Scientific Manuscript Skill
Craft and refine manuscripts for high-impact journals through structured feedback, comparative analysis with exemplar papers, and sentence-level prose craft.
Core Focus Areas
This skill emphasizes four dimensions of high-impact writing:
- •Narrative arc — how the story builds across sections and paragraphs
- •Paragraph architecture — how individual paragraphs create momentum and impact
- •Sentence-level craft — concise, punchy prose with word economy
- •Strategic rhetoric — calculated use of adjectives and flourishes
Reference Files
Section-Specific Guides
| Section | Reference File |
|---|---|
| Abstract | references/abstract.md |
| Introduction | references/introduction.md |
| Results | references/results.md |
| Discussion | references/discussion.md |
| Methods | references/methods.md |
| Figures | references/figures.md |
Craft-Level Guides (Load for any section)
| Focus | Reference File | When to Load |
|---|---|---|
| Narrative structure | references/narrative-structure.md | Story arc, section flow, momentum |
| Prose craft | references/prose-craft.md | Sentence-level style, word economy, rhetoric |
| Evaluation | references/rubrics.md | Systematic scoring |
Annotated Examples
| Paper | File | Best for |
|---|---|---|
| Musser 2021 Science | references/examples/musser_2021_science.md | Paradox hooks, cell type papers |
| Ruperti 2024 Curr Biol | references/examples/ruperti_2024_curbio.md | Challenging paradigms, quantitative prose |
| Tarashansky 2021 eLife | references/examples/tarashansky_2021_elife.md | Methods papers, comparative analysis |
| Vergara 2021 Cell | references/examples/vergara_2021_cell.md | Resource papers, multimodal data |
Feedback Modes
Mode 1: Narrative Analysis
Analyze story arc and momentum. Use when:
- •Draft feels flat or disjointed
- •User asks about "flow" or "structure"
- •Sections don't build toward a conclusion
Load: references/narrative-structure.md
Format:
**Arc diagnosis**: [Where tension is established, where it resolves, what's missing] **Momentum check**: [Which paragraphs build vs. stall] **Pivot analysis**: [How you transition from known → unknown → your contribution] **Suggested restructuring**: [Concrete reordering or additions]
Mode 2: Prose Craft Review
Sentence-level style analysis. Use when:
- •User asks about "style" or "writing quality"
- •Prose feels bloated or academic
- •User wants text to be "punchier" or "more concise"
Load: references/prose-craft.md
Format:
**Bloat patterns**: [Specific phrases to cut with rewrites] **Verb weakness**: [Weak verbs → strong verb suggestions] **Sentence rhythm**: [Where variation is needed] **Adjective audit**: [Which add meaning vs. clutter] **Power positions**: [Sentences where key info is buried]
Mode 3: Comparative Critique
Compare to exemplar papers. Use when:
- •User wants to see "how good papers do it"
- •Draft has rhetorical issues best shown by contrast
Load: Relevant example file from references/examples/
Format:
**Your draft**: [quote passage] **Exemplar**: [quote from example paper] **Key difference**: [What the exemplar does that yours doesn't] **Principle**: [The generalizable technique] **Suggested revision**: [Concrete rewrite applying the principle]
Mode 4: Rubric Evaluation
Systematic scoring. Use when:
- •User asks "Is this ready for submission?"
- •Comprehensive assessment needed
Load: references/rubrics.md
Mode 5: Iterative Dialogue
Socratic questioning. Use when:
- •Logic or argument needs development
- •User refining specific claims
Quick Diagnostics
The Arc Check
For any section, ask:
- •Where is the tension established?
- •Where does it resolve?
- •Does each paragraph advance toward resolution?
The First/Last Test
- •First sentence of each paragraph: Does it state the main point?
- •Last sentence of the paper: Is it memorable and quotable?
- •Last sentence of each section: Does it transition or conclude powerfully?
The Economy Test
Flag these bloat patterns:
- •"It is important to note that" → [delete]
- •"plays a role in" → "regulates" / "drives"
- •"is involved in" → [specific verb]
- •"in order to" → "to"
- •Stacked adjectives → choose one
The Flourish Audit
Flourishes should appear at:
- •Paper opening (hook)
- •Key conceptual pivot
- •Paper closing (take-home)
NOT in: routine findings, methods, figure descriptions
Handling Requests
"Review my introduction"
→ Load introduction.md + narrative-structure.md, analyze arc and pivot, check prose craft
"Make this punchier"
→ Load prose-craft.md, do sentence-level audit, provide rewrites
"How does this compare to good examples?" → Load relevant example file, do comparative critique
"Is the narrative working?"
→ Load narrative-structure.md, analyze tension-resolution arc, check paragraph momentum
"Help me cut this down"
→ Load prose-craft.md, identify bloat patterns, suggest cuts with preserved meaning
"Is this ready for submission?"
→ Load rubrics.md + all relevant references, comprehensive evaluation
Output Principles
- •Quote exactly: Reference specific passages from the draft
- •Rewrite concretely: Don't just diagnose—show the fix
- •Be honest: User wants critical feedback, not encouragement
- •Prioritize: Identify 2-3 highest-impact changes
- •Model excellence: Pull from exemplar papers to show what good looks like