Compiled Chemistry: Structural Inheritance and the Deep Origins of Biological Function

The transition from prebiotic chemistry to genetic inheritance represents a fundamental gap in our understanding of life's origins. While origin-of-life research demonstrates that complex chemical systems can maintain functional organization through environmental energy sources, coherent frameworks explaining how these systems became encoded in DNA remain lacking. This paper examines the Chemical-Genetic Integration Model (CGIM): a proposed mechanism whereby genetic systems emerged through selective incorporation of pre-existing, functionally organized chemical networks including iron-sulfur clusters, mineral scaffolds, and autocatalytic systems. The framework suggests this integration was incomplete and differential, with lineages potentially retaining varying degrees of pre-genetic functional architecture. Analysis of early-diverging animals reveals organizational patterns consistent with preserved chemical inheritance. Ctenophores exhibit constitutive protein expression activated by environmental conditions rather than transcriptional regulation, resembling proposed pre-genetic chemical networks. Tardigrades deploy intrinsically disordered proteins that function through physical rather than regulatory mechanisms. Genomic analysis identifies cross-kingdom sequence conservation patterns in taxonomically problematic organisms that may represent molecular signatures of chemical inheritance. The CGIM framework generates testable predictions for systematic identification of chemical inheritance in modern organisms, including quantitative criteria for distinguishing runtime from modular biological organization and genomic archaeology methods for detecting ancient chemical signatures. The approach provides a mechanistic hypothesis for the chemistry-to-genetics transition that can be evaluated through computational analysis, experimental validation, and systematic discovery protocols.