MachineSex/figures
Giorgio Gilestro 6b5591c92f third review round: mathematical corrections + operator separation + headline calibration
The five priority fixes, in the PNAS draft and propagated to the
long-form document and results documentation:

1. The averaging proposition now proves what it claims: a FIRST-ORDER
   cancellation of the multi-parent retention gain under output-mean
   inheritance in the rare-item regime (n·p/K << 1), with the convexity
   boundary stated (averaging's variance reduction can reduce extinction
   outside that regime — the reviewer's argument) and the union
   operator's renormalisation + oracle requirement explicit. "Adding
   parents cannot help" deleted everywhere.
2. Grounding: g*~=0.05 restated as an operational threshold (equilibrium
   smooth in g — no phase transition); m·p floor restated as
   1−exp(−m·p) per-batch observation probability with
   retention/occupancy/reintroduction distinguished; the deep-tail rule
   de-categoricalised (stratified sampling; recombination recovers only
   what parents retain).
3. Grounded INHERITANCE (data channel) separated from grounded
   EVALUATION (fitness channel) in the society section; retitled to
   "complementary contributions"; general joint necessity disclaimed.
   Table 1 + v6 ledger updated.
4. Alignment contradiction removed everywhere ("cannot be an alignment
   failure" -> the reviewer's formulation); abstract says "remaining
   after permutation-and-rescaling alignment"; group = search space,
   control recovery != global optimality; "specialisation is merge-safe"
   -> "do not treat divergence/specialisation alone as evidence of
   incompatibility".
5. Significance headline matched to the bounded evidence; seed-
   dependence sensitivity added (per-seed rho stable +0.37..+0.53 for
   functional measures, ~0 for geometry, gradient alignment
   seed-UNSTABLE −0.11..−0.55 — reported as its own caveat; LOSO ranges
   in stats script).

Presentation: review-process meta-language stripped; "exact" reserved
for closed forms ("analytic model" labels); headroom rule qualitative;
directed-sex phrasing per review; ratchet = consequence-level
correspondence; compact results table (Table 2) added. Response letter:
paper/response-to-review-3.md. Both PDFs rebuilt; 151 tests green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
2026-09-06 19:29:09 +01:00
..
_figlib.py Layer 1 core: Wright-Fisher knowledge-transmission model with E1-E2 2026-07-04 18:10:18 +02:00
mnist_montage.py neural: real-MNIST external-validity tier (collapse + grounding) 2026-07-05 09:19:36 +01:00
plot_architectures.py neural: grounding refinement + all five Layer-1.5 figures 2026-07-05 08:14:19 +01:00
plot_bridge.py neural: grounding refinement + all five Layer-1.5 figures 2026-07-05 08:14:19 +01:00
plot_collapse.py neural: grounding refinement + all five Layer-1.5 figures 2026-07-05 08:14:19 +01:00
plot_E1.py Layer 1 core: Wright-Fisher knowledge-transmission model with E1-E2 2026-07-04 18:10:18 +02:00
plot_E2.py Layer 1 complete: E3-E6 + E2 analysis add-ons 2026-07-04 18:54:42 +02:00
plot_E3.py Layer 1 complete: E3-E6 + E2 analysis add-ons 2026-07-04 18:54:42 +02:00
plot_E4.py Layer 1 complete: E3-E6 + E2 analysis add-ons 2026-07-04 18:54:42 +02:00
plot_E5.py Layer 1 complete: E3-E6 + E2 analysis add-ons 2026-07-04 18:54:42 +02:00
plot_E6.py Layer 1 complete: E3-E6 + E2 analysis add-ons 2026-07-04 18:54:42 +02:00
plot_E7.py society: multi-locus recombination frame — the vertical claim (E7/E8) 2026-07-05 10:51:41 +01:00
plot_E8.py society: multi-locus recombination frame — the vertical claim (E7/E8) 2026-07-05 10:51:41 +01:00
plot_E9.py society: make the sexual-transmission model rigorous (E9 epistasis, E10 directed sex) 2026-07-05 11:13:37 +01:00
plot_E10.py society: make the sexual-transmission model rigorous (E9 epistasis, E10 directed sex) 2026-07-05 11:13:37 +01:00
plot_E11.py society: the dynamic Lamarckian society — the vertical claim (E11 / C3) 2026-07-05 12:34:01 +01:00
plot_E12.py E12: model speciation — the merge-compatibility limit of the sexual society 2026-07-08 22:40:02 +01:00
plot_E14.py E14: mating systems — monogamy vs promiscuity (mate-pool breadth) 2026-07-09 12:38:50 +01:00
plot_grounding.py neural: grounding refinement + all five Layer-1.5 figures 2026-07-05 08:14:19 +01:00
plot_kernel.py knowledge: learning kernel — model the estimator bias, not just sampling 2026-07-05 10:23:33 +01:00
plot_llm_directed.py llm_directed: directed sex (breed offspring + select on verifier) — E10 in real weights 2026-07-05 18:35:04 +01:00
plot_llm_epistasis.py second review round: tempered claims, robust statistics, corrected technical statements 2026-09-06 17:55:46 +01:00
plot_llm_merge.py llm_merge_hpc: the 7B firm-up makes the Fisher-Muller sign decisive 2026-07-05 17:32:51 +01:00
plot_llm_moe.py llm_moe: the union operator (route/max-merge) vs fusion — and the regime flips at scale 2026-07-05 17:53:47 +01:00
plot_llm_seeds.py Phase 3: LLM-tier speciation + multi-seed firm-up of the recombination claims 2026-09-06 15:39:15 +01:00
plot_llm_speciation.py second review round: tempered claims, robust statistics, corrected technical statements 2026-09-06 17:55:46 +01:00
plot_mnist.py neural: real-MNIST external-validity tier (collapse + grounding) 2026-07-05 09:19:36 +01:00
plot_recombination.py neural: grounding refinement + all five Layer-1.5 figures 2026-07-05 08:14:19 +01:00
plot_speciation_real.py E13b/c: harden real-weight speciation — full symmetry group + emergent-divergence null 2026-09-06 12:35:14 +01:00
stats_llm_epistasis.py third review round: mathematical corrections + operator separation + headline calibration 2026-09-06 19:29:09 +01:00