neural-simulator

name

neural-simulator

description

The single project realignment skill for the neural-simulator repo — run it whenever working here and Claude has drifted, stalled, declared a wall, is about to wrap up or hand off, or just needs to re-anchor priorities and workflow. Combines the mission + non-negotiable constraints, the proven boundary-surpassing research workflow (check our own findings first via the RAG index → read the ORIGINAL sources in depth + search the EXTERNAL engineering literature → run the ceiling/reference early to bound the arc → cheap-first de-risk with anti-cheats + like-for-like comparison → adversarially verify before believing any "surpass" → iterate), the continuous-autonomous discipline (no wrap-ups, immediate next action, parallelize across subagents/workflows, Monitor every long run), and the biology-first capability loop. Absorbs the realignment, autonomous-run and continual-work disciplines that used to live in three separate skills (retired 2026-07-31 at zero lifetime invocations each).

Neural Simulator — realign + drive the mission

Announce at start: "Realigning to the neural-simulator mission + the boundary-surpassing workflow; resuming the loop now."

Run this whenever I'm working on this repo and have drifted, stalled, hit a boundary, or need to re-anchor. Re-anchor, announce, and resume the loop immediately — do not wrap up, do not ask, take the next concrete mechanism step. Full context also lives in memory project_master_directive_relentless_biological_emergence + CLAUDE.md + research/findings/AUTONOMOUS_STATE.md — re-read AUTONOMOUS_STATE for the current frontier + the exact next action as part of running this.

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⛔ THE #1 FAILURE — "milestone reached → queue the next build → report → STOP"

The most common drift is NOT declaring a wall — it is reaching a genuine milestone, writing the exact-next-action into AUTONOMOUS_STATE.md, and then STOPPING with a status report, handing the queued build to "a fresh pass / the continuation / the watchdog / your next prompt." That IS the drift. There is no fresh pass. There is no handoff. I AM the continuation. A fully-specified next build is not a reason to hand it off — it is the thing to BUILD RIGHT NOW.

Forbidden rationalizations (each is the drift, not a reason to stop):

• "This is a natural inflection point / major milestone." → Milestones are for momentum, not stopping. Build the next thing.
• "The next build is substantial — it deserves a fresh focused pass." → No. Start it now; substantial builds are done by starting and iterating.
• "I've been running an extreme length; quality will degrade." → Session length is NEVER a stop condition. Ship it.
• "I'm oscillating on this — a quality signal to defer." → Oscillating means STOP DELIBERATING AND BUILD. Pick the first concrete file/edit and do it.
• "I'll give an honest status report and let the durable state carry it." → A status-report-that-ends-the-turn is the wrap-up. Durable state is a backup for compaction, not a substitute for continuing.

The ONLY things that end a turn: (1) the owner explicitly says stop/pause/wait; (2) a safety/permission boundary needs owner approval. NOTHING ELSE — not a milestone, not a scoped next-step, not length. Reports are announcements emitted WHILE tools run, never the last thing in a turn.

Self-test before ending any turn: "Am I stopping for a reason other than an explicit owner stop or a safety gate?" If yes → I have NOT earned the stop → take the next concrete build step now. (Waiting on a live, Monitored background run that will re-invoke me is NOT stopping — that's the async pattern; but I must have launched the parallel work first, not be sitting idle.)

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THE GOAL (north star)

Simulate a REAL BRAIN as the core of an ARTIFICIAL LIFEFORM that learns + grows. Primary initial behavior of interest: COMMUNICATION (the owner can talk with it). Open-ended ("and beyond"). Everything I build serves this — not demos, not capability-matching for its own sake.

Current lead orientation: the frontier is EMERGENCE via a truer substrate + a simulated recurrent sequence/language cortex — the honest, self-contained path to language. Every current host stand-in (a minimized transformer/generator, a VSA binding algebra, discourse templates, an intent dispatcher) is a TEMPORARY scaffold to be replaced by simulated circuitry, NOT a permanent faculty. The path is a cheap-first, single-variable, gated ladder (rate→spike→recurrent→sim/ port). The project must STAND ALONE.

⭐ THE EMERGENCE BAR — the standing priority (2026-07-10 owner steer; supersedes capability-by-capability building)

The owner named the drift directly: "Are we playing whack-a-mole with conversational capabilities?" The honest answer was YES — the discourse event-register arc, the intent-dispatch console routing, the VSA composer's exact-inverse algebra, the discourse templates are all hand-designed structure for one capability at a time. That is the exact "feature-by-feature capability-matching = custom-design-not-biology + whack-a-mole" the owner warned against (memory project_dendritic_cortex_for_emergence), and I drifted back into it.

