Agent Skills: Academic writing and research methodology

Academic writing and research methodology

Systematic approaches for scholarly writing, research design, and academic communication.

Research design fundamentals

Research question development

## Crafting a research question

### The FINER criteria
- **F**easible: Can you actually do this research?
- **I**nteresting: Does it matter to the field?
- **N**ovel: Does it add new knowledge?
- **E**thical: Can it be done ethically?
- **R**elevant: Does it address a real problem?

### Question types
| Type | Purpose | Example |
|------|---------|---------|
| Descriptive | Document phenomena | "What are the characteristics of X?" |
| Comparative | Compare groups/conditions | "How does X differ between groups?" |
| Correlational | Examine relationships | "Is there a relationship between X and Y?" |
| Causal | Establish causation | "Does X cause Y?" |
| Exploratory | Generate hypotheses | "What factors might explain X?" |

### Refining your question
Start broad → Narrow progressively

Draft 1: "How does social media affect politics?"
Draft 2: "How does Twitter use affect political polarization?"
Draft 3: "How does exposure to partisan Twitter accounts affect
         political attitude polarization among US adults?"
Draft 4: "Does increased exposure to ideologically homogeneous Twitter
         feeds increase affective polarization among politically
         engaged US adults aged 18-35?"

Literature review strategy

## Systematic literature search

### Database selection by field
- **Multidisciplinary**: Web of Science, Scopus, Google Scholar
- **Social Sciences**: JSTOR, ProQuest, SSRN
- **Communication**: Communication Abstracts, ComAbstracts
- **Health**: PubMed, MEDLINE, CINAHL
- **Education**: ERIC
- **Business**: Business Source Complete

### Search strategy template
1. **Identify key concepts** from research question
2. **Generate synonyms** for each concept
3. **Combine with Boolean operators**

Example for: "social media political polarization"

Concept 1: social media
- OR: Twitter, Facebook, Instagram, "social networking sites",
      "online platforms", "digital media"

Concept 2: political
- OR: partisan, ideological, electoral, civic

Concept 3: polarization
- OR: division, extremism, "attitude change", radicalization

Combined search:
(Twitter OR Facebook OR "social media" OR "social networking")
AND (political OR partisan OR ideological)
AND (polarization OR division OR extremism)

### Inclusion/exclusion criteria
Document your criteria:
- Publication date range: [X to present]
- Languages: [English only / multiple]
- Publication types: [Peer-reviewed only / include preprints]
- Geographic scope: [Global / specific countries]
- Methodologies: [All / specific approaches]

### Managing your search
- Save searches to re-run later
- Export results to reference manager
- Track number of results at each stage
- Document date of each search

Citation management

# Zotero/reference manager integration patterns

# For automated citation workflows
CITATION_STYLES = {
    'apa7': 'American Psychological Association 7th edition',
    'mla9': 'Modern Language Association 9th edition',
    'chicago': 'Chicago Manual of Style 17th edition',
    'harvard': 'Harvard Reference format',
    'ieee': 'IEEE',
    'vancouver': 'Vancouver (medicine)',
}

# BibTeX entry template
BIBTEX_ARTICLE = """
@article{{{citekey},
    author = {{{author}}},
    title = {{{title}}},
    journal = {{{journal}}},
    year = {{{year}}},
    volume = {{{volume}}},
    number = {{{number}}},
    pages = {{{pages}}},
    doi = {{{doi}}}
}}
"""

# Common citation patterns by context
CITATION_CONTEXTS = {
    'introducing_concept': "According to Author (Year), ...",
    'supporting_claim': "Research has shown that X (Author, Year; Author, Year).",
    'contrasting': "While Author (Year) argues X, Author (Year) contends Y.",
    'methodology_reference': "Following the method developed by Author (Year), ...",
    'direct_quote': 'Author (Year) states that "exact quote" (p. X).',
}

Paper structure and writing

IMRaD structure (scientific papers)

## Standard research paper sections

### Abstract (150-300 words typically)
- Background (1-2 sentences)
- Purpose/objective (1 sentence)
- Methods (2-3 sentences)
- Results (2-3 sentences)
- Conclusions (1-2 sentences)

### Introduction
**Funnel structure:**
1. Broad context - Why does this topic matter?
2. Narrow focus - What's the specific problem?
3. Gap identification - What don't we know?
4. Research question/hypothesis - What will you investigate?
5. Contribution preview - Why does this study matter?

