Manuscript revision and pending experiment work, snapshot before restructuring

Clarity pass over the main text (36-item audit), Discussion rewrite and cut,
acknowledgements, Souly et al. as ref 62, lettered SI panels, model section
moved under Results; plus the untracked curriculum/society/compose/smol
configs, runners, figures, stats and tests that the SI already cites.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm

tasks/lessons.md

@@ -50,3 +50,120 @@ Rules: (1) never mutate `.venv` while a background job is running against it —
 throwaway venv elsewhere; (2) `uv sync` is *declarative* — always pass **every** extra the project
 needs, or it removes the ones you omit; (3) the repo now pins `.python-version` (3.14) so the
 interpreter can never drift silently.
+
+## Before a compute campaign, derive the design from the theory and read the analytic code beside the neural code (2026-09-07)
+The v1 `llm_society` campaign (4 seeds, ~13 L40S-h) returned a null that was *structurally guaranteed*:
+3 families over 8 agents made founders near-clones (E8's ρ=1 control: recombining clones buys nothing);
+2^3 competence states left no room for a child to be "new" (E8 needs L=12); sex was a linear blend at
+0.5B (E4/`llm_moe`: the dilution regime); parents were truncated before breeding (E11 selects on
+survival over parents+offspring — v1 threw away half the families at gen 1 with no operator to
+restore them); `n_test`=40 put every contrast inside one SE. GG caught the first fault by asking what
+the founders knew; the rest fell out of comparing `dynamic_society.py` with `society.py` line by line.
+Rules: (1) a Layer-2 instantiation of an analytic experiment must be checked *operator by operator*
+against the analytic code, not against its description; (2) every free parameter that the theory
+constrains (ρ, L, the operator regime, the observation floor, selection intensity) is set by a
+prediction or a calibration measurement, never by feel; (3) write the falsifiers with numbers and the
+power analysis *before* submission — the pre-registration is `tasks/prereg-llm-society-v2.md`.
+
+## Calibrate the inheritance channel before the population (2026-09-07, evening)
+Nine local GPU-hours of calibration found three ceilings a 96-GPU-hour campaign would have hidden:
+(1) with 3 skills over 8 agents, founders were near-clones (E8 ρ=1 → recombination buys nothing);
+(2) a fresh LoRA distilled from a one-skill parent's answers on nine families retains only 0.6–0.8 of
+the skill — interference from confident off-expertise answers, not the E2 observation floor, and
+removable by gating on the source's own confidence; (3) a two-skill child holds each skill at
+~0.85× of its parents at ANY training budget (rank 64 overfits) — the learning budget, not the
+sample budget, is the conserved quantity, and it caps how many skills one adapter can carry. GG's
+call was no-go at 0.5B rather than a campaign that could only test the ablations. Rules: (a) measure
+transmission fidelity of the inheritance channel for one skill, then two, before breeding populations;
+(b) when a gate fails, re-derive it from the data you already have (the conflict gate moved 0.35→0.41
+from the epistasis grid's own outcomes) rather than by feel, and record it as an amendment; (c) a
+pre-registration that ends in a no-go has done its job — write the ceiling up, don't route around it.
+
+## A plan for reader-facing prose must carry the dual-audience standard explicitly (2026-09-09)
+GG rejected the approved-in-substance manuscript-revision plan until it stated, as a first-class
+section, that every term from either field is defined at first use with an example from each world.
+The plan had the right content and structure but treated accessibility as a verification
+afterthought; GG's rule is that it is "paramount" and must be designed in, not checked for. Rule:
+before drafting any passage for a mixed readership, build the term table (term / one-clause
+definition / biology example / model example) *in the plan*, and put a two-reader pass in
+verification. The same applies to my status reports — GG twice said "I am lost with all these C3,
+E9, H1"; spell codenames out.
+
+## 2026-09-11 — check the figure panel inventory before flagging cross-references
+In the manuscript review I flagged Table 1's "Fig. 4C–E" and "Fig. 3C" as inconsistent with the text. They were
+correct: `make_figs.py` puts the E11 ablation in Fig. 4's bottom row and the predictive grid in Fig. 3C–D; the text
+simply failed to cite them. Rule: before calling a cross-reference wrong, read `paper/pnas/make_figs.py` and the
+captions in `build.py` for the panel inventory; the fix is usually a missing citation in the text, not a wrong table.
+
+## 2026-09-11 — never type a result number that a script has not printed
+Writing the stop3 README I filled the per-seed cells from memory of the mean and had three rows wrong
+until the loader's pivot table exposed it. Rule: every number in a README, SI table or manuscript is
+pasted from a stats-script printout produced in the same step; if the script has not printed it,
+print it first. This is the same rule the plan stated ("copied from the stats-script output, not
+typed") and I broke it within the hour.
+
+## Reference numbers hardcoded outside the renumber path (2026-09-11)
+`renumber_refs.py` rewrites main.md, si.md and build.py captions, but `make_figs.py` carries a literal "(refs. N, M)" in the fig1a grounding cell, which went stale after references were added. Rule: after any renumber, grep `refs\.` and `ref\.` across `paper/pnas/*.py` and fix by hand (or extend renumber_refs.py to cover make_figs.py). Also: fig text is rendered, so verify by `pdftotext figs/fig1a.pdf`, not by grepping the source alone.
