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Lesson 5 12 min

Writing Your Paper

Draft, edit, and polish publication-ready manuscripts with AI — from abstract to conclusion — while maintaining your scientific voice and meeting journal standards.

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The blank page is a scientist’s second biggest enemy (after the blank grant application). Writing a paper takes months not because the science is complicated, but because translating complex findings into clear, publishable prose is a different skill than doing the research. AI won’t write your paper for you — but it can get you from blank page to solid first draft in hours instead of weeks.

🔄 Quick Recall: In the previous lesson, you analyzed your data with AI — selecting statistical tests, checking assumptions, and generating visualizations. Now you’ll transform those results into a manuscript, section by section.

The AI-Assisted Writing Workflow

Important: AI assists with structure, clarity, and language. It does not contribute scientific ideas, interpret results, or make authorship-worthy contributions. You write the science; AI polishes the prose.

Manuscript Section	How AI Helps	What You Must Do
Abstract	Summarize from completed sections	Verify every number and claim matches the paper
Introduction	Structure the narrative, suggest organization	Verify every citation, ensure the gap is real
Methods	Format consistently, check completeness	Ensure reproducibility, add AI disclosure
Results	Structure reporting, check APA formatting	Verify all statistics match your analysis output
Discussion	Improve clarity, connect to literature	Interpret meaning, write limitations honestly
References	Format consistently	Verify every single reference exists and is correct

Section-by-Section Writing Prompts

Introduction

Help me structure the introduction for my paper:

Topic: [your research topic]
Key gap: [what's missing in the literature]
Hypothesis: [what you tested]
3-5 key background papers: [list with brief notes on each]

Generate a structured outline:
1. Opening: broad context (why this topic matters)
2. Background: what's known (organized by theme, not chronologically)
3. Gap: what's missing or contradictory
4. Purpose: what this study addresses and how
5. Hypothesis: specific prediction with rationale

Rules:
- Each paragraph should have one main point
- Avoid "to the best of our knowledge" (reviewers hate this)
- End with a clear thesis statement connecting the gap to your study

Methods

Review my methods section for completeness:

Study design: [description]
Participants/samples: [who/what, how recruited/selected]
Materials/instruments: [what you used]
Procedure: [what you did, step by step]
Analysis plan: [statistical methods]

Check:
1. Could another researcher replicate this study from my description?
2. Are all measures described with reliability/validity info?
3. Are ethical approvals and consent mentioned?
4. Is the analysis plan specific enough (test names, software, corrections)?
5. Are AI tools used in the study properly disclosed?
6. What's missing?

✅ Quick Check: Your Methods section says “Participants were recruited from the university.” Is this sufficient? (Answer: No. Specify: how many, inclusion/exclusion criteria, demographics, recruitment method (flyers, online, course credit), compensation, IRB approval number, and consent process. Underdescribed Methods = unreplicable study.)

Results

Help me structure the Results section:

Analyses performed:
1. [Analysis 1 — test, variables, result]
2. [Analysis 2 — test, variables, result]
3. [Analysis 3 — test, variables, result]

For each result, format in journal style:
- Report the test statistic, degrees of freedom, p-value, and effect size
- Example: "A one-way ANOVA revealed a significant effect of treatment on growth rate, F(2, 87) = 4.52, p = .013, η² = .094"
- Describe the direction of effects in plain language
- Reference the relevant figure or table

Organize by:
- Primary analyses first (confirmatory)
- Secondary analyses second (exploratory — clearly labeled)
- Report non-significant results too

Discussion

Help me structure the Discussion section:

Main findings: [2-3 key results]
How they relate to the literature: [which papers they support/contradict]
Practical implications: [what this means for the field]
Limitations I know about: [list honestly]
Future directions: [what should be studied next]

Structure:
1. Summary of main findings (1 paragraph — don't repeat Results)
2. Interpretation: what do the findings mean?
3. Connection to literature: how do they fit with what's known?
4. Limitations (mandatory — never skip this)
5. Implications and future directions
6. Concluding statement

AI Editing Tools

After drafting, AI editing tools improve clarity and language quality.

