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skills/hypothesis-generation/assets/hypothesis_output_template.md

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+# Scientific Hypothesis Generation: [Phenomenon Name]
+
+## 1. Background & Context
+
+### Phenomenon Description
+[Clear description of the observation, pattern, or question that requires explanation. Include:
+- What was observed or what question needs answering
+- The specific context or system in which it occurs
+- Any relevant constraints or boundary conditions
+- Why this phenomenon is interesting or important]
+
+### Current Understanding
+[Synthesis of existing literature, including:
+- What is already known about this phenomenon
+- Established mechanisms or theories that may be relevant
+- Key findings from recent research
+- Gaps or limitations in current understanding
+- Conflicting findings or unresolved debates
+
+Include citations to key papers (Author et al., Year, Journal)]
+
+### Knowledge Gaps
+[Specific aspects that remain unexplained or poorly understood:
+- What aspects of the phenomenon lack clear explanation?
+- What contradictions exist in current understanding?
+- What questions remain unanswered?]
+
+---
+
+## 2. Competing Hypotheses
+
+### Hypothesis 1: [Concise Title]
+
+**Mechanistic Explanation:**
+[Detailed explanation of the proposed mechanism. This should explain HOW and WHY the phenomenon occurs, not just describe WHAT occurs. Include:
+- Specific molecular, cellular, physiological, or population-level mechanisms
+- Causal chain from initial trigger to observed outcome
+- Key components, pathways, or factors involved
+- Scale or level of explanation (molecular, cellular, organ, organism, population)]
+
+**Supporting Evidence:**
+[Evidence from literature that supports this hypothesis:
+- Analogous mechanisms in related systems
+- Direct evidence from relevant studies
+- Theoretical frameworks that align with this hypothesis
+- Include citations]
+
+**Key Assumptions:**
+[Explicit statement of assumptions underlying this hypothesis:
+- What must be true for this hypothesis to hold?
+- What conditions or contexts does it require?]
+
+---
+
+### Hypothesis 2: [Concise Title]
+
+**Mechanistic Explanation:**
+[Detailed mechanistic explanation distinct from Hypothesis 1]
+
+**Supporting Evidence:**
+[Evidence supporting this alternative explanation]
+
+**Key Assumptions:**
+[Assumptions underlying this hypothesis]
+
+---
+
+### Hypothesis 3: [Concise Title]
+
+**Mechanistic Explanation:**
+[Detailed mechanistic explanation distinct from previous hypotheses]
+
+**Supporting Evidence:**
+[Evidence supporting this explanation]
+
+**Key Assumptions:**
+[Assumptions underlying this hypothesis]
+
+---
+
+[Continue for Hypothesis 4, 5, etc. if applicable]
+
+---
+
+## 3. Quality Assessment
+
+### Evaluation Against Core Criteria
+
+| Criterion | Hypothesis 1 | Hypothesis 2 | Hypothesis 3 | [H4] | [H5] |
+|-----------|--------------|--------------|--------------|------|------|
+| **Testability** | [Rating & brief note] | [Rating & brief note] | [Rating & brief note] | | |
+| **Falsifiability** | [Rating & brief note] | [Rating & brief note] | [Rating & brief note] | | |
+| **Parsimony** | [Rating & brief note] | [Rating & brief note] | [Rating & brief note] | | |
+| **Explanatory Power** | [Rating & brief note] | [Rating & brief note] | [Rating & brief note] | | |
+| **Scope** | [Rating & brief note] | [Rating & brief note] | [Rating & brief note] | | |
+| **Consistency** | [Rating & brief note] | [Rating & brief note] | [Rating & brief note] | | |
+
+**Rating scale:** Strong / Moderate / Weak
+
+### Detailed Evaluation
+
+#### Hypothesis 1
+**Strengths:**
+- [Specific strength 1]
+- [Specific strength 2]
+
+**Weaknesses:**
+- [Specific weakness 1]
+- [Specific weakness 2]
+
+**Overall Assessment:**
+[Brief summary of hypothesis quality and viability]
+
+#### Hypothesis 2
+[Similar structure]
+
+#### Hypothesis 3
+[Similar structure]
+
+---
+
+## 4. Experimental Designs
+
+### Testing Hypothesis 1: [Title]
+
+**Experiment 1A: [Brief title]**
+
+*Design Type:* [e.g., In vitro dose-response / In vivo knockout / Clinical RCT / Observational cohort / Computational model]
+
+*Objective:* [What specific aspect of the hypothesis does this test?]
+
+*Methods:*
+- **System/Model:** [What system, organism, or population?]
+- **Intervention/Manipulation:** [What is varied or manipulated?]
+- **Measurements:** [What outcomes are measured?]
+- **Controls:** [What control conditions?]
