incubation-loop

name	incubation-loop
description	Autonomous iterative thinking loop - processes active topics using rotating analytical moves (ACH, Bayesian updating, steelmanning, cross-domain bridging, implication checks) and persists reasoning state across scheduled runs
automation	autonomous
schedule	0 7 * * *
allowed-tools	Read, Write, Grep, Glob, Bash
user-invocable	true
argument-hint	[topic-slug] (optional - processes all active topics if omitted)

Incubation Loop

Autonomous thinking engine. Each scheduled run advances all active thinking topics by one analytical move, persisting reasoning state across runs until convergence.

Purpose

Continuous intellectual iteration on open questions. Uses a rotating set of research-validated analytical moves (ACH, Bayesian updating, dialectical steelmanning, cross-domain bridging) to build toward well-grounded conclusions - without requiring human presence in each cycle.

Design principle: Each run does one move per topic. Depth accumulates across runs. No single run tries to "solve" the question.

State Dependencies

Source	Location	Read	Write	Description
Thinking Registry	Brain/05-Meta/Thinking/THINKING-REGISTRY.md	✓	✓	Active topics + status
Thinking Files	Brain/05-Meta/Thinking/[topic-slug].md	✓	✓	Per-topic reasoning journal
Local Brain Search	resources/local-brain-search/	✓		Semantic search for KB evidence
Permanent Notes	Brain/02-Permanent/	✓		Primary evidence source
Session Changelogs	Brain/05-Meta/Changelogs/		✓	Run log

Prerequisites

• Registry file exists at Brain/05-Meta/Thinking/THINKING-REGISTRY.md
• At least one active topic seeded (see Seeding section below)
• Local Brain Search index up-to-date

---

Process

Step 1: Get Date and Load Registry

date '+%Y-%m-%d'

Read Brain/05-Meta/Thinking/THINKING-REGISTRY.md. Parse all topics with status: active.

If registry does not exist, create it:

---
created: YYYY-MM-DD
updated: YYYY-MM-DD
created_by: claude-sonnet-4-6
updated_by: claude-sonnet-4-6
agent_version: 01.25
---

# Thinking Registry

Active questions under continuous analysis.

| Topic Slug | Central Question | Status | Runs | Last Run |
|------------|-----------------|--------|------|----------|

If no active topics found, log to changelog and exit cleanly.

Step 2: For Each Active Topic - Load State

Read Brain/05-Meta/Thinking/[topic-slug].md.

Parse:

• run_count - how many iterations completed
• move_sequence - which moves have been applied (determines next move)
• current_hypotheses - list with confidence scores
• status - active / converged / crystallized
• Last run's conclusions

Step 3: Determine Next Thinking Move

Rotate through this sequence. Position = run_count mod 6:

Position	Move	Research Basis
0	ACH Audit	Heuer (CIA) - Analysis of Competing Hypotheses
1	Bayesian Update	Information theory - explicit confidence tracking
2	Steelman Opposition	Socratic dialectic - steel-man the opposite
3	Cross-Domain Bridge	Consilience method - what does an unrelated field say?
4	Implication Check	Falsificationism (Popper) - if true, what follows? Is that true?
5	Assumption Audit	Intelligence SAT - which premises are load-bearing and shakiest?

Step 4: Run KB Search for Evidence

Use Local Brain Search to find relevant notes:

cd "$(git rev-parse --show-toplevel)"
python3 resources/local-brain-search/search.py "[central question]" --limit 8 --mode spreading 2>/dev/null
python3 resources/local-brain-search/search.py "[leading hypothesis]" --limit 5 --mode spreading 2>/dev/null

Read the top 3-4 most relevant notes in full. These are the evidence base for this iteration.

Step 5: Apply the Thinking Move

Execute the move based on what was determined in Step 3. For each move:

ACH Audit

• List all current competing hypotheses
• For each piece of KB evidence found: does it support, contradict, or not apply to each hypothesis?
• Build a simple diagnostic matrix (evidence × hypotheses)
• Eliminate any hypothesis that is contradicted by multiple pieces of evidence
• Update confidence scores for surviving hypotheses
• Output: Pruned hypothesis list with updated confidence levels

Bayesian Update

• State prior confidence in leading hypothesis (from last run)
• Identify new evidence from KB search
• Explicitly reason: "Given this evidence, should I be more or less confident? By how much?"
• Use rough likelihood ratios (e.g., "this evidence is 3x more likely if H1 is true than if H2 is true")
• Compute and record updated posterior confidence
• Output: New confidence scores with explicit reasoning for the change

Steelman Opposition

• State the current leading hypothesis clearly
• Construct the strongest possible argument AGAINST it - not a strawman
• Search KB explicitly for evidence supporting the opposing view
• Assess: does the steelman change the leading hypothesis, or does it survive?
• If the steelman reveals a genuine weakness, revise the hypothesis
• Output: Steel-manned opposition + response + any hypothesis revision

Cross-Domain Bridge

• Identify the core mechanism or pattern in the current question
• Run KB search from an unrelated domain (e.g., if topic is about AI, search neuroscience or Buddhism)
• Find analogous patterns or contradictory evidence from that domain
• Extract what the foreign domain implies about the current question
• Output: Cross-domain insight + revised framing of the question (if warranted)

Implication Check

• Take the current leading hypothesis as given (temporarily)
• Derive 3-5 concrete, testable implications that should be true if the hypothesis holds
• Search KB and reason about whether those implications are actually supported
• If an implication is clearly false, that is disconfirming evidence for the hypothesis
• Output: Implications assessed as supported/unsupported/unknown + impact on hypothesis confidence