Tool	Best For	Pricing
Writefull	Academic-specific language editing, title/abstract generation	Free tier + premium
Paperpal	Grammar, clarity, journal-specific suggestions	Free tier + premium
AI assistants	Restructuring paragraphs, explaining complex ideas more clearly	Varies

Editing prompt for AI assistants:

Edit this paragraph for clarity and conciseness.
Keep the scientific meaning exactly the same.
Do NOT change technical terms or add claims.
Do NOT remove limitation statements or hedging language
  that reflects genuine uncertainty.
Target journal: [name]

[paste paragraph]

✅ Quick Check: AI suggests changing “Our results suggest a possible association between X and Y” to “Our results demonstrate that X causes Y.” Should you accept this edit? (Answer: Absolutely not. “Suggest a possible association” reflects appropriate scientific caution for correlational data. “Demonstrate that X causes Y” implies causation from correlation — a serious scientific error. AI optimizes for strong, confident writing; science requires precision about what your evidence actually supports.)

The Abstract — Write Last

Write your abstract after the paper is complete, not before.

Generate a structured abstract from my completed manuscript:

Background: [1-2 sentences from Introduction]
Methods: [1-2 sentences — design, participants, measures]
Results: [2-3 sentences — key findings with statistics]
Conclusion: [1-2 sentences — what this means]

Word limit: [journal's limit, typically 150-300 words]

Rules:
- Every number in the abstract must match the paper exactly
- Don't include findings not in the Results
- Don't make claims stronger than the Discussion supports

Practice Exercise

Pick one section of a paper you’re currently writing and run it through the appropriate structural prompt
Use an AI editing tool (Writefull or an AI assistant) to edit one paragraph — then compare the original and edited versions for accuracy, not just readability
Check if any AI edits subtly changed the scientific meaning of your claims

Key Takeaways

AI assists with structure, clarity, and language — not scientific ideas, interpretation, or authorship
Verify every citation AI includes in your introduction — fabricated references are the highest-risk AI error
Methods sections must disclose AI tools with specificity: tool name, version, what it did, how outputs were verified
Never let AI remove limitation statements — they’re a required component of academic writing, not a weakness to edit out
Write the abstract last, from the completed paper — and verify every number matches
AI optimizes for confident, clear language; science requires precise hedging when evidence is uncertain

Up Next

In the next lesson, you’ll create publication-quality figures, captions, and supplementary materials — the visual elements that make or break a paper’s impact.

Knowledge Check

1. You ask AI to write the introduction of your paper. It produces a well-structured, clearly written section. What's the most important thing you should check?

Whether the writing style matches the target journal Whether every claim has a real, verified citation and whether the narrative accurately represents the literature. AI constructs plausible-sounding arguments with fabricated or misrepresented references. Your introduction must reflect what the literature actually says, not what AI thinks it should say. Check every citation exists, verify the cited papers actually support the claims made, and ensure the gap statement reflects a genuine gap — not one AI invented Whether it's long enough for the target journal

2. Your Methods section needs to describe the AI tools you used for data analysis. How detailed should this description be?

Just mention you used AI — 'AI-assisted analysis was performed' Specify: the tool name and version, exactly which analyses it performed, how outputs were verified, and any modifications you made. Example: 'Initial statistical test selection was performed using [Tool] (v2.1). All assumptions were verified manually using Shapiro-Wilk tests and Q-Q plots. The AI-suggested ANOVA was confirmed appropriate and executed in [Software]. All results were independently replicated in R (v4.3)' Don't mention AI tools at all — focus on the statistical methods used

3. AI-edited your Discussion section, making it 30% shorter and more readable. But in the process, it removed a paragraph about your study's limitations. Should you keep the shorter version?

Yes — shorter and more readable is always better for publication Add the limitations paragraph back. Every Discussion must include limitations — reviewers will flag their absence, and omitting them suggests you either aren't aware of your study's weaknesses or are hiding them. AI optimizes for readability but doesn't understand that certain 'imperfections' in academic writing serve essential functions Ask AI to move the limitations to the Supplementary Materials instead

Answer all questions to check

Complete the quiz above first