trace-origin

name	trace-origin
description	Trace a paper's intellectual roots: find the 1-2 deepest knowledge trunks it recombines. Based on the Innovation Depth principle — innovation magnitude scales with recombination depth. Use standalone or as an enrichment layer for /read-ken or any bib-note pipeline.
allowed-tools	["Read","WebSearch","WebFetch","Grep","Glob","Bash","Agent"]

Trace-Origin: Intellectual Ancestry Tracer

Usage: /trace-origin [PDF path | citation key | paper description]

Purpose: Find the 1-2 deepest intellectual roots (knowledge trunks) that a paper recombines. Not "what does this paper cite?" but "what deep traditions collide here?"

Theory (Innovation Depth): Innovation magnitude scales with recombination depth. Leaf recombination → incremental papers. Branch recombination → new subfields. Trunk recombination → paradigm shifts. This skill measures that depth.

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Core Metaphor: The Knowledge Tree

ROOT        Physics / Mathematics / Philosophy
             │
TRUNK       Information Theory    Evolutionary Biology    Economics
             │                     │                       │
BRANCH      Coding theory         Population genetics     Trade theory
             │                     │                       │
TWIG        Error-correcting      Neutral theory          Gravity models
             │                     │                       │
LEAF        Specific 2024 paper   Specific 2024 paper     Specific 2024 paper

The question: When a paper recombines ideas, how deep is the last common ancestor of those ideas? A paper fusing two 2020 papers from the same lab = leaf LCA. A paper fusing information theory with evolutionary biology = trunk LCA. The deeper the LCA, the bigger the innovation.

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ENFORCED 4-PHASE WORKFLOW

Complete all phases IN ORDER.

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Phase 1: Paper Identification

Case A: PDF path provided

pdftotext -f 1 -l 3 -layout "[PDF path]" - 2>/dev/null | head -80

Extract: title, authors, abstract, and crucially the introduction's framing — how do the authors position their contribution?

Case B: Citation key provided (e.g., "Bettencourt2007")

Ask the user for the PDF, or do a web search for the paper by author + year.

Case C: Paper description provided

WebSearch: "[description] paper [year if known]"

Extract the Paper's Self-Declared Lineage

From the introduction, identify:

• What fields does the paper claim to bridge? (explicit interdisciplinary framing)
• What seminal works does the intro cite? (not all references — just the ones framing the contribution)
• What problem framing do they use? (the metaphor/framework reveals the trunk)

Output: 2-4 candidate lineage threads (the paper's own declared ancestry).

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Phase 2: Trace Roots Backward (The Dig)

For each candidate lineage thread from Phase 1, trace it backward toward the trunk.

Step 2a: Identify Seminal Anchors

The paper cites recent work, which cites earlier work, which eventually reaches a seminal anchor — a paper/book/idea that founded or defined a field.

Strategy: Use the 2-hop rule.

1. From the paper's key references, pick the 1-2 most foundational (oldest, most cited, most field-defining)
2. Web search those foundational references to find THEIR intellectual origins

WebSearch: "[seminal paper/author] intellectual origins influenced by history of [field]"
WebSearch: "[foundational concept] origin history who invented"

🔴 PARALLELIZE: Launch 2-4 WebSearches simultaneously (one per lineage thread).

Step 2b: Determine Depth Level

For each lineage thread, classify its depth:

Depth	Definition	Example
Root	Foundational discipline (math, physics, philosophy)	Calculus, thermodynamics, logic
Trunk	Major intellectual tradition (>50 years, >1 field)	Information theory, natural selection, general equilibrium
Branch	Established subfield (10-50 years)	Urban scaling, neutral ecology, deep learning
Twig	Active research program (5-15 years)	CD index, transformer architecture
Leaf	Specific recent contribution (<5 years)	A particular 2024 paper

Goal: Find the deepest divergence point between the paper's lineage threads. That's the innovation depth.

