Abstract
The nature of the product to be discovered guides the reasoning to discover it. Biologists and medical researchers often search for mechanisms. The “new mechanistic philosophy of science” provides resources about the nature of biological mechanisms that aid the discovery of mechanisms. Here, we apply these resources to the discovery of mechanisms in medicine. A new diagrammatic representation of a disease mechanism chain indicates both what is known and, most significantly, what is not known at a given time, thereby guiding the researcher and collaborators in discovery. Mechanisms of genetic diseases provide the examples.
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References
Abrahamsen, A. A., & Bechtel, W. (2015). Diagrams as tools for scientific reasoning. Review of Psychology and Philosophy, 6, 117–131.
Abrahamsen, A., Benjamin, S., & William, B. (2017). Explaining visually: Mechanism diagrams. In S. Glennan & P. Illari (Eds.), The routledge handbook of mechanisms and mechanical philosophy (pp. 238–254). New York: Routledge.
Andersen, H. (2012). Mechanisms: What are they evidence for in evidence-based medicine? Journal of Evaluation in Clinical Practice, 18(5), 992–999.
Arp, R., Smith, B., & Spear, A. D. (2015). Building ontologies with basic formal ontology. Cambridge, MA: MIT Press.
Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. In C. F. Craver & L. Darden (Eds.), Special issue: Mechanisms in biology. Studies in History and Philosophy of Biological and Biomedical Sciences (vol. 36, pp. 421–441).
Bechtel, W., & Abrahamsen, A. A. (2013). Thinking dynamically about biological mechanisms: Networks of coupled oscillators. Foundations of Science, 18, 707–723.
Bechtel, W., & Richardson, R. C. (1993). Discovering complexity: Decomposition and localization as strategies in scientific research. Princeton, NJ: Princeton University Press.
Craver, C. F. (2007). Explaining the brain: Mechanisms and the mosaic unity of neuroscience. New York: Oxford University Press.
Craver, C. F. (2008). Physical law and mechanistic explanation in the Hodgkin and Huxley model of the action potential. Philosophy of Science, 75(5), 1022–1033.
Craver, C. F., & Darden, L. (2013). In search of mechanisms: Discoveries across the life sciences. Chicago, IL: University of Chicago Press.
Darden, L. (2002). Strategies for discovering mechanisms: Schema instantiation, modular subassembly, forward/backward chaining. Philosophy of Science, 69(Proceedings), S354–S365.
Darden, L. (2006). Reasoning in biological discoveries: Mechanisms, interfield relations, and anomaly resolution. New York: Cambridge University Press.
Darden, L. (2013). Mechanisms versus causes in biology and medicine. In H. K. Chao, S. T. Chen, & R. L. Millstein (Eds.), Mechanism and causality in biology and economics (pp. 19–34). The Netherlands: Springer.
Darden, L., & Craver, C. F. (2002). Strategies in the interfield discovery of the mechanism of protein synthesis. Studies in History and Philosophy of Biological and Biomedical Sciences, 33, 1–28. Reprinted with corrections in Darden (2006, Chap. 3).
de Lange, K. M., et al. (2017). Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nature Genetics, 49, 256–261. https://doi.org/10.1038/ng.3760.
Gebharter, A., & Kaiser, M. I. (2014). Causal graphs and biological mechanisms. In M. I. Kaiser, O. R. Scholz, D. Plenge, & A. Hüttemann (Eds.), Explanation in the special sciences (Vol. 367, pp. 55–85). Dordrecht: Synthese Library.
Gene Ontology Consortium. (2015). The gene ontology consortium: Going forward. Nucleic Acids Research, 43(database issue), D1049–D1056.
Glennan, S. S. (1996). Mechanisms and the nature of causation. Erkenntnis, 44, 49–71.
Glennan, S., & Illari, P. (Eds.). (2017). Routledge handbook of mechanisms and mechanical philosophy. New York: Routledge.
Gorlatova, N., Chao, K., Pal, L. R., Araj, R. H., Galkin, A., Turko, I., et al. (2011). Protein characterization of a candidate mechanism SNP for Crohn’s disease: The macrophage stimulating protein R689C substitution. PLOS ONE (open access). http://dx.doi.org/10.1371/journal.pone.0027269.
Howick, J. (2011). Exposing the vanities—And a qualified defense—Of mechanistic reasoning in health care decision making. Philosophy of Science, 78, 926–940.
Jin, L., Xiao-Yu, Z., Wei-Yang, S., Xiao-Lei, Z., Man-Qiong, Y., Li-Zhen, H., et al. (2014). Pathway-based analysis tools for complex diseases: A review. Genomics, Proteomics & Bioinformatics, 12(5), 210–220. https://doi.org/10.1016/j.gpb.2014.10.002.
Kanehisa, M., Furumichi, M., Tanabe, M., Sata, Y., & Norishima, K. (2017). KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Research, 45(D1), D353–D361. https://doi.org/10.1093/nar/gkw1092.
Kaiser, M. I. (2016). On the limits of causal modeling: Spatially-structured complex biological phenomena. Philosophy of Science, 83(5), 921–933.
Li, G. M. (2008). Mechanisms and functions of DNA mismatch repair. Cell Research, 18, 85–98.
Lindee, S., & Mueller, R. (2011). Is cystic fibrosis genetic medicine’s canary? Perspectives in Biology and Medicine, 54(3), 316–331.
Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67, 1–25.
Plutynski, A. (2013). Cancer and the goals of integration. Studies in the History and Philosophy of Biological and Biomedical Sciences, 4, 466–476.
Plutynski, A. (forthcoming). Explaining Cancer: Finding Order in Disorder.
Russo, F., & Williamson, J. (2007). Interpreting causality in the health sciences. International Studies in the Philosophy of Science, 21(2), 157–170.
Sheredos, B., Burston, D., Abrahamsen, A., & Bechtel, W. (2013). Why do biologists use so many diagrams? Philosophy of Science, 80(5), 931–944.
Solomon, M. (2015). Making medical knowledge. New York: Oxford University Press.
Thagard, P. (1998). Explaining disease: Causes, correlations, and mechanisms. Minds and Machines, 8, 61–78.
Thagard, P. (1999). How scientists explain disease. Princeton, NJ: Princeton University Press.
Thagard, P. (2003). Pathways to biomedical discovery. Philosophy of Science, 70, 235–254.
Weber, M. (2016). On the incompatibility of dynamical biological mechanisms and causal graphs. Philosophy of Science, 83(5), 959–971.
Wilkenfeld, D. (2013). Understanding as representation manipulability. Synthese, 190, 997–1016. https://doi.org/10.1007/s11229-011-0055-x.
Acknowledgements
LD thanks Emiliano Ippoliti and his colleagues at Sapienza University in Rome for the invitation to the Building Theories Workshop, and to them and all the participants for lively discussions of discovery heuristics. For helpful suggestions on earlier drafts, she thanks Carl Craver, Giamila Fantuzzi, Nancy Hall, and an anonymous reviewer, as well as Kal Kalewold and the other students in her graduate seminar on mechanisms and ontology. This work was supported in part by NIH (US National Institutes of Health) grants R01GM102810 and R01GM104436 to JM.
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Darden, L., Pal, L.R., Kundu, K., Moult, J. (2018). The Product Guides the Process: Discovering Disease Mechanisms. In: Danks, D., Ippoliti, E. (eds) Building Theories. Studies in Applied Philosophy, Epistemology and Rational Ethics, vol 41. Springer, Cham. https://doi.org/10.1007/978-3-319-72787-5_6
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