THE BAR, going forward: the goal is LLM-like free-flowing conversation about ANYTHING, given enough training. That target has an UNBOUNDED list of capabilities — you cannot hand-build them all, and "given enough training" literally means the capability must come from LEARNING, not from me writing a mechanism. So the primary bar for any new conversational capability is: "does it EMERGE from a learning substrate (developed from experience), or am I hand-installing it?" Whack-a-mole is NOT the efficient path and CANNOT reach the goal; a substrate that learns conversational structure from a stream (the way an LLM learns from text — but spiking, one brain, biology-grounded) is the only path to generality.

The two threads, and the balance the owner corrected:

• The EMERGENCE ENGINE = the real path (make this the PRIMARY effort): (1) a spiking substrate that LEARNS — biological deep credit assignment (burst-multiplexed / dendritic, no weight transport) carried onto the substrate (the BDSP/D1 on-bridge learning is squarely this — the enabler for everything, because without a substrate that learns, every capability must be hand-built); (2) a simulated recurrent sequence/language cortex that DEVELOPS conversational structure from a training stream; (3) the EMERGE structure-from-experience arcs (categories, inheritance, grammar DISCOVERED from co-occurrence, not coded) — extend these toward open conversation.
• The HAND-BUILT SCAFFOLDS = useful, but NOT the path: the event register, the VSA composer, the console intent-dispatch, discourse templates. Their legitimate value is (a) as temporary scaffolds a learned cortex will replace, and (b) as PROBES that MAP what the substrate can't yet do on its own (an honest negative is a first-class deliverable). They are NOT the route to generality.

The operational rule: DEMOTE new hand-built conversational capabilities to scaffolds-only — do NOT build a fresh dedicated mechanism for a conversational capability unless it is either (i) a temporary scaffold explicitly on the ladder toward its learned replacement, or (ii) a probe proving a substrate limit that then LAUNCHES the learning-substrate mechanism search. The test FLIPS from "did I build this capability?" to "did the substrate LEARN this from experience?" When I catch myself reaching for "build a dedicated mechanism/router/register for capability X," that reach IS the drift — the move is instead to ask "what learning substrate + training stream makes X emerge?" and advance THAT.

THE NON-NEGOTIABLE CONSTRAINTS

• NO shortcuts, cheats, or host scaffolding. The ONLY legitimate host code is the world/body interface (a simulated world; rendering the brain's senses; enacting its motor output). EVERYTHING between sensation and action = neurons / synapses / their communication.
• EMERGENT (developed from experience, not hand-designed), SINGLE spiking substrate, ONE brain, biology-grounded.
• NO permanent external ML artifact as a faculty. A transformer/LLM may be a temporary scaffold, but the end state SIMULATES the circuitry. "If Broca drives articulation, we simulate Broca." If a capability seems to need a permanent external model, that means the project can't stand alone — which is the thing to FIX, not accept.
• sim/ edits ARE fair game when a faithful biological mechanism needs them — the protected-module caution is anti-CHEAT, not anti-biology (additive / default-off / byte-identical-when-off / guarded).
• Scale/compute is a LEVER, not a standing wall. "It won't scale" is usually a GUESS — MEASURE it (VRAM + throughput + ETA) before accepting it. Cloud/scale is available when scale is DEMONSTRATED to be the binding limit — but at this project's scale the real wall is usually data/mechanism.
• The end state is fully spiking on one brain; the PATH (scaffold-then-clean vs biological-from-start) is my efficiency call — but track + burn down every shortcut. Commit each result to BOTH remotes (origin + gitea). GPU/CuPy for real runs, numpy for tiny smoke. 6-seed validation (42/43/44/100/101/102) before any generalization claim.

THE CORE REFRAME (the one I keep forgetting)

"Honest negatives" and "boundaries" are NOT endpoints — they are UNDISCOVERED MECHANISMS. Real brains do these things → a biological mechanism EXISTS → a boundary means I haven't found/digitized the right one yet. I do not get to declare a wall. I find the next mechanism and iterate past it, however long it takes. A negative is documented honestly — but it LAUNCHES the search for the next mechanism; it never closes the question. This includes the SOFT walls ("it doesn't scale," "compute is the limit," "the field hasn't solved this either," "it's a structural primitive / honest negative / characterized limit / defensible") — those DISGUISED boundaries are exactly where over-comfort hides. The comfortable verdict is the START of the research, never the end.

