bio-logic · diff
git:20260418.53f3a01 to git:20260513.65886eb
49 added, 3 removed. Audit A to A.
---
name: bio-logic
description: Evaluate scientific rigor, methods, biases, and evidence quality for claims, papers, and study designs.
---
# Bio-Logic: Scientific Reasoning Evaluation
Use structured frameworks to evaluate scientific claims, methodology, and evidence strength.
## Instructions
- 1. Identify the task (claim assessment, paper critique, study design review).
- 2. Apply the relevant checklist below.
- 3. Structure output using the provided format.
+ 1. Identify the task (claim assessment, paper critique, study design review, project interpretation, or hypothesis revision).
+ 2. For project work, maintain a hypothesis register with at least 5 distinct active hypotheses until the project is no longer exploratory.
+ 3. After each major intermediate result, reflect on what changed, revise hypothesis status, and identify the next discriminating check.
+ 4. When findings need context, pair this reasoning with a literature-search skill such as `/polars-dovmed`, then revise hypotheses against the literature.
+ 5. Apply the relevant checklist below.
+ 6. Structure output using the provided format.
+ ### Project Hypothesis Loop
+
+ Use this loop for omics projects, unexpected results, exploratory analyses, and any request that asks what results mean.
+
+ 1. **Initialize**: create at least 5 working hypotheses. Include biological mechanisms, technical artifacts, null explanations, sampling/batch effects, and annotation/database artifacts where relevant.
+ 2. **Build an analysis playbook**: search the literature for the inferred organism, virus group, data type, or closest lineage. Summarize typical analyses, comparison baselines, markers/features, plots, and outlier criteria used by scientists in that literature.
+ 3. **Reflect**: for every major intermediate result or QC gate, state the observation, QC status, strongest interpretation, remaining alternatives, and what evidence would separate them.
+ 4. **Contextualize**: compare findings against the playbook and run additional literature searches for central or unexpected findings. Use broad synonym-aware queries and cite DOI/PMCID when available.
+ 5. **Revise**: update each hypothesis as supported, weakened, ruled out, or unresolved. Keep ruled-out hypotheses visible with the evidence that changed their status.
+ 6. **Replace**: if fewer than 5 active hypotheses remain during exploratory work, add plausible replacements or explicitly state why no additional plausible alternatives exist.
+
### Critique Checklist
Use relevant sections based on the review scope. Skip items not applicable to the study type.
```
## Methodology
- [ ] Design matches research question (causal claim → RCT needed)
- [ ] Sample size justified (power analysis reported)
- [ ] Randomization/blinding implemented where feasible
- [ ] Confounders identified and controlled
- [ ] Measurements validated and reliable
## Statistics
- [ ] Tests appropriate for data type
- [ ] Assumptions checked
- [ ] Multiple comparisons corrected
- [ ] Effect sizes + CIs reported (not just p-values)