+
+## 2026-09-12 — GG's manuscript comments: heralds, undefined terms, and phantom SI references
+Forty-five comments on the ODT. Three patterns. (1) **Herald sentences** ("Two boundaries follow.",
+"Modifier theory predicts its fate:", "X is the measurement no other arm produces") — GG: "Breaking
+down sentences like this is also a claudism." Now a HERALD block in the declaudify detector; run
+`--list herald` before handing over any draft. (2) **Every technical term defined at first use, with
+one word per concept**: item/capability/allele, mass, refit, verified real samples, Zipf source,
+practitioner, "which trained networks" — the dual-audience rule from 2026-09-09 applied to *my own*
+vocabulary, not only the biology. Rule: after drafting, grep each noun of art for its first
+occurrence and check a definition precedes it. (3) **Never cite the SI for something the SI does not
+contain.** The text cited "the SI separates three cases" and "the proof is Poisson thinning" and
+neither existed; and every "(SI)" pointer must name a figure or text number. Rule: before writing
+"(SI)" grep si.md for the claim; if absent, write it (SI Text S4) or drop the sentence.
+
+## 2026-09-12 (round 2) — the Discussion must discuss; novelty is flagged where the result is shown
+GG on the "What is borrowed and what is new" inventory: "The discussion should discuss, not list."
+And on the Limits paragraph: stating small-scale limits "is usually done by undergraduate students";
+either run the experiment or discuss only problems too big for the paper. Rules: (a) never write a
+Discussion paragraph that is a list of prior-art citations or of caveats; each Discussion paragraph
+argues one point; (b) attribute novelty at the point of the result, with the figure panel, and name
+the prior finding it explains or extends in the same sentence ("an observation reported by others
+and left unexplained (60)"); (c) "much/some/most of X was known" is a hedge that gives novelty away
+without saying what is new; replace with the specific thing prior work lacks. Also: after
+`renumber_refs.py --apply`, the fig1a literal (refs. 22, 33) went stale (Shumailov became 23); the lesson from 2026-09-11 held.
+
+## 2026-09-12 — a prediction written into the Discussion must be run before it is printed
+The revised Discussion predicted that differential reproduction would turn recombination's speed
+advantage into a level advantage. Three GPU-hours later it did not (parity, 3/3 seeds). Rules:
+(a) when a Discussion sentence forecasts the outcome of an experiment we can run in under a day,
+run it in the same revision; (b) check adapter/cache directories for seed- and base-specificity
+before any HPC array (speciation shared one dir across seeds; the specialist cache would have loaded
+Qwen adapters into SmolLM2); (c) the local smoke gate for a new base (termination, base accuracy in
+(0.05, 0.95), sample generations) cost 4 minutes and is worth running every time.
+
+## 2026-09-13 — a figure must be readable without its caption
+GG on the manuscript figures after reading the student guide: "too unclear, cryptic"; figures should
+"give some clear information without the need to read the legend". The house rule in make_figs.py
+("no per-panel headline titles; interpretation lives in the captions") was the wrong rule for this
+audience and is reversed. Rules: (a) every data panel carries a one-line headline stating its
+finding plus a grey line naming the system and its size; (b) legend entries say in words what is
+plotted ("accuracy on the model's weakest task family", not "worst_family"); (c) where the set-up is
+not obvious, a schematic panel explains it inside the figure; (d) bar comparisons carry the test
+(paired over seeds, stars, key printed under the legend). Layout lesson: headlines longer than the
+panel run into the neighbour; wrap at ~40 characters per line for a half-width panel, ~70 for full
+width, and render before trusting.
+
+## 2026-09-13 — figure layout rules I should apply without being told
+GG had to ask three times for things a careful eye catches: headlines running past their panel,
+a schematic strip narrower than the data panels beneath it and not flush with their left edge,
+and a large blank band between a strip and the next row. Rules, now encoded in make_figs.py:
+(a) any panel placed by hand (schematics) is positioned from the neighbouring data axes' geometry:
+left edge = the data panels' frame, right edge = the last panel's frame, bottom = a fixed 0.75 in
+above the headline below, height from the content's designed aspect (never let equal-aspect centre
+a too-wide axes); (b) text wraps to its own panel width (`headline()` measures the axes); (c) after
+every regeneration, render at ≥ 90 dpi and check four things before reporting: nothing crosses a
+panel boundary, nothing overlaps, blank bands are no larger than the row gaps, and left edges of
+stacked panels line up. Report only after that check passes.
+
+## 2026-09-13 — prose: no staccato fragments
+- GG flagged "These results say X. They do not say where. The inheritance model does, in closed form."
+  as a claudism. Breaking a thought into short declaratives is rarely necessary; join them (colon,
+  "because", "and", "but"). Clarity comes from stating the concrete object, not from short sentences.
+- After any rewrite pass, scan for sentences of ≤7 words introduced by the edit and rejoin them.