Giorgio Gilestro
2d8f661924
"Model" now means an AI model everywhere; the Wright-Fisher construct is "the
biological model" throughout (19 occurrences): tier header, section title (now
"The biological model, and where trained learners depart from it"), Table 1
support column ("Exact" -> "Closed form"; "Analytic model" -> "Biological
model"), Results, Discussion, Methods ("Biological-model tier"), and all
figure captions. "Exact" survives only in technical noun phrases (exact-match
verifier, exact oracle, exact equilibrium, exact recovery); the abstract's
"exactly Wright-Fisher" is now "literally Wright-Fisher".
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
3.2 KiB
2026-08-11 — Stop padding time estimates. GG: "You generally massively overestimate the time it takes to do some work... You're fast." Phase-1 items I scoped as "Week 1" took ~an hour. Rule: state what will be done and in what order; give a duration only when compute-bound (training walltime), and base it on measured runtimes, not human-project heuristics.
2026-08-11 — Correspondence is not identity; interpretation is not prediction (manuscript reviews). The external review's core corrections, to internalise for all paper claims: (1) distinguish interpretation / explanation / prediction and claim only the level the evidence supports; (2) a minimal model being exactly Wright-Fisher does not make real training "literally" WF — our own learning-kernel result says otherwise (cite it against ourselves); (3) name the operator every claim is about (output-mean vs weight-average vs max-with-oracle vs routing are different objects with different budgets); (4) don't write "nobody has / none imports" — invite no priority disputes; say "to our knowledge" and state the positive contribution; (5) negative results (E13b) are strengths — lead with them; (6) "control theory" needs states/controls/dynamics/rule or it's a "framework".
2026-08-11 — tmux does NOT survive SSH disconnects on this machine. The tmux server starts inside
the SSH session's systemd scope and gets reaped on logout (lost ~20 min of the epistasis grid; GG:
"SSH disconnected"). Reliable pattern here: systemd-run --user --collect --unit=<name> --working-directory="$PWD" bash -c '<cmd>' — lands in user@.service (kept alive by the desktop
session), survives disconnects; check with systemctl --user is-active <name>, logs via redirect.
2026-08-11 — Internal deliberations must not leak into reader-facing prose. GG (on the convergence paragraph): it "carries all the ghosts of our internal brainstorming that should be completely alien to the readers (this is, alas, a recurring problem with your writing)." The pattern: strategic concerns from the working process (priority anxieties -> "we cite for priority of publication"; calibration debates -> "the honest statement"; positioning battles -> "nobody has") surface as defensive or self-referential prose. Rule: before finalising any reader-facing passage, ask "does understanding this sentence require knowing how we worked?" If yes, rewrite it as a plain statement about the literature or the result. Confident papers situate; they do not litigate. (Promoted to a general rule in the global ~/.claude/CLAUDE.md, 2026-08-11 — it applies to all reader-facing prose in every project.)
Terminology: "model" is overloaded in this project (2026-09-07)
In the PNAS manuscript and figures, "model" must mean an AI model. The settled term for the pop-gen construct is "the biological model" (GG decision, 2026-09-07) — used everywhere ("the multi-locus biological model", "Biological-model tier"), never "minimal model", "analytic model", or "exact model"; GG also vetoed "(exact)" as a tier label (the guarantee line "closed forms · bitwise-reproducible" carries that content). Support level formerly "Exact" is now "Closed form". Keep "exact" only in technical noun phrases (exact-match verifier, exact oracle, exact equilibrium, exact recovery).