paper-write-nature

name	paper-write-nature
description	Draft a Nature-style LaTeX paper with hourglass structure, reader-first logic, and publication-quality English. Use when user says 'Nature paper', 'Nature writing', 'SCI writing', or needs high-impact journal manuscript drafting.
argument-hint	["venue-or-section"]
allowed-tools	Bash(*), Read, Write, Edit, Grep, Glob, Agent, WebSearch, WebFetch, mcp__codex__codex, mcp__codex__codex-reply

Nature-Style Paper Writing

Draft a Nature-quality LaTeX paper based on: $ARGUMENTS

Constants

• TARGET_VENUE = Nature — Override via Additional Parameters. Supported: Nature, Nature Methods, Nature Machine Intelligence, Communications journals.

• MAX_PAGES — Nature Article: ~5 pages main text + Methods. Override via Additional Parameters.

• ANONYMOUS = false — Nature uses non-anonymous submission.

• DBLP_BIBTEX = true — Fetch real BibTeX from DBLP/CrossRef. Never fabricate.

• CUSTOM_REQUIREMENTS — Highest priority.

• REVIEWER_SCRIPT — External reviewer script.

Inputs

1. PAPER_PLAN.md — outline with claims-evidence matrix, figure plan

2. RESULTS.md — structured experiment results

3. figures/ — SVGs/PDFs + latex_includes.tex

4. Existing .bib file (or will create)

If no PAPER_PLAN.md, generate minimal outline from available docs.

Core Architecture

1. Identify Paper Type First

Before writing, determine the paper type:

• Research paper: why the phenomenon matters → what was done → what was found → what it means

• Methods paper: does the method work → is it reproducible → is it better under fair comparison

• Hypothesis-based: establish or rule out a causal explanation

• Algorithmic/device: propose procedure/tool/system → show reliable and advantageous performance

Do not use one narrative logic for all paper types.

2. Reader-First Writing Order

Write for the reader's cognitive sequence:

1. Is this relevant to me? (Introduction hook)

2. What is new here? (Contribution statement)

3. Do I trust it? (Results + Methods)

4. Can I reuse it? (Methods detail + Data Availability)

5. What does it mean? (Discussion + boundaries)

3. Productive Writing Order

For research articles, write in this order:

1. Results — anchor everything in evidence

2. Introduction — frame the gap now that you know the findings

3. Title — crystallize the contribution

4. Discussion — interpret and bound

5. Materials and Methods — reproducibility

6. Abstract — mini-paper summary last

4. Hourglass Structure

• Introduction: open broadly → narrow to specific gap → state question/hypothesis

• Discussion/Conclusion: widen again → connect findings to literature → explain how gap was filled

5. Paragraph Architecture: Claim-Evidence-Boundary

Every paragraph follows:

• Claim: one controlling idea (topic sentence)

• Evidence: data, comparison, explanation, literature support

• Boundary: limitation, scope, or transition to next claim

Section Responsibilities

Title

• ≤ 75 characters including spaces (Nature guideline)

• Searchable, specific, restrained, defensible

• Pattern: [Core entity] in/through/by [mechanism or context]

• No vague hooks, no unverified "first"

Abstract (150–200 words)

Mini-paper structure: context/problem → gap → approach → key result with numbers → implication

Introduction (~600–800 words for Nature)

• Hook: why the topic matters broadly

• Known: what is established

• Gap: what remains unresolved

• Aim: what this study asks/does

• Value: brief indication of approach and significance

• Do NOT summarize Results or Conclusion here

• Short paragraphs OK (Nature style allows 3–4 sentence paragraphs)

Results

• Past tense: report what was observed

• Orient reader to figure/table → state main observation → quantitative detail → patterns

• Results = what happened, NOT what it means

• Each result paragraph tied to a specific figure or table

• Active voice preferred: "We observed..." not "It was observed that..."

Discussion

• Restate main finding → plausible explanations → compare with earlier work → limitations → implications → future work

• Short rule: Results = what we observed; Discussion = how we understand it and when it may fail

• Three-part close: contribution → key evidence → implication with boundary

Materials and Methods

• Specific, complete, transparent, reproducible

• Another group must determine: ethical conformity, materials/conditions, key parameters, data processing, statistical tests, software versions

• Never: "under standard conditions", "using routine methods", "data were analyzed statistically"

Data Availability Statement

Generate using Nature data policy principles:

• Map each dataset to access route: public repository, controlled access, within supplement, reused source, third-party restricted

• Prefer DOI/accession numbers over personal websites

• Pattern: "The [data type] generated in this study have been deposited in [repository] under accession code [XXX]. Source data are provided with this paper."