### Literature Review
**Organize thematically, not chronologically:**
1. Theme 1: Key findings, debates, gaps
2. Theme 2: Key findings, debates, gaps
3. Theme 3: Key findings, debates, gaps
4. Synthesis: How themes connect to your study

### Methods
**The reproducibility test:** Could another researcher replicate your study from this section alone?

Include:
- Participants/sample (who, how selected, N)
- Materials/measures (what instruments, their validity)
- Procedure (step-by-step what happened)
- Analysis approach (statistical tests, qualitative methods)
- Ethical considerations (IRB, consent)

### Results
**Report, don't interpret:**
- Present findings systematically
- Use tables/figures for complex data
- Report effect sizes, not just p-values
- Address each research question/hypothesis

### Discussion
**Reverse funnel structure:**
1. Summary of key findings
2. Interpretation in context of literature
3. Theoretical implications
4. Practical implications
5. Limitations
6. Future research directions
7. Conclusion

Academic writing style

## Writing conventions

### Voice and tense
| Section | Tense | Example |
|---------|-------|---------|
| Abstract | Past (methods/results), Present (conclusions) | "We found... This suggests..." |
| Introduction | Present (established knowledge) | "Research shows..." |
| Methods | Past | "Participants completed..." |
| Results | Past | "Analysis revealed..." |
| Discussion | Present + Past | "These findings indicate... We found..." |

### Hedging language
Appropriate hedging (avoiding overclaiming):
- "This suggests that..." (not "This proves that...")
- "may be related to" (not "causes")
- "Results indicate..." (not "Results demonstrate conclusively...")
- "One possible explanation..." (not "The explanation...")

### Transition words by function
**Addition:** furthermore, moreover, additionally, in addition
**Contrast:** however, nevertheless, conversely, in contrast
**Cause/effect:** therefore, consequently, as a result, thus
**Example:** for instance, specifically, to illustrate
**Sequence:** first, subsequently, finally, meanwhile
**Summary:** in summary, overall, in conclusion

### Paragraphs
Each paragraph should:
1. Begin with a topic sentence
2. Contain one main idea
3. Include supporting evidence
4. Connect to adjacent paragraphs
5. Average 100-200 words (varies by field)

Common writing problems

## Issues to avoid

### Wordiness
❌ "It is important to note that the results demonstrate..."
✅ "Results demonstrate..."

❌ "In order to investigate..."
✅ "To investigate..."

❌ "A total of 50 participants..."
✅ "Fifty participants..."

### Weak verbs
❌ "The study was conducted by the researchers"
✅ "The researchers conducted the study"

❌ "There was a significant difference found"
✅ "We found a significant difference"

### Vague language
❌ "Several studies have shown..."
✅ "Three studies (Author, Year; Author, Year; Author, Year) showed..."

❌ "The results were significant"
✅ "The results were statistically significant (p < .05, d = 0.45)"

### Unnecessary jargon
- Define technical terms on first use
- Use simpler words when equally precise
- Consider your audience's expertise level

### Citation problems
❌ Citing secondary sources without noting
✅ "(Author, Year, as cited in Author, Year)"

❌ String citations without synthesis
✅ Group citations that make the same point; distinguish those that differ

Peer review and revision

Responding to reviewers

## Response letter template

Dear Editor and Reviewers,

Thank you for the thoughtful feedback on our manuscript titled "[Title]"
(Manuscript ID: [Number]). We have carefully considered all comments and
revised the manuscript accordingly. Below, we provide point-by-point
responses to each comment.

---

## Reviewer 1

### Comment 1.1
[Quote or paraphrase the reviewer's comment]

**Response:**
[Your response explaining what you did]

**Changes made:**
[Quote the specific changes with page/line numbers]
"New text here..." (p. X, lines XX-XX)

### Comment 1.2
[Continue for each comment]

---

## Reviewer 2
[Same format]

---

We believe these revisions have substantially strengthened the manuscript
and hope you will find it suitable for publication in [Journal Name].

Sincerely,
[Authors]

Handling criticism

## Types of reviewer feedback

### Must address
- Methodological concerns
- Missing literature
- Unclear writing
- Logical gaps in argument
- Statistical errors

### Negotiate carefully
- Requests for additional analyses
- Suggestions to restructure
- Disagreements on interpretation

### Pushback appropriately
- Requests outside scope
- Misunderstandings of your argument
- Contradictory advice from reviewers

### Response strategies
**Agreement:** "We thank the reviewer for this suggestion. We have [action]."
**Partial agreement:** "We appreciate this point. While [acknowledge validity], we [explain your approach]. However, we have [partial accommodation]."
**Respectful disagreement:** "We thank the reviewer for raising this issue. We have considered this carefully; however, [explanation]. We hope the reviewer will find this reasoning persuasive."

Grant proposals

Proposal structure (NSF/NIH style)

## Standard grant components

### Specific aims (1 page)
**Opening paragraph:** What's the problem? Why does it matter?
**Gap statement:** What's missing from current understanding?
**Long-term goal:** Your research program vision
**Objective:** What this specific project will accomplish
**Central hypothesis:** Your testable prediction
**Aims:** 2-4 specific, achievable objectives
**Impact statement:** Why funding this matters

### Significance (2-3 pages)
- Importance of the problem
- Gaps in current knowledge
- How your work advances the field
- Potential impact if successful

### Innovation (1 page)
- What's new about your approach?
- Conceptual innovation
- Methodological innovation
- Technical innovation

### Approach (6-12 pages)
For each aim:
- Rationale
- Preliminary data (if any)
- Research design
- Methods
- Expected outcomes
- Potential problems and alternatives
- Timeline

