Contingent Molecular Coding in a Specified Reaction Architecture: Formation, Causal Heredity, and Output-Mediated Maintenance

The formation of a molecular assignment and the origin of the capabilities that implement it are distinct explanatory problems. This paper studies assignment formation within a specified recognition, assembly, templating, and readout architecture whose initial state contains no cross-domain carrier or privileged mapping. The principal result is a joint existence theorem: one fixed, independently assignment-symmetric reaction--compartment grammar supports contingent readout, topology-dependent causal heredity, and output-mediated maintenance on a common admissible parameter regime, without a mapping-quality reward or an externally activated reaction stage. Local assembly and nonlinear reinforcement generate two symmetry-related organizations that mediate opposite symbol-conditioned channels. Matched interventions distinguish the channel's dependence on its carrier, the effect of inherited pairing topology on descendant channels, and the contribution of decoded outputs to future interpreter capacity. An elementary fuel-driven mass-action realization retains these properties under the stated scale separation. Genesis has strictly positive probability; high-probability lineage retention is established separately from constructed exact-balanced mature parents, over horizons growing exponentially with compartment scale. Finite-system reset and local free-rider bounds delimit that retention. The contribution is a compatible construction and a set of quantitative causal discriminators for a restricted operational molecular code. It does not derive the molecular origin of the supplied capabilities, mapping-sensitive interpreter self-construction, a high-probability complete origin history, or a historical pathway to the Standard Genetic Code. The construction makes precise what remains to be explained when a model generates a coding relation within an already specified architecture.

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Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-09-05
DOI
https://doi.org/10.5281/zenodo.22377651
Primary Topic
Gene Regulatory Network Analysis
Type
preprint
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Contingent Molecular Coding in a Specified Reaction Architecture: Formation, Causal Heredity, and Output-Mediated Maintenance

Kai Liang
Zenodo (CERN European Organization for Nuclear Research)
Gene Regulatory Network Analysis
preprint

Contingent Molecular Coding in a Specified Reaction Architecture: Formation, Causal Heredity, and Output-Mediated Maintenance

Kai Liang
preprint en

Abstract

The formation of a molecular assignment and the origin of the capabilities that implement it are distinct explanatory problems. This paper studies assignment formation within a specified recognition, assembly, templating, and readout architecture whose initial state contains no cross-domain carrier or privileged mapping. The principal result is a joint existence theorem: one fixed, independently assignment-symmetric reaction--compartment grammar supports contingent readout, topology-dependent causal heredity, and output-mediated maintenance on a common admissible parameter regime, without a mapping-quality reward or an externally activated reaction stage. Local assembly and nonlinear reinforcement generate two symmetry-related organizations that mediate opposite symbol-conditioned channels. Matched interventions distinguish the channel's dependence on its carrier, the effect of inherited pairing topology on descendant channels, and the contribution of decoded outputs to future interpreter capacity. An elementary fuel-driven mass-action realization retains these properties under the stated scale separation. Genesis has strictly positive probability; high-probability lineage retention is established separately from constructed exact-balanced mature parents, over horizons growing exponentially with compartment scale. Finite-system reset and local free-rider bounds delimit that retention. The contribution is a compatible construction and a set of quantitative causal discriminators for a restricted operational molecular code. It does not derive the molecular origin of the supplied capabilities, mapping-sensitive interpreter self-construction, a high-probability complete origin history, or a historical pathway to the Standard Genetic Code. The construction makes precise what remains to be explained when a model generates a coding relation within an already specified architecture.

Zenodo (CERN European Organization for Nuclear Research)
Reduced inequalities
Gene Regulatory Network Analysis
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Contingent Molecular Coding in a Specified Reaction Architecture: Formation, Causal Heredity, and Output-Mediated Maintenance — Kai Liang · Zenodo (CERN European Organization for Nuclear Research) (2026) | TGRS Research Map | TGRS