From Form to Program: Medium-Range Conditional Codon Syntax Inside Real Genes (Preprint, Pipeline v13 & Results)

Abstract

This repository contains the preprint of the paper "From Form to Program" and the full source code for the autonomous audit of conditional codon syntax (pipeline v13). Building upon the "Form/Substance" lens introduced by J.-C. Perez, this study mathematically separates the static macroscopic invariants of the genome (form: codon populations, fractals, mirror symmetry) from the dynamic, program-like sequential order inside real coding sequences (substance/program). Key Features & Scientific Contributions: Broad Phylogenetic Scope: Analyzes real true-frame CDS sequences from 13 RefSeq taxa, spanning mammals, a vertebrate bridge (zebrafish, chicken), an insect, a plant, a nematode, a fungus, two bacteria, and two archaea. Strict Null-Model Ladder (H0–H7): The empirical codon-bigram model is tested against an unprecedented hierarchy of nulls, including amino-acid syntax with codon-pair bias (H2b), nucleotide trigrams (H3b), and local block-shuffle (H4). Codon-Mirror-Symmetry Control (H7): Introduces a novel shuffle model that strictly preserves the exact static populations of the 32 Watson-Crick reverse-complement codon pairs (the first symmetry axis of Perez, 2013) while destroying sequential order. All 13 species successfully pass this control, proving that dynamic conditional syntax is orthogonal to static mirror symmetry. Two-Scale Cross-Species Transfer: Coarse Scale: Recovers a broad, symmetric vertebrate-level conserved grammatical layer across human, chimp, mouse, zebrafish, and chicken. Fine Scale: Uncovers a sharper, directionally asymmetric mammalian codon-choice core using a corrected target-scored H5 metric. GC3/Acidic-Proteome Artifact Control: Explicitly separates true lineage divergence from extreme environmental form mismatches (e.g., salt adaptation in H. salinarum), ensuring that compositional artifacts are not misread as conserved program syntax. Included Files: code_logos_perez_v3.tex.pdf — The full text of the updated preprint in PDF format. code_logos_perez_v3.tex — The LaTeX source code of the manuscript. super_codon_autonomous_v13.py — The autonomous Python script (v13) to fully reproduce the results. It features 1-click execution with automatic NCBI CDS downloading, one-gene-one-vote paralog filtering, and the application of all null models. logs.zip / full.json / full.md — The detailed execution logs, statistical matrices, and Markdown reports generated by the autonomous pipeline. Attribution Note: This pipeline measures the dynamical/program layer and treats static mirror/composition symmetry as form. Universal static attractors (such as the Human Genome Optimum) remain a separate orthogonal measurement within the same overarching form/substance programme.