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.
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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.jsonartifacts - parent review artifacts
- active
state/STRATEGY_PLAN.json
Outputs:
hypotheses/<id>/HYPOTHESIS.jsonhypotheses/<id>/HYPOTHESIS.mdhypotheses/<id>/ORIGIN.json
Context Loading:
- Open
skills/shared-references/schema-index.md. - Read
packages/agent_contracts/hypothesis.pyand confirm the exactHypothesisContractshape before writinghypotheses/<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.statementmust name concrete materials, catalysts, reaction conditions, mechanistic variables, or experimental targets from the parent and research goal.origin.content.mechanismmust explain a causal chain; do not write only generic phrases such asimproved mechanism,targeted improvement, orreview-identified weaknesses.origin.content.experimental_designmust 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, orValidate 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
summaryandcategory.
- Emit the canonical
Execution Steps:
- Open
skills/shared-references/schema-index.md, then readpackages/agent_contracts/hypothesis.pybefore writinghypotheses/<id>/HYPOTHESIS.json. - Identify the coherence failures in the parent set.
- Produce exactly one corrected child hypothesis.
- Persist canonical
HYPOTHESIS.json,HYPOTHESIS.md, andORIGIN.json. - Validate the emitted hypothesis artifact.
Completion Rule:
- This skill is complete only when one logically improved child hypothesis has been written in canonical form.