# Scientific Critical Thinking

> Audit scientific claims, assumptions, causal language, bias, confounding, and evidence quality without drafting a formal referee report. Use for critical appraisal, evidence grading, or teaching claim evaluation; use peer-review for a manuscript review and statistical-analysis for new calculations.

- Skill: `timsmykov/scientific-critical-thinking` (Agent Skill, multi-file: 9 files)
- Install (CLI): `npx skillmds@latest add timsmykov/scientific-critical-thinking`
- Raw SKILL.md: https://api.skillmd.com/api/skills/timsmykov/scientific-critical-thinking/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Security
- License: MIT
- Author: timsmykov (https://skillmd.com/u/timsmykov)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/timsmykov/scientific-critical-thinking

---


# Scientific Critical Thinking

## Overview

Critical thinking is a systematic process for evaluating scientific rigor. Assess methodology, experimental design, statistical validity, biases, confounding, and evidence quality using GRADE and Cochrane ROB frameworks. Apply this skill for critical analysis of scientific claims.

## Evidence Lab operating contract

- Define the claim and the supplied evidence set before evaluating it; do not imply that an incomplete set is exhaustive.
- Separate observations, author interpretations, reviewer inferences, and unresolved questions.
- Apply a named framework only when it fits the study type, and state any domain expertise the assessment lacks.
- Ask the researcher to confirm the intended decision context when it changes the standard of evidence.
- Return a provisional audit, not a clinical, regulatory, legal, or publication decision.

## When to Use This Skill

This skill should be used when:
- Evaluating research methodology and experimental design
- Assessing statistical validity and evidence quality
- Identifying biases and confounding in studies
- Reviewing scientific claims and conclusions
- Conducting systematic reviews or meta-analyses
- Applying GRADE or Cochrane risk of bias assessments
- Providing critical analysis of research papers

If a diagram materially improves the audit, route it separately to `markdown-mermaid-writing`; do not make visualization a condition of critical appraisal.

## Core Capabilities

Seven capability areas, each with the questions to ask and what the answers imply, are in
[references/core_capabilities.md](references/core_capabilities.md):

1. **Methodology critique** — design, controls, confounding, and whether the method can
   answer the question asked.
2. **Bias detection** — selection, measurement, publication, and cognitive biases.
3. **Statistical analysis evaluation** — power, multiplicity, p-value misuse, effect sizes.
4. **Evidence quality assessment** — study hierarchy, replication, and strength of inference.
5. **Logical fallacy identification** — the fallacies that recur in scientific argument.
6. **Research design guidance** — how to strengthen a design before data collection.
7. **Claim evaluation** — separating what was shown from what is being asserted.

Per-topic detail is in [references/scientific_method.md](references/scientific_method.md),
[references/common_biases.md](references/common_biases.md),
[references/statistical_pitfalls.md](references/statistical_pitfalls.md),
[references/evidence_hierarchy.md](references/evidence_hierarchy.md),
[references/logical_fallacies.md](references/logical_fallacies.md), and
[references/experimental_design.md](references/experimental_design.md).

## Application Guidelines

### General Approach

1. **Be Constructive**
   - Identify strengths as well as weaknesses
   - Suggest improvements rather than just criticizing
   - Distinguish between fatal flaws and minor limitations
   - Recognize that all research has limitations

2. **Be Specific**
   - Point to specific instances (e.g., "Table 2 shows..." or "In the Methods section...")
   - Quote problematic statements
   - Provide concrete examples of issues
   - Reference specific principles or standards violated

3. **Be Proportionate**
   - Match criticism severity to issue importance
   - Distinguish between major threats to validity and minor concerns
   - Consider whether issues affect primary conclusions
   - Acknowledge uncertainty in your own assessments

4. **Apply Consistent Standards**
   - Use same criteria across all studies
   - Don't apply stricter standards to findings you dislike
   - Acknowledge your own potential biases
   - Base judgments on methodology, not results

5. **Consider Context**
   - Acknowledge practical and ethical constraints
   - Consider field-specific norms for effect sizes and methods
   - Recognize exploratory vs. confirmatory contexts
   - Account for resource limitations in evaluating studies

### When Providing Critique

**Structure feedback as:**

1. **Summary:** Brief overview of what was evaluated
2. **Strengths:** What was done well (important for credibility and learning)
3. **Concerns:** Issues organized by severity
   - Critical issues (threaten validity of main conclusions)
   - Important issues (affect interpretation but not fatally)
   - Minor issues (worth noting but don't change conclusions)
4. **Specific Recommendations:** Actionable suggestions for improvement
5. **Overall Assessment:** Balanced conclusion about evidence quality and what can be concluded

**Use precise terminology:**
- Name specific biases, fallacies, and methodological issues
- Reference established standards and guidelines
- Cite principles from scientific methodology
- Use technical terms accurately

### When Uncertain

- **Acknowledge uncertainty:** "This could be X or Y; additional information needed is Z"
- **Ask clarifying questions:** "Was [methodological detail] done? This affects interpretation."
- **Provide conditional assessments:** "If X was done, then Y follows; if not, then Z is concern"
- **Note what additional information would resolve uncertainty**

## Reference Materials

This skill includes comprehensive reference materials that provide detailed frameworks for critical evaluation:

- **`references/scientific_method.md`** - Core principles of scientific methodology, the scientific process, critical evaluation criteria, red flags in scientific claims, causal inference standards, peer review, and open science principles

- **`references/common_biases.md`** - Comprehensive taxonomy of cognitive, experimental, methodological, statistical, and analysis biases with detection and mitigation strategies

- **`references/statistical_pitfalls.md`** - Common statistical errors and misinterpretations including p-value misunderstandings, multiple comparisons problems, sample size issues, effect size mistakes, correlation/causation confusion, regression pitfalls, and meta-analysis issues

- **`references/evidence_hierarchy.md`** - Traditional evidence hierarchy, GRADE system, study quality assessment criteria, domain-specific considerations, evidence synthesis principles, and practical decision frameworks

- **`references/logical_fallacies.md`** - Logical fallacies common in scientific discourse organized by type (causation, generalization, authority, relevance, structure, statistical) with examples and detection strategies

- **`references/experimental_design.md`** - Comprehensive experimental design checklist covering research questions, hypotheses, study design selection, variables, sampling, blinding, randomization, control groups, procedures, measurement, bias minimization, data management, statistical planning, ethical considerations, validity threats, and reporting standards

**When to consult references:**
- Load references into context when detailed frameworks are needed
- Use grep to search references for specific topics: `grep -r "pattern" references/`
- References provide depth; SKILL.md provides procedural guidance
- Consult references for comprehensive lists, detailed criteria, and specific examples

## Remember

**Scientific critical thinking is about:**
- Systematic evaluation using established principles
- Constructive critique that improves science
- Proportional confidence to evidence strength
- Transparency about uncertainty and limitations
- Consistent application of standards
- Recognition that all research has limitations
- Balance between skepticism and openness to evidence

**Always distinguish between:**
- Data (what was observed) and interpretation (what it means)
- Correlation and causation
- Statistical significance and practical importance
- Exploratory and confirmatory findings
- What is known and what is uncertain
- Evidence against a claim and evidence for the null

**Goals of critical thinking:**
1. Identify strengths and weaknesses accurately
2. Determine what conclusions are supported
3. Recognize limitations and uncertainties
4. Suggest improvements for future work
5. Advance scientific understanding