Canonical Inventory: What Exists, What Maps, What's Needed
Purpose: Comprehensive inventory across all methodology directories. What canonical analyses exist, what can be pulled from v1_revision, and what needs to be written.
1. Directory Structure
methodology/
├── abstract_info_domain_analysis/ — Abstract mirrors of information substrates
├── biology_domain_analysis/ — Biology chain: chemistry → biology → organism → ecosystem
│ └── cognitive_substrate_domain_analysis/ — Cognition chain: cog substrate → cog arch → culture
├── entity_domain_analysis/ — Entity chain: digital → entity system → app arch → digital eco
├── math_information_domain_analysis/ — Mathematical info domains: IT, CC, DS, NT, info-comp core
├── methdology_domain_analysis/ — Methodology self-analysis: L1, L2, L3
├── methodology.md — The methodology document itself (v2)
└── v1_revision/ — Historical work (preserved as-is)
2. abstract_info_domain_analysis/
Currently has
| File | Status | Notes |
|---|
| analysis-abstract-information-substrate.md | NEW (this session) | 6 primitives {En,St,Ev,Dr,Op,Bd}. Full 12-step. Canonical. |
| analysis-info-comp-core.md | MISPLACED | This is actually information theory. Copy moved to math_information as analysis-information_theory.md. Should be removed or replaced. |
| exploration-info-comp-core-revision.md | NEW (this session) | Exploration comparing info-comp core vs IT vs abstract substrate. Working doc. |
Needs from v1_revision
| What | v1 source | Work needed |
|---|
| Abstract surface analysis | v1_biology_domain_analysis/abstract_conclusions/analysis-abstract-domains-full-expansion.md Part 2 | Extract Part 2, clean up into canonical form. 7+2 primitives {St,Or,Rg,Pr,Ac,Pt,Ex,[Rs],[Gn]}. |
| Abstract ecosystem analysis | Same file, Part 3 | Extract Part 3, clean up. 9 primitives {Pd,Tf,Cy,Dv,In,Rg,Sp,Tp,Ct}. |
| SSA topology analysis | v1_biology_domain_analysis/bio_v2/exploration-situated-substrate-architecture.md | Extract topology description, clean up. 7 primitives {En,Vr,Mc,Sf,Cx,Cm,Se}. |
| Connections between abstract domains | abstract_conclusions/exploration-abstract-structure-and-info-comp-revision.md | Extract the abstract bridge analysis and inter-abstract-domain edges. |
Cleanup
- Remove
analysis-info-comp-core.md (now in math_information as information theory)
- Decide: does the exploration-info-comp-core-revision.md stay here or move?
3. biology_domain_analysis/
Currently has
Empty (except cognitive_substrate_domain_analysis/ subfolder).
Needs from v1_revision
| What | v1 source | Work needed |
|---|
| Chemistry domain analysis | v1_biology_domain_analysis/bio_v1/biology-bridges.md (contains chemistry primitives) | Extract chemistry 6 primitives, write canonical analysis. |
| Biology substrate analysis | bio_v1/biology-domain.md | Has full analysis of {G,T,R,P,Reg,Mem}. Clean up into canonical form. |
| Chemistry→Biology bridge | bio_v1/biology-bridges.md + bio_v1/exploration-developmental-bridges.md | 6 bridge primitives {Cd,Cat,Gr,Fx,Cmp,Fb}. Extract and canonicalize. |
| Organism architecture | bio_v1/organism-architecture.md | 9 primitives. Full analysis exists. Canonicalize. |
| Biology→Organism bridge | bio_v1/exploration-developmental-bridges.md | 12 developmental mechanisms. Extract and canonicalize. |
| Environment | bio_v1/exploration-environment-and-ecosystem.md | 6 primitives. Extract. |
| Organism→Ecosystem bridge | bio_v2/exploration-graph-topology-and-cross-cutting-edges.md | 10 ecological mechanisms. Extract. |
| Ecosystem | bio_v1/exploration-environment-and-ecosystem.md | 9 primitives. Extract. |
| Case studies + manifestations | bio_v1/review-case-studies-and-critical-analysis.md | 13 species positioned. |
| Unified manifestation | bio_v1/exploration-unified-manifestation.md | E. coli etc. across all lattices. |
cognitive_substrate_domain_analysis/
Currently has
Empty.
