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  1. On the Limits of Causal Modeling: Spatially-Structurally Complex Biological Phenomena.Marie I. Kaiser - 2016 - Philosophy of Science 83 (5):921-933.
    This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models is due (...)
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  • A Causal Bayes Net Analysis of Glennan’s Mechanistic Account of Higher-Level Causation.Alexander Gebharter - 2022 - British Journal for the Philosophy of Science 73 (1):185-210.
    One of Stuart Glennan's most prominent contributions to the new mechanist debate consists in his reductive analysis of higher-level causation in terms of mechanisms (Glennan, 1996). In this paper I employ the causal Bayes net framework to reconstruct his analysis. This allows for specifying general assumptions which have to be satis ed to get Glennan's approach working. I show that once these assumptions are in place, they imply (against the background of the causal Bayes net machinery) that higher-level causation indeed (...)
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  • A Modeling Approach for Mechanisms Featuring Causal Cycles.Alexander Gebharter & Gerhard Schurz - 2016 - Philosophy of Science 83 (5):934-945.
    Mechanisms play an important role in many sciences when it comes to questions concerning explanation, prediction, and control. Answering such questions in a quantitative way requires a formal represention of mechanisms. Gebharter (2014) suggests to represent mechanisms by means of one or more causal arrows of an acyclic causal net. In this paper we show how this approach can be extended in such a way that it can also be fruitfully applied to mechanisms featuring causal feedback.
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  • Combining Causal Bayes Nets and Cellular Automata: A Hybrid Modelling Approach to Mechanisms.Alexander Gebharter & Daniel Koch - 2021 - British Journal for the Philosophy of Science 72 (3):839-864.
    Causal Bayes nets (CBNs) can be used to model causal relationships up to whole mechanisms. Though modelling mechanisms with CBNs comes with many advantages, CBNs might fail to adequately represent some biological mechanisms because—as Kaiser (2016) pointed out—they have problems with capturing relevant spatial and structural information. In this paper we propose a hybrid approach for modelling mechanisms that combines CBNs and cellular automata. Our approach can incorporate spatial and structural information while, at the same time, it comes with all (...)
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  • Intervening on Time Derivatives.Toby Friend - 2021 - Studies in History and Philosophy of Science Part A 89:74-83.
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  • From Interventions to Mechanistic Explanations.Tudor Baetu - 2016 - Synthese 193 (10).
    An important strategy in the discovery of biological mechanisms involves the piecing together of experimental results from interventions. However, if mechanisms are investigated by means of ideal interventions, as defined by James Woodward and others, then the kind of information revealed is insufficient to discriminate between modular and non-modular causal contributions. Ideal interventions suffice for constructing webs of causal dependencies that can be used to make some predictions about experimental outcomes, but tell us little about how causally relevant factors are (...)
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  • The Compatibility of Differential Equations and Causal Models Reconsidered.Wes Anderson - 2020 - Erkenntnis 85 (2):317-332.
    Weber argues that causal modelers face a dilemma when they attempt to model systems in which the underlying mechanism operates according to some set of differential equations. The first horn is that causal models of these systems leave out certain causal effects. The second horn is that causal models of these systems leave out time-dependent derivatives, and doing so distorts reality. Either way causal models of these systems leave something important out. I argue that Weber’s reasons for thinking causal modeling (...)
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  • Philosophy of Developmental Biology.Marcel Weber - 2022 - Cambridge: Cambridge University Press.
    The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...)
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