+- **Sample Size:** [Estimated n, with justification if possible]
+- **Analysis:** [Statistical or analytical approach]
+
+*Expected Timeline:* [Rough estimate]
+
+*Feasibility:* [High/Medium/Low, with brief justification]
+
+**Experiment 1B: [Brief title - alternative or complementary approach]**
+[Similar structure to 1A]
+
+---
+
+### Testing Hypothesis 2: [Title]
+
+**Experiment 2A: [Brief title]**
+[Structure as above]
+
+**Experiment 2B: [Brief title]**
+[Structure as above]
+
+---
+
+### Testing Hypothesis 3: [Title]
+
+**Experiment 3A: [Brief title]**
+[Structure as above]
+
+---
+
+## 5. Testable Predictions
+
+### Predictions from Hypothesis 1
+
+1. **Prediction 1.1:** [Specific, measurable prediction]
+   - **Conditions:** [Under what conditions should this be observed?]
+   - **Magnitude:** [Expected effect size or direction, if quantifiable]
+   - **Falsification:** [What observation would falsify this prediction?]
+
+2. **Prediction 1.2:** [Specific, measurable prediction]
+   - **Conditions:** [Conditions]
+   - **Magnitude:** [Expected effect]
+   - **Falsification:** [Falsifying observation]
+
+3. **Prediction 1.3:** [Additional prediction]
+
+---
+
+### Predictions from Hypothesis 2
+
+1. **Prediction 2.1:** [Specific, measurable prediction]
+   - **Conditions:** [Conditions]
+   - **Magnitude:** [Expected effect]
+   - **Falsification:** [Falsifying observation]
+
+2. **Prediction 2.2:** [Additional prediction]
+
+---
+
+### Predictions from Hypothesis 3
+
+1. **Prediction 3.1:** [Specific, measurable prediction]
+   - **Conditions:** [Conditions]
+   - **Magnitude:** [Expected effect]
+   - **Falsification:** [Falsifying observation]
+
+---
+
+## 6. Critical Comparisons
+
+### Distinguishing Between Hypotheses
+
+**Comparison: Hypothesis 1 vs. Hypothesis 2**
+
+*Key Distinguishing Feature:*
+[What is the fundamental difference in mechanism or prediction?]
+
+*Discriminating Experiment:*
+[What experiment or observation would clearly favor one over the other?]
+
+*Outcome Interpretation:*
+- If [Result A], then Hypothesis 1 is supported
+- If [Result B], then Hypothesis 2 is supported
+- If [Result C], then both/neither are supported
+
+---
+
+**Comparison: Hypothesis 1 vs. Hypothesis 3**
+[Similar structure]
+
+---
+
+**Comparison: Hypothesis 2 vs. Hypothesis 3**
+[Similar structure]
+
+---
+
+### Priority Experiments
+
+**Highest Priority Test:**
+[Which experiment would most efficiently distinguish between hypotheses or most definitively test a hypothesis?]
+
+**Justification:**
+[Why is this the highest priority? Consider informativeness, feasibility, and cost]
+
+**Secondary Priority Tests:**
+1. [Second most important experiment]
+2. [Third most important]
+
+---
+
+## 7. Summary & Recommendations
+
+### Summary of Hypotheses
+
+[Brief paragraph summarizing the competing hypotheses and their relationships]
+
+### Recommended Testing Sequence
+
+**Phase 1 (Initial Tests):**
+[Which experiments should be done first? Why?]
+
+**Phase 2 (Contingent on Phase 1 results):**
+[What follow-up experiments depend on initial results?]
+
+**Phase 3 (Validation and Extension):**
+[How to validate findings and extend to broader contexts?]
+
+### Expected Outcomes and Implications
+
+**If Hypothesis 1 is supported:**
+[What would this mean for the field? What new questions arise?]
+
+**If Hypothesis 2 is supported:**
+[Implications and new questions]
+
+**If Hypothesis 3 is supported:**
+[Implications and new questions]
+
+**If multiple hypotheses are partially supported:**
+[How might mechanisms combine or interact?]
+
+### Open Questions
+
+[What questions remain even after these hypotheses are tested?]
+
+---
+
+## References
+
+[List key papers cited in the document, formatted consistently]
+
+1. Author1, A.B., & Author2, C.D. (Year). Title of paper. *Journal Name*, Volume(Issue), pages. DOI or URL
+
+2. [Continue for all citations]
+
+---
+
+## Notes on Using This Template
+
+- Replace all bracketed instructions with actual content
+- Not all sections are mandatory - adapt to your specific hypothesis generation task
+- For simpler phenomena, 3 hypotheses may be sufficient; complex phenomena may warrant 4-5
+- Experimental designs should be detailed enough to be actionable but can be refined later
+- Predictions should be as specific and quantitative as possible
+- The template emphasizes both generating hypotheses and planning how to test them
+- Citation format can be adjusted to field-specific standards