Mechanisms, Pathways, and Networks: On Their Description and Explanation

Recent literature in the philosophy of science has increasingly recognized that explanations in the biomedical sciences aim to account for the behavior of complex systems. These explanations often depend on some understanding of causal relationships and typically involve multilevel analyses, where various explanatory layers must be integrated to adequately explain the system as a whole. This paper examines scientific explanation in molecular biology and medicine by focusing on the relationship between explanation and description. We argue that the notion of "description" must be carefully disambiguated in order to clarify the precise connections between these two distinct epistemic practices. To this end, we emphasize the need to distinguish—and relate—three interrelated types of biological and philosophical inquiry: the study of molecular mechanisms, molecular pathways (or processes), and molecular networks (particularly interactomes). A deeper exploration of these conceptual approaches, along with the explanatory models associated with them, will illuminate the distinctive features of explanation in molecular biology. It will also help clarify how description and explanation are connected. Although they are distinct epistemic acts, we argue that their relationship is closer than has often been acknowledged in the literature.