### Broader impacts
- Training opportunities
- Dissemination plans
- Benefits to society
- Diversity and inclusion

Budget justification

## Budget categories

### Personnel
- PI salary and effort (% time)
- Co-investigators
- Postdocs (salary + benefits)
- Graduate students (stipend + tuition + benefits)
- Undergraduate researchers
- Technical staff

### Equipment
- Items over $5,000 (check sponsor threshold)
- Justify necessity for project

### Supplies
- Lab consumables
- Software licenses
- Participant payments

### Travel
- Conference presentations
- Data collection sites
- Collaborator visits

### Other direct costs
- Publication costs
- Participant incentives
- Transcription services
- Equipment maintenance

### Indirect costs (F&A)
- Negotiated rate with institution
- Typically 50-60% of direct costs

Publishing strategy

Journal selection

## Evaluating journals

### Quality indicators
- Impact factor (use cautiously)
- Acceptance rate
- Review time
- Time to publication
- Reputation in your field
- Indexing (Web of Science, Scopus)

### Fit indicators
- Scope alignment
- Audience match
- Open access options
- Article type (empirical, theoretical, review)

### Red flags (predatory journals)
- Aggressive email solicitation
- Rapid "peer review" (days)
- Unclear editorial board
- Not indexed in major databases
- "Pay to publish" with no clear OA model
- Poor website quality

### Resources
- Beall's List (archived versions)
- Think. Check. Submit. (thinkchecksubmit.org)
- DOAJ (Directory of Open Access Journals)
- Journal Citation Reports

Cover letter template

Dear Dr. [Editor's name],

We are pleased to submit our manuscript titled "[Full title]" for
consideration as a [article type] in [Journal Name].

**Summary (2-3 sentences):**
[What you did and what you found]

**Significance (2-3 sentences):**
[Why this matters for the journal's readership]

**Fit statement:**
[Why this journal specifically]

**Declarations:**
- This manuscript is original and not under consideration elsewhere
- All authors have approved the submission
- [Conflict of interest statement]
- [Funding acknowledgment]

**Suggested reviewers (if requested):**
1. [Name, affiliation, email] - Expert in [relevant area]
2. [Name, affiliation, email] - Expert in [relevant area]
3. [Name, affiliation, email] - Expert in [relevant area]

**Reviewers to exclude (if any):**
[Name] - [Brief, professional reason]

We look forward to your response.

Sincerely,
[Corresponding author name]
[Title, affiliation]
[Contact information]

Research ethics

Ethical considerations checklist

## Before starting research

### Human subjects
- [ ] IRB/ethics board approval obtained
- [ ] Informed consent procedures established
- [ ] Vulnerable populations identified and protected
- [ ] Privacy and confidentiality measures in place
- [ ] Data security plan established
- [ ] Risk/benefit ratio acceptable

### Data management
- [ ] Data management plan created
- [ ] Secure storage arranged
- [ ] Sharing/archiving plans documented
- [ ] Retention period determined
- [ ] Destruction procedures established

### Authorship
- [ ] Contribution criteria discussed
- [ ] Author order agreed upon
- [ ] All contributors will meet authorship criteria
- [ ] Acknowledgments planned for non-author contributors

### Conflicts of interest
- [ ] Financial conflicts identified
- [ ] Non-financial conflicts identified
- [ ] Disclosure plan established

### Reproducibility
- [ ] Analysis plan pre-registered (if applicable)
- [ ] Code will be shared
- [ ] Data will be shared (if possible)
- [ ] Materials will be shared

Avoiding research misconduct

## Types of misconduct

### Fabrication
- Making up data or results
- Never acceptable under any circumstances

### Falsification
- Manipulating data, equipment, or processes
- Selectively omitting data to change conclusions
- Image manipulation beyond acceptable adjustment

### Plagiarism
- Using others' words without attribution
- Self-plagiarism (reusing own published work without acknowledgment)
- Paraphrasing too closely

### Other questionable practices
- P-hacking (running multiple analyses until significant)
- HARKing (hypothesizing after results known)
- Salami slicing (fragmenting one study into many papers)
- Gift/ghost authorship
- Selective reporting of results

Productivity and workflow

Writing routine

## Sustainable academic writing

### Daily writing practice
- Write at same time daily (habit formation)
- Start with minimum viable goal (e.g., 30 minutes)
- Track progress (word counts, time)
- Protect writing time from meetings/email

### Managing large projects
1. Break into smallest possible tasks
2. Set deadlines for each component
3. Schedule regular writing blocks
4. Build in buffer time
5. Get feedback early and often

### Overcoming blocks
- Start with easiest section
- Write a "shitty first draft" (Anne Lamott)
- Use placeholders for citations/data
- Talk through ideas with colleague
- Change environment
- Return to outline/structure

Tools for academics

| Purpose | Tools | |---------|-------| | Reference management | Zotero, Mendeley, EndNote | | Writing | Scrivener, Overleaf, Word | | Collaboration | Google Docs, Overleaf | | Version control | Git/GitHub, Track Changes | | Task management | Todoist, Notion, Trello | | Focus | Forest, Freedom, Cold Turkey | | Analysis | R, Python, SPSS, Stata, NVivo | | Visualization | R/ggplot2, Python/matplotlib, Tableau |