasts that highlight the effects of specific difference-makers. However, causal contrast diagrams are not an obvious and easy to recognize category because they appear in many guises. In this paper, four case studies are presented to examine how causal contrast diagrams appear in a wide range of scientific reports, from experimental to observational and even purely theoretical studies. It is shown that causal contrasts can be (...)
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  15.  16
    Alex Rosenberg and Robert Arp : Philosophy of Biology: An Anthology: Wiley-Blackwell, Chichester, 2010, Ix + 464 Pp, ISBN: 978-1-4051-8316-1.Raphael Scholl - 2013 - Acta Biotheoretica 61 (2):285-288.
  16.  36
    Confessions of a Complexity Skeptic.Raphael Scholl - unknown
    Three objections to Max Urchs's paper on complexity are discussed. First, Urchs's macroeconomic illustrations of the benefits of complexity thinking are open to more conventional interpretations. Second, Urchs formulates a thesis concerning the relationship between science and society which is untenable if taken as a historical claim and insufficiently developed if taken as a metaphor. Third, methodological problems in history and philosophy of science plague Urchs's discussion of neuroscience.
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  17.  50
    Elliott Sober: Did Darwin Write the Origin Backwards? Philosophical Essays on Darwin’s Theory: Prometheus Books, Amherst, NY, 2011, 230 Pp, ISBN 978-1-61614-230-8.Raphael Scholl - 2012 - Acta Biotheoretica 60 (3):323-328.
    Elliott Sober: Did Darwin Write the Origin Backwards? Philosophical Essays on Darwin’s Theory Content Type Journal Article Category Book Review Pages 1-6 DOI 10.1007/s10441-012-9151-7 Authors Raphael Scholl, History and Philosophy of Science, Institute of Philosophy, University of Bern, Länggassstr. 49a, 3012 Bern, Switzerland Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342.
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  18. Introduction.Raphael Scholl & Tilman Sauer - 2016 - In Raphael Scholl & Tilman Sauer (eds.), The Philosophy of Historical Case Studies. Springer.
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