Explanation in Systems Biology: Is It All About Mechanisms?

Abstract

As the mechanistic understanding of how biological systems function continues to become more refined, the power of scientists to manipulate and control them for the sake of achieving concrete practical goals increases. Proponents of the recent movement for a new mechanistic philosophy of biology have taken up the task of defining the theoretical conditions that would promote such understanding. In this paper, the case of systems biology serves to highlight some of the limitations of the explanatory models that are grounded on their philosophical accounts of mechanism. In light of the prominent role played by mechanisms in top-down and bottom-up systems biology, I argue that a purely mechanism-based framework that complies with the constraints stipulated by the new mechanists is adequate for producing useful explanations of biological phenomena in the context of the systems approach. Nevertheless, this framework remains limited in its capacity to carry out the comprehensive explanatory integration demanded for the holistic understanding of complex biological systems whose attainment constitutes systems biology’s most ambitious objective. In addition, in their current formulation the models endorsed by the new mechanists are not sufficient for capturing the rich explanatory pluralism that characterizes the practice of systems biology. The fact that a pragmatic view of the practice of systems biology reveals its pluralistic character suggests that moving beyond theoretical considerations provides useful insights into the nature of explanation. I propose, however, that philosophers do not need to make a choice between adopting either a theoretical or a pragmatic attitude: both perspectives contribute in a mutually complementary way to constructive thinking about explanation in biology.