hypothesis-generation

Files (7)

• SKILL.md
• FORMATTING_GUIDE.md · assets/
• hypothesis_generation.sty · assets/
• hypothesis_report_template.tex · assets/
• experimental_design_patterns.md · references/
• hypothesis_quality_criteria.md · references/
• literature_search_strategies.md · references/

SKILL.md (first lines)

# Scientific Hypothesis Generation

## Overview

Hypothesis generation is a systematic process for developing testable explanations. Formulate evidence-based hypotheses from observations, design experiments, explore competing explanations, and develop predictions. Apply this skill for scientific inquiry across domains.

## When to Use This Skill

This skill should be used when:
- Developing hypotheses from observations or preliminary data
- Designing experiments to test scientific questions
- Exploring competing explanations for phenomena
- Formulating testable predictions for research
- Conducting literature-based hypothesis generation
- Running a lightweight HypoGeniC-style workflow when the user explicitly asks for automated hypothesis generation/testing
- Planning mechanistic studies across scientific domains

## Outputs

Produce a structured hypothesis report when useful:

- Core observation or anomaly to explain
- Competing mechanistic hypotheses
- Testable predictions for each hypothesis
- Minimal validation experiments or studies
- Decision criteria for supporting, revising, or rejecting each hypothesis

Figures or diagrams may be included when they clarify the hypothesis structure, but this skill does not require a second skill or helper expert to create them.

---

## Workflow

Follow this systematic process to generate robust scientific hypotheses:

### 1. Understand the Phenomenon

Start by clarifying the observation, question, or phenomenon that requires explanation:

- Identify the core observation or pattern that needs explanation
- Define the scope and boundaries of the phenomenon
- Note any constraints or specific contexts
- Clarify what is already known vs. what is uncertain
- Identify the relevant scientific domain(s)

### 2. Conduct Comprehensive Literature Search

Search existing scientific literature to ground hypotheses in current evidence. Use both PubMed (for biomedical topics) and general web search (for broader scientific domains):

**For biomedical topics:**
- Use WebFetch with PubMed URLs to access relevant literature
- Search for recent reviews, meta-analyses, and primary research
- Look for similar phenomena, related mechanisms, or analogous systems

**For all scientific domains:**
- Use WebSearch to find recent papers, preprints, and reviews
- Search for established theories, mechanisms, or frameworks
- Identify gaps in current understanding

**Search strategy:**
- Begin with broad searches to understand the landscape
- Narrow to specific mechanisms, pathways, or theories
- Look for contradictory findings or unresolved debates
- Consult `references/literature_search_strategies.md` for detailed search techniques

### 3. Synthesize Existing Evidence

Analyze and integrate findings from literature search:

- Summarize current understanding of the phenomenon
- Identify established mechanisms or theories that may apply
- Note conflicting evidence or alternative viewpoints
- Recognize gaps, limitations, or unanswered questions
- Identify analogies from related systems or domains

### 4. Generate Competing Hypotheses

Develop 3-5 distinct hypotheses that could explain the phenomenon. Each hypothesis should:

- Provide a mechanistic explanation (not just description)
- Be distinguishable from other hypotheses
- Draw on evidence from the literature synthesis
- Consider different levels of explanation (molecular, cellular, systemic, population, etc.)

**Strategies for generating hypotheses:**
- Apply known mechanisms from analogous systems
- Consider multiple causative pathways
- Explore different scales of explanation
- Question assumptions in existing explanations
- Combine mechanisms in novel ways

### 5. Evaluate Hypothesis Quality

Assess each hypothesis against established quality criteria from `references/hypothesis_quality_criteria.md`:

**Testability:** Can the hypothesis be empirically tested?
**Falsifiability:** What observations would disprove it?
**Parsimony:** Is it the simplest explanation that fits the evidence?
**Explanatory Power:** How much of the phenomenon does it explain?
**Scope:** What range of observations does it cover?
**Consistency:** Does it align with established principles?
**Novelty:** Does it offer new insights beyond existing explanations?

Explicitly note the strengths and weaknesses of each hypothesis.

### 6. Design Experimental Tests

For each viable hypothesis, propose specific experiments or studies to test it. Consult `references/experimental_design_patterns.md` for common approaches:

**Experimental design elements:**
- What would be measured or observed?
- What comparisons or controls are needed?
- What methods or techniques would be used?
- What sample sizes or statistical approaches are appropriate?
- What are potential confounds and how to address them?

**Consider multiple approaches:**
- Laboratory experiments (in vitro, in vivo, computational)
- Observational studies (cross-sectional, longitudinal, case-control)

From foryourhealth111-pixel/Vibe-Skills, MIT.

More from foryourhealth111-pixel/Vibe-Skills