Needs from v1_revision
| What | v1 source | Work needed |
|---|
| Cognitive substrate | bio_v2/exploration-cognitive-substrate-and-culture.md | 6 primitives {Rp,Ct,As,Sq,Sy,Ev}. Extract and canonicalize. |
| Cog substrate → Cog arch bridge | bio_v2/cognitive-bridge-mechanisms.md | 10 mechanisms. Extract. |
| Cognitive architecture | bio_v2/individual-cognitive-architecture.md | 9 primitives {Kw,Sk,Dc,Pl,Co,Jd,Cr,Si,Id}. Extract. |
| Cog arch → Cultural ecosystem bridge | bio_v2/cognitive-bridge-mechanisms.md | 10 social transmission mechanisms. Extract. |
| Cultural ecosystem | bio_v2/exploration-cognitive-substrate-and-culture.md | 9 primitives {Pr,Ex,Tr,Dv,Cd,Gv,Te,Sc,Ct}. Extract. |
4. entity_domain_analysis/
Currently has
Empty.
Needs from v1_revision
| What | v1 source | Work needed |
|---|
| Entity system substrate | v1_entity_domain_analysis/entity-system.md | 6 primitives {E,I,T,M,X,P}. Canonical analysis likely exists. |
| Digital computing domain | Not formally analyzed in v1 | Need new analysis or stub. 6 primitives named but not analyzed. |
| Entity→Digital bridge | v1_entity_domain_analysis/entity-system-extensions.md + methodology.md §6.2 | 6 bridge primitives {Enc,Hsh,Prt,Prs,Sch,Net}. Documented in methodology. |
| App architecture | v1_entity_domain_analysis/application-architecture.md | 9 primitives. Analysis exists. |
| Entity→App bridge | v1_entity_domain_analysis/entity-system-extensions.md | 12 system extensions as bridges. Partially analyzed. |
| Digital ecosystem | NOT analyzed | Major gap. Needs new analysis. |
5. math_information_domain_analysis/
Currently has
| File | Status |
|---|
| analysis-information_theory.md | Moved from abstract_info. 7 primitives {Σ,P,C,Ke,Kd,μ,Γ}. Needs header update to clarify it's IT not info-comp core. |
Needs from v1_revision
| What | v1 source | Work needed |
|---|
| Computational complexity | v1_full_analysis/information-computational-landscape.md §3 | 6 primitives. Extract and canonicalize. |
| Dynamical systems | Same file §4 | ~5 primitives. Extract and canonicalize. |
| Network theory | Same file §5 | 6 primitives. Extract and canonicalize. |
| Info-comp core (ACTUAL) | Same file §20 | 6→7 primitives {St,Str,Tf,Ev,Me,Co,Pa}. Needs full revision with Tr→Tf+Ev split. |
| Statistical mechanics | v1_full_analysis/thermodynamics-and-statistical-mechanics.md | 7 primitives. Extract and canonicalize. |
6. methdology_domain_analysis/
Currently has (complete for current purposes)
| File | Status |
|---|
| analysis-domain-analysis.md | Canonical L1 analysis |
| analysis-graph-construction.md | Canonical L2 analysis |
| analysis-graph-semantics.md | Canonical L3 analysis |
| exploration-synthesis-and-unified-manifestation.md | Working doc |
| exploration-inter-layer-edges-and-graph-constraints.md | Working doc |
| review-stress-test.md | Review doc |
| methodology-v2-draft.md | Draft methodology document |
Needs
- Finalize methodology-v2-draft.md → promote to methodology/methodology.md when ready
- May need advanced topics companion document
7. Priority order for populating
Immediate: Complete abstract_info_domain_analysis
Abstract information substrate DONE- Abstract surface (from v1 Part 2) — canonicalize
- Abstract ecosystem (from v1 Part 3) — canonicalize
- SSA topology (from v1 substrate architecture) — canonicalize
- Clean up: remove misplaced info-comp-core.md, update headers
Next: Fix math_information_domain_analysis
- Update analysis-information_theory.md header (clarify it's IT, not info-comp core)
- Extract CC, DS, NT from v1 landscape analysis
- Write revised info-comp core with Tr→Tf+Ev split
Then: Populate biology_domain_analysis
- Biology substrate — from bio_v1
- Chemistry — from bio_v1
- Chemistry→Biology bridge — from bio_v1
- Organism architecture — from bio_v1
- Biology→Organism bridge — from bio_v1
- Environment + Ecosystem — from bio_v1
Then: cognitive_substrate_domain_analysis
- Cognitive substrate — from bio_v2
- Cognitive architecture — from bio_v2
- Bridge mechanisms — from bio_v2
- Cultural ecosystem — from bio_v2
Then: entity_domain_analysis
- Entity system substrate — from v1_entity
- App architecture — from v1_entity
- Entity→Digital bridge — from methodology
- Entity→App bridge (extensions) — from v1_entity
- Digital ecosystem — NEW (gap)
Last: Finalize methodology
- methodology.md v2 finalized
- Advanced topics updated