Quantum Biology MOC — Version History
Tracking the evolution of our knowledge pipeline from empty template to data-driven corpus analysis.
Version Timeline
| Version | Date | Location | Focus |
|---|---|---|---|
| v0 | Feb 2 | knowledge-rag/docs/ | 6 Axioms (A1-A6), gap detection framework |
| v1 | Jan 27 | notes.shdwnet.org | Empty Dataview template |
| v2 | Jan 31 | a872c76 | Basic structure, topic list |
| v3 | Feb 1 | 589278f | Book library integration |
| v4 | Feb 2 | b873bf9 | Kruse framework, concept notes |
| v5 | Feb 2 | 80e1382 | Entity extraction data |
V0: Axiom Framework (PatentBot Native) ⭐
Location: ~/projects/knowledge-rag/docs/QB_MOC.md
Commit: 2ad2e7a — PatentBot repo
The original QB MOC, created for gap detection. Lives in the PatentBot codebase, not Obsidian.
6 Foundational Axioms
| Axiom | Name | Anchor |
|---|---|---|
| A1 | Quantum Coherence in Biological Systems | Decoherence timescales |
| A2 | Quantum Tunneling in Enzyme Catalysis | Kinetic isotope effects (KIE) |
| A3 | Radical Pair Magnetoreception | Cryptochrome proteins |
| A4 | Quantum Effects in Photosynthesis | FMO complex |
| A5 | Olfaction Vibration Theory | IETS model |
| A6 | Quantum Biology of Consciousness | Orch-OR (speculative) |
Structure
- Entity domain tables (Materials, Processes, Properties, Applications)
- Cross-domain connections (QB↔Medicine, Engineering, Neuro)
- Gap detection priorities
- Literature anchors (Engel 2007, Ritz 2000, etc.)
- Corpus source analysis
What it was: Designed for PatentBot gap detection, not human navigation. Academic axiom structure with placeholder tables awaiting entity extraction.
Key insight: This is the analytical MOC. The Obsidian versions are navigational MOCs. Different purposes.
V1: Empty Template (Jan 27)
Commit: a37701c — Initial setup
# 🧬 Quantum Biology & Photobiomodulation
## Active Projects
-
## Key Resources
-
## Notes
\`\`\`dataview
LIST FROM "02-Areas/QuantumBio-Photobiomod"
\`\`\`What it was: Bare Dataview scaffold. No content, just structure placeholder.
V2: Basic Structure (Jan 31)
Commit: a872c76 — Restructure notes
Added:
- Area hub link
- Key topics list (bullet points)
- Related section
Topics introduced:
- Photobiomodulation / Red Light Therapy
- Mitochondrial function & ATP
- Circadian biology
- Biophotons
- Quantum coherence in biology
What changed: First real content. Manual topic list based on domain knowledge.
V3: Book Library (Feb 1)
Commit: 589278f — Add Book Library
Added:
- Link to quantum book collection (150+ titles)
- Key texts list (Bohm, Heisenberg, Feynman, Schrödinger)
What changed: Integration with physical corpus. Books now tracked.
V4: Kruse Framework (Feb 2, morning)
Commit: b873bf9 — Consolidate QB MOCs
Major expansion:
- Three Levers framework (Light, Water, Magnetism)
- Academic quantum biology axioms table
- Concept notes structure (placeholder links)
- Classical QBio phenomena table
- Corpus reference (378k chunks mentioned)
- Protocol notes
What changed: First domain-specific framework. Kruse philosophy integrated. Still manually curated content.
V5: Entity Extraction Data (Feb 2, night) ⭐
Commit: 80e1382 — Entity extraction from 40k Kruse chunks
Data-driven rewrite:
Corpus Stats Added
| Source | Chunks |
|---|---|
| kruse_patreon | 40,002 |
| Conscious Life | 150 |
| Quantum Theory Brain | 150 |
| Quantum Neuroscience | 129 |
| Bohm Implicate Order | 126 |
| Total enriched | 40,557 |
Top Entities (extracted, not manual)
| Entity | Mentions |
|---|---|
| Mitochondria | 4,550 |
| Melanin | 3,822 |
| Deuterium | 2,349 |
| Melatonin | 1,939 |
| DDW | 1,827 |
Top Concepts (extracted)
| Concept | Mentions |
|---|---|
| Melanin Evolution | 507 |
| Kinetic Isotope Effect | 480 |
| Heteroplasmy | 403 |
| Cold Thermogenesis | 384 |
Domain Distribution (from enrichment)
| Domain | Chunks |
|---|---|
| Biophysics | 4,395 |
| Quantum Biology | 2,955 |
| Chronobiology | 2,349 |
What changed:
- Content now driven by actual entity extraction pipeline
- Numbers reflect real corpus analysis
- Concepts ranked by frequency, not assumption
- Reproducible from pipeline output
Pipeline Evolution
V0: Axiom framework (PatentBot) ← Gap detection structure
↓ (lives in knowledge-rag repo)
V1: Empty Obsidian template
↓
V2: Manual topic list
↓
V3: Book inventory added
↓
V4: Domain framework (Kruse) ← Merged axiom thinking
↓
V5: LLM entity extraction (40k) ← Data-driven content
↓
V6: [NEXT] Cross-corpus analysis
+ Pharmakon Miner integration
+ physicists_corpus merge
+ Merge V0 axioms back in
Two MOC Lineages
| Lineage | Location | Purpose |
|---|---|---|
| Analytical | knowledge-rag/docs/QB_MOC.md | PatentBot gap detection |
| Navigational | notes.shdwnet.org/Maps/ | Human quick-reference |
The analytical MOC (v0) informed v4’s structure, but they serve different audiences.
Key Learnings
- Start with structure — Even empty templates help organize later work
- Manual → Automated — Human curation bootstraps, extraction scales
- Domain frameworks matter — Kruse’s Three Levers organized chaotic data
- Entity extraction reveals priorities — Melanin (3,822 mentions) > expected
- Corpus stats = credibility — Numbers prove the pipeline works
Next Steps
- Merge physicists_corpus entities (when indexing completes)
- Cross-reference with Pharmakon Miner Greek terms
- Build concept relationship graph
- Auto-generate MOC updates from new enrichment runs
View current MOC: 🧬 Quantum Biology MOC
This document tracks pipeline maturity, not just content.