{
  "ai.module": "evolutionary_biology.rtt1",
  "ai.version": "1.0",
  "ai.purpose": "RTT/1 engine layer for Evolutionary Biology: operator grammar, dimensional mapping, adaptive behavior, and minimal coherence examples.",
  "ai.keywords": [
    "evolution",
    "selection",
    "variation",
    "inheritance",
    "lineage",
    "adaptation",
    "operator grammar",
    "rtt1"
  ],

  "engine": {
    "layer": "RTT/1",
    "description": "Defines the operator grammar and dimensional behavior of evolutionary processes within the RTT substrate."
  },

  "operators": {
    "core": {
      "variation": {
        "type": "generator",
        "description": "Introduces differences among individuals through mutation, recombination, and developmental noise.",
        "signals": ["novelty", "trait_distribution_shift"]
      },
      "selection": {
        "type": "filter",
        "description": "Differential reproductive success based on environmental fit.",
        "signals": ["fitness_gradient", "trait_frequency_change"]
      },
      "inheritance": {
        "type": "memory",
        "description": "Transmission of lineage information across generations.",
        "signals": ["genetic_stability", "trait_heritability"]
      },
      "drift": {
        "type": "stochastic_operator",
        "description": "Random fluctuations in allele frequencies due to finite population size.",
        "signals": ["frequency_noise", "bottleneck_effects"]
      },
      "adaptation": {
        "type": "emergent_behavior",
        "description": "Population-level alignment with environmental constraints through repeated selection cycles.",
        "signals": ["fitness_increase", "trait_optimization"]
      }
    },

    "supporting": {
      "gene_flow": {
        "type": "exchange",
        "description": "Movement of genetic material between populations."
      },
      "population_structure": {
        "type": "constraint",
        "description": "Spatial or social organization that shapes evolutionary dynamics."
      },
      "environmental_pressure": {
        "type": "external_operator",
        "description": "Environmental constraints that shape selection gradients."
      }
    }
  },

  "dimensional_mapping": {
    "R1": "Primitive replicator dynamics; minimal lineage memory; high stochasticity.",
    "R2": "Genetic mechanisms and molecular variation; partial expression of adaptive patterns.",
    "R3": "Full population-level evolutionary dynamics; stable selection and adaptation cycles."
  },

  "coherence": {
    "markers": [
      "stable inheritance patterns",
      "predictable selection gradients",
      "consistent trait frequency shifts",
      "population-level adaptation"
    ],
    "instability_signals": [
      "loss of lineage continuity",
      "environmental collapse",
      "genetic bottlenecks",
      "excessive stochastic drift"
    ]
  },

  "examples": {
    "minimal": [
      {
        "name": "Peppered Moth (Industrial Melanism)",
        "demonstrates": ["selection", "adaptation"]
      },
      {
        "name": "Founder Effect",
        "demonstrates": ["drift", "lineage_constraint"]
      },
      {
        "name": "Mutation-Driven Variation",
        "demonstrates": ["variation"]
      }
    ]
  },

  "integration": {
    "cross_module": [
      "genetics.rtt1",
      "ecology.rtt1",
      "information_theory.rtt1"
    ],
    "notes": "RTT/1 treats evolution as an operator-driven adaptive system; deeper resonance and lineage structures are resolved in RTT/2 and RTT/3."
  }
}