From 07b2ea47844eee077fd8fbfa11647a9854fba7c1 Mon Sep 17 00:00:00 2001 From: Allaun Silverfox <28494262+allaunthefox@users.noreply.github.com> Date: Tue, 5 May 2026 02:01:27 -0500 Subject: [PATCH] Add genetics information substrate boundary --- ...genetics_information_substrate_boundary.md | 163 ++++++++++++++++++ 1 file changed, 163 insertions(+) create mode 100644 0-Core-Formalism/otom/docs/genetics_information_substrate_boundary.md diff --git a/0-Core-Formalism/otom/docs/genetics_information_substrate_boundary.md b/0-Core-Formalism/otom/docs/genetics_information_substrate_boundary.md new file mode 100644 index 00000000..4f9f3878 --- /dev/null +++ b/0-Core-Formalism/otom/docs/genetics_information_substrate_boundary.md @@ -0,0 +1,163 @@ +--- +project: OTOM +domain: axis-04-formalization +type: BoundaryRecord +settlement: FORMING +authority: registry +route_signature: otom/axis-04-formalization/boundaryrecord/genetics-information-substrate/v0 +claim_state: BEAUTIFUL_PROVISIONAL +source_audit: uploaded-codemap-2026-05-05 +--- + +# Genetics Information Substrate Boundary + +## Purpose + +This boundary record separates genuinely plumbed genetics-information models from +registry-only, ghost, aspirational, and misfiled entries. + +The immediate goal is claim-state hygiene: + +```text +Do not claim the genetics layer is fully implemented when only part of it has +compiled Lean, running data code, or executable evidence receipts. +``` + +## Canonical boundary statement + +```text +The Research Stack currently has a partial but real genetics-information +substrate: compiled codon/peptide/compression formalizations, one real-data +population-genetics script, and a larger registry of unplumbed or ghost model +entries. Claims about genetics information capacity must cite the plumbed +substrate or remain BEAUTIFUL_PROVISIONAL. +``` + +## Classification buckets + +| Bucket | Meaning | Promotion rule | +|---|---|---| +| `CANONICAL_PLUMBED` | compiled Lean module or running real-data script | may support bounded claims | +| `REGISTRY_ONLY` | equation/model exists in registry but has no executable path | may support roadmap claims only | +| `GHOST_ENTRY` | marked complete/available but no corresponding implementation found | must be demoted or implemented | +| `MISFILED` | present near genetics but not genetics-relevant | relocate or mark out-of-scope | +| `ASPIRATIONAL_MIXTURE_PRIMITIVE` | taxonomy concept without proof/data path | BEAUTIFUL_PROVISIONAL only | + +## Plumbed genetics substrate + +### Lean / formalized substrate + +The audit identifies the following as the strongest plumbed genetics-connected +information models: + +| Module | Information-holding mechanism | Genetics tie | Status | +|---|---|---|---| +| `GeneticCode.lean` | NCBI Table 1 codon-to-amino-acid map; 64 codon states plus outputs | canonical translation and codon degeneracy | `CANONICAL_PLUMBED` | +| `CodonOTOM.lean` | codon efficiency functional, mutation delta, selection condition | codon usage bias and mutation-selection balance | `CANONICAL_PLUMBED` | +| `PeptideMoE.lean` | peptide state, Ramachandran coordinates, internal energy, entropy | conformational search as information geometry | `CANONICAL_PLUMBED` | +| `GenomicCompression.lean` | compression windows, phiGenomic, Q16_16 arithmetic | formal sequence-compression substrate | `CANONICAL_PLUMBED` | +| `SyntheticGeneticCoding.lean` | coding and biological parameter projections | normalized biological parameter projection | `CANONICAL_PLUMBED` | +| `GeneticGroundUp.lean` | nucleotide-state encoding, expression probability, binding energy, fold angle | synthetic biology / nucleotide-state model | `CANONICAL_PLUMBED` | +| `HachimojiPipeline.lean` | 8-symbol expanded genetic alphabet analog | expanded DNA/RNA coding regime | `CANONICAL_PLUMBED` | + +### Running data substrate + +| File | Information-holding mechanism | Genetics tie | Status | +|---|---|---|---| +| `Allelica.py` | Hardy-Weinberg genotype-frequency model over real gnomAD data | p² + 2pq + q² = 1 applied to real allele/genotype data | `CANONICAL_PLUMBED` | + +## Registry-only model surface + +These models may be scientifically relevant