Musings on mechanism: quest for a quark theory of proteins?

The give and take between biology and physics is an important part of the history of modern science, with this partnership perhaps now more intimate than ever. In this essay, I explore the ways in which these different fields can strengthen each other through their distinct outlooks on some of the most important questions being asked about the living world. In particular, I highlight three areas where the perspective from physics might lead to deeper insights into the workings of cells. First, I consider what it means for two ostensibly unrelated problems to be the same, and how such sameness can provide unexpected insights into apparently unrelated phenomena. Second, I consider different conceptions of what constitutes a mechanistic understanding of a given phenomenon with an emphasis on nonmolecular notions of mechanism. The third idea is the importance of "toy problems" as a way of providing foundational insights into the real problems. Though my focus here is primarily on ways in which physics approaches might prove interesting in biology, I close with an example of how biology might substantially alter physics by providing a forum and the tools to uncover a fundamental understanding of nonequilibrium phenomena.-Phillips, R. Musings on mechanism: quest for a quark theory of proteins? © FASEB.