Scientific Writing Outline

Scientific Writing — Stage 2: Outline

Overview

Turn story.md into a bulleted outline whose every claim is backed — by a concrete repo artifact (results bullets) or a web-verified citation (background bullets). Multi-pass, modeled on superpowers:executing-plans. Outputs outline.md + references.md in the story dir.

Foundational rule: no bullet without backing. Inventing a citation or a number to fill a bullet is the cardinal failure of this stage.

Step 0 — confirm the venue

Ask the user the target journal/format (e.g. Nature/Science/Cell biological article; CS conference; BMC-style software article). This selects the section scaffold. Record the choice + rationale in the outline.md header. Common scaffolds:

• Nature/Cell biological: Abstract, Intro, Results, Discussion, Methods.
• BMC software article: Background, Implementation, Results, Conclusions.
• CS conference: Abstract, Intro, Related Work, Method, Experiments, Conclusion.

Section structure — Steps 3–12

This stage is Steps 3–12 of the fifteen steps (detail: scientific-writing/fifteen-steps.md). Build every section from lists first, prose never, and give each section its required shape:

• Methods (Steps 3–5). A numbered method list, one per line mirroring the code, each with a to-clause rationale ("To estimate richness, rarefaction was performed"). Every method leads to a result; every result traces to a method.
• Results (Step 5). One observation/measurement/statistic per bullet, clear and unembellished — each backed by a repo artifact + figure panel (the loop already enforces this).
• Introduction (Step 6 — CARS). The first three paragraphs are the three moves, in order: Territory (general context, centrality, prior work) → Niche (the gap — what existing knowledge lacks) → Occupy (a clear objectives/hypotheses statement linking to methods and results).
• Discussion (Steps 7–9). Two halves. First half = findings: results placed in interpretive context, each tied to a problem raised in the Introduction (findings ≠ results). Second half = problem→response pairs: list caveats/limitations/objections (Step 8), each with one paired response (Step 9, 1:1). Do not dump caveats as a flat "limitations" list.
• Closing paragraph (Step 10). Give it its own thesis, connected to the main one. End on a positive note; never end on a caveat or "need for further research." Close on a declaration of the main finding, a new question, or a concrete application.

Purpose statements (Step 11). Give every planned paragraph a one-line purpose statement naming its role in advancing the thesis (e.g. "This paragraph justifies the Cormack–Jolly–Seber model over band recovery"). These carry into the draft as topic-sentence seeds — record one per planned paragraph in outline.md.

Figures (Step 12). Order figures by the narrative arc; cut any that doesn't illuminate the thesis. Each caption's topic sentence is a complete sentence readable as the figure's title (not a label), and the sequence of caption topic sentences should read as an abbreviation of the whole narrative.

Multi-pass loop (per block of ~3–8 bullets)

1. Implement — write the bullets for the current section block.
2. Story review — consistent with story.md's thesis/beats? Are non-result (background/motivation) bullets backed by literature?
3. Technical review — is each result bullet backed by a named repo artifact (script/result CSV/plot/notebook)? Is every "magic number" (e.g. an RNA-seq count threshold, an x-fold ratio) backed by a principled source — an in-repo empirical result or a citation? Add the pointer inline. Also name the figure panel each result bullet maps to (e.g. Fig. 2C) so Stage 3 can attach the callout without inventing one.
4. Citation web-check — for each new citation, dispatch a subagent (parallelize with superpowers:dispatching-parallel-agents) to verify via web: (a) does the paper exist (authors, venue, year)? (b) does its content support the specific claim? Log every verdict to references.md.

Final review (whole outline)

• Sections/bullets coherent with each other; everything ties back to the thesis and story.md.
• Every bullet has a backing pointer (repo artifact) or a references.md entry marked verified.
• Connector test (Step 7): put the results list beside the findings list and draw a line from each result to the finding it supports. No result may lead to no finding, and no finding may be unsupported by a result — fix any unconnected item by adding the missing partner, connecting it, or cutting it.
• Every planned paragraph has a purpose statement (Step 11); the Introduction's first three paragraphs are the three CARS moves; the Discussion is findings then problem→response pairs.
• Then hand off to the user, explicitly listing any ambiguities/concerns raised during review (e.g. a number you couldn't back, a citation that only partially supports its claim).

outline.md header template

# Outline — <title>
Venue: <journal/format>   |   Chosen because: <rationale>   |   Scaffold: <sections>
Backing legend: [repo: <path>] | [cite: <key> ✓verified]

## <Section>
**Purpose (¶1): <one-line Step-11 purpose statement>**
- <bullet>  [repo: <path> → Fig. 2C] | [cite: <key> ✓verified]
**Purpose (¶2): <…>**
- <bullet> …

references.md template

| key | citation | exists? | supports claim? | claim it backs | source URL |
|-----|----------|---------|-----------------|----------------|------------|

Red flags — STOP and fix

• A bullet you can't point to an artifact or verified citation for → mark UNBACKED and flag to user; do not paper over it.
• "I'll verify citations later" → verify now; that's this stage's job.
• Citing a paper from memory without the web-check → not allowed.
• Picking a section scaffold before confirming the venue → ask first.

Next stage

Once the user approves outline.md, invoke scientific-writing-draft.