{
  "module": "evolutionary_biology",
  "version": "1.0",
  "identity": "multi-scale adaptive resonance system",
  "description": "Simulation hooks for variation, selection, inheritance, lineage coherence, and regime-aware evolutionary dynamics.",

  "hooks": {
    "initialize_population": {
      "purpose": "Create the base population with trait distributions and coherence structure.",
      "inputs": ["population_size", "trait_space", "initial_distribution"],
      "outputs": ["population_state"],
      "constraints": [
        "no teleology",
        "traits must be structurally defined",
        "population must be regime-compatible"
      ]
    },

    "generate_variation": {
      "purpose": "Apply variation as a distinction-generation operator.",
      "inputs": ["population_state", "variation_rates", "environment_profile"],
      "outputs": ["variant_population"],
      "constraints": [
        "variation is non-purposeful",
        "no adaptation-as-intent",
        "variation must preserve structural validity"
      ]
    },

    "apply_selection": {
      "purpose": "Filter variants using selection as a coherence-filtering operator.",
      "inputs": ["variant_population", "environment_profile", "fitness_operator"],
      "outputs": ["selected_population"],
      "constraints": [
        "selection is not purpose-driven",
        "selection must be operator-defined",
        "no progress narratives"
      ]
    },

    "apply_inheritance": {
      "purpose": "Propagate traits across generations using inheritance as a coherence operator.",
      "inputs": ["selected_population", "inheritance_rules"],
      "outputs": ["next_generation_population"],
      "constraints": [
        "inheritance must preserve coherence",
        "no gene-centric reductionism",
        "multi-scale inheritance allowed (genetic, epigenetic, cultural)"
      ]
    },

    "evaluate_lineage_coherence": {
      "purpose": "Evaluate coherence across generations.",
      "inputs": ["population_history", "trait_dynamics"],
      "outputs": ["coherence_score"],
      "constraints": [
        "coherence = lineage stability",
        "no teleological metrics",
        "coherence must be structural"
      ]
    },

    "ecosystem_interaction": {
      "purpose": "Model interactions between populations and ecological operators.",
      "inputs": ["population_state", "ecosystem_state", "interaction_rules"],
      "outputs": ["updated_population_state", "updated_ecosystem_state"],
      "constraints": [
        "ecosystems are multi-operator environments",
        "interactions must preserve ecological coherence",
        "no purpose metaphors"
      ]
    },

    "regime_transition": {
      "purpose": "Transition evolutionary behavior across RTT regimes.",
      "inputs": ["population_state", "from_regime", "to_regime"],
      "outputs": ["transitioned_population_state"],
      "constraints": [
        "R0: pre-evolutionary distinctions",
        "R1: stable variation-inheritance cycle",
        "R2: selection operators active",
        "R3: multi-scale adaptive resonance",
        "transitions must preserve lineage coherence"
      ]
    },

    "detect_evolutionary_collapse": {
      "purpose": "Classify failure modes in evolutionary dynamics.",
      "inputs": ["population_state"],
      "outputs": ["collapse_mode"],
      "modes": {
        "E1": "variation collapse (no distinctions)",
        "E2": "selection collapse (operator invalid)",
        "E3": "inheritance collapse (propagation failure)",
        "E4": "lineage incoherence (trajectory failure)",
        "E5": "ecosystem collapse (environmental incompatibility)"
      }
    },

    "reinforce_adaptive_resonance": {
      "purpose": "Stabilize evolutionary dynamics through repeated coherent cycles.",
      "inputs": ["population_history", "environment_history"],
      "outputs": ["reinforced_population_state"],
      "constraints": [
        "reinforcement must increase coherence",
        "reinforcement is structural, not teleological",
        "no introduction of purpose-driven mechanisms"
      ]
    }
  }
}