but should not be promoted as +implemented until a Lean module, Python script, test fixture, or receipt path +exists. + +| Model family | Examples | Status | +|---|---|---| +| Population genetics registry | Wright-Fisher drift, Fisher fundamental theorem, Price equation | `REGISTRY_ONLY` | +| Sequence information registry | Shannon entropy, per-position entropy, Jensen-Shannon divergence, Jukes-Cantor distance, ANI/AAI, mutation rate, novel mutation count | `REGISTRY_ONLY` unless connected to compiled module | +| Thermodynamic/folding registry | RNA folding delta-G, Gibbs free energy, fitness-entropy tradeoff, Waddington potential | `REGISTRY_ONLY` | +| Cellular/regulatory registry | Central Dogma ODE, Gierer-Meinhardt pattern formation | `REGISTRY_ONLY` | + +## Ghost entries requiring demotion or implementation + +The audit reports these as present in the registry but not backed by a found Lean +module, Python implementation, or data pipeline: + +| Ghost entry | Why it matters | Recommended action | +|---|---|---| +| Quasispecies equation | mutation-selection balance, error threshold, viral evolution | implement Lean skeleton + simulator | +| Replicator equation | evolutionary game dynamics | implement only if tied to population-genetics or ecology use case | +| Neutral theory / Kimura | drift-mutation balance | implement after drift/selection metrics | +| Masked language modeling loss for DNA | sequence-prediction information model | defer until corpus/data pipeline exists | +| pTM / TM-score | structural biology information metric | defer until protein-structure pipeline exists | + +## Misfiled entry + +| Entry | Reason | Action | +|---|---|---| +| `parametric-learn` | Three.js/TensorFlow.js parametric surface fitting demo; no biological sequence, population, or genetics-information role found | mark `MISFILED` or relocate outside genetics | + +## Missing canonical gaps + +| Missing area | Why it matters | Suggested implementation route | +|---|---|---| +| Selection detection | identifies signatures of selection in sequence/population data | implement Tajima's D and FST first | +| Phylogenetic tree inference | reconstructs evolutionary history as tree-structured information | use Jukes-Cantor distance, then neighbor-joining | +| Population structure | ancestry/latent-variable information | PCA/admixture after real genotype fixtures exist | +| Epigenetic HMM / chromatin states | regulatory information layer | HMM implementation plus receipt schema | +| Splicing / isoform quantification | transcript-level information | defer until RNA-seq or transcript fixtures exist | +| Variant calling | raw read to variant state inference | hard; requires aligner/error model | +| Comparative genomics | synteny/CNE/regulatory homology | hard; defer | + +## Mass Number interpretation for genetics + +Genetics is a communication regime, not a human-language regime. + +```text +DNA sequence + -> transcriptional decoder + -> RNA folding / splicing decoder + -> codon translation decoder + -> peptide folding decoder + -> cellular phenotype decoder + -> population-selection decoder +``` + +Recommended Mass Number classes: + +```text +MN-BIO-GEN Genetic sequence mass +MN-BIO-COD Codon / translation mass +MN-BIO-FOLD Folding / conformation mass +MN-BIO-POP Population-genetic mass +MN-BIO-REG Regulatory / epigenetic mass +MN-BIO-EVO Evolutionary trajectory mass +``` + +## Promotion policy + +A genetics model may be promoted beyond `BEAUTIFUL_PROVISIONAL` only when it has +at least one of: + +1. compiled Lean theorem or executable definition; +2. running Python/Rust pipeline with test fixtures; +3. real-data receipt with source provenance; +4. adversarial or benchmark receipt; +5. explicit connection to MassNumber admissibility or SemanticMass carrier scoring. + +## Immediate promotion candidate + +Implement selection metrics first: + +```text +Tajima's D + FST +``` + +Rationale: + +- low implementation difficulty; +- high genetics-information value; +- direct path from allele/genotype state to population selection signal; +- good MassNumber gate candidate for deciding whether selection evidence is + strong enough to promote a registry model.