Phase 3: LLM-tier speciation + multi-seed firm-up of the recombination claims

llm_speciation (new kind; src/llm/speciation.py): E13 in LLM weights.
LoRA children share the frozen base's coordinates, so merge failure is
functional by construction. CONFLICT (ambiguous sort prompts learned
under opposite conventions — the BDM structure): function-specific
hybrid breakdown — merged coherence 0.02-0.08 falls below BOTH parents
(~0.2) on the conflicted function; and in the de-confounded `add` design
(private budget fixed, conflict added on top; 3 seeds after a
single-seed pilot showed one anomalous point) the merge's private-family
accuracy shows NO trend with conflict — the damage is surgical, not
global. DURATION (over-trained disjoint specialists, 1->12 epochs): the
merge improves (0.84->0.94) and stays above the best parent — the MLP
"no emergent isolation" null generalises; relevant to the
expert-training-duration report (2607.11997), with the epistasis
prediction left to the decisive experiment.

Multi-seed firm-up (seeds threaded into specialist caches; `seeds:` list
support in the runner; fixed test sets): all three recombination claims
hold with CIs — merges beat every specialist (5 seeds, ties
0.647±0.027 > best spec 0.592±0.009; worst-family 0.28 vs <=0.16); union
0.274±0.026 > fusion 0.174±0.102 on hard (3 seeds); directed 0.221±0.026
> soup. NEW finding: fusion is seed-FRAGILE where headroom exists
(CI ±0.10) while routing/directed selection are stable (±0.026) — the
union/selection operators win on reliability, not just mean.

Figures (llm_speciation 3-panel; llm_seeds 3-panel with 95% CI), READMEs,
+1 convention test (150 green), make llm-speciation / llm-seeds targets.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v

tasks/workorder-pnas-submission.md

@@ -62,7 +62,9 @@ barriers). Patch before the preprint goes up.
     (no growth ⇒ "models are safer to merge than biology predicts" — an honest bound).
   - Tests + README + fold into figure. Pre-register the falsifier language before running.
 
-## Phase 2 — arXiv preprint (priority stake) — end of Week 1
+## Phase 2 — arXiv preprint package (GG decision 2026-08-11: DO NOT POST until all experiments
+and analysis are complete — the preprint goes up after Phase 3, with the final analysis folded in;
+re-run md2tex + tectonic at that point)
 
 - [x] Citation refresh in `paper/the-evolution-of-sex-for-ai.md` *(done 2026-08-11; author names verified against arXiv API)*: **new concessions** —
   First-Extinction Law (2509.20101), quantitative-trait collapse (2407.17493), verifier-injection
@@ -74,12 +76,18 @@ barriers). Patch before the preprint goes up.
 - [x] Fold E13b/c results into the speciation section (whatever they show — honestly). *(Done: full-symmetry residual + hybrid-fitness cliff + the emergent converse, in abstract, §5, §13 and the accessible version.)*
 - [x] LaTeX conversion: `paper/arxiv/` (md2tex.py block-based converter from the Markdown source of
   truth; main.tex; 3 figures; builds clean under tectonic, 20 pp; arXiv pdflatex hint guarded).
-- [ ] **Post to arXiv (GG action — package ready):** upload `paper/arxiv/{main.tex,body.tex,figs/}`;
-  categories, license note, and a ≤1,920-char abstract are prepared in `paper/arxiv/ARXIV-SUBMISSION.md`.
+- [ ] **Post to arXiv — DEFERRED until all experiments/analysis are done (GG).** Package is ready
+  (`paper/arxiv/`, instructions in `ARXIV-SUBMISSION.md`); rebuild after the Phase-3 results are
+  folded into the manuscript, then upload.
 
