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
31 lines
2.3 KiB
Markdown
31 lines
2.3 KiB
Markdown
# E7 — the advantage of sex: recombination adapts faster than clonal reproduction
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**Claim tested.** The dynamic mechanism behind E8: *why* can a recombining society reach capability a
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lone lineage cannot? Because recombination reassorts beneficial variants that arise in different
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sub-lineages, while an asexual (clonal) lineage suffers **clonal interference** — the variants compete
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and cannot combine.
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**Setup.** A single population (distribution over `2^L` genotypes, `L=12`) adapts from **all-wrong**
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toward the multi-locus optimum under the composed step: selection (fitness-proportional) + drift
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(resample `n=150`) + mutation (per-locus flips, `μ=0.02`) + recombination. Two arms — **asexual**
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(`recomb_rate=0`) vs **sexual** (`recomb_rate=1`). 20 replicates.
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### Symbols
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- **asexual/clonal** = offspring are whole-genotype copies (Layer-1's regime) · **sexual** = loci reassorted across the population each generation.
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- **fitness** = number of correct loci (optimum = `L`) · **linkage disequilibrium |D|** = how far the loci are from statistical independence (correct alleles scattered across different genotypes).
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### The two panels
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1. **Advantage of sex.** Mean fitness over generations: the **sexual lineage (red) climbs faster**
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than the asexual one (grey) through the adaptation phase (gen ~10–35). *Honest scope:* both plateau
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near the optimum by gen ~40 in this tractable regime — this is a **speed** advantage, not a
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permanent gap (the single-population Muller's ratchet is subtle to force; E8 carries the headline).
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2. **Mechanism.** Linkage disequilibrium over generations: the asexual lineage spikes to `|D|≈0.04`
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during adaptation (beneficial alleles held apart, scattered across genotypes), while the sexual
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lineage stays at `|D|≈0` — it *assembles* them. The LD gap is exactly why sexual adapts faster.
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### Takeaway
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Recombination's advantage is real and classical: it combines good ideas that arose independently,
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which clonal reproduction cannot. This is the population-level reason a single evolving model lineage
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degrades or stalls where a recombining **society** climbs — and it grounds the E8 vertical result in
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the evolution-of-sex theory. **Falsifier (not triggered):** if the sexual lineage adapted no faster
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than the asexual one (and kept the same LD), recombination would do no work.
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