A Novel Paradigm: The Extinct Equilibrium Host Theory for Pathogen-Host Mismatch Arising from Ancient Host Extinctions

This conceptual paper introduces the Extinct Equilibrium Host Theory (EEHT), positing that many contemporary diseases arise not from inherent pathogenicity but from evolutionary mismatches between pathogens and their current hosts, stemming from the extinction of ancient equilibrium hosts. We formalize this through multidimensional mathematical models, incorporating epidemiological dynamics, evolutionary pressures, and extinction events. Rigorous derivations of equilibrium states, stability analyses, and stochastic extensions are provided. Empirical support is drawn from paleovirology and zoonotic spillover data, with Python-based simulations using real-world rabies virus parameters for reproducibility. Advanced sensitivity analysis, quantitative statistics, Bayesian inference, uncertainty quantification, and falsifiability criteria are integrated. A multi-stage roadmap from experimentation to potential therapeutic manufacturing is outlined. The manuscript is self-contained with all data and code embedded.Keywords: Host-pathogen coevolution, Paleovirology, Zoonotic diseases, Evolutionary mismatch, Extinction dynamics