Hostname: page-component-586b7cd67f-r5fsc Total loading time: 0 Render date: 2024-12-04T20:22:25.330Z Has data issue: false hasContentIssue false
  • English
  • Français

On the Limits of Causal Modeling: Spatially-Structurally Complex Biological Phenomena

Published online by Cambridge University Press:  01 January 2022

Marie I. Kaiser
Get access Rights & Permissions [Opens in a new window]

Abstract

This article examines the adequacy of causal graph theory as a tool for modeling biological phenomena. I argue that the causal graph approach reaches its limits when it comes to modeling biological phenomena that involve complex spatial and chemical-structural relations. Using a case study from molecular biology, I show why causal graph models fail to adequately represent and explain biological phenomena of this kind. The inadequacy of these models is due to their failure to include relevant spatial-structural information in a way that does not render the models nonexplanatory, unmanageable, or inconsistent with basic assumptions of causal graph theory.

Type
Adequacy of Causal Graphs and Bayes Networks
Information
Philosophy of Science , Volume 83 , Issue 5 , December 2016 , pp. 921 - 933
Copyright
Copyright © The Philosophy of Science Association

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

†

This paper arose from a collaboration with Marcel Weber during my time at the University of Geneva, and it profited much from our stimulating discussions. I also thank Benjamin Jantzen, Christopher Hitchcock, Lorenzo Casini, Alexander Gebharter, Maximilian Huber, and the members of my DFG Research Group “Causation and Explanation” for their helpful comments on earlier versions of the paper. This material is based on work supported by the German Research Foundation (DFG; FOR 1063).

References

Baumgartner, Michael, and Gebharter, Alexander. 2015. “Constitutive Relevance, Mutual Manipulability, and Fat-Handedness.” British Journal for the Philosophy of Science, published online February 20. doi:10.1093/bjps/axv003.CrossRefGoogle Scholar
Cai, Yu-Hang, and Huang, He. 2012. “Advances in the Study of Protein–DNA Interaction.” Amino Acids 43:1141–46.CrossRefGoogle Scholar
Casini, Lorenzo, Illari, Phyllis McKay, Russo, Federica, and Williamson, Jon. 2011. “Models for Prediction, Explanation and Control: Recursive Bayesian Networks.” Theoria 70 (1): 5–33.Google Scholar
Clarke, Brendan, Leuridan, Bert, and Williamson, Jon. 2014. “Modelling Mechanisms with Causal Cycles.” Synthese 191 (8): 1–31.CrossRefGoogle Scholar
Gebharter, Alexander, and Kaiser, Marie I.. 2014. “Causal Graphs and Biological Mechanisms.” In Explanation in the Special Sciences, ed. Kaiser, M. I., Scholz, Oliver R., Plenge, Daniel, and Hüttemann, Andreas, 55–85. Berlin: Springer.CrossRefGoogle Scholar
Harrison, Stephen C. 1991. “A Structural Taxonomy of DNA-Binding Domains.” Nature 353:715–19.CrossRefGoogle ScholarPubMed
Kaiser, Marie I. 2015. Reductive Explanation in the Biological Sciences. Cham: Springer.CrossRefGoogle Scholar
Pavletich, Nikola P., and Pabo, Carl O. 1991. “Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1A.” Science 252:809–17.CrossRefGoogle Scholar
Pearl, Judea. 2000. Causality: Models, Reasoning, and Inference. Cambridge: Cambridge University Press.Google Scholar
Rohs, Remo, Jin, Xiangshu, West, Sean M., Joshi, Rohit, Honig, Barry, and Mann, Richard S.. 2010. “Origins of Specificity in Protein–DNA Recognition.” Annual Review Biochemistry 79:233–69.CrossRefGoogle ScholarPubMed
Spirtes, Peter, Glymour, Clarke, and Scheines, Richard. 2000. Causation, Prediction, and Search. Cambridge, MA: MIT Press.Google Scholar
Stormo, Gary D., and Zhao, Yue. 2010. “Determining the Specificity of Protein–DNA Interactions.” Nature Reviews Genetics 11:751–60.CrossRefGoogle ScholarPubMed
Strauch, Mark A. 2001. “Protein–DNA Complexes: Specific.” In Encyclopedia of Life Sciences. Nature Publishing Group.Google Scholar
Weber, Marcel. 2016. “On the Incompatibility of Dynamical Biological Mechanisms and Causal Graphs.” Philosophy of Science, in this issue.CrossRefGoogle Scholar
Woodward, Jim. 2003. Making Things Happen: A Theory of Causal Explanation. New York: Oxford University Press.Google Scholar
Woodward, Jim 2011. “Mechanisms Revisited.” Synthese 183 (3): 409–27.CrossRefGoogle Scholar
Woodward, Jim 2013. “Mechanistic Explanation: Its Scope and Limits.” Proceedings of the Aristotelian Society Supplementary Volume 87 (1): 39–65.CrossRefGoogle Scholar
Woodward, Jim 2015. “Interventionism and Causal Exclusion.” Philosophy and Phenomenological Research 91 (2): 303–47.CrossRefGoogle Scholar
Woodward, Jim, and Hitchcock, Christopher 2003. “Explanatory Generalizations, Part I: A Counterfactual Account.” Noûs 37 (1): 1–24.CrossRefGoogle Scholar