From Form to Program: Medium-Range Conditional Codon Syntax Inside Real Genes (Preprint, Pipeline v10 & 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 v10). 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). Key Features & Results: Broad Phylogenetic Scope: Analyzed real 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. Hierarchy of Strict Null Models (H0–H7): The empirical codon-bigram model is tested against an unprecedented ladder of nulls, including marginal frequencies, amino-acid syntax (H2), codon-pair bias (H2b), nucleotide trigrams (H3b), and block-shuffle (H4). Unique Mirror-Symmetry Control (H7): Introduces a novel shuffle model that strictly preserves the static populations of the 32 Watson-Crick codon pairs (the codon-mirror symmetry of Perez, 2013) while destroying order. All 13 species successfully passed this control, proving that conditional syntax is not reducible to static mirror symmetry. The Vertebrate Bridge: A cross-species transfer matrix with an amino-acid-preserving surrogate control (H5) revealed a conserved codon-specific grammar shared across the entire vertebrate clade (human, chimp, mouse, zebrafish, chicken), whereas other taxa exhibit phylogenetically isolated syntax. Conclusion: Establishes the existence of medium-range (approx. 30 codons) conditional syntax, representing an evolving, clade-specific biological "software" operating within the fixed topological boundaries ("hardware") of DNA. Included Files: code_logos_perez_v2.tex.pdf — The full text of the preprint in PDF format. code_logos_perez_v2.tex — The LaTeX source code of the manuscript. super_codon_proof_v10.py — The autonomous Python script (version 10) to fully reproduce the results, including automatic NCBI CDS downloading and the application of all null models. super_codon_proof_v10.md — The detailed report and final matrices (in Markdown format) generated by the pipeline.