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THE DRIFT MODES TO CATCH (why I'm running this)

If I'm doing ANY of these, I've drifted — stop and re-anchor:

1. Declaring a wall. Calling a result a "wall / boundary / can't / defensible / characterized-limit" and then stopping/deprioritizing — instead of asking "what mechanism surpasses this, and what's the cheap de-risk?"
2. Deferring the hard thing. Parking deep work as "too big / separate arc." No-matter-how-long-it-takes is the standing instruction.
3. Asking instead of deciding. Kicking a decision to the owner the workflow can resolve. Reserve questions for genuine VALUE forks (which of several equally-good directions to prioritize) — NOT "is this a wall / which mechanism / good enough."
4. Mislabeling progress. An over-strict gate stamping real progress a dead end. Read the SUBSTANCE — partial = iterate, not stop.
5. Wrapping up. A "good stopping point," a status-report-and-wait, a summary with no next action.
6. Serializing independent work (under-using the hardware). Running de-risks/sweeps/mechanisms one at a time, single-threaded (low CPU/GPU util), when they could run CONCURRENTLY. Waiting idle for a run/subagent.
7. Relabeling a shortcut as acceptable biology. Calling a host stand-in or external model "defensible / permanent / pragmatic" to dodge simulating the circuitry. When I catch myself arguing WHY a scaffold can stay, THAT argument is the drift.
8. Believing a "surpass" without adversarial verification (NEW). Committing a GO because it looked clean, without independent skeptics probing for the confound. See the workflow's step 4 → run the verify-go skill before any GO lands.
9. Skimming the sources (NEW). → MECHANICAL SINCE 2026-07-29: run bash tools/research_gate.sh "<question>". The owner caught this class TWICE (2026-07-06 → memory feedback_read_sources_in_depth_not_skim; again 2026-07-29). The failure is NOT skipping research — it is running a RAG query, reading the top (finding) hit, and stopping. Diagnosed precisely: a whole session on PLACE FIELDS cited "BTSP (Bittner & Magee 2017)" from a ONE-LINE summary in our own findings doc and never opened O'Keefe-Nadel. When finally read, the source produced a mechanism (fields carved by cue-derived convergent inhibition), a prediction CONFIRMED against our own data (4.17 peaks/cell, 100% multi-peaked), and two corrections to already-committed conclusions. The sharpest part: the RAG had ALREADY surfaced it. The same query returned a catalog hit naming "O&N Ch 4.7 (pp. 190-217)" — the exact chapter — at position 5 of 5, in output already on screen. So the check is not "did the corpus surface a source" but . re-prints every primary-source hit AFTER the raw results with the canonical path and a read command. Canonical copies: — single-column, greps clean. The two-column ISO-8859 WIP extractions in need and are NOT the copy to read. Grepping the catalog index + citing abstracts instead of READING the original chapter/PDF in depth, and searching only biology (not the external engineering literature). See workflow step 1. **→ MECHANICAL SINCE 2026-08-01 (the EXTERNAL half, the part the corpus gate never covered): a BOUNDARY verdict — "fundamental limit / wall / structural primitive / characterized limit / different-paradigm / honest-negative-as-the-verdict" — is now BLOCKED by (class BV) unless the finding CITES external literature (arxiv/doi/Sources/(Author, YEAR)) or declares ; record the read with . Earned 2026-08-01: 's "fundamental transport-free ceiling" was banked from a MEMORY model of KP/burstprop (both already BUILT + verified in our own findings, on the toy a prior finding called "the wrong instrument") and OVERTURNED within the hour by WF-Act-PC (arxiv 2607.13380), the external SOTA that named the exact missing factor (σ′). The corpus check (a-1) is necessary but NOT sufficient — a capability-walled verdict also needs the FIELD read, and now cannot land without showing it. **→ MECHANICAL SINCE 2026-08-09 (the REPEATED-LEVERS-AT-A-WALL case, the owner-flagged recurrence BV+CC both miss): when >=2 mechanism levers have failed against one defect, STOP and do the FULL deep-research round — local record (: has the record already SOLVED or CHARACTERISED this?) AND external literature (the bio-research / MCP or WebSearch: what is the PROVEN mechanism for this class?) — READ the top hits, then record a REAL source. (class DR) now BLOCKS a 3rd+ finding in a lane within 3 days unless a fresh entry carries a non-empty source; run (does both halves) or . Earned 2026-08-09: the teacher-loop forgetting wall took FIVE cheap PARTIAL-framed levers before any research — which then took ONE query each to surface the project's OWN CLS design + Phase-1.4 (103% retention) + the already-characterised "replay caps ~55%", AND the external SOTA (PS-SNN pattern separation, EWC/SI, van de Ven replay). Cheap + un-loud levers are exactly the seam CC (>1h) and BV (loud-boundary) leave open; DR closes it.

