Scientific Thinking

Scientific Thinking

Enforces the scientific method as an investigation discipline. Governs hypothesis formulation, predictions, experiment design, and evidence-based conclusions.

Shared Resources

Load these references at the start of any investigation. A references index is available for a quick map of all shared files.

• Unified Investigation Template — output structure for all investigation work
• Investigation Workflow — mermaid diagrams of the full scientific method flow

Companion Skill

evidence-first-debugging handles observation recording, evidence IDs, and causality validation. Both skills use the same Unified Investigation Template output structure. Load evidence-first-debugging when the task requires structured evidence tracking alongside hypothesis work.

Activation Triggers

Activate this skill when the prompt contains:

• "unknown cause", "strange behavior", "intermittent"
• "architecture decision", "previous attempts failed"
• "root cause", "investigation"

Scope Boundary

Apply this skill to problems with genuine uncertainty — unknowns, failed attempts, complex architecture trade-offs.

Tasks outside scope: typo fixes, simple additions, tasks with explicit step-by-step instructions already provided. For those, execute directly.

Investigation Stages

Enforce stages in this order. Each stage gates the next.

flowchart TD
    S0[Stage 0-3: Observation<br>Record ONLY factual observations<br>No interpretation] --> S4
    S4[Stage 4: Hypothesis Formulation<br>State H0 null and H1 alternative<br>Both must be falsifiable] --> S5
    S5[Stage 5: Prediction<br>Write: If H1 is true, we should observe...] --> S6
    S6[Stage 6-7: Experiment Design<br>Define Path A and Path B<br>Identify confounds] --> S8
    S8[Stage 8-9: Execute<br>Run experiments<br>Record results verbatim] --> S10
    S10[Stage 10-11: Conclusion<br>Classify causality<br>State decision<br>Cite evidence IDs] --> Done
    Done{status?}
    Done -->|resolved-verified| Retro[Notify user: retrospective-analyst<br>agent can produce mermaid timeline<br>and retrospective from iteration log]
    Done -->|unresolved or mitigated| S0

Stage Rules

Observation (sections 0-3):

• Record only what is directly observable — no causal language, no interpretations
• Each observation requires an evidence ID (delegated to evidence-first-debugging)

Hypothesis Formulation (section 4):

• H0 (null): the default assumption — no effect, no cause
• H1 (alternative): the proposed cause or mechanism
• Both must be falsifiable — if a hypothesis cannot be tested, rewrite it

Prediction (section 5):

• Write one sentence per hypothesis: "If H1 is true, we should observe X when we do Y"
• Predictions must reference observable, measurable outcomes

Experiment Design (sections 6-7):

• Path A: test that would confirm H1
• Path B: test that would refute H1 (controls for confounds)
• List confounds explicitly — variables that could produce the same result without H1 being true

Execute (sections 8-9):

• Run experiments exactly as designed — record results verbatim, not summarized
• If execution diverges from design, restart from Experiment Design with updated constraints

Conclusion (sections 10-11):

• Classify each action-result link: causal-supported, correlated-only, unrelated, or unknown
• State the decision derived from evidence
• Every claim must cite an evidence ID — no unsupported assertions