Hostname: page-component-848d4c4894-nr4z6 Total loading time: 0 Render date: 2024-05-03T21:07:12.944Z Has data issue: false hasContentIssue false
  • English
  • Français

Synthetic Modeling and Mechanistic Account: Material Recombination and Beyond

Published online by Cambridge University Press:  01 January 2022

Tarja Knuuttila  and
Andrea Loettgers
Get access Rights & Permissions [Opens in a new window]

Abstract

Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic modeling as a kind of material recomposition strategy also points beyond the mechanistic paradigm.

Type
General Philosophy of Science
Information
Philosophy of Science , Volume 80 , Issue 5 , December 2013 , pp. 874 - 885
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.)

References

Bechtel, William. 2011. “Mechanism and Biological Explanation.” Philosophy of Science 78:533–57.CrossRefGoogle Scholar
Bechtel, William, and Abrahamsen, Adele. 2009. “Decomposing, Recomposing, and Situating Circadian Mechanisms: Three Tasks in Developing Mechanistic Explanations.” In Reduction and Elimination in Philosophy of Mind and Philosophy of Neuroscience, ed. Leitgeb, Hannes and Hieke, Alexander, 173–86. Frankfurt: Ontos.Google Scholar
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
Bechtel, William, and Abrahamsen, Adele. 2011. “Complex Biological Mechanisms: Cyclic, Oscillatory, and Autonomous.” In Philosophy of Complex Systems, vol. 10 of Handbook of the Philosophy of Science, ed. Hooker, C. A., 257–85. Oxford: Elsevier.Google Scholar
Cookson, Natalia A., Tsimring, Lev S., and Hasty, Jeff. 2009. “The Pedestrian Watchmaker: Genetic Clocks from Engineered Oscillators.” FEBS Letters 583:3931–37.CrossRefGoogle ScholarPubMed
Craver, Carl F. 2006. “When Mechanistic Models Explain.” Synthese 153:355–76.CrossRefGoogle Scholar
Darden, Lindley. 2007. “Mechanisms and Models.” In Cambridge Companion to Philosophy of Biology, ed. Hull, David L. and Ruse, Michael, 139–59. New York: Cambridge University Press.Google Scholar
Darden, Lindley, and Craver, Carl. 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.CrossRefGoogle Scholar
Elowitz, Michael B., and Leibler, Stanislas. 2000. “A Synthetic Oscillatory Network of Transcriptional Regulators.” Nature 403:335–38.CrossRefGoogle ScholarPubMed
Glennan, Stuart S. 2005. “Modeling Mechanisms.” Studies in History and Philosophy of Biological and Biomedical Sciences 36:443–64.CrossRefGoogle ScholarPubMed
Hasty, Jeff, Dolnik, Milos, Rottschäfer, Vivi, and Collins, James J.. 2002. “Synthetic Gene Network for Entraining and Amplifying Cellular Oscillations.” Physical Review Letters 88:148101–1–4.CrossRefGoogle ScholarPubMed
Machamer, Peter, Darden, Lindley, and Craver, Carl F.. 2000. “Thinking about Mechanisms.” Philosophy of Science 67:1–25.CrossRefGoogle Scholar
Morgan, Mary. 2003. “Experiments without Material Intervention: Model Experiments, Virtual Experiments and Virtually Experiments.” In Philosophy of Scientific Experimentation, ed. Radder, Hans, 216–35. Pittsburgh: University of Pittsburgh Press.Google Scholar
Nandagopal, Nagarajan, and Elowitz, Michael B.. 2011. “Synthetic Biology: Integrated Gene Circuits.” Science 333:1244–48.CrossRefGoogle ScholarPubMed
Sprinzak, David, and Elowitz, Michael B.. 2005. “Reconstruction of Genetic Circuits.” Nature 438:442–48.CrossRefGoogle ScholarPubMed
Stepp, Nigel, Chemero, Anthony, and Turvey, Michael T.. 2011. “Philosophy of the Rest of Cognitive Science.” Topics in Cognitive Science 3:425–37.CrossRefGoogle ScholarPubMed
Stricker, Jesse, Cookson, Scott, Bennet, Matthew R., Mather, William H., Tsimring, Lev S., and Hasty, Jeff. 2008. “A Fast, Robust and Tunable Synthetic Gene Oscillator.” Nature 456:516–19.CrossRefGoogle ScholarPubMed
Strogatz, Steven H. 1994. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Cambridge, MA: Perseus.Google Scholar
Swain, Peter S., Elowitz, Michael B., and Siggia, Eric D.. 2002. “Intrinsic and Extrinsic Contributions to Stochasticity in Gene Expression.” Proceedings of the National Academy of Sciences of the United States of America 99 (20): 12795–12800..CrossRefGoogle ScholarPubMed