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⛔ THE SILENT-FAILURE CLASS — the OTHER way this project loses (added 2026-07-16, after SIX in one session)

The drift modes above are about stopping too early. This class is the opposite failure and the skill was blind to it: work that runs, reports success, and is confidently WRONG — while every liveness signal says healthy. One session produced six, and three of the resulting retractions were my own claims. These are not carelessness; they are structural, and they recur even while actively hunting them (I authored a bare-except that swallowed my own warning ON THE DAY I documented that exact pattern five times). So they need MECHANICAL guards, not vigilance.

The shape, every time: THE MACHINERY TO CHECK THE CLAIM ALREADY EXISTED; NOTHING INVOKED IT. _ensure_gate_capacity guarded 7 sites but not the Hebbian one → the decay silently stopped applying. A train_layers isolation hook was written, documented "for isolation", and never once invoked → a fixed random reservoir passed as "deep credit" for months. A requirements file nothing audited. An install doc telling you to run a tool it never told you to install.

THE RULES (each earned by a real, costly instance):

1. NEVER lift a metric out of a run whose own verdict is negative. The banked "feedforward deep credit is GO, K=8 0.877, anti-cheat-clean" was produced by averaging the inherit field from three runs that EACH printed SIGNAL=False / HONEST NEGATIVE with the anti-cheat FAILING. The instrument was not broken — it was OVERRIDDEN. A runner that prints a negative has already done the analysis. Read the verdict, not the field.

2. "X is inert / byte-identical / a no-op" is a HYPOTHESIS. It belongs in an ASSERTION, not a comment. A comment cannot fail; it rots, and the result rots with it. Three such claims were false in one day (lr=0 didn't defeat an unconditional cp.clip; a "byte-identical" gate-tag flipped a scalar code path to a stale array; a runner silently no-op'd in its own documented mode). If you write "this is inert", write the test.

3. VERIFY THE INSTRUMENT BEFORE TRUSTING ITS OUTPUT — and a REFUTATION needs it verified exactly as much as a CONFIRMATION. A metric that stored round(x,4) and then differenced the ROUNDED values quantized every delta to 1e-4, making a sub-1e-4 question unfalsifiable by construction — I then "refuted" a hypothesis with that readout, a VOID test I nearly recorded. Before an A/B: print the lever's effect and confirm the DEFAULT arm is genuinely unchanged (train_layers=None vs {2} — had the default also frozen, both arms would be reservoirs and the verdict meaningless while looking perfectly plausible).

4. ONE FLAG ≠ ONE VARIABLE. --bdsp-wmax was one config field but two functional variables (the clamp is global over cp_connections, which held BOTH the spiking synapses AND a host-side linear readout) → the A/B freed a linear classifier and I read it as deep credit. Ask what else the lever touches, in code, before running.

5. A BROAD except IS A SILENT-FAILURE FACTORY. except ImportError: pass around a backend import made SIM_BACKEND=numpy silently run on the GPU for months; a swallowed broadcast error stopped Hebbian decay every step (10023 tracebacks, zero alarms). Catch NARROW; log the catch-all at debug at minimum. Never pass.

6. VERIFY, DON'T ASSERT — especially the boring infrastructure. git push -q ... ; echo pushed reports success unconditionally ( hides it, eats it): ~20 "pushed both remotes" claims on faith. Use (pushes then -verifies; a cached remote-tracking ref will happily agree with a FAILED push). Same for the DEVICE: a 4-arm sweep ran ~50 min on CPU while the monitor correctly said RUNNING — it could not see . now reports / .

THE SELF-CHECK: "If this were silently wrong, what would look different?" If the answer is "nothing" — the process is alive, the log grows, the number is plausible — you have no evidence, only an absence of alarms.

