Biological Genomes as Functional State Space Specifications:A Formal Framework for Genomic Function and Regulation

We propose that biological genomes encode functional state space (FSS) specifications through which cellular systems navigate via constraint-preserving operator composition. DNA sequences are reinterpreted as generators of closed operator families, with regulatory genes implementing homeostatic control parameters. This framework unifies gene knockout effects, synthetic lethality, developmental timing, and disease mutations under single mathematical structure. Critically, we advocate theory-and-simulation-first validation using existing databases before experimental intervention. Part 1 establishes foundations: mathematical formalism, genomic interpretation, and theoretical predictions. Parts 2-3 (separate documents) provide empirical tests and strongly-typed appendices.