Assumption Audit

• List the 3-5 key assumptions the current reasoning rests on
• Rank by: (a) how load-bearing for the conclusion, and (b) how uncertain/shaky
• Focus scrutiny on high load-bearing + high uncertainty assumptions
• For the shakiest assumption: search KB for evidence bearing on it
• Output: Assumption vulnerability map + revised conclusion if key assumption weakens

Step 6: Write Updated Thinking File

Append to Brain/05-Meta/Thinking/[topic-slug].md:

### Run [N]: [Move Name] - [YYYY-MM-DD]

**KB Evidence Consulted:**
- [[Note A]] - [one line on relevance]
- [[Note B]] - [one line on relevance]

**Analysis:**
[2-4 paragraphs of actual reasoning from the move]

**Updated Hypotheses:**
| Hypothesis | Confidence | Change |
|-----------|------------|--------|
| H1: [statement] | X% | ↑/↓/→ from Y% |
| H2: [statement] | X% | ↑/↓/→ from Y% |

**Current Best Answer:** [1-2 sentences - the leading position after this run]

**Open Questions for Next Run:** [What remains unresolved or most worth probing]

Update the frontmatter: updated, updated_by, run_count, last_run.

Step 7: Check Convergence

A topic has converged when ALL of:

• run_count >= 4 (minimum 4 cycles)
• Same hypothesis has led for 3+ consecutive runs
• Confidence delta between last two runs < 5 percentage points
• No major open questions flagged in last run

If converged:

• Set status: converged in the thinking file frontmatter
• Add note: **CONVERGED** - Ready for crystallization via /synthesize-insights
• Update registry status to converged

If not converged: continue to next topic.

Step 8: Update Registry

Update Brain/05-Meta/Thinking/THINKING-REGISTRY.md:

• Increment run count for each processed topic
• Update last_run date
• Update status (active → converged where applicable)

Step 9: Write Session Changelog

Write to Brain/05-Meta/Changelogs/CHANGELOG - Incubation Loop YYYY-MM-DD.md:

---
created: YYYY-MM-DD
updated: YYYY-MM-DD
created_by: claude-sonnet-4-6
updated_by: claude-sonnet-4-6
agent_version: 01.25
---

# Incubation Loop Session: YYYY-MM-DD

## Topics Processed

| Topic | Move Applied | Confidence Shift | Status |
|-------|-------------|-----------------|--------|
| [slug] | [move name] | [leading H]: Y% → Z% | active/converged |

## Notable Shifts
[Any hypothesis revisions, convergences, or surprising KB evidence]

## Converged Topics (Ready for Crystallization)
[List any topics that reached convergence this run]

---

Seeding a New Topic

To add a topic to the loop, create Brain/05-Meta/Thinking/[topic-slug].md:

---
created: YYYY-MM-DD
updated: YYYY-MM-DD
created_by: claude-sonnet-4-6
updated_by: claude-sonnet-4-6
agent_version: 01.25
topic: "[exact question being analyzed]"
run_count: 0
last_run: null
status: active
---

# Thinking: [Topic Title]

## Central Question
[The exact question. Precise framing matters - ambiguous questions stay ambiguous.]

## Why This Question Matters
[1-2 sentences on stakes or relevance]

## Initial Hypotheses
| Hypothesis | Initial Confidence | Basis |
|-----------|-------------------|-------|
| H1: [statement] | X% | [prior knowledge or intuition] |
| H2: [statement] | X% | [prior knowledge or intuition] |

## Known Evidence (Pre-Run)
[Any notes or sources already known to be relevant]

## Constraints and Assumptions
[What are you taking as given? What's out of scope?]

---
*[Analytical runs will be appended below by the incubation loop]*

Then add to THINKING-REGISTRY.md:

| [topic-slug] | [central question] | active | 0 | null |

---

Crystallization (Manual)

When a topic reaches status: converged, the human should:

1. Read the full thinking file
2. Run /synthesize-insights [topic-slug] to graduate conclusions to a permanent note
3. Archive thinking file: set status: crystallized
4. The permanent note becomes part of the KB for future searches

Do not automate crystallization - judgment calls about what conclusions deserve permanence belong to the human.

---

Error Handling

Error	Recovery
Registry missing	Create empty registry, log, exit cleanly
No active topics	Log to changelog, exit cleanly
KB search returns empty	Try alternate search terms from hypothesis text; if still empty, note in run log and skip KB-grounding for this move
Thinking file missing for active topic	Log warning in registry, skip topic
Run exceeds 45 minutes	Process topics in order; skip remaining, log which were skipped

---

Completion Checklist

• Registry read - active topics identified
• Each active topic: KB searched with relevant queries
• Each active topic: correct move in rotation applied
• Each active topic: thinking file updated with reasoning + confidence scores
• Convergence checked for each topic
• Registry updated (run counts, dates, status changes)
• Session changelog written to Brain/05-Meta/Changelogs/

---

Self-Improvement

After completing this skill's primary task, consider tactical improvements:

• Review execution: Were there friction points, unclear steps, or inefficiencies?
• Identify improvements: Could the thinking moves, convergence criteria, or file structure be sharper?
• Scope check: Only execution changes - NOT changes to the ACH/Bayesian/dialectic framework itself
• Apply improvement (if identified):
  • Edit this SKILL.md with the specific improvement
  • Keep changes minimal and focused
• Version control:
  • git add .claude/skills/incubation-loop/SKILL.md
  • git commit -m "refactor(incubation-loop): <brief improvement>"