- paper/pnas -> paper/manuscript (venue-neutral)
- configs/layer1 -> configs/inheritance, src/knowledge -> src/inheritance
(imported as `inheritance`), make layer1 -> make inheritance; layer2 alias dropped
- inheritance and trained-network bundles named after the manuscript figure
they feed (fig2_grounding_sweep, figS3_rebaselining, ...), or descriptively
where they feed none; configs keep their `experiment:` value so parquet
hashes are unchanged, only output.dir moves
- figure scripts, SI figure sources, notebooks, REPRODUCING.md, README and the
SI Methods/tables updated; make clean no longer deletes tracked manifests;
reproduce.sh hashes the s{seed}/ layouts too
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm
An audit of the figure pipeline found real sync gaps, now closed:
- `paper/pnas/make_figs.py` (which draws every manuscript figure) was invoked
by NO Makefile target or script - a manual step. Added `make paper-figures`.
- `configs/llm/epistasis{,_compat}.yaml` were reachable from nothing at all,
despite producing Fig. 3C-D. Added `make llm-epistasis` (+ its statistics).
- `make figures` never regenerated the MNIST montage that Fig. 2B embeds;
it now runs with the `mnist` target (it needs torch - it re-simulates).
- Added `make llm-society`, `env-notebooks`, `notebooks`.
New REPRODUCING.md is the authoritative map: every manuscript panel -> the
artifact it plots -> the config that produced it -> that config's seed, plus
the determinism policy (biological tier bitwise; GPU tiers statistical), the
seed-provenance statement, and an artifact-hash verification snippet. All 44
committed bundles currently hash-match their manifests, and figure
regeneration is pixel-identical (verified by comparison).
reproduce.sh delivers the one-command reproduction the paper's Methods
promises, writing REPRODUCED.md with recomputed hashes per bundle.
Two executed notebooks: 01 builds the Wright-Fisher model from scratch and
checks both closed forms interactively (runs in ~1 min on a laptop); 02
verifies artifact hashes then regenerates and displays all seven manuscript
figures. Both execute end-to-end (`make notebooks`).
Also pins `.python-version` to 3.14: the interpreter was previously
unpinned, and a `uv sync` silently switched it to 3.11 mid-session (see
tasks/lessons.md). README rewritten - it still described a Layer-1-only repo
of E1-E6 and pointed at a figure_manifest.md that does not exist.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BkRLcc18rwT2Lysu6PbG7v
Rewrite the-lamarckian-society-v4.md -> v5, making sexual reproduction the
central engine and lifting accessibility for a cross-disciplinary audience
(geneticists, ML engineers, neuroscientists) — every field's jargon glossed
inline, big picture kept legible, measured tone, honest about scope (the
evidence is from minimal models, not LLMs).
Core reframe (section 5): single-teacher distillation is asexual copying,
which collapses (Muller's ratchet = model collapse); the cure is to ground
every birth in reality and to reproduce SEXUALLY — recombining many
complementary parents so offspring can exceed any parent (Fisher-Muller).
Adds the honest limits (outbreeding depression on entangled skills) and the
distinctly-AI advantage (directed sex: choose mates, screen offspring,
unbounded parents). Turns the old "a companion paper will..." into "what we
built and found," folding in the demonstrated results (E1-E11, neural +
MNIST, the learning kernel) and the Riis positioning (concede collapse=drift
as prior art; claim the control-theory cure). Update CLAUDE.md / README
references; results-summary noted alongside.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Scaffold plus the Layer 1 analytical core and the first two experiments.
- knowledge/: truth, metrics, teachers (2.7.1 shared-switch construction),
step, lineage, experiment, config, seeding (imported as `knowledge`).
- Validation spine green: neutral decay (Pred 1), fixation (Pred 2), exact
mutation-drift equilibrium (Pred 3), union coverage (Pred 5). 68 tests pass.
- E1 reproduces tail-first collapse. E2 delivers the headline: a grounding
phase boundary g* << 1, with stationary H tracking the exact H_eq closed
form (g=0.005 -> 68% of truth diversity; g=0.05 -> 96%).
- Reproducibility: uv venv from a hash-pinned uv.lock is the source of truth;
every run writes results.parquet + resolved_config.yaml + manifest.json
(lib versions, git commit, sha256). Figures and manifests tracked; the
large regenerable parquet is gitignored.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
