Quantum Biology — Map of Content (MOC)
Definitive axioms and anchor concepts for the quantum_biology corpus 312,900 chunks | Last updated: 2026-02-02
🔬 FOUNDATIONAL AXIOMS
A1. Quantum Coherence in Biological Systems
The persistence of quantum superposition states in warm, wet biological environments
- Anchor: Decoherence timescales in protein environments
- Key tension: How do biological systems maintain coherence despite thermal noise?
- Related: A2, A5
A2. Quantum Tunneling in Enzyme Catalysis
Proton and electron transfer via quantum tunneling enables reaction rates impossible classically
- Anchor: Kinetic isotope effects (KIE) as tunneling signatures
- Key enzymes: Alcohol dehydrogenase, aromatic amine dehydrogenase
- Related: A1, A3
A3. Radical Pair Mechanism in Magnetoreception
Spin-correlated radical pairs enable magnetic field sensing in birds/insects
- Anchor: Cryptochrome proteins in avian retina
- Key phenomenon: Singlet-triplet interconversion under Earth-strength fields
- Related: A4, A6
A4. Quantum Effects in Photosynthesis
Near-unity energy transfer efficiency via quantum coherent exciton transport
- Anchor: Fenna-Matthews-Olson (FMO) complex
- Key finding: 2D electronic spectroscopy evidence of long-lived coherence
- Related: A1, A3
A5. Olfaction and Vibration Theory
Molecular vibration frequencies (not just shape) determine smell perception
- Anchor: Inelastic electron tunneling spectroscopy (IETS) model
- Key debate: Shape vs. vibration controversy
- Related: A2
A6. Quantum Biology of Consciousness (Speculative)
Microtubule quantum computations as substrate for consciousness
- Anchor: Orchestrated Objective Reduction (Orch-OR) theory
- Proponents: Penrose, Hameroff
- Status: Highly controversial, limited experimental support
- Related: A1
📊 ENTITY DOMAINS
Materials & Molecules
(Populated from corpus entity extraction)
| Category | Top Entities | Chunk Count |
|---|---|---|
| Proteins | cryptochrome, chlorophyll, cytochrome | TBD |
| Cofactors | flavin adenine dinucleotide (FAD), porphyrins | TBD |
| Structures | FMO complex, reaction centers, microtubules | TBD |
| Small molecules | ATP, NADH, radical species | TBD |
Processes & Mechanisms
| Category | Top Entities | Chunk Count |
|---|---|---|
| Energy transfer | Förster resonance (FRET), exciton coupling | TBD |
| Electron transfer | Marcus theory, superexchange | TBD |
| Spin dynamics | Radical pair mechanism, intersystem crossing | TBD |
| Tunneling | Proton-coupled electron transfer (PCET) | TBD |
Properties & Observables
| Category | Top Entities | Chunk Count |
|---|---|---|
| Spectroscopic | 2D electronic spectroscopy, EPR, NMR | TBD |
| Kinetic | Isotope effects, temperature dependence | TBD |
| Quantum | Coherence lifetime, entanglement | TBD |
Applications & Organisms
| Category | Top Entities | Chunk Count |
|---|---|---|
| Organisms | Cryptophyte algae, migratory birds, bacteria | TBD |
| Applications | Quantum sensors, artificial photosynthesis | TBD |
| Medical | Cancer therapy (PDT), drug design | TBD |
🔗 CROSS-DOMAIN CONNECTIONS
QB ↔ Medicine
- Photodynamic therapy (PDT) - quantum yield optimization
- Drug-protein tunneling interactions
- Radical damage in DNA/aging
QB ↔ Engineering
- Bio-inspired solar cells (dye-sensitized)
- Quantum dot fluorescent probes
- Biomimetic magnetometers
QB ↔ Neuroscience
- Anesthesia mechanisms
- Neural quantum effects (controversial)
- Circadian rhythm magnetoreception
🎯 GAP DETECTION PRIORITIES
Based on entity co-occurrence analysis, investigate:
- Low-hanging fruit: Common entities that never appear together
- Mechanism gaps: Known processes lacking proposed quantum mechanisms
- Measurement gaps: Predictions without experimental methodology
- Application gaps: Understood mechanisms without engineering translation
📚 KEY LITERATURE ANCHORS
Foundational papers to trace citation networks
- Engel et al. (2007) - “Evidence for wavelike energy transfer” (Nature)
- Ritz et al. (2000) - “A model for photoreceptor-based magnetoreception”
- Klinman & Kohen (2013) - “Hydrogen tunneling in enzyme catalysis”
- Turin (1996) - “A spectroscopic mechanism for primary olfactory reception”
- Lambert et al. (2013) - “Quantum biology” (Nature Physics review)
📖 CORPUS SOURCE ANALYSIS
Semantic query results showing primary sources per concept
| Concept | Primary Sources |
|---|---|
| Quantum coherence + photosynthesis | kruse_patreon (dominant) |
| Cryptochrome magnetoreception | Conscious Life, kruse_patreon |
| Enzyme tunneling | Encyclopedia of Cell Biology, Medical Biochemistry (Godkar) |
| Radical pair mechanism | kruse_patreon (dominant) |
| Olfaction vibration theory | Molecular Spectroscopy, Photochemistry texts |
| Microtubule consciousness | kruse_patreon (dominant) |
| FMO complex energy transfer | Biochemistry textbooks (Lal) |
| Proton-coupled electron transfer | Biochemistry textbooks, kruse_patreon |
Source Distribution Notes
- kruse_patreon: Heavy representation of Jack Kruse’s quantum biology content
- Conscious Life (Torday & Sacco 2025): Recent monograph bridging QB and consciousness
- Textbooks: Godkar, Lal biochemistry — foundational mechanisms
- Spectroscopy texts: Sathyanarayana, Turro — physical chemistry basis
Entity Extraction Status
⚠️ PENDING: Entity extraction (materials/processes/properties/applications) not yet run on quantum_biology collection. Current metadata: {chunk, source} only.
Action Required: Run python patentbot.py reindex on quantum_biology to enable gap detection.
🔄 MOC MAINTENANCE
- Populate entity tables from corpus extraction
- Add chunk count references to each axiom
- Build citation network graph
- Identify highest-confidence gap candidates
- Cross-reference with patent databases
This MOC serves as the conceptual backbone for PatentBot gap detection in the quantum biology domain.