CDFD Part II: Origins of Life and Tri-Regime Bioenergetics

This release contains the public Part II origins-of-life archive for the Constraint-Driven Flux Dynamics project.

Author

Steve Bico Mujjabi, MD
Independent Researcher
Founder, Vura Labs
Kampala, Uganda
ORCID: https://orcid.org/0009-0001-0556-5516

Institutional home: Vura Labs

Release Naming

CDFD Part II: Origins of Life and Tri-Regime Bioenergetics

Keywords

Constraint-Driven Flux Dynamics; CDFD; origins of life; abiogenesis; prebiotic chemistry; geochemistry; redox chemistry; alkaline hydrothermal vents; hot-spring hypothesis; iron-sulfur chemistry; magnetite; mixed-valence minerals; interfacial water; proton gradients; proto-chemiosmosis; wet-dry cycling; thermal gradients; phosphate activation; autocatalysis; chemical memory; chemical alphabets; homochirality; coacervates; liquid-liquid phase separation; protocells; vesicles; thioesters; RNA aminoacylation; peptide-RNA chemistry; RNA world; metabolism-first; error threshold; parasitic threshold; photochemistry; photoredox chemistry; overload stabilization; tri-regime bioenergetics; Life Number; Mujjabi Life Number; CDFL; CDFD Runtime; reproducible research; open science; preprint.

GitHub Topics

cdfd, cdfd-runtime, cdfl, constraint-driven-flux-dynamics, origins-of-life, abiogenesis, prebiotic-chemistry, bioenergetics, geochemistry, redox-chemistry, hydrothermal-vents, iron-sulfur, protocells, autocatalysis, coacervates, homochirality, rna-world, chemiosmosis, photochemistry, reproducible-research

Contents

• Part_II_Origins_of_Life_and_Tri_Regime_Bioenergetics/ - Part II manuscripts, PDFs, supplementary scripts, generated outputs, bibliography, named laws/tests, interactive panels, and reproducibility instructions.
• CITATION.cff - GitHub citation metadata.
• .zenodo.json - Zenodo deposit metadata.
• requirements.txt - Python dependencies for the public supplementary scripts.
• environment.yml - Conda environment for the public science stack.
• LICENSE - CC BY 4.0 release license.
• LICENSE_BOUNDARY.md - explains the boundary between this scholarly archive and the separately licensed public CDFD Runtime.

Final Part II Architecture

The final edit turns Part II into a twelve-paper dependency chain rather than a compressed origin story. The series moves from thermodynamic vocabulary to Fe-S redox, distributed mineral transport, proton/ion coupling, environmental cycling, autocatalytic closure, chemical alphabets, adaptive boundaries, replication, parasitic failure, photochemical expansion, and the master tri-regime synthesis.

This release explicitly cites Part I as the source of the public CDFD flow-constraint-memory grammar, here named CDFL: https://doi.org/10.5281/zenodo.20250821

Review Status

These manuscripts are archived as research/preprint materials and are not peer reviewed. The supplementary scripts reproduce toy diagnostics, figures, tables, and consistency checks. They do not establish empirical validation of any historical origin-of-life pathway.

Suggested Reading Order

1. Part_II_Origins_of_Life_and_Tri_Regime_Bioenergetics/README.md
2. Part_II_Origins_of_Life_and_Tri_Regime_Bioenergetics/MUJJABI_LIFE_LAWS_AND_TESTS.md
3. Part_II_Origins_of_Life_and_Tri_Regime_Bioenergetics/REPRODUCIBILITY.md
4. Part_II_Origins_of_Life_and_Tri_Regime_Bioenergetics/outputs/interactive_index.html
5. Part_II_Origins_of_Life_and_Tri_Regime_Bioenergetics/PDFs/

Reproducibility

See Part_II_Origins_of_Life_and_Tri_Regime_Bioenergetics/REPRODUCIBILITY.md for rebuild and verification commands. The active release is script-first. It does not include placeholder notebooks. Output folders are included only where a paper cites a generated figure, table, or diagnostic. The optional make_interactive_panels.py script builds local HTML viewers over those generated outputs.

The May 2026 follow-up adds a guarded Paper 7 aromatic source-mix diagnostic (outputs/paper_07/aromatic_source_mix.csv) and keeps Paper 11 eumelanin language as a mature photochemical endpoint example, not an origin requirement. The best retained source-mix row is mixed_source_surface_trap with functional score 0.610; the result is a provenance guardrail, not historical proof.

Public CDFD Runtime

The CDFD Runtime is the reusable implementation target for CDFL, the flow-constraint-memory language used across the CDFD series. This Part II release remains a scholarly archive: its paper-local Python scripts and outputs reproduce the diagnostics cited by the origins-of-life manuscripts.

Cite and license the two layers separately until a combined CDFD Runtime release DOI exists.

Reference Verification

All DOI-backed bibliography entries were checked online against Crossref or DataCite on 2026-05-18. The 2024-2026 release anchors used for the final sweep were rechecked against publisher or PubMed records on 2026-05-20. The Murchison aromatic/organic and eumelanin endpoint anchors added after release were rechecked against publisher, PubMed, or DOI records on 2026-05-30. The bibliography includes real DOI-backed references, Part II Zenodo DOI, plus the Part I Zenodo DOI.

License

This release is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). See LICENSE and LICENSE_BOUNDARY.md.

Citation

Mujjabi, S. B. (2026). CDFD Part II: Origins of Life and Tri-Regime Bioenergetics - Constraint-Driven Flux Dynamics. Zenodo. https://doi.org/10.5281/zenodo.20264779

Steve Bico Mujjabi, MD. CDFD Part I: Fundamental Physics. Zenodo. https://doi.org/10.5281/zenodo.20250821