Functional Stability Theory III: Biological Stability and Nash Frustration (DRAFT)

DRAFT version. This preprint is part of an active research programme and remains subject to revision, correction, and journal review. A unified framework for biological organization spanning molecular to ecosystem scales, grounded in thermodynamic game theory and the Maximum Entropy Production Principle (MEPP). We argue that biological systems are dissipative structures whose stable configurations can be characterized as Nash equilibria at multiple organizational levels. The framework integrates England's dissipative adaptation theory, Friston's Free Energy Principle, Kauffman's Boolean network dynamics, and classical evolutionary game theory into a coherent hierarchy. As a concrete application, we introduce Nash frustration for protein structures and provide a proof-of-concept test against NMR chemical shift perturbation data (Spearman rhoS = 0. 44, p = 0. 033, n = 24). Series position FST-III is the biology / evolutionary stability companion (Level 1c) of the FST application series. The programmatic umbrella is the FST Hub (Concept-DOI 10. 5281/zenodo. 20130499). Sibling application companions: FST-I Particles, FST-II Chemistry, FST-IV Cosmology. Code the previously listed DOI 10. 1006/jmbi. 1999. 3363 belonged to an unrelated Holliday-junction paper. BMRB provenance clarified: BMRB 4428 is identified as the HP67/1QQV villin-headpiece NMR dataset, mapped to the C-terminal HP35/1YRF subdomain for the benchmark; BMRB DOI 10. 13018/BMR4428 added. Self-citation metadata updated: FST-I, FST-II, RH Landscape, RH Even Dominance and RFEP/Spectrum Duality references now use stable Zenodo Concept-DOIs. Files rebuilt: EN, DE and combined v3 PDFs generated after the source check. Version 1. 1 (May 2026) Hub-link corrected: "FST-IV Overview" references replaced by "FST Hub" (programmatic umbrella). The Hub paper holds Concept-DOI 10. 5281/zenodo. 20130499 and is no-numeral; FST-IV is now the cosmological collector slot. GitHub source link added. Related Identifier: FST-DE reference relabelled to "FST-IV Cosmology / FST-DE". Version 1. 0 (May 2026) Initial release as part of the FST series. Status: ~7. 5/10 readiness; remaining open items per referee moderate-revision verdict: η-calibration (QUANT-III-2 via BMRB 4428 + McKnight 1996 protection factors), cosmology-section relocation, TP53 mutational analysis with calibrated η, falsifiable predictions with quantitative thresholds, MEPP-as-heuristic framing.