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:

Finding	Alternative checked	Excluded?	Evidence
...	Confounder X	Yes / No	...

Rationalization Firewall

You will hear yourself say...	Reality check
"The effect is too strong to be confounding"	Strong effects can still be confounded. Check anyway.
"We controlled for the obvious variables"	Obvious to you. What about reviewer #2's favorite confounder?
"Correlation is enough for this paper"	Correlation is enough only if you DON'T claim mechanism.
"Batch correction was applied"	Did you verify it worked? Show before/after.