 ## Phase 3 — New experiments for impact & robustness — Weeks 2–3
 
-- [ ] **`llm_speciation` — the cliff at the LLM tier (new, highest-impact addition).**
+- [x] **`llm_speciation` — the cliff at the LLM tier.** *(Run 2026-08-11, 0.5B: DURATION NULL —
+  over-trained disjoint specialists merge better not worse (0.84->0.94, above best parent throughout);
+  the MLP "no emergent isolation" null generalises. CONFLICT — function-specific hybrid breakdown:
+  merged coherence 0.02-0.08 falls below BOTH parents (~0.2) on the conflicted function. Caught a
+  design confound (replace mode ties conflict_frac to private-data budget) -> built the de-confounded
+  `add` variant (conflict_mode: add; configs/llm/speciation_add.yaml). 7B confirm optional later.)*
   Speciation demonstrated at all three tiers (analytic → MLP → LLM) makes the headline
   unassailable. Structural bonus to state in the paper: LoRA deltas live in the frozen base's
   coordinate system, so there is **no permutation ambiguity by construction** — any LoRA-merge
@@ -93,12 +101,46 @@ barriers). Patch before the preprint goes up.
     (2607.11997: optimal expert duration) as *our theory explaining their data* — a strong PNAS
     move.
   - 0.5B locally first; one 7B CX3 confirm if the sign is clean (`hpc/` PBS, minutes).
-- [ ] **Multi-seed the LLM arc (robustness — removes the "one seed" objection).**
+- [x] **Multi-seed the LLM arc (0.5B tier done 2026-08-11).** All three claims hold with CIs
+  (merge>every specialist; union 0.274±0.026 > fusion 0.174±0.102 hard; directed 0.221±0.026 > soup)
+  + NEW finding: fusion is seed-FRAGILE on hard tasks (±0.10) while routing/directed are stable
+  (±0.026) — the union/selection operators are the reliable ones. results/llm_*_seeds/ + llm_seeds
+  figure. Remaining: 7B CX3 seeds (1-3) when HPC convenient.
   - Thread the seed into specialist cache keys (`spec_<family>[_hard]_s<seed>`); verify nothing
     else assumes the old names.
   - 0.5B: seeds 1–5 × {merge, moe, directed} × {easy, hard}. 7B on CX3: seeds 1–3 × hard
     {merge, moe, directed} (8–25 min walltimes → trivial). Aggregate figures with 95% CI; update
     READMEs; the headroom law now carries error bars.
+- [ ] **`epistasis_predicts` — the DECISIVE experiment (from the external review, 2026-08-11; highest
+  priority after llm_speciation lands).** The review's exact bar: population-genetic quantities must
+  *predict* (not re-describe) — forecast merge success **before merging**, and beat existing
+  predictors. Design, reusing the llm_speciation machinery:
+  1. Parents with independently controlled interaction structure: sweep `conflict_frac` (ground-truth
+     epistasis) *and* compatible/disjoint + duration variants (spread in divergence WITHOUT conflict),
+     so functional conflict and divergence are decorrelated by construction.
+  2. Pre-merge predictors, none of which touches a merged model: (a) **operational epistasis** =
+     functional-disagreement mass between the parents on a shared probe set (the μ(S) estimate — ours);
+     (b) **gradient alignment** (the Zhou et al. 2601.22285 predictor); (c) **weight-space geometry**
+     (LoRA-delta cosine / norm distance).
+  3. Outcome: merged (soup) performance on private families + convention coherence, held-out test,
+     multi-seed.
+  4. The claim to test: at matched geometric divergence, the epistasis measure predicts merge outcome
+     and the geometry measures do not (R² comparison + an operator-choice decision test — merge vs
+     route — under matched budgets).
+  Pre-registered falsifier: if gradient/geometry predictors match the epistasis measure, the paper's
+  "epistasis, not divergence, sets the cliff" claim stays analytic-only and is labelled as such.
+- [x] **Manuscript claim-narrowing (external review, 2026-08-11) — done.** Softened identity claims
+  (WF exact only in the minimal model + learning-kernel cited against ourselves; ratchet scoped to the
+  irreversible arm), removed "nobody has / none imports / theory outrun" (priority-dispute bait),
+  added the interpretation/explanation/prediction ladder to §1, stated the merge-don't-average
+  operator boundaries (output-mean vs weight-avg vs routing vs max-with-oracle, budgets, oracle,
+  capacity), added a "what these experiments do and do not establish" scope block to the speciation
+  section (impossibility floor is information-theoretic, not genetic; snowball/epistasis-cliff =
+  hypotheses at the neural tier), replaced "control theory" with "framework" (subtitle included —
+  GG can veto), fixed the §3/§11 overstatements (frozen core ≠ frozen behaviour; Baldwin = echo not
+  identity; archive vs operational irreversibility), added the **claims-at-a-glance table**
+  (status/assumptions/evidence/limits) to §13 + table support in md2tex, and matched the calibration
+  in the accessible version. Adopted the review's framing sentence as the stated core contribution.
 - [ ] **(Optional, SI-grade) ambiguous-families router stress test** — overlapping-skill families
   where the router is no longer trivially perfect; documents the honest limit of union-by-routing.
   Do only if time permits; otherwise keep the existing rider sentence.