title: Using computational models to discover and understand mechanisms.
abstract: Areas of biology such as cell and molecular biology have been dominated by research directed at constructing mechanistic explanations that identify parts and operations that when organized appropriately are responsible for the various phenomena they investigate. Increasingly the mechanisms hypothesized involve non-sequential organization of non-linear operations and so exceed the ability of researchers to mentally rehearse their behavior. Accordingly, scientists rely on tools of computational modeling and dynamical systems theory in advancing dynamic mechanistic explanations. Using circadian rhythm research as an exemplar, this paper explores the variety of roles computational modeling is playing. They serve not just to determine whether the mechanism will produce the desired behavior, but in the discovery process of hypothesizing mechanisms and in understanding why proposed mechanisms behave as they do.
authors.affiliation: Department of Philosophy and Center for Circadian Biology, University of California, La Jolla, CA 92093-0119, United States. Electronic address: bechtel@ucsd.edu.
authors.forename: William
authors.initials: W
authors.lastname: Bechtel
mesh_terms: D000818:Animals; D055881:Chronobiology Discipline; D002940:Circadian Rhythm; D019295:Computational Biology; D000458:Cyanobacteria / Q000502:physiology*; D007448:Invertebrates / Q000502:physiology*; D008954:Models, Biological; D014714:Vertebrates / Q000502:physiology*
keywords: Circadian rhythms; Computational modeling; Design principles; Discovery; Mechanistic explanation; Understanding