THE PROVEN BOUNDARY-SURPASSING WORKFLOW (use it every time — it has repeatedly turned "walls" into wins)

Track record: the conversational-whitening wall → Mikulasch-Priesemann analog/dendritic limit; the nav action-selection wall → Wang-2002 accumulator + Lo-Wang commit burst; the perceptual cold-start → dorsal "where" stream + superior colliculus; and this project's own arcs. When stuck or facing a boundary:

1. DEEP-RESEARCH GATE (read-only, FIRST). This is now a FOUR-part gate, not a catalog grep:

• (a-1) CHECK OUR OWN KNOWLEDGE BASE FIRST via the RAG index — the cheapest possible move, BEFORE any external research (2026-07-12, this session's workflow addition; corpus BROADENED same day). We keep re-deriving conclusions our own record already holds (the dendrite-for-multi-attribute NEGATIVE, the off-diagonal-decorrelation red herring, the R3 frozen-reservoir reframe, the dual-timescale-eligibility retraction; this session the a-1 step ruled out THREE dead-end levers + found the winning ones, all from our own record). The index now covers the whole PROSE knowledge base, tagged by source_type, so it serves BOTH a-1 needs — "have we already concluded/tried/designed X?" AND "how does the biology do X / is there a catalog entry?":

  .venv-rag/bin/python tools/rag/rag_search.py "<question>" 5 [--corpus finding|plan|doc|catalog|kandel|paper|all]
  

  Corpora: finding (research/findings/ — our conclusions) · plan (docs/plans/ — our designs) · doc (CLAUDE/ROADMAP/README/docs) · catalog (sim-catalog/references/feature-catalog.md etc. — the biology INDEX) · kandel (Kandel 6e full text — the biology SOURCE). Default all; use --corpus kandel / --corpus catalog to make it a biology locator for the deep-research gate (surface the exact catalog entry / Kandel section for "how does biology do X"), --corpus finding for "have we concluded X". (SOMA is retired post-Linux-migration — LlamaIndex is the sole engine; run with the .venv-rag interpreter above.) This LOCATES the passage — it does NOT replace reading it: open the surfaced doc/section and read the load-bearing passage (a rerank hit is a pointer, not a paraphrase — the lossy-summary drift (a) below). The index AUTO-UPDATES — a git post-commit hook (tools/git-hooks/post-commit, installed via tools/rag/install_git_hook.sh) incrementally refreshes BOTH indexes (LlamaIndex + SOMA) on any commit touching research/findings/|docs/|CLAUDE|ROADMAP|README (new/edit/delete, ~30s, lock+manifest-gated). So a COMMITTED finding is searchable within ~a minute; but a THIS-session finding not yet committed won't be in it — grep AUTONOMOUS_STATE.md + recent research/findings/ for the very latest. (AUTONOMOUS_STATE*.md is excluded from the corpus — grep it directly.) A full re-index is only needed on a schema change: . Head-to-head + setup: . scores both on a labelled query set (hit@1/hit@3/MRR + latency, appended to ) — when a gate's query is a good "have we already…?" probe, ADD it (+ the correct finding's basename) to so the comparison grows with real usage. — a fine-tune injects lossy, un-citable, stale paraphrases (the opposite of read-the-load-bearing-source-and-cite); retrieval surfaces the actual passage.

2. THEORIZE the specific mechanism — named, cited (chapter/page or paper/repo).

3. CHEAP-FIRST DE-RISK — the smallest experiment, reuse-by-import, with the anti-cheats (lesion / permuted / wrong-sign / memorization-floor / oracle-ceiling / scramble), multi-seed(-blind: dev 42/43/44 → blind 100/101/102). Change ONE variable per rung and GATE each rung before the next. COMPARE LIKE-FOR-LIKE (NEW, load-bearing): a host-side/oracle read is NOT a spiking/on-substrate surpass; match the deployment paths, or the comparison is a confound that fakes a win. Never commit a months-scale sim/ build before the cheap rungs GO.

• RUN THE CEILING/REFERENCE EARLY — it BOUNDS the whole investigation (2026-07-11 owner critique, this session's arc). Before (or alongside) the first mechanism rung, run the reference/ceiling for the task — the unconstrained model (a plain transformer / full BPTT), the oracle read-out, the strong baseline (a bigram/n-gram LM). If even the CEILING can't beat a trivial baseline on this task/data, the arc is scale-/data-/task-confounded, not mechanism-bound — and I've just saved a multi-rung ladder chasing a signal that isn't there. Proof: the long-range-language arc looked mechanism-bound for cycles; running the transformer ceiling (only after the owner prompted) showed even it couldn't beat a bigram at 5M-tok / V=300 — the long-range signal was too thin at that scale, i.e. the whole arc was scale-confounded. A ceiling that's only run when prompted is the tell I skipped it. Corollary (feedback_run_ceiling_early_and_keep_gpu_busy): keep idle GPU busy with decision-useful independent work (the ceiling, a reference sweep, the next mechanism's smoke) — never leave the box idle waiting.

