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Explanation of Molecular Processes without Tracking Mechanism Operation

Published online by Cambridge University Press:  01 January 2022

Ingo Brigandt
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Abstract

Philosophical discussions of systems biology have enriched the notion of mechanistic explanation by pointing to the role of mathematical modeling. However, such accounts still focus on explanation in terms of tracking a mechanism’s operation across time (by means of mental or computational simulation). My contention is that there are explanations of molecular systems in which the explanatory understanding does not consist in tracking a mechanism’s operation and productive continuity. I make this case by a discussion of bifurcation analysis in dynamical systems, articulating the distinctive way in which explanatory understanding is provided, especially about the reversibility or irreversibility of molecular processes.

Type
Research Article
Information
Philosophy of Science , Volume 85 , Issue 5 , December 2018 , pp. 984 - 997
Copyright
Copyright © The Philosophy of Science Association

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Footnotes

†

Earlier versions of this article have been presented to audiences at S-ANU 2015, ISHPSSB 2015, CSHPS 2016, and PSA 2016. Special thanks go to Arnon Levy and Bill Bechtel for submitting the PSA 2016 symposium proposal. I am also grateful to Arnon Levy and two reviewers for comments on a written version of this article. The work on this article was supported by the Social Sciences and Humanities Research Council of Canada (Insight Grant 435-2016-0500).

References

Bechtel, William. 2010. “The Downs and Ups of Mechanistic Research: Circadian Rhythm Research as an Exemplar.” Erkenntnis 73:313–28.CrossRefGoogle Scholar
Bechtel, William 2011. “Mechanism and Biological Explanation.” Philosophy of Science 78:533–57.CrossRefGoogle Scholar
Bechtel, William 2012. “Understanding Endogenously Active Mechanisms: A Scientific and Philosophical Challenge.” European Journal for Philosophy of Science 2:233–48.CrossRefGoogle Scholar
Bechtel, William, and Abrahamsen, Adele. 2005. “Explanation: A Mechanist Alternative.” Studies in History and Philosophy of Biological and Biomedical Sciences 36:421–41.CrossRefGoogle ScholarPubMed
Bechtel, William, and Abrahamsen, Adele 2010. “Dynamic Mechanistic Explanation: Computational Modeling of Circadian Rhythms as an Exemplar for Cognitive Science.” Studies in History and Philosophy of Science 41:321–33.CrossRefGoogle ScholarPubMed
Braillard, Pierre-Alain. 2010. “Systems Biology and the Mechanistic Framework.” History and Philosophy of the Life Sciences 32:43–62.Google ScholarPubMed
Brigandt, Ingo. 2013. “Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation.” Studies in History and Philosophy of Biological and Biomedical Sciences 44:477–92.CrossRefGoogle ScholarPubMed
Brigandt, Ingo 2015. “Evolutionary Developmental Biology and the Limits of Philosophical Accounts of Mechanistic Explanation.” In Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences, ed. Braillard, Pierre-Alain and Malaterre, Christophe, 135–73. Dordrecht: Springer.Google Scholar
Brigandt, Ingo, Green, Sara, and O’Malley, Maureen A.. 2017. “Systems Biology and Mechanistic Explanation.” In The Routledge Handbook of Mechanisms and Mechanical Philosophy, ed. Glennan, Stuart and Illari, Phyllis, 362–74. New York: Routledge.Google Scholar
Chen, Katherine C., Csikasz-Nagy, Attila, Gyorffy, Bela, Val, John, Novak, Bela, and Tyson, John J.. 2000. “Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle.” Molecular Biology of the Cell 11:369–91.CrossRefGoogle ScholarPubMed
Craver, Carl F., and Darden, Lindley. 2013. In Search of Mechanisms: Discoveries across the Life Sciences. Chicago: University of Chicago Press.CrossRefGoogle Scholar
Eissing, Thomas, Conzelmann, Holger, Gilles, Ernst D., Allgöwer, Frank, Bullinger, Eric, and Scheurich, Peter. 2004. “Bistability Analyses of a Caspase Activation Model for Receptor-Induced Apoptosis.” Journal of Biological Chemistry 279:36892–7.CrossRefGoogle ScholarPubMed
Ferrell, James E. Jr. 2012. “Bistability, Bifurcations, and Waddington’s Epigenetic Landscape.” Current Biology 22:R458–R466.CrossRefGoogle ScholarPubMed
Green, Sara, Şerban, Maria, Scholl, Raphael, Jones, Nicholaos, Brigandt, Ingo, and Bechtel, William. 2018. “Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.” Synthese 195 (4): 1751–77..CrossRefGoogle Scholar
Huneman, Philippe. 2010. “Topological Explanations and Robustness in Biological Sciences.” Synthese 177:213–45.CrossRefGoogle Scholar
Huneman, Philippe 2018. “Outlines of a Theory of Structural Explanations.” Philosophical Studies 175 (3): 665–702..CrossRefGoogle Scholar
Issad, Tarik, and Malaterre, Christophe. 2015. “Are Dynamic Mechanistic Explanations Still Mechanistic?” In Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences, ed. Braillard, Pierre-Alain and Malaterre, Christophe, 265–92. Dordrecht: Springer.Google Scholar
Legewie, Stefan, Blüthgen, Nils, and Herzel, Hanspeter. 2006. “Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability.” PLoS Computational Biology 2:e120.CrossRefGoogle ScholarPubMed
Levy, Arnon, and Bechtel, William. 2013. “Abstraction and the Organization of Mechanisms.” Philosophy of Science 80:241–61.CrossRefGoogle Scholar
Levy, Arnon, and Bechtel, William 2016. “Towards Mechanism 2.0: Expanding the Scope of Mechanistic Explanation.” Paper presented at the Biennial Meeting of the Philosophy of Science Association, Atlanta, November 3–6. http://philsci-archive.pitt.edu/id/eprint/12567.Google Scholar
Novak, Bela, Csikasz-Nagy, Attila, Gyorffy, Bela, Nasmyth, Kim, and Tyson, John J.. 1998. “Model Scenarios for Evolution of the Eukaryotic Cell Cycle.” Philosophical Transactions of the Royal Society B 353:2063–76.CrossRefGoogle ScholarPubMed
Sterelny, Kim. 1996. “Explanatory Pluralism in Evolutionary Biology.” Biology and Philosophy 11:193–214.CrossRefGoogle Scholar