• Flag "available upon request" as weak unless legally/ethically required

Failure Mode Diagnosis

Before editing any section, diagnose the main problem in priority order:

1. Paper type — wrong narrative logic for this paper type?

2. Section job — section not fulfilling its rhetorical responsibility?

3. Paragraph logic — claim without evidence? evidence without claim? missing boundary?

4. Sentence polish — clutter, passive voice, overclaim?

Fix from top down. Do not polish sentences while reasoning is broken.

Nature-Specific Style Rules

Sentence control

• Each sentence ≤ 30 words

• One core subject-verb proposition per sentence

• Split overloaded sentences rather than polishing cosmetically

• Active voice preferred: "We show..." not "It is shown that..."

Paragraph control

• Short paragraphs OK (3–5 sentences typical for Nature)

• Each paragraph: one controlling idea + support

• Thematic linking, not repetitive "This suggests..." openings

De-AI Polish Rules

Remove or replace these AI-typical words:

• "delve" → "examine", "investigate"

• "pivotal" → "important", "central"

• "landscape" → "field", "area"

• "multifaceted" → "complex"

• "underscores" → "shows", "highlights"

• "leveraging" → "using"

• "novel" (overused) → "new", or remove if claim is clear from context

• "groundbreaking" → remove or use specific evidence

• "paradigm shift" → describe the actual change

• "in conclusion" → just state the conclusion directly

Hedging (Academic Phrasebank patterns)

• "These results suggest that..."

• "A possible explanation is that..."

• "This discrepancy may reflect..."

• "To our knowledge, this is the first..."

• "Further work is needed to determine whether..."

Transitions

• Contrast: "However,", "By contrast,", "Nevertheless,"

• Addition: "Moreover,", "Furthermore,", "In addition,"

• Cause: "Consequently,", "As a result,", "Therefore,"

• Concession: "Although...,", "Despite...,", "Notwithstanding,"

Limitations acknowledgment

• "These results should be interpreted with caution because..."

• "A limitation of this study is that..."

• "The generalizability of these findings is limited by..."

Workflow

Step 1: Read inputs and plan

Read PAPER_PLAN.md, RESULTS.md, figures/. Identify paper type and writing order.

Step 2: Draft Results first

Write Results section anchored to figures and data. Each paragraph: orient → observe → quantify → pattern.

Step 3: Draft Introduction

Frame the gap now that findings are known. Hourglass: broad → narrow → specific aim.

Step 4: Draft Title

Crystallize contribution in ≤ 75 characters.

Step 5: Draft Discussion

Interpret findings, compare with literature, acknowledge limitations, state implications.

Step 6: Draft Methods

Complete, reproducible, specific. Include statistical tests, software versions, parameters.

Step 7: Draft Abstract

150–200 words. Context → gap → approach → key result → implication.

Step 8: Data Availability + Author Contributions

Generate Data Availability statement. Add Author Contributions template.

Step 9: Self-review

Run failure mode diagnosis on each section. Check:

• Hourglass structure intact

• Each paragraph has claim-evidence-boundary

• No AI-typical language remaining

• Active voice dominant

• Sentences ≤ 30 words

• Title ≤ 75 characters

• Abstract 150–200 words

• No fabricated references

• Hedging appropriate (no overclaim)

• Data Availability complete

Step 10: Compile

Save to paper/main.tex with proper Nature formatting. Generate paper/references.bib.

Related Files

| File | Open when |

|------|-----------|

| references/section-moves.md | Section-specific move patterns and phrase families |

| references/style-guardrails.md | Academic style checks, hedging, transitions |

| shared-scripts/writing_rules.md | General LaTeX writing rules |

| shared-scripts/compile_check.sh | Compilation verification |

Key Rules

• ⛔ Never fabricate references — use DBLP/CrossRef or flag with [VERIFY]

• ⛔ Never upgrade association to causation

• ⛔ Never let AI draft the core scientific argument from scratch

• ⛔ No plt.title() in figures — captions in LaTeX only

• Language serves argument — do not polish sentences while reasoning is broken

• Write with empathy for the reader: relevance → novelty → trust → reuse → meaning

• If the draft is structurally rough, reconstruct logic first, prose second

• Nature allows short paragraphs — do not pad for length

• Direct claims with evidence, not hedged-to-meaninglessness