Darwin — genome · universe · library · theory of the ecosystem

Named after Charles Darwin (evolution). This repository is the 𝕌_local of a three-organ AI ecosystem: its genome (structure), its environment ℛ / reality (the external arbiter; invariants grounded in it), its library (external sources), its theory (formal model). Three organs live in it and are shaped by it:

• M = mirabilis (sandbox / mechanism phenotype) — "coral" · github.com/AlexShchuka/mirabilis
• N = neuro-matrix (harness / behaviour phenotype) — "seahorse" · github.com/AlexShchuka/neuro-matrix
• S = SolitaryEquilibriumShield (knowledge / epistemos phenotype — α_S, knowledge-lane) · github.com/AlexShchuka/SolitaryEquilibriumShield

What this repo is / is not

• IS the complete, dense, modular description of the ecosystem's reality — readable by humans AND other AIs that mine it for ideas (the role the cross-AI advisory exemplar plays today; that pattern moves here).
• IS NOT a code repo (organs hold the code) · NOT a GitHub-issues tracker (issues = "dangling leaves" → migrate into Γ: theory→dept/, transient threads→vectors/) · NOT an archive (genome ≠ archive: raw per-session logs stay OUT, in SCRATCH).

Self-description — how to operate Darwin so the whole universe evolves · [INVARIANT]

The operating loop is invariant machinery (fixed, like transcription); the content it moves is evolvable.

PRE-0  NAVIGATE, not transcribe: start at README (this map), route task→chain via the Map + §H index,
       read ONLY that chain. Repo-link + task-prompt suffice to reach the needed chain. (§J PRE-0; R6/liu-2023)
PRE-1  PRESENCE NEVER ASSUMED: every pointer (repo, file, tool, MCP) is HYPO-until-verified against reality.
       Absence/rot is normal — re-anchor, provision, or report; never proceed blind. (§J PRE-1; R1/inv#1/§B)
1 READ    Γ = GENOME + genome/ + archive/ + dept/ + vectors/   → full picture (¬dangling-leaves)   [invariant #22]
2 LOCATE  dept/graph-plan-{harness,sandbox,communication}        → "what & how to improve" (to detail)
3 ACT     mutate organ M or N  (variation V) via role agents
4 SELECT  reality/owner judge (R→S): AskMe + eval + tests        → FACT                              [directed]
5 WRITE   compress the session → delta over {genes, invariants, Λ, Vec, dept} ;  raw → SCRATCH, outside Γ  (genome ≠ archive)
          ~/.claude/memory = first-order collector (staging) → compressed into Γ
6 SHARE   other AIs read Γ → extract ideas                                                            [the cross-AI advisory exemplar]

Invariant: every cycle reads Γ before it acts; the content mutates while the operating loop stays fixed.

Strata — graded by stability (§G)

CORE     GENOME.md           foundation: formal model · evolution rules · density · CONST→FUNC · operating loop.  change = fundamental
BODY     genome/ + archive/  genome content (registries 𝒢 · projections · mined-candidates · Λ); evolves by selection
DEPT     dept/               INTERMEDIATE · preserved · DECOUPLED: the R→S audit + graph-plans.  a change here does not touch CORE
Vec      vectors/            transient working-state (open fixes/bugs/migrating issues); implemented → discard
SCRATCH  (outside Γ)         session-dump · critic-findings → /workspace/  short-lived checking, exported as entropy

Encoding & discipline

English + first-order predicate logic where a real formal object exists; honest dense prose elsewhere — the densest faithful encoding (§C). Density is preserved-meaning per token: a guiding heuristic, not a computed fitness function (preserved-meaning is not measurable). Per-claim tag FACT | ASSOC | HYPO | Q. Content is evolvable, not axioms; constants → functions (§A.3). We are engineers, not blind evolution: get the initial invariant set right while keeping every invariant mutable.

Map

README.md                  this — invariant self-description + tiers + map
GENOME.md                  CORE: §A carriers/𝕌_local · §A.1 completeness · §A.2 engineering · §A.3 CONST→FUNC
                           · §B gene algebra · §C density · §D evolution · §E independence · §F externalization / asymmetric gene-loss lens (seahorse depends on coral; not symmetric peers)
                           · §G strata (stability tiers) · §H registry index · §I ledger · §J operating loop
genome/registry-M.md       𝒢|M coral genes (sandbox anatomy + work-items + INV-D/E/F)
genome/registry-N.md       𝒢|N seahorse genes (invariants + agents + skills + hooks + eval + scripts + refs)
genome/registry-new.md     𝒢|+ new genes (know/fleet/obs+/domain/route) + channel genes (sci/web/code)
genome/projections.md      proj_M / proj_N : two graphs from one 𝒢 + ecosystem-graph (5 nodes: M,N,Γ,S + ℛ-external)
genome/mission.md          owner vision: raid-target (T1/T2/T3) + owner–AI generation loop [HYPO/ASSOC]
genome/mined-invariants.md candidate invariants from the memory dump (CI-1..14 + comms primitives)
genome/design-principles.md design principles G0–G13 (sandbox/engineering; home for all Gn references)
archive/archive.md         Λ external sources by department (dedup; upstream research-anchors.md)
dept/theory-of-everything.md     the R→S audit — formal-methods spec + cross-disciplinary graph + dev-vector R→S/V1–V7
dept/graph-plan-harness.md       what & how to improve N (vector: close R→S first)
dept/graph-plan-sandbox.md       what & how to improve M (work-items W1–W8, by gene)
dept/graph-plan-communication.md communication systems (AskMe/codebook/protocol/Telegram/translator/caveman)
vectors/vectors.md         Vec index + lifecycle
vectors/bugs.md            open fixes (N eval-gate + M token-opt §M-iter open residue)
vectors/idea-exchange.md   the cross-AI advisory exemplar migrated (public-Γ; patterns → compress into Λ)