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assets/hypothesis_output_template.md

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]
  2. Conditions: [Under what conditions should this be observed?]
  3. Magnitude: [Expected effect size or direction, if quantifiable]

  4. Falsification: [What observation would falsify this prediction?]

  5. Prediction 1.2: [Specific, measurable prediction]

  6. Conditions: [Conditions]
  7. Magnitude: [Expected effect]

  8. Falsification: [Falsifying observation]

  9. Prediction 1.3: [Additional prediction]

Predictions from Hypothesis 2

  1. Prediction 2.1: [Specific, measurable prediction]
  2. Conditions: [Conditions]
  3. Magnitude: [Expected effect]

  4. Falsification: [Falsifying observation]

  5. Prediction 2.2: [Additional prediction]

Predictions from Hypothesis 3

  1. Prediction 3.1: [Specific, measurable prediction]
  2. Conditions: [Conditions]
  3. Magnitude: [Expected effect]
  4. 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]

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
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