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:

Broad context (1-2 paragraphs): field importance
Literature review (2-4 paragraphs): what is known, organized thematically
Gap identification (1 paragraph): what remains unknown
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

Systematic reviews/meta-analyses (strongest synthesis)
Randomized controlled trials (causal inference)
Prospective cohort studies (temporal precedence)
Cross-sectional studies (associations)
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

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

Stage 2: Drafting

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

Stage 3: Revision

Check logical flow throughout
Verify terminology consistency
Confirm reporting guideline adherence
Verify all citations accurate
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

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