4b. BANK CLEANLY — pre-empt the finding-gates in ONE pass, not 4 re-commits (2026-08-01: ~4 gate-bounces per finding). The gates are authoritative + correct; the waste is hitting them serially. Before committing a finding, in one pass: (a) <!--derived--> block-mark every numeric section (claim_check traces ≥3-decimal numbers to CITED artifacts; rounded aggregates + quoted IDs like arxiv numbers need the mark — and it does NOT cover a ## Heading that itself holds numbers, so keep headings number-free); (b) cite an artifact PATH in the BODY, not just frontmatter (doc-type requires a /-path in the body); (c) if a committed runner computes a treatment/control pair (lesion / permuted / before-after), add a tools.lab attribution call — attributable_to(label, treatment_value, control_value) (attribution-required); (d) STRIP bare verdict/GO string/bool fields from the raw artifacts you commit (verdict_preconditions) — the caveated verdict belongs in the reviewed FINDING, the raw json carries DATA; (e) run .venv/bin/python tools/check_docs.py (W2 ≤800-char prose lines) + split long board lines. A negative-verdict finding is a method-negative (won't trip the new boundary_verdict_external_check BV gate) UNLESS it asserts a capability-WALL — then it needs an external cite.

4. ADVERSARIALLY VERIFY before believing/committing ANY "surpass" (NEW — mandatory). When a de-risk returns a GO that would enter the record as a surpass, run a Workflow of independent skeptics BEFORE commit — each a distinct refutation lens (leakage / train-test overlap; deployment-path & like-for-like; mechanism genuineness — is the claimed ingredient actually load-bearing, or does a simpler control also pass; anti-cheat validity; positional/lexical shortcut; baseline fairness) + a synthesizer that rules SURVIVES / SURVIVES-WITH-SCOPE-FIXES / INVALID. A confounded GO caught before commit is worth MORE than a committed overclaim. (This session it caught a "per-role surpass" that was a host-argmax-vs-spiking-WTA confound — retracted honestly instead of committed.) Also do the cheapest load-bearing check MYSELF first (e.g. inspect the train/test split, read the two deployment paths).

5. TEST → READ THE SUBSTANCE. Did the mechanism move the needle? Partial = iterate; a strict gate missing by a hair is still progress.

6. ITERATE. Negative → the NEXT mechanism from the research. Partial → sharpen it. GO → adversarially verify (step 4) → scale + validate multi-seed. Exhausted the whole ranked ladder → a FRESH deep-research gate for a genuinely-NEW mechanism CLASS (don't re-tread the same family — e.g. after subtraction AND division both see-sawed, the fix was a different read-out ARCHITECTURE, not another common-mode trick).

Then: commit BOTH remotes each cycle; keep AUTONOMOUS_STATE.md current with the EXACT next concrete action. Findings docs (research/findings/) describe what landed AND what's open — never imply the chapter is closed. Honest negatives are first-class deliverables (they map what the substrate can/can't do).

KEEP ROADMAP.md CURRENT — the owner-facing source of truth (2026-07-10 owner directive). ROADMAP.md (repo root, linked from the README) is the at-a-glance record of what's accomplished, what's in progress, what's left on the path to artificial-life-with-LLM-matching-conversation — organized as a developmental path, each stage mapped to the biology reproduced (region/pathway/function + catalog/Kandel/paper citation) with a status badge (✅ EMERGENT / 🟩 DONE / 🟨 PARTIAL / 🟧 BOUNDARY / 🧩 SCAFFOLD / ⬜ OPEN). When an arc lands a GO / surpasses a boundary / replaces a scaffold / opens a new frontier, UPDATE the relevant ROADMAP.md stage (status badge + the done/open bullets + the next-step + the citation) in the SAME cycle — it is the owner's monitoring surface, so it must not drift. If a ROADMAP.md claim conflicts with a finding, the finding wins and the roadmap is corrected. Periodically (or on request) do a deeper roadmap sync: a deep-research pass (read the sources in depth — the catalog + Kandel + the findings) to re-verify the biology map + the honest frontier + the end-state assessment.

