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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
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Based on SOC occupation classification
Use when designing the evaluation protocol for a method development project — locks primary metrics, datasets, seeds, statistical tests, and baseline list into an immutable contract
Use when G2 (plan freeze) and G3 (execution readiness) gates have passed — handles all implementation, baseline reproduction, experimentation, and iteration for both Type M and Type D projects; this is Phase 4
Use when research direction is validated (G1 passed) and the project needs method design, analysis framework, evaluation protocol, or story line — this is Phase 3 and must complete before any code or experiments
Reusable protocol for multi-agent discussions that iterate until convergence. Used by results-integration (Phase 5) and paper-writing (Phase 6) to ensure discussions actually resolve issues rather than just noting them.
Use when and ONLY when the user explicitly requests paper writing and G4 (write-ready) gate has passed — handles LaTeX structure, senior-level writing, reference verification, and iterative refinement
Use when Phase 1 (research-direction-exploration) is complete and G1 gate has passed — subjects the research problem to adversarial defense-style questioning, classifies project intent, re-evaluates venue target, and produces a final feasibility ruling before any method design begins
| 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 |
Discipline layer skill. Active during Phase 4–5 for Type D and Type H projects.
NO MECHANISM CLAIMS WITHOUT EXCLUDING ALTERNATIVE EXPLANATIONS
For each major finding, systematically check:
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
For each finding, produce a table:
| Finding | Alternative checked | Excluded? | Evidence |
|---|---|---|---|
| ... | Confounder X | Yes / No | ... |
| 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. |
