Using genetics as a tool, we can learn much about how important biogeochemical reactions occur. Moreover, understanding these mechanisms at the molecular level enables us to construct testable hypotheses regarding the evolution of geochemically relevant metabolisms. To illustrate this, I will discuss our approach to the problem of bacterial respiration of minerals and some of the surprising insights we are gaining along the way. Specifically, I will focus on the role of small molecules in serving as electron shuttles between microbes and minerals, paying particular attention to their origin (microbially-produced v. exogenous), structure, and domain of activity.