Scientific Writing

Write publication-ready scientific manuscripts using established academic conventions and evidence-based practices.

Core Principles

Evidence-Based Claims

Every substantive claim requires support from peer-reviewed literature. Use appropriate hedging: "suggests" for correlational evidence, "demonstrates" for causal evidence. Never assert without citation or data support.

Clarity Over Flourish

Scientific writing prioritizes precision. Use domain-specific terminology correctly, define terms on first use, prefer active voice in methods, and avoid vague qualifiers ("very significant" → "statistically significant, p < 0.001").

Reproducibility Standard

Methods must enable replication: include all parameters, software versions, statistical tests, sample sizes, inclusion/exclusion criteria, effect sizes alongside p-values, and relevant reporting guideline compliance.

Two-Stage Writing Process

Stage 1: Outline with Evidence Create structured outlines with bullet points marking main arguments, key citations, data points, and logical flow. This is scaffolding—not the final manuscript.

Stage 2: Convert to Prose Transform outlines into complete paragraphs with proper transitions, integrated citations, and logical sentence flow. Final manuscripts contain NO bullet points except in specific Methods subsections (inclusion criteria, materials lists).

Manuscript Structure (IMRAD)

Abstract

Write as flowing paragraph(s), NOT labeled sections. Cover: (1) context/problem, (2) methods summary, (3) key findings with statistics, (4) significance. Typically 150-300 words. Only use structured format if journal explicitly requires it.

Example structure:

[Context sentence establishing importance]. [Gap or problem addressed]. 
[Study objective]. [Methods: design, N, key measures]. [Primary result with 
statistics]. [Secondary findings]. [Conclusion and implications].

Introduction

Follow funnel structure:

1. Broad context (1-2 paragraphs): field importance
2. Literature review (2-4 paragraphs): what is known, organized thematically
3. Gap identification (1 paragraph): what remains unknown
4. Present study (1 paragraph): objectives, hypotheses, approach

Methods

Standard subsections:

• Participants/Subjects: demographics, recruitment, ethics approval
• Materials/Stimuli: detailed descriptions, validated instrument citations
• Procedure: chronological protocol with timing
• Data Analysis: statistical approach, software, multiple comparison corrections

Include power analysis. Report all conditions. Enable replication.

Results

Structure: (1) preliminary analyses, (2) primary hypotheses, (3) secondary/exploratory (labeled).

Report consistently:

• Descriptive: M ± SD or Mdn (IQR)
• Inferential with effect sizes: "t(48) = 2.31, p = .025, d = 0.67"
• Confidence intervals when possible

No interpretation here—save for Discussion.

Discussion

Structure: (1) summary without statistics, (2) interpretation in literature context, (3) limitations, (4) implications, (5) future directions, (6) conclusion.

Address alternative explanations. Avoid overclaiming.

Citation Practices

Source Hierarchy

1. Systematic reviews/meta-analyses (strongest synthesis)
2. Randomized controlled trials (causal inference)
3. Prospective cohort studies (temporal precedence)
4. Cross-sectional studies (associations)
5. Case studies/expert opinion (hypothesis-generating)

Best Practices

• Cite primary sources, not secondary summaries
• Balance recent work (last 5 years) with foundational papers
• Verify claims against original sources
• Flag contradictory evidence rather than omitting it
• Self-citations <20%

For detailed citation formatting by style, see references/citation_styles.md.

Reporting Guidelines

Match guideline to study type:

• CONSORT: Randomized controlled trials
• STROBE: Observational studies (cohort, case-control, cross-sectional)
• PRISMA: Systematic reviews and meta-analyses
• STARD: Diagnostic accuracy studies
• TRIPOD: Prediction models
• ARRIVE: Animal research
• CARE: Case reports

For checklists and details, see references/reporting_guidelines.md.

Writing Style

Verb Tense

Section	Tense
Introduction (established facts)	Present
Introduction (prior studies)	Past
Methods	Past
Results	Past
Discussion (your findings)	Past
Discussion (interpretations)	Present
Conclusions	Present

Common Errors

Error	Correction
"Data shows..."	"Data show..." (plural)
"Proves that..."	"Suggests/demonstrates that..."
"Significant" (colloquial)	"Substantial" or "statistically significant"
"In order to"	"To"
"Due to the fact that"	"Because"

Paragraph Structure

• Open with topic sentence stating main point
• Provide evidence and elaboration
• Connect logically to next paragraph
• Typical length: 4-8 sentences

Field-Specific Conventions

Biomedical/Clinical

• Use precise anatomical/clinical terminology
• Follow standardized nomenclature (ICD, DSM, SNOMED-CT)
• Generic drug names first, brands in parentheses
• "Patients" for clinical, "participants" for community research

Molecular Biology

• Gene symbols italicized (TP53), proteins regular (p53)
• Species-specific: human uppercase (BRCA1), mouse sentence case (Brca1)
• Full species name first, then abbreviation (Escherichia coli → E. coli)

Chemistry

• IUPAC nomenclature for compounds
• Concentrations with units (mM, μM, nM)
• Standard notation (SMILES, InChI)

For comprehensive field conventions, see references/field_conventions.md.

Figures and Tables

When to Use Which

• Tables: Precise numerical data, exact values needed
• Figures: Trends, patterns, relationships, visual comparisons

Requirements

• Self-explanatory with complete captions
• Consistent formatting and terminology
• All axes/columns labeled with units
• Sample sizes (n) and statistical annotations
• No duplication between text, tables, and figures

For detailed guidance, see references/figures_tables.md.

Workflow Summary

Stage 1: Planning

1. Identify target journal, review author guidelines
2. Determine applicable reporting guideline
3. Outline manuscript structure
4. Plan figures/tables as data story backbone

Stage 2: Drafting

1. Start with figures/tables
2. Draft Methods first (easiest)
3. Write Results (describe figures/tables)
4. Compose Discussion (interpret findings)
5. Write Introduction (set up research question)
6. Craft Abstract last (summarize complete work)

Stage 3: Revision

1. Check logical flow throughout
2. Verify terminology consistency
3. Confirm reporting guideline adherence
4. Verify all citations accurate
5. Proofread for clarity

Pre-Submission Checklist

• Abstract accurately reflects content (written as prose, not labeled sections)
• All claims have citations or data support
• Methods enable replication
• Statistics include effect sizes and CIs
• Figures have informative captions
• References follow target journal style
• Reporting guideline checklist completed
• Word count within limits
• Author contributions and conflicts declared