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docs: genetics and inheritance design (ADR 0006, Phase 4, PR 1/5) - #97
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Record the Phase 4 design before any code: a per-organism immutable genome (physical, sensory, metabolic, behavioral, reproduction, brain, learning), table-driven per-kind mutation, explicit recombination (blend crossover for continuous genes, per-block segment crossover for neural weights so both parents' brains contribute), validate/repair/compare operations, a lineage store that outlives organisms, and learning inheritance as a pure function wired in Phase 5. Capability is coupled to cost (body-size-derived energy capacity and basal cost, sensor cost scaling with sensor radius, reproduction cost scaling with offspring investment) so no gene is a free lunch; at the baseline genome every quantity equals its Phase 3 value, which lets the behavior-preserving PR prove it changes nothing. Also adds docs/genetics/genome.md (gene tables, ranges, operators, weight layout, lineage API), hash schema v3 layout in determinism.md, the genome-reading pipeline notes in update-order.md, and brings the configuration.md field table up to date (it was missing the Phase 3 fields). Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
This was referenced Oct 24, 2026
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Summary
First of five Phase 4 PRs. Design only; no code or behavior changes. Records the genetics design before implementation, as ADR 0005 did for Phase 3.
Genome(physical, sensory, metabolic, behavioral, reproduction, brain, learning); table-driven per-kind mutation (gaussian, point, bit-flip, circular, trait-shift, learning-parameter, brain-weight); explicit recombination (blend crossover for continuous genes, per-block single-point crossover for neural weights so both parents' brains contribute);validateGenome/repairGenome/genomeDistance; aLineageStorethat outlives organisms; learning inheritance (baldwinian / partial / lamarckian) as a pure function wired in Phase 5.docs/genetics/genome.md: gene table with baselines, ranges, rates and stds; derived quantities; brain weight block layout; operators; validation rules; lineage API; config surface.determinism.md: hash schema v3 layout (appendsnextGenomeIdand each organism's genome); v2 stays documented.update-order.md: systems read the organism's own genes; reproduction builds the child genome on thegeneticsstream; death marks the lineage record.configuration.md: field table brought up to date. It was missing the Phase 3 fields; this adds those plus the Phase 4geneticssection, and marksorganisms.*/reproduction.*as the founder baseline.Decisions made with the owner
Notes for review
reproduction.energyCost/offspringEnergywill be replaced byoffspringInvestment+overheadFraction(baseline values reproduce Phase 3's 20 paid / 25 to child). No external users, so no compatibility shim.Test plan
pnpm format:checkclean in a fresh clonepnpm checkgreen in a fresh clone (docs-only, no code touched)🤖 Generated with Claude Code