Mutation by Natural Dominance (TMD): a testable framework for evolution and the origin of life — software & data (v0.8)

Short description

Plain summary. Mutation by Natural Dominance (TMD) is a testable framework for predicting which adaptive genetic route appears first when several solutions are available. The core rule is simple: the chance that a route wins first is proportional to its mutation rate (μ) × genome accessibility (A) × fixation probability (F). This record releases an execution‑grade toolkit (code, docs, figures) to run preregistered tests (G1–G3), design studies, and reproduce the plots shown in the accompanying materials.

 

Long description

# Mutation by Natural Dominance (TMD) — Zenodo record (v0.8)

 

**Status**: testable framework (pre‑theory). When preregistered gates G1–G3 pass, cite as “The Theory of Mutation by Natural Dominance (TMD).”

 

**Core idea (plain language)**

Evolution often follows the *easiest* genetic path. Some mutations occur more often (chemistry), and some genome regions are more exposed (architecture). The route with the largest **MDI = μ × A × F** tends to win first.

 

**What’s in this record**

- **Software kits**: `TMD_kit_v0_2.zip` … `TMD_kit_v0_8.zip` (pipelines for G1–G5, power calculators, dominance/ridge plots, replicator–mutator and Poisson‑race simulators).

- **Figures bundle**: publication‑ready PNGs (power surfaces, dominance ridge, timecourses, first‑fix histograms).

- **Design data**: example JSON/CSV templates; power and ridge tables.

- **Docs**: whitepaper draft, submission pack, explainer, prereg blocks, figure captions.

 

**How to run (one‑liners)**

- G3 “who fixes first?”: `python pipelines/gillespie_first_fix.py 5e-3 2e-3 5000`

- CTMC timecourse (full Λ): `python pipelines/rm_timecourse_ctmc2.py examples/ctmc_params_general.json 1e84000`

- Dominance ridge (μ‑ratio at P1=0.5): `python pipelines/ridge_from_params.py 0.02 0.015`

 

**Licensing inside the bundle**

- **Code**: MIT (see `CODE_LICENSE_MIT.txt`)

- **Text & figures**: CC BY 4.0 (see `DOCS_LICENSE_CC_BY_4_0.txt`)

 

**Reproducibility notes**

- File inventory + hashes: `TMD_Zenodo_file_inventory.(md|csv)`

• Exact figure captions: `figure_captions.md`

 

Maldonado, R. (2025). Mutation by Natural Dominance (TMD): a testable framework for evolution and the origin of life — software & data (v0.8) [Software]. Zenodo. https://doi.org/10.5281/zenodo.17335715