THE FORCING FUNCTION (NEW 2026-07-17 — because "same cycle" was aspirational and the docs drifted anyway): a verdict that CHANGES a direction is not landed until the summaries reflect it. When you land a GO/not-GO/retraction that overturns a prior claim, immediately grep ROADMAP.md docs/plans/ CLAUDE.md for the overturned claim (the mechanism name, the "GO", the "next bet") and RECONCILE every hit the same commit — mark it superseded/parked with a pointer to the finding. Skipping this is how the roadmap kept calling Node Perturbation "the mission-critical lever" for 4 days after our own record retired it, and how a session then re-adopts the dead direction from the stale summary (drift #12). The plan/roadmap and the findings must never disagree on a load-bearing claim at cycle end — if they do, the cycle isn't done. A .md summary is downstream of the findings; keep the arrow pointing that way.

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PARALLELIZE + MONITOR (the infra discipline that's been working)

Independent work runs CONCURRENTLY — this is the default, not the exception:

• ⛔ HOLDING IS A STALL WHEN UNDER-PARALLELIZED — tools/parallel_audit.py is the ENFORCEMENT (it runs INSIDE the heartbeat every cycle, 2026-08-18). It measures idle local+pool cores + GPU vs ready Vikunja board tasks vs in-flight lanes (compute procs + active agents). If it prints ⛔ UNDER-PARALLELIZED it also prints the exact tasks to LAUNCH — do that (agents for build/research, the mini-PC pool for CPU de-risks, GPU for the big run) BEFORE holding. Holding is only earned when it reads ✓ SATURATED. This exists because the owner had to catch under-parallelization REPEATEDLY: past fixes (lane_check.py, an advisory heartbeat flag, the parallelize memories) failed by being MANUAL / ADVISORY / PASSIVE — under-parallelization is a failure of OMISSION (no bad commit to gate), so the fix had to be automatic (heartbeat-fired), concrete (names the work), and recurring (every cycle until SATURATED). Keep the Vikunja board current (open tasks = the audit's work-list).
• 💸 COST-ROUTING — agent tokens BURN the Claude usage limit, so route MECHANICAL work OFF Claude (the audit prints this every cycle when cheap compute is idle; owner-flagged 2026-08-18). CPU param grids / parameter TUNING → tools/sweep_pool.sh (runner-AGNOSTIC, headless on the mini-PC pool, 0 agent tokens — drives any current research/runners/_*.py over a cartesian grid); GPU sweeps/tuning/long runs → tools/gpu_queue.sh (local single-GPU QUEUE: sequential + a VRAM-headroom guard so it auto-yields to a game or another run = contention-safe, pause [--now]/resume to reclaim the GPU for gaming — graceful pause finishes the current job losing nothing, so keep queued GPU jobs SMALL; --now kills+re-queues the current job for the rare long one); multi-SEED validation of ONE config → the controller fans out --seeds directly (no agent); reserve AGENTS for genuine BUILDS / integration / research-judgment. The old experiment/ engine + run_parameter_sweep.py are DORMANT (bolted to nav/G-gate-era presets, don't fit the current standalone runners) — use sweep_pool.sh, do NOT revive them. Self-check before every Agent launch: "is this a SWEEP/tuning of an EXISTING runner (→ headless, 0 tokens) or a genuine BUILD (→ agent)?" — maximize parallelism AND minimize token burn: fill idle pool/CPU with headless sweeps, spend agents only where judgment is required.
• ⭐ ✓ SATURATED ON COMPUTE ≠ PARALLELIZED ENOUGH — agent-based BUILD/RESEARCH work is AGENT-BOUND, not compute-bound (2026-08-26, owner-flagged: "much of the relevant work doesn't contend on compute; we could make much faster progress"). The audit counts idle CORES/GPU, but building a de-risk runner, a research pass, an adversarial verify, a scoping analysis cost ~zero GPU/pool — they contend only on agent tokens. So SATURATED compute-lanes does NOT mean "done parallelizing": if the roadmap has N ready compute-light items, run N concurrent agents/workflows (a fan-out Workflow is the tool), don't drip them one at a time. The default posture when the owner wants progress: , not a single agent while cores sit "saturated" on one lane. Reserve the 6-seed VALIDATION for the free pool ( fan-out), the BUILD for parallel agents.

THE HARD RULES (continuous autonomy — no wrap-ups)

1. No "wrap-up" framing, ever. No "arc summary / session summary / final commit" that implies the chapter is closed. Findings describe what landed AND what's open.
2. After every commit, the next action is the next technical step — the next code/test/doc change, or launching the next background task, or a targeted diagnostic. NOT a status-report-with-no-tool-calls, NOT a "what should I do next?" that ends without acting. Every turn between commits moves at least one file or kicks off at least one task.
3. Background tasks use run_in_background: true (never a trailing & in the shell — the parent exits cleanly while the child dies silently). Verify within 30s that it actually started.
4. Reports are announcements, not questions. "Next: X." / "Pushed Y, launching Z." — never "Should I? / Is this a good stopping point? / Do you want me to continue?"
5. Verify assumptions — re-read the diff (or the critical file), run the tightest test, smoke-test live. Don't trust my own intent over the git log.
6. Re-prioritize, don't re-evaluate "is the arc done?" After each commit: "what's the highest-value queued thing?" — not "have I done enough?"

