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 (...) the investigation of organizational properties of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological complexity. (shrink)

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 (...) should instead be understood in the context of explanatory abstractions in complete causal models of evolutionary change. Once the debate is reframed in this way, the proximate–ultimate distinction’s role in arguments against the theoretical significance of evo-devo is seen to rely on a generally implicit premise: that the variation produced by development is abundant, small and undirected. We show that a “lean version” of the proximate–ultimate distinction can be maintained even when this isotropy assumption does not hold. Finally, we connect these considerations to biological practice. We show that the investigation of developmental constraints in evolutionary transitions has long relied on a methodology which foregrounds the explanatory role of developmental processes. It is, however, entirely compatible with the lean version of the proximate–ultimate distinction. (shrink)

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 (...) study of inheritance and development (Stanford’s case study) and extend it into the twentieth century, focusing in particular on both classical Mendelian genetics and the studies by Avery et al. on the chemical nature of the hereditary substance. Our extended case studies show the preference of the biological community for a different methodological standard: the vera causa ideal, which requires that purported causes be shown on non-explanatory grounds to exist and be competent to produce their effects. On this basis, we defend a prospective realism about the biological sciences. (shrink)

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 (...) philosophical viewpoints? What are the criteria that a case study has to fulfill in order to be philosophically relevant? Bringing together leading practitioners in the fields of history and philosophy of the physical and the life sciences, this volume addresses this methodological problem and proposes ways of rendering explicit philosophical assumptions of historical work. (shrink)

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 (...) have gone unappreciated in the existing literature. I show that a causal reasoning approach makes sense of the multitude of tables in Semmelweis’s main text, which in later editions were often abridged because they appeared redundant.Moreover, the existing literature tends to focus on Semmelweis’s clinical intervention and on the extent to which it alone confirms his theoretical conclusions. This neglects Semmelweis’s efforts to show by animal experiments that his clinical results are in agreement with a demonstrable mechanism of puerperal fever pathogenesis. I argue that the full evidential force of Semmelweis’s argument can only be appreciated if both his clinical and his laboratory investigations are taken into account. (shrink)

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-analyse the nineteenth-century (...) study of inheritance and development (Stanford’s case study) and extend it into the twentieth century, focusing in particular on both classical Mendelian genetics and the studies by Avery et al. on the chemical nature of the hereditary substance. Our extended case studies show the preference of the biological community for a different methodological standard: the vera causa ideal, which requires that purported causes be shown on non-explanatory grounds to exist and be competent to produce their effects. On this basis, we defend a prospective realism about the biological sciences. 1 Introduction2 Stanford on Unconceived Alternatives3 Pangenesis: A Re-analysis4 The Vera Causa Ideal I: Negative Aspect5 Rendering Heredity Accessible6 The Vera Causa Ideal II: Positive Aspect7 Implications for Scientific Realism8 Conclusion. (shrink)

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 (...) choosing the strategy of modeling. Second, we show that the development of the model follows a trajectory from a “how possibly” to a “how actually” model. We discuss how and to what extent Volterra and D’Ancona were able to advance their model along that trajectory. It turns out they were unable to establish that their model was fully applicable to any system. Third, we consider another instance of model-based science: Darwin’s model of the origin and distribution of coral atolls in the Pacific Ocean. Darwin argued more successfully that his model faithfully represents the causal structure of the target system, and hence that it is a “how actually” model. (shrink)

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. (...) This framing can be taken to suggest an unprofitable one-off confrontation between particular historical facts and general philosophical theories. I outline more recent accounts of empirical inquiry, which describe an iterative back-and-forth movement between concrete empirical exemplars to their abstract descriptions. Reframed along similar lines, the confrontation model continues to offer both conceptual insight and practical guidance for a naturalized philosophy of science. (shrink)

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 (...) and the problem of inferred differences. Lipton claimed that these two problems show Mill’s method of difference to be largely unworkable unless it is embedded in an explanationist framework. Here I consider both arguments as well as the best Millian defense against them. Since the existing Millian defense is only partially successful, I will develop a new and improved account. As an integral part of the argument, I show that my solutions to the problems of multiple and inferred differences offer new insight into Lipton’s main case study: Ignaz Semmelweis’s discovery of the cause of childbed fever. I conclude that the method of difference can overcome Lipton’s challenges outside an explanationist framework. (shrink)

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 (...) case study with a long history: Semmelweis’s discovery of the cause of childbed fever. (shrink)

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 (...) beyond simple extrapolation or analogy; the causal–mechanistic approach to discovery permits a middle course between the extremes of a completely substrate-neutral and a completely domain-specific view of scientific discovery; the existing literature on mechanism discovery underemphasizes the role of combinatorial approaches in defining and exploring search spaces of possible problem solutions; there is a subtle interplay between a fine-grained mechanistic and a more coarse-grained causal level of analysis, and both are needed to make discovery processes intelligible. (shrink)

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 (...) beyond simple extrapolation or analogy; the causal–mechanistic approach to discovery permits a middle course between the extremes of a completely substrate-neutral and a completely domain-specific view of scientific discovery; the existing literature on mechanism discovery underemphasizes the role of combinatorial approaches in defining and exploring search spaces of possible problem solutions; there is a subtle interplay between a fine-grained mechanistic and a more coarse-grained causal level of analysis, and both are needed to make discovery processes intelligible. (shrink)

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 (...) expressed in starkly different formats, including photographs of complexly visualized macromolecules as well as line graphs, bar graphs, or plots of state spaces. Despite surface differences, however, there is a measure of conceptual unity among such diagrams. In empirical studies they generally serve not only to infer and communicate specific causal claims, but also as evidence for them. The key data of some studies is given nowhere except in the diagrams. Many diagrams show multiple causal contrasts in order to demonstrate both that an effect exists and that the effect is specific -- that is, to narrowly circumscribe the phenomenon to be explained. In a large range of scientific reports, causal contrast diagrams reflect the core epistemic claims of the researchers. (shrink)

John Stuart Mills Wissenschaftstheorie wird von den meisten Autoren mit wenig Wohlwollen betrachtet. Mills Vorstellungen der Ziele und Methoden der empirischen Wissenschaften, die er in seinem ASystem of Logic darstellte, werden sowohl für einfältig als auch für realitätsfern gehalten. Einfältig, weil die von Mill skizzierten empirischen Methoden bei näherer philosophischer Betrachtung unschlüssig und kraftlos erscheinen. Realitätsfern, weil Mill angeblich die Vertrautheit mit der Geschichte und Praxis der Wissenschaften fehlte, die Voraussetzung für eine erfolgreiche philosophische Analyse gewesen wäre. Im Licht der (...) jüngeren Wissenschaftsforschung ist allerdings in vielen Punkten eine günstigere Beurteilung der Mill’schen Position möglich, als traditionellerweise angeboten wird. (shrink)

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.

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.