Representing Temporal Organization in Molecular Biology: A Structuralist Approach

The New Mechanism has traditionally focused on identifying constitutively relevant components in mechanistic explanation but has largely overlooked how temporal organization encompassing order, duration, and rate should be formally represented. This paper develops a structuralist approach to mechanistic explanation by integrating insights from scientific representation and category theory. Drawing on Hughes’ DDI (Denotation, Demonstration, Interpretation) account, it establishes a representational framework for modeling temporal constraints as explanatory targets. Category–theoretic tools including index categories, functorial mappings, and Petri nets are employed to formally encode dynamical and sequential structures. Using protein synthesis as a case study, the paper demonstrates that mechanistic explanation must account not only for token–level causal dependencies but also for type–level structural constraints. By bridging the theory of scientific representation with mechanistic explanation, it clarifies how temporal organization underlies and enables explanatory models in biology.