alternative-hypothesis-check

name: alternative-hypothesis-check description: "Use when analyzing results in Type D or Type H projects before making mechanistic or causal claims — requires systematic exclusion of confounders, batch effects, technical noise, and other alternative explanations"

Alternative Hypothesis Check

Discipline layer skill. Active during Phase 4–5 for Type D and Type H projects.

Iron Law

NO MECHANISM CLAIMS WITHOUT EXCLUDING ALTERNATIVE EXPLANATIONS

Systematic Check

For each major finding, systematically check:

• □ Confounders — variables that could explain the association independently of your proposed mechanism
• □ Batch effects [bioinformatics] — technical variation masquerading as biology (plate, lane, date, operator)
• □ Technical noise — measurement artifacts, instrument drift, reagent lot differences
• □ Sample selection bias — non-random inclusion criteria that correlate with the outcome
• □ Multiple testing inflation — testing many hypotheses means some will be significant by chance; confirm FDR/Bonferroni was applied
• □ Correlation ≠ causation — temporal precedence, dose-response, and intervention evidence must be present before causal language is used

When an Alternative Explanation Cannot Be Excluded

If an alternative explanation cannot be excluded:

→ It must be stated as a limitation in the paper → Language must be weakened ("associated with" not "causes") → It cannot be presented as a mechanistic finding

Checklist Format

For each finding, produce a table:

Rationalization Firewall