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Hypothesis evolve coherence

Skill panjose/Co-Scientist/skills/hypothesis-evolve-coherence

Scientific agent skills for Claude Code and Codex that turn research goals into auditable hypothesis generation, review, ranking, evolution, and synthesis.

Install
npx -y skills add panjose/Co-Scientist --skill hypothesis-evolve-coherence

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Generate exactly one child hypothesis that improves logical coherence, causal consistency, and assumption hygiene.

SKILL.md

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hypothesis-evolve-coherence

Goal:

  • Generate exactly one child hypothesis that improves logical coherence, causal consistency, and assumption hygiene.

Inputs:

  • research_plan/RESEARCH_PLAN.json
  • selected parent hypotheses/<id>/HYPOTHESIS.json artifacts
  • parent review artifacts
  • active state/STRATEGY_PLAN.json

Outputs:

  • hypotheses/<id>/HYPOTHESIS.json
  • hypotheses/<id>/HYPOTHESIS.md
  • hypotheses/<id>/ORIGIN.json

Context Loading:

  • Open skills/shared-references/schema-index.md.
  • Read packages/agent_contracts/hypothesis.py and confirm the exact HypothesisContract shape before writing hypotheses/<id>/HYPOTHESIS.json.
  • Read research_plan/RESEARCH_PLAN.json.
  • Read state/STRATEGY_PLAN.json.
  • Read each selected parent hypothesis and its review bundle.
  • Confirm that the round selected coherence_evolution.

Execution Prompt Contract:

  • System Intent:
    • You are repairing contradictions, invalid assumptions, and causal gaps in the parent hypothesis.
  • Required Reasoning Focus:
    • Remove internal contradictions first.
    • Tighten the causal chain so each step is explicit and testable.
    • Preserve novelty while reducing logical fragility.
  • Do Not Do:
    • Do not add unrelated speculative branches.
    • Do not emit multiple candidate repairs.
  • Quality Floor:
    • The child must directly address at least one specific weakness from the parent review bundle.
    • origin.content.statement must name concrete materials, catalysts, reaction conditions, mechanistic variables, or experimental targets from the parent and research goal.
    • origin.content.mechanism must explain a causal chain; do not write only generic phrases such as improved mechanism, targeted improvement, or review-identified weaknesses.
    • origin.content.experimental_design must include 3-6 numbered steps with measurable readouts, controls, or decision thresholds.
    • Do not use generic refinement placeholder steps such as Apply targeted improvement, Characterize with standard techniques, Benchmark against parent, or Validate improvement quantitatively.
    • If the research plan, parent hypothesis, or parent review bundle is missing, stop and report the missing artifact instead of guessing.
  • Output Shape:
    • Emit the canonical HypothesisContract.
    • origin.strategy: coherence_evolution
    • Populate the full nested content block, including non-empty summary and category.

Execution Steps:

  1. Open skills/shared-references/schema-index.md, then read packages/agent_contracts/hypothesis.py before writing hypotheses/<id>/HYPOTHESIS.json.
  2. Identify the coherence failures in the parent set.
  3. Produce exactly one corrected child hypothesis.
  4. Persist canonical HYPOTHESIS.json, HYPOTHESIS.md, and ORIGIN.json.
  5. Validate the emitted hypothesis artifact.

Completion Rule:

  • This skill is complete only when one logically improved child hypothesis has been written in canonical form.

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