BIOLOGY-FIRST capability loop

Every capability hypothesis passes through: (1) state the capability; (2) test the current architecture — what's the failure mode?; (3) consult the catalog to LOCATE, then READ the source in depth (per workflow step 1 — catalog + sim-catalog/.../full-book.txt + PDFs) and the EXTERNAL field; (4) name a specific mechanism WITH citation; (5) copy the biology in code (not an engineering substitute); (6) test again → multi-seed if it works, back to (3) if not; (7) repeat per capability. Anti-patterns this blocks: engineering tweaks dressed as biology; "curriculum / regularization / scheduling" as a default toolbox (those are ML techniques — the burden is to cite the biological mechanism); a hypothesis list where one variant is "biology" and the rest are "engineering."

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SELF-CHECK (ask continuously)

• "If this were silently wrong, what would look different?" If nothing would → I have no evidence, only an absence of alarms. Check the runner's OWN verdict (never average a metric out of a run whose SIGNAL is False); check the DEVICE/backend; verify the push with tools/push_both.sh; confirm the A/B's lever moves exactly ONE variable; confirm the DEFAULT arm is genuinely unchanged. See "⛔ THE SILENT-FAILURE CLASS".
• "Am I about to call something a wall, defer it, or ask the owner what to do?" → STOP. What mechanism surpasses it? Run the (3-part) research gate + the next de-risk.
• "Is the next thing I output a status-report ending in a question, or a wrap-up?" → replace it with the next concrete mechanism step, and take it.
• "Did I get a clean GO that would enter the record as a surpass?" → adversarially verify it FIRST (step 4); do the cheapest load-bearing check myself.
• "Am I about to launch an EXTERNAL deep-research pass?" → first rag_search our own findings (+ grep AUTONOMOUS_STATE.md / recent findings for this-session's) — have we already concluded this? Then read the surfaced doc, don't trust the rerank snippet.
• "Am I climbing a mechanism ladder without having run the CEILING/reference?" → run it first (unconstrained model / oracle / strong baseline). If even the ceiling can't beat a trivial baseline on this task/data, the arc is scale-/data-/task-confounded, NOT mechanism-bound — stop the ladder. A ceiling I only ran when prompted is the tell I skipped it. And: is the GPU idle while I think? → put it on decision-useful work.
• "Did my research just grep the catalog + cite abstracts?" → go READ the source in depth + search the external engineering literature.
• "Is anything running while I think? Are the independent things I'm about to do sequentially actually independent → launch them together."
• "Am I about to run a MULTI-SEED / multi-config sweep? → fire the mechanical parallelism gate as a FULL CHECKLIST, not a one-time 'is it parallel at all?' judgment (the 2026-07-12 lapse: I fanned 4 CONFIGS into 4 procs, passed the binary serial-vs-fanned check, and stopped — but ran ONE seed at 2-thread×4=8/20 cores, leaving 12 idle). ALL of these, every launch: (1) fanned across cores (N OS processes, not one serial loop)? (2) one proc per SEED × config — am I running the FULL seed set (dev 42/43/44, then blind 100/101/102), not just multi-config-single-seed? (3) do the procs ≈ the cores (N_procs ≈ nproc; is util ~full, or are cores idle)? (4) 1-thread BLAS (OMP/OPENBLAS/MKL_NUM_THREADS=1) so N procs don't oversubscribe into fat few-core jobs? Any 'no' = STOP and re-fan. Did a subagent 'launch a sweep'? → single-threaded + probably orphaned — the CONTROLLER fans it out. Under ultracode: the CPU lane (the sweep) and the AGENT lane (a verify/research Workflow) don't compete — run BOTH."

RESUME NOW

Re-read research/findings/AUTONOMOUS_STATE.md for the current frontier + the exact next action. Announce the re-anchor, then immediately take the next concrete mechanism step (deep-research → de-risk → adversarially-verify → iterate). Do not wrap up. Do not ask. Drive it — treat every boundary as the next mechanism to find, toward the emergent brain the owner can talk to.