William Bechtel (UCSD), Constructing and Analyzing Networks to Discover Mechanisms: Applications in Yeast and Cancer Biology

William Bechtel (Department of Philosophy and Center for Circadian Biology, University of California, San Diego, USA)

Constructing and Analyzing Networks to Discover Mechanisms: Applications in Yeast and Cancer Biology

Abstract:

With the development in systems biology and systems medicine of high-throughput technologies, large databases to collect the resulting data, and platforms such as Cytoscape to represent and analyze data in networks, one might think that the project of mechanistic explanation in biology has been supplanted. However, the very researchers developing and using these new tools still advance accounts of mechanisms. I contend that what the new tools provide are novel strategies for discovering mechanisms. They also provide new insights into what mechanisms are and how they function in the context of living organisms. Rather than starting by identifying a given phenomenon with an already differentiated mechanism or a few of its parts, the research I discuss starts with data about a multitude of interactions of genes and proteins in cells. Researchers represent genes and proteins in networks to which they apply a variety of analytic tools to reveal modules. In many cases these modules correspond approximately to mechanisms as traditionally investigated and the research results in identifying new components in these mechanisms. In other cases, modules are taken to represent previously undiscovered mechanisms. In either case, the investigations reveal a multitude of ways mechanisms are interconnected with other cell mechanism and often that they are far more transitory and malleable than traditionally conceived. I employ examples from yeast and cancer biology to illustrate both the strategies being employed to discover mechanisms and how the resulting mechanisms figure in explanations in both basic science and cancer research.

For audio file of the talk, please contact Thomas Pradeu.