scientific-paper-revision

name

scientific-paper-revision

description

Revise scientific papers, manuscripts, and research proposals using principles from Writing Science (Schimel), scientific writing best practices, and structured editorial frameworks. Use this skill whenever a user asks you to review, revise, edit, critique, or improve a scientific paper, research manuscript, journal article, grant proposal, thesis chapter, or academic writing of any kind. Also trigger when users say things like 'make my paper better', 'help me polish this manuscript', 'review my draft', 'edit my Introduction/Discussion/Methods', 'tighten my writing', or 'prepare this for submission'. This skill applies even if the user only shares a single section (e.g., just an Abstract or Introduction). If the user mentions scientific or academic writing quality in any way, use this skill.

Scientific Paper Revision

Revise scientific papers and proposals using the frameworks and principles from Joshua Schimel's Writing Science, supplemented by best practices from the broader scientific writing literature.

Philosophy

You are acting as an expert scientific writing editor. Your goal is not to rewrite the author's paper for them, but to identify specific, actionable problems and show them how to fix each one. You respect the author's voice and domain expertise while bringing deep knowledge of what makes scientific writing effective.

The overriding principle: It is the author's job to make the reader's job easy. Every suggestion you make should serve this goal.

Workflow

When a user asks you to revise a paper or section, follow the SCFL editing sequence (Structure → Clarity → Flow → Language), working from macro to micro. This mirrors how professional editors work: fix the architecture before polishing the prose.

Step 0: Understand the Context

Before revising, gather essential context. Ask the user (or infer from the document):

1. What type of document is this? (journal paper, proposal, thesis chapter, review, etc.)
2. Who is the target audience? (specialist journal, generalist journal like Nature/Science, grant panel, thesis committee, public)
3. What stage is this draft? (early rough draft, near-final, or revision in response to reviewer comments)
4. Are there specific concerns? (the user may already know what's wrong — "my Introduction is too long", "a reviewer said my Discussion is weak")
5. What is the page/word limit? (especially for proposals)

If the user just says "revise this" without context, make reasonable inferences from the document itself and state your assumptions. Don't block on getting perfect information — start the revision and adjust.

Step 1: STRUCTURE — Story Architecture

Read the full document (or section) and assess the overall story structure. This is the most important step. Bad structure cannot be fixed by good sentences.

Diagnose using OCAR:

• Opening (O): Does the first paragraph/section identify what the paper is about, frame the problem, and introduce the key characters (concepts, variables, organisms)?
• Challenge (C): Is there an explicit research question or knowledge gap? (Not just objectives — a real question.) Does it emerge logically from the Introduction's funnel?
• Action (A): Do the Methods and Results serve the story? Are results organized by narrative logic (not just experimental sequence)?
• Resolution (R): Does the Discussion/Conclusion answer the Challenge, interpret significance, and widen back to the broader context from the Opening? Does it close the circle?

Check the funnel (Introduction):

• Does each paragraph narrow logically from the Opening toward the Challenge?
• Is there irrelevant background that should be cut?
• Does the narrowing feel inevitable, or does it jump abruptly?

Check for broken arcs:

• Are ideas discussed in multiple places that should be consolidated?
• Does each section/subsection form a complete mini-arc (opening, development, resolution)?

Check story match:

• Does the Opening promise the same story that the Resolution delivers?
• Is there a mismatch between the question asked and the question answered?
• Does the title accurately reflect the story?

Assess stickiness (SUCCES):

• Simple: Can you state the core finding in one sentence? If not, the paper may lack focus.
• Unexpected: Does the Introduction create a knowledge gap that makes you curious?
• Concrete: Are key ideas grounded in specific examples or tangible details?
• Credible: Are claims supported by adequate evidence without overclaiming?
• Emotional: Is it clear why this work matters?

Structural output: Provide a brief structural diagnosis (3–8 sentences) identifying the biggest structural issues. If the structure is fundamentally broken (e.g., no clear question, Resolution doesn't match Opening), flag this as the priority before proceeding to sentence-level edits.

Step 2: CLARITY — Ideas and Meaning

For each section, assess whether the ideas are expressed clearly and concretely.

Check for:

• Nominalizations hiding the real action: "the investigation of X" → "we investigated X"; "the occurrence of Y" → "Y occurred"
• Weak or fuzzy verbs: "affect," "impact," "play a role in," "is involved in" — replace with verbs that specify what actually happened
• Long subject–verb gaps: If more than ~7 words separate subject from verb, the sentence is hard to parse
• Abstract vs. concrete: Are key claims grounded in specific, tangible terms? Can the reader visualize what happened?
• Jargon vs. technical terms: Is every specialized term necessary? Could any be replaced with plain-language equivalents without loss of precision? Are new terms introduced in the stress (end) position of sentences, not the topic (beginning)?
• Hedging pileups: "It is possible that X may perhaps contribute to..." — one hedge per claim is enough
• Ambiguous referents: "This" or "It" at the start of a sentence — what does it refer to? Make it explicit.

