Energy and Metabolism: The Economy of Topological Organization—Volume III of the Axiomatization of Biology in the Global-Realism Framework

Abstract

This manuscript develops the third biological volume of the global-realist axiomatization program. It derives metabolism and biological energy transduction from previously established physical, chemical, cellular, and genetic foundations. Metabolism is defined as a stoichiometrically constrained, enzyme-realized open reaction network carrying matter, charge, reducing equivalents, and free-energy flux. The paper derives flux balance, thermodynamic feasibility, cycle affinities, enzyme-control coefficients, and robustness conditions. It reconstructs ATP-mediated energy transfer, glycolysis, pyruvate oxidation, the tricarboxylic-acid cycle, respiratory electron transport, proton-motive storage, oxidative phosphorylation, photosynthetic charge separation, and carbon fixation within a unified nonequilibrium framework. Each theoretical layer is equipped with explicit definitions, conservation laws, dimensionless controls, approximation conditions, empirical interfaces, and noncircular closure criteria. **Keywords** Global realism; metabolism; biological energy transduction; ATP; metabolic networks; oxidative phosphorylation; chemiosmosis; photosynthesis; nonequilibrium thermodynamics; topological organization.