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Phase 3: Construct the Root Diagram

Step 3a: Draw the Ancestry

For each root (1-2, ideally 2), construct a lineage chain:

ROOT 1: [Trunk-level tradition]
  └─ [Branch]: [key figure/work, year]
    └─ [Twig]: [more recent development]
      └─ THIS PAPER's contribution from this thread

ROOT 2: [Trunk-level tradition]
  └─ [Branch]: [key figure/work, year]
    └─ [Twig]: [more recent development]
      └─ THIS PAPER's contribution from this thread

RECOMBINATION DEPTH: [Trunk / Branch / Twig / Leaf]
The last common ancestor of Root 1 and Root 2 is at the [X] level.

Step 3b: Name the Innovation Type

Based on recombination depth:

LCA Depth	Innovation Type	Rarity	Example
Trunk–Trunk	Paradigm shift	Very rare	Darwin (geology × economics → evolution)
Trunk–Branch	Field creation	Rare	Bettencourt (physics × urban studies → urban scaling)
Branch–Branch	Subfield innovation	Common	Most interdisciplinary papers
Twig–Twig	Incremental extension	Very common	Most papers
Leaf–Leaf	Replication/refinement	Routine	Follow-up studies

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Phase 4: Output

Standalone Output (when run as /trace-origin)

Present the results as a structured summary:

## Intellectual Roots: [Paper Citation]

### Root 1: [Tradition Name]
**Lineage**: [Root] → [Branch] → [Twig] → this paper
**Key ancestor**: [Seminal work/figure]
**What this paper inherits**: [specific concept, method, or framing]

### Root 2: [Tradition Name]
**Lineage**: [Root] → [Branch] → [Twig] → this paper
**Key ancestor**: [Seminal work/figure]
**What this paper inherits**: [specific concept, method, or framing]

### Recombination Analysis
**LCA depth**: [Trunk / Branch / Twig / Leaf]
**Innovation type**: [from table above]
**The recombination**: [1 sentence: what collision of ideas makes this paper possible]

Integration Output (when called from another skill)

Return a compact block to be inserted into the bib note:

## Intellectual Roots
- **Root 1**: [Tradition] via [Seminal Work] → [what this paper inherits]
- **Root 2**: [Tradition] via [Seminal Work] → [what this paper inherits]
- **Recombination depth**: [Level] — [1-sentence explanation]

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Integration Notes (for chaining with other skills)

Where it fits in /read-ken: After Phase 3 (Field Context). The intellectual roots enrich the "So What?" section with deeper historical grounding.

Where it fits in any bib-note pipeline: Between field-context analysis and connection discovery. trace-origin provides the deep ancestry; connection discovery maps to your existing notes.

How to call from another skill: Spawn as subagent:

Agent: trace-origin analysis
  subagent_type: general-purpose
  prompt: "Run /trace-origin for [paper]. Return the compact integration output block."

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Examples

Example: Bettencourt et al. (2007) "Growth, Innovation, Scaling"

Root 1: Allometric scaling (biology) └─ Kleiber's law (1932): metabolic rate ~ mass^0.75 └─ West, Brown, Enquist (1997): fractal network theory └─ THIS PAPER: applies scaling framework to cities

Root 2: Urban economics └─ Marshall (1890): agglomeration economies └─ Jacobs (1961): diversity drives urban vitality └─ THIS PAPER: social network density as mechanism

LCA depth: Trunk–Trunk (biology × economics) Innovation type: Field creation (urban scaling as new field) The recombination: What if cities are organisms? Metabolic scaling theory meets agglomeration economics.

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Design Philosophy

This skill operationalizes the Innovation Depth principle: every paper has roots, and the depth of those roots tells you the magnitude of the innovation. Most papers are leaf-level recombinations. The ones that matter recombine trunks.

The skill is deliberately lean — it doesn't replace /read-ken's author research or any other skill's connection discovery. It adds one thing: the vertical dimension. Where those skills map the horizontal network (what connects to what), trace-origin maps the vertical ancestry (where does this come from, and how deep?).

Origin

This skill formalizes a habit Mingzhen learned from Lars Hedin (Princeton ecology). When reading a paper, Lars would ask: where does this idea really come from? Not the immediate citation, but the deep root. That habit of digging past the bibliography into the intellectual ancestry is what this skill automates.