Mechanist idealisation in systems biology
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Mechanist idealisation in systems biology Dingmar van Eck1,2 · Cory Wright3 Received: 28 February 2019 / Accepted: 28 July 2020 © Springer Nature B.V. 2020
Abstract This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering heat shock—the heat shock response (HSR) system—in Escherichia coli (E. coli) bacteria. This research also reinforces a more general lesson: ontic constraint accounts in the literature on mechanistic explanation provide insufficiently informative normative appraisals of mechanistic models. We close by outlining an alternative view on the explanatory norms governing mechanistic representation. Keywords Idealisation · Mechanistic model · Heat shock response · Systems biology · Mechanistic explanation
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Dingmar van Eck [email protected]; [email protected] Cory Wright [email protected]
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Department of Philosophy and Moral Sciences, Centre for Logic and Philosophy of Science, Ghent University, Blandijnberg 2, 9000 Ghent, Belgium
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Department of Philosophy, Institute for Logic, Language and Computation, University of Amsterdam, Oude Turfmarkt 143, 1012 GC Amsterdam, The Netherlands
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Department of Philosophy, California State University Long Beach, Long Beach, USA
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Synthese
1 Explanatory idealisation 1.1 Introduction Idealisations abound in scientific practice, and there are many accounts of them available. One such account, which is predominant in the literature on scientific explanation, may be called the ‘misrepresent irrelevancies’ account (MIA) of idealisation (see Mäki 1992, 2009; Nowak 1980). According to MIA, the main function of idealizations is to highlight explanatorily irrelevancies. While MIA is one among many accounts of idealisations, there is a paucity of specifically mechanistic analyses of idealisation in scientific modelling and explanation. Among the few on offer is a recent one from Glennan (2017), who harnesses MIA because of its putative use in constructing general mechanistic explanations. Glennan develops this application as follows: (1) features that differ from case to case or from token system to system are misrepresented, such that (2) these idealisations make salient that those (misrepresented) features have no significant explanatory import in the general explanations that are sought; (3) deploying idealisations is then a means to ‘help us find generality in a world of mechanisms that are ultimately particular, localized, and heterogeneous’ (Glennan 2017: p. 83). While the application of
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