Genetics and the Genome: Inheritance and Variation of Information Topology (Volume II of the Axiomatization of Biology in the Global‑Realism Framework) Abstract

Abstract

This second volume of the global‑realist biology program derives genetics as a lawful continuation of already closed physical, chemical, and first‑biological layers. Without introducing “gene”, “allele”, “recombination”, or “genome” as primitive terms, we construct them from sequence topology, molecular recognition, and nonequilibrium thermodynamics. A gene is defined as a functional DNA interval with upstream recognition, transcribed region, termination, and an expressed output map. Semiconservative replication is proved to be the unique resolution of antiparallel duplex templating under polymerase directionality, and its fidelity is quantified as a product of initial discrimination, proofreading, and mismatch repair. Transcription and translation are factorized into operator chains that convert DNA topology into RNA and finally into protein folds, with explicit free‑energy budgets and error bounds. Regulation – operon switches, chromatin accessibility, enhancer contacts, RNA processing, and noncoding RNA control – is unified as gated occupancy and sequence‑dependent free‑energy barriers. Chromosome‑scale phenomena (packaging, telomeres, centromeres, replication timing, transposons) are treated as topological and energetic constraints on a confined polymer. Classical Mendelian laws, linkage, quantitative genetics, GWAS, and population genetics are reinterpreted as statistical mechanics of chromosome transmission and reproductive‑work filtering. Every major concept is equipped with an admissibility margin, a thermodynamic payment bound, and a multiscale audit that ensures conservative extension from physics and chemistry. The output is an explicit export bundle for later biological volumes on development, physiology, and evolution