Giorgio Gilestro
ab3dc10587
- 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
29 lines
1.3 KiB
YAML
29 lines
1.3 KiB
YAML
experiment: E7
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kind: genotype_lineage
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seed: 20260705
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n_replicates: 20
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# (The advantage of sex — the dynamic mechanism behind E8): a single population adapts from all-wrong
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# toward a multi-locus optimum under selection + drift + mutation. Beneficial alleles arise in
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# different sub-lineages; recombination reassorts them into one genotype, while an asexual lineage
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# suffers clonal interference (the alleles compete and cannot combine). Expect the SEXUAL lineage
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# (recomb_rate=1) to climb toward the optimum faster than the ASEXUAL one (recomb_rate=0) — the
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# classical advantage of sex, and the reason a lone model lineage cannot do what a recombining
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# society can. Honest scope: a SPEED advantage, not a dramatic permanent gap (the single-population
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# ratchet is subtle); E8 carries the headline. Falsifier: sexual adapts no faster than asexual.
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genotype:
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L: 12
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n: 150 # population/resample size (drift strength)
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mu: 0.02 # per-locus mutation (flip) rate
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base: 1.3 # multiplicative selection: fitness weight = base^(#correct loci)
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recomb_rate: 0.0 # overwritten per arm by the sweep
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init: wrong # start all-wrong (load L); adapt upward
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generations: 120
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sweep:
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- param: genotype.recomb_rate
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values: [0.0, 1.0] # asexual vs sexual
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output: {dir: results/sexual_vs_asexual_lineage}
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