scientific-manuscript-review

What this skill does

# Scientific Manuscript Review

## Table of Contents
- [Core Principles](#core-principles)
- [Workflow](#workflow)
- [Section-by-Section Review](#section-by-section-review)
- [Language Guidelines](#language-guidelines)
- [Guardrails](#guardrails)
- [Quick Reference](#quick-reference)

**Related skills:** Grant proposals → `grant-proposal-assistant` | Recommendation letters → `academic-letter-architect` | Emails → `scientific-email-polishing`

## Core Principles

Seven foundational beliefs guiding manuscript review:

1. **Clarity over cleverness**: Scientific clarity is more important than stylistic elegance
2. **Narrative shapes comprehension**: Structure and story arc determine reader understanding
3. **Audience dictates tone**: Expert vs. general audience requires different depth and framing
4. **Format signals credibility**: Professional formatting reflects scientific rigor
5. **Claims require evidence**: Strong assertions need strong data and appropriate hedging
6. **Each section has a job**: Introduction sells the problem, Results show the data, Discussion interprets
7. **Constraints shape structure**: Word limits and journal guidelines determine emphasis

## Workflow

Copy this checklist and track your progress:

```
Manuscript Review Progress:
- [ ] Step 1: Identify manuscript type and extract core message
- [ ] Step 2: Structural pass - map and evaluate overall organization
- [ ] Step 3: Introduction review - gap statement, focus, hypothesis
- [ ] Step 4: Results review - question, approach, finding, interpretation
- [ ] Step 5: Discussion review - synthesis, context, limitations
- [ ] Step 6: Scientific clarity check - claims, controls, hedging
- [ ] Step 7: Language polish - terminology, voice, jargon
- [ ] Step 8: Formatting check - journal compliance
```

**Step 1: Identify Manuscript Type and Core Message**

Determine document type (research article, review, perspective, short communication). Extract the ONE finding or message readers must remember. Ask: "If readers remember only one thing, what should it be?" See [resources/methodology.md](resources/methodology.md#core-message-extraction) for extraction techniques.

**Step 2: Structural Pass**

Map overall organization against standard IMRaD (Introduction, Methods, Results, Discussion) or review structure. Check logical sequencing - does each section flow into the next? Identify unclear transitions or missing context. See [resources/methodology.md](resources/methodology.md#structural-assessment) for structure evaluation.

**Step 3: Introduction Review**

Evaluate using the Introduction Arc: Broad context → Narrow focus → Knowledge gap → Hypothesis/Objective. Check that gap statement is explicit and compelling. Verify ending with clear hypothesis or objective. See [resources/template.md](resources/template.md#introduction-arc) for template.

**Step 4: Results Review**

For each figure/table/experiment: Question addressed? → Approach used? → Key finding (with statistics)? → Interpretation (what it means)? Flag data-dump writing that lacks interpretation. Ensure findings build toward core message. See [resources/template.md](resources/template.md#results-paragraph) for results structure.

**Step 5: Discussion Review**

Verify structure: Revisit hypothesis → Interpret findings in field context → Place in broader literature → Acknowledge limitations → Suggest future directions. Check for overclaiming (speculation presented as fact). Ensure clear separation of data interpretation vs. speculation. See [resources/methodology.md](resources/methodology.md#discussion-structure) for discussion framework.

**Step 6: Scientific Clarity Check**

Run the clarity checklist: Claims supported by data? Quantitative details present (statistics, n values)? Controls adequately described? Interpretations appropriately hedged? Mechanistic explanations where needed? See [resources/template.md](resources/template.md#clarity-checklist) for full checklist.

**Step 7: Language Polish**

Ensure terminology consistency throughout. Remove or define jargon on first use. Prefer active voice when it aids clarity. Standardize abbreviations. Check for hedging language ("suggests" vs "proves"). See [resources/methodology.md](resources/methodology.md#language-guidelines) for specific guidance.

**Step 8: Formatting Check**

Verify compliance with target journal guidelines (word limits, reference format, figure requirements). Check section headings match journal requirements. Ensure abstract follows structured/unstructured requirement. Validate using [resources/evaluators/rubric_scientific_manuscript.json](resources/evaluators/rubric_scientific_manuscript.json). **Minimum standard**: Average score ≥ 3.5.

## Section-by-Section Review

### Introduction Structure

**Goal:** Convince readers the problem matters and your approach is sound

**The Funnel Structure:**
```
[Broad context - establish field importance, 1-2 sentences]
        ↓
[Narrow to specific area - what's been done]
        ↓
[Knowledge gap - what's missing, why it matters]
        ↓
[Your hypothesis/objective - what you will address]
```

**Common problems:**
- Gap statement buried or implicit (make it explicit: "However, X remains unknown")
- Too broad opening (readers don't need history of the universe)
- No clear hypothesis at end (readers don't know what to expect)
- Overlong literature review (move details to Discussion)

### Results Structure

**Goal:** Present data clearly with interpretation, not just numbers

**Per-paragraph/figure structure:**
```
[Question this experiment addresses]
[Approach/method used]
[Key finding - with quantification]
[Brief interpretation - what this means]
```

**Common problems:**
- Data dump (listing results without interpretation)
- Missing statistics (p-values, n values, confidence intervals)
- Vague descriptions ("we found differences" vs "we found 3-fold increase")
- Figures not referenced in logical order
- Key findings buried in text (highlight important results)

### Discussion Structure

**Goal:** Interpret findings and place in broader context

**Standard flow:**
```
[Restate main finding and hypothesis status]
        ↓
[Interpret key results in field context]
        ↓
[Compare to prior literature - agreements/disagreements]
        ↓
[Mechanistic implications (if applicable)]
        ↓
[Limitations - honest acknowledgment]
        ↓
[Future directions - what comes next]
        ↓
[Concluding statement - big picture significance]
```

**Common problems:**
- Overclaiming (data doesn't support conclusions)
- Repeating Results section (discuss, don't recapitulate)
- Missing limitations (reviewers will note them anyway)
- Speculation unmarked (clearly label "we speculate that...")
- No connection to field (discuss in isolation)

## Language Guidelines

**Active vs. Passive Voice:**
- Use active for clarity: "We measured" not "Measurements were made"
- Use passive when agent is obvious or unimportant: "Samples were incubated at 37°C"
- Avoid dangling modifiers: Not "Having analyzed the data, the conclusion was..." but "Having analyzed the data, we concluded..."

**Hedging Language:**
- Strong data: "demonstrates", "shows", "establishes"
- Moderate confidence: "suggests", "indicates", "supports"
- Speculation: "may", "might", "could potentially"
- Match hedge strength to evidence strength

**Jargon Management:**
- Define on first use: "polymerase chain reaction (PCR)"
- Avoid unnecessary jargon when plain language works
- Field-standard terms don't need definition (DNA, protein, cell)
- Reader-appropriate: more definition for broad audience journals

**Terminology Consistency:**
- Pick one term and stick with it (don't alternate between "subjects", "participants", "patients")
- Create terminology table for complex manuscripts
- Check abbreviations defined before use

## Guardrails

**Key requirements:**

1. **Preserve author voice**: Edit for clarity, not voice. Avoid inventing claims or changing meaning. Mark suggesti