Antibiotic Resistance as a Geometric Phenomenon: A Taxonomy of Resistance Mechanisms and Counter-Intervention by Attractor Class

This paper proposes that antibiotic resistance is not a chemical phenomenon but a geometric one. Every primary mechanism of bacterial resistance — efflux pump polyspecificity, beta-lactamase active site recognition, target site modification, outer membrane exclusion, and horizontal gene transfer — operates through shape recognition: the identification, binding, or exclusion of molecular structures by their geometric properties rather than their chemical identity. Evidence from isolated cave microbiomes (Lechuguilla Cave, 4 million years), ancient cave ice (Scărișoara Cave, Romania, 5,000 years), and Siberian permafrost (15,000–1.8 million years) demonstrates that antibiotic resistance predates pharmaceutical pressure by millions of years, consistent with geometric recognition of attractor class membership rather than chemical-specific adaptation. A seventh geometric attractor class — the fused beta-lactam class — is proposed. The existing counter-interventions that work best (avibactam, cefiderocol, cyclic boronates) are classified as corrective geometric interventions that target the resistance machinery rather than redesigning the antibiotic compound. Four distinguishing predictions are derived. The honest limits of the framework are identified, including enzymatic modification resistance mechanisms not yet accommodated by the taxonomy. This paper is a companion to: Hilbert (2026a), "Aromatic surface geometry as a primary mechanism of nanoplastic endocrine disruption: A cyclodextrin competition hypothesis," and Hilbert (2026b), "Geometric attractor classes as a unifying principle of pre-cognitive biological intervention." No clinical claims are made. Preprint — not peer reviewed.