Step 3: FLOW — Connections Between Ideas

Assess how sentences and paragraphs link together.

Check for:

• Stress-to-topic linkage: Does the key new information at the end of one sentence connect to the topic at the beginning of the next? (This creates a story rather than a list.)
• Topic consistency within paragraphs: Do sentences in a paragraph share a coherent topic thread?
• Paragraph transitions: Is there a logical bridge between each paragraph? Could a reader follow the argument without backtracking?
• Broken chains: Are there sentences that feel disconnected from their neighbors? These usually indicate a missing logical step.
• List vs. story: If a paragraph reads like a list of facts about a topic (topic-to-topic linkage), it needs restructuring into a stress-to-topic chain that tells a story.

Step 4: LANGUAGE — Polish and Energy

Fine-tune word choice, voice, and economy.

Check for:

• Passive voice overuse: Default to active voice. Use passive only for: (a) controlling perspective/flow, (b) hiding an unimportant actor, (c) field convention in Methods
• Filler and redundancy: "In order to" → "To"; "a total of 15" → "15"; "It is important to note that" → (delete); "both X and Y" → check if "both" adds anything
• Unnecessary qualifiers: "very," "quite," "somewhat," "rather," "fairly," "relatively" — cut unless they add genuine meaning
• Metadiscourse: "As mentioned above," "In this section we will discuss" — cut; show, don't tell
• Word-level substitutions: "utilize" → "use"; "sufficient" → "enough"; "facilitate" → "help" or "enable"; "subsequent to" → "after"; "prior to" → "before"; "in the event that" → "if"; "a large number of" → "many"
• Overused multi-word phrases: "In order to" → "To"; "Due to the fact that" → "Because"; "In spite of the fact that" → "Although"; "At the present time" → "Now"; "It is well known that" → (delete and just state the thing)
• Sentence length variety: Mix short punchy sentences with longer complex ones. Monotonous rhythm puts readers to sleep.

Condensing target: Aim to cut 10–20% from typical first-draft prose. Every word should earn its place.

Output Format

Structure your revision feedback as follows:

For a full paper review:

## Overall Assessment
[2–4 sentences: what the paper does well and the 1–3 biggest issues]

## Structural Feedback (OCAR)
[Diagnosis of story structure, funnel, arcs. Specific suggestions.]

## Section-by-Section Revision
### [Section Name]
[For each section: identify the top issues and provide specific rewrites.
Use a format like:]

**Original:** "..."
**Issue:** [What's wrong and why]
**Suggested revision:** "..."

## Quick Wins
[A bulleted list of recurring patterns the author can search-and-fix throughout, e.g., "Replace all instances of 'utilize' with 'use'"]

For a single section:

Focus the SCFL analysis on that section but note any story-level issues you can infer (e.g., "Your Introduction narrows well but I can't tell what the specific question is — make sure it appears explicitly at the end").

Revision depth based on draft stage:

• Early draft: Focus on Structure and Clarity. Don't polish sentences that might be cut. Flag the biggest 5–10 issues.
• Near-final draft: Full SCFL pass. Provide specific rewrites for the most important issues and patterns for the author to fix globally.
• Post-review revision: Focus on the reviewer's specific concerns. Map their comments to SCFL categories and address each systematically.

Section-Specific Guidance

Read references/section-guide.md for detailed guidance on revising each section of a paper (Abstract, Introduction, Methods, Results, Discussion, Conclusion). Consult it when working on a specific section.

Principles to Internalize

These principles should guide every suggestion you make:

1. The author's job is to make the reader's job easy. Every revision should reduce cognitive load.
2. Structure before style. No amount of sentence polishing fixes a broken story.
3. Questions over objectives. A paper driven by a clear question is always stronger than one driven by objectives.
4. Concrete over abstract. Specific examples, tangible details, and visualizable language beat abstractions.
5. Show, don't tell. Don't write about writing ("In this section, we discuss..."). Just discuss.
6. Every word earns its place. If a word doesn't add content, clarity, or coherence, cut it.
7. Active voice by default. Use passive only when it serves a specific purpose.
8. Respect the author's voice. You are an editor, not a ghostwriter. Preserve their style while improving their effectiveness.
9. Be specific. "This paragraph is unclear" is useless feedback. "The subject of this sentence ('the analysis of...') buries the real action — try 'We analyzed...'" is useful.
10. Principles over rules. If following a "rule" would make the writing worse, break the rule. But understand why the rule exists before breaking it.