gh-k-dense-ai-claude-scientific-writer-claude-scientific-writer/skills/scientific-critical-thinking/references/scientific_method.md

Scientific Method Core Principles

Fundamental Principles

1. Empiricism

• Knowledge derives from observable, measurable evidence
• Claims must be testable through observation or experiment
• Subjective experience alone is insufficient for scientific conclusions

2. Falsifiability (Popper's Criterion)

• A hypothesis must be capable of being proven false
• Unfalsifiable claims are not scientific (e.g., "invisible, undetectable forces")
• Good hypotheses make specific, testable predictions

3. Reproducibility

• Results must be replicable by independent researchers
• Methods must be described with sufficient detail for replication
• Single studies are rarely definitive; replication strengthens confidence

4. Parsimony (Occam's Razor)

• Prefer simpler explanations over complex ones when both fit the data
• Don't multiply entities unnecessarily
• Extraordinary claims require extraordinary evidence

5. Systematic Observation

• Use standardized, rigorous methods
• Control for confounding variables
• Minimize observer bias through blinding and protocols

The Scientific Process

1. Question Formation

• Identify a specific, answerable question
• Ensure the question is within the scope of scientific inquiry
• Consider whether current methods can address the question

2. Literature Review

• Survey existing knowledge
• Identify gaps and contradictions
• Build on previous work rather than reinventing

3. Hypothesis Development

• State a clear, testable prediction
• Define variables operationally
• Specify the expected relationship between variables

4. Experimental Design

• Choose appropriate methodology
• Identify independent and dependent variables
• Control confounding variables
• Select appropriate sample size and population
• Plan statistical analyses in advance

5. Data Collection

• Follow protocols consistently
• Record all observations, including unexpected results
• Maintain detailed lab notebooks or data logs
• Use validated measurement instruments

6. Analysis

• Apply appropriate statistical methods
• Test assumptions of statistical tests
• Consider effect size, not just significance
• Look for alternative explanations

7. Interpretation

• Distinguish between correlation and causation
• Acknowledge limitations
• Consider alternative interpretations
• Avoid overgeneralizing beyond the data

8. Communication

• Report methods transparently
• Include negative results
• Acknowledge conflicts of interest
• Make data and code available when possible

Critical Evaluation Criteria

When Reviewing Scientific Work, Ask:

Validity Questions:

• Does the study measure what it claims to measure?
• Are the methods appropriate for the research question?
• Were controls adequate?
• Could confounding variables explain the results?

Reliability Questions:

• Are measurements consistent?
• Would the study produce similar results if repeated?
• Are inter-rater reliability and measurement precision reported?

Generalizability Questions:

• Is the sample representative of the target population?
• Are the conditions realistic or artificial?
• Do the results apply beyond the specific context?

Statistical Questions:

• Is the sample size adequate for the analysis?
• Are the statistical tests appropriate?
• Are effect sizes reported alongside p-values?
• Were multiple comparisons corrected?

Logical Questions:

• Do the conclusions follow from the data?
• Are alternative explanations considered?
• Are causal claims supported by the study design?
• Are limitations acknowledged?

Red Flags in Scientific Claims

1. Cherry-picking data - Highlighting only supporting evidence
2. Moving goalposts - Changing predictions after seeing results
3. Ad hoc hypotheses - Adding explanations to rescue a failed prediction
4. Appeal to authority - "Expert X says" without evidence
5. Anecdotal evidence - Relying on personal stories over systematic data
6. Correlation implies causation - Confusing association with causality
7. Post hoc rationalization - Explaining results after the fact without prediction
8. Ignoring base rates - Not considering prior probability
9. Confirmation bias - Seeking only evidence that supports beliefs
10. Publication bias - Only positive results get published

Standards for Causal Inference

Bradford Hill Criteria (adapted)

1. Strength - Strong associations are more likely causal
2. Consistency - Repeated observations by different researchers
3. Specificity - Specific outcomes from specific causes
4. Temporality - Cause precedes effect (essential)
5. Biological gradient - Dose-response relationship
6. Plausibility - Coherent with existing knowledge
7. Coherence - Consistent with other evidence
8. Experiment - Experimental evidence supports causation
9. Analogy - Similar cause-effect relationships exist

Establishing Causation Requires:

• Temporal precedence (cause before effect)
• Covariation (cause and effect correlate)
• Elimination of alternative explanations
• Ideally: experimental manipulation showing cause produces effect

Peer Review and Scientific Consensus

Understanding Peer Review

• Filters obvious errors but isn't perfect
• Reviewers can miss problems or have biases
• Published ≠ proven; it means "passed initial scrutiny"
• Retraction mechanisms exist for flawed papers

Scientific Consensus

• Emerges from convergence of multiple independent lines of evidence
• Consensus can change with new evidence
• Individual studies rarely overturn consensus
• Consider the weight of evidence, not individual papers

Open Science Principles

Transparency Practices

• Preregistration of hypotheses and methods
• Open data sharing
• Open-source code
• Preprints for rapid dissemination
• Registered reports (peer review before data collection)

Why Transparency Matters

• Reduces publication bias
• Enables verification
• Prevents p-hacking and HARKing (Hypothesizing After Results are Known)
• Accelerates scientific progress