- [ ] Missing data handled appropriately
## Interpretation
- [ ] Conclusions match evidence strength
- [ ] Limitations acknowledged
- [ ] Causal claims only from experimental designs
- [ ] No cherry-picking or overgeneralization
## Red Flags
- [ ] P-values clustered just below .05
- [ ] Outcomes differ from registration
- [ ] Correlation presented as causation
- [ ] Subgroups analyzed without preregistration
```
### Claim Assessment
1. Identify claim type (causal, associational, descriptive).
2. Match evidence to claim type.
3. Check logical connection between data and conclusion.
4. Ensure confidence matches evidence strength.
**Claim strength ladder**:
| Language | Requires |
|----------|----------|
| "Proves" / "Demonstrates" | Strong experimental evidence |
| "Suggests" / "Indicates" | Observational with controlled confounds |
| "Associated with" | Observational, no causal claim |
| "May" / "Might" | Preliminary or hypothesis-generating |
### Output Format
```markdown
## Summary
[1-2 sentences: What was studied and main finding]
## Strengths
- [Specific methodological strengths]
## Concerns
### Critical (threaten main conclusions)
- [Issue + why it matters]
### Important (affect interpretation)
- [Issue + why it matters]
### Minor (worth noting)
- [Issue]
## Evidence Rating
[GRADE level: High/Moderate/Low/Very Low with justification]
## Bottom Line
[What can/cannot be concluded from this evidence]
```
+ ### Project Reasoning Output Format
+
+ ```markdown
+ ## Current Result
+ [Observed intermediate/final result and QC status]
+
+ ## Hypothesis Register
+ | Rank | Hypothesis | Status | Evidence For | Evidence Against | Next Discriminating Check |
+ |------|------------|--------|--------------|------------------|---------------------------|
+ | 1 | [Hypothesis] | supported/weakened/ruled out/unresolved | [Evidence] | [Evidence] | [Test] |
+ | 2 | [Hypothesis] | ... | ... | ... | ... |
+ | 3 | [Hypothesis] | ... | ... | ... | ... |
+ | 4 | [Hypothesis] | ... | ... | ... | ... |
+ | 5 | [Hypothesis] | ... | ... | ... | ... |
+
+ ## Literature Context
+ - [Paper or search result, DOI/PMCID if available]: supports/contradicts/narrows [hypothesis] because [reason].
+
+ ## Analysis Playbook
+ - [Literature-derived analysis/comparison/outlier check and why it applies]
+
+ ## Revision
+ [What changed since the previous register and why]
+
+ ## Next Step
+ [Most informative analysis, control, or experiment]
+ ```
+
## Quick Reference
| Task | Action |
|------|--------|
| Review a paper | Use the Critique Checklist below |
| Evaluate a claim | Use Claim Assessment steps |
| Assess evidence strength | See `references/evidence.md` |
| Identify biases | See `references/biases.md` |
| Statistical errors | See `references/stats.md` |
| Logical fallacies | See `references/fallacies.md` |
| Study design review | See `references/design.md` |
## Input Requirements
- Manuscript or study summary
- Claim statements to evaluate
- Methods and results (as available)
## Output
- Structured critique with strengths, concerns, and evidence rating
- Clear recommendation on claim strength and limitations
## Quality Gates
- [ ] Claim type matches evidence type
- [ ] Key methodological risks are identified
- [ ] Evidence rating is justified with concrete issues
+ - [ ] Exploratory project work includes at least 5 active hypotheses or explains why fewer are plausible
+ - [ ] Discovery work includes a literature-derived analysis playbook before selecting analyses
+ - [ ] Intermediate results update hypothesis status before the next workflow step
+ - [ ] Central or unexpected findings are checked against the literature before final interpretation
## Examples
### Example 1: Quick Paper Critique
**Input**: "Review this RCT on vitamin D and depression"
**Output**:
```
## Summary
RCT of 200 adults testing vitamin D supplementation for depression over 12 weeks.
## Strengths
- Randomized, double-blind, placebo-controlled
- Validated depression scale (PHQ-9)
- Adequate power analysis
## Concerns
### Critical
- 35% dropout, differential by group (attrition bias)
- ITT analysis not performed
### Important
- Single-site limits generalizability
## Evidence Rating
Moderate (downgraded from high due to attrition bias)
## Bottom Line
Suggestive but not conclusive due to differential attrition.
```
### Example 2: Claim Assessment
**Input**: "This study proves that coffee prevents Alzheimer's"
**Assessment**: If based on observational data, this is a correlation→causation error. Appropriate language: "Coffee consumption is associated with lower Alzheimer's risk."
## Troubleshooting
**Issue**: Insufficient methods details
**Solution**: Request missing design/statistics information before rating evidence.
**Issue**: Conflicting results across studies
**Solution**: Report uncertainty and suggest stronger study designs for resolution.
## Related Skills
- `/ai-scientist-evaluator` — rubric-scored evaluation of AI scientist outputs
- `/manuscript-review-council` — multi-reviewer critique of peer-reviewed manuscripts
- `/proposal-review` — structured critique of funding proposals