Theory of Mutation by Natural Dominance (TMD) — v2.5.4: ETLR + gamma‑race time + information‑geometry decomposition

Overview

This deposit contains TMD (Theory of Mutation by Natural Dominance) — a reproducible, prereg‑friendly framework for quantifying evidence, predictability, and mechanistic structure in mutation outcomes from experimental evolution / parallel evolution panels.

Scope note: This deposit is an analysis framework + locked benchmark/unit-test harness. It does not claim new experimental validation beyond included panels.

TMD’s core objects are:

• Evidence vs null: Bayesian evidence (Bayes factor) for observed winner-route counts under a chosen null distribution q (uniform or mechanistic).

• Predictability: entropy‑based predictability of the winner distribution.

• Planning leverage: a practical “replicates needed” metric for achieving target evidence thresholds under post‑mean planning.

This version extends the framework along two axes:

1. ETLR — Exponential‑Tilting Low‑Rank residuals: a compact, testable bridge between a mechanistic null and observed data, emphasizing low‑rank residual structure across panels/contexts.

2. Gamma‑race time module — a falsifier suite for time‑to‑first‑winner data under a gamma‑mixed hazard race, producing sharp predictions (e.g., Lomax/Pareto‑II pooled survival form and winner–time independence).

What’s new in v2.5.4

• Gamma‑race time falsifiers (optional, when replicate‑level arrival times exist)

  • Lomax (Pareto‑II) survival signature under gamma mixing

  • Winner–time independence as a sharp falsifiable signature

   

• Information‑geometry framing for decomposing evidence and time structure

• Updated locked analysis unit test pack (deterministic; fixed seeds) with optional time module

• Updated paper draft and falsifier sheets to reflect these additions

Included files (top level)

This deposit is distributed as a small set of “share” bundles and locked outputs:

• TMD_share_pack_2026-02-04.zip

  A curated pack containing:

  • TMD_v2_5_4_candidate_release_bundle_2026-02-03.zip (core release bundle)

  • paper draft, falsifier sheets, prereg blocks, templates, and notes

   

• TMD_locked_run_2026-02-04_outputs.zip

  Deterministic locked run outputs for the unit‑test panels (for independent verification).

• TMD_locked_unit_test_repro_check_2026-02-04.md

  A checksum‑style reproducibility note confirming that the locked run matches the committed expectations.

• TMD_progress_summary_2026-02-05.md and TMD_next_steps_2026-02-04.md

  Short “where we are / what’s next” summaries.

Reproducibility

A “locked” runner + unit‑test pack is included so independent reviewers can reproduce the main plots/tables deterministically (fixed seeds, pinned dependencies) and verify checksums against the included reproducibility note.

Prereg + falsification workflow

This deposit includes:

• a prereg‑ready text block for OSF,

• falsifier sheets (including time‑module falsifiers),

• and a gate checklist that specifies what must be locked before looking at the held‑out results.