Research Skills and Critical Thinking

(A Guide for the Research Skills Academy)

Date:

Aug 17, 2025

Author:

Mark Galassi <mark@galassi.org>

Author:

Andrea Bruno <bruno.andrea.191@gmail.com>

Author:

Karina Higginson <karinajhigginson@gmail.com>

Author:

Juno Kerelis <ajkerelis@gmail.com>

License:

This is a free book. You may adapt and redistribute it under the terms of the Creative Commons Attribution-ShareAlike 4.0 International license (CC BY-SA 4.0) described at https://creativecommons.org/licenses/by-sa/4.0/

Caution

This web book is a work in progress.

Contents:

• 1. The Academy
  • 1.1. The Schedule
  • 1.2. What is Research?
  • 1.3. Transfer of metaphor
  • 1.4. What Students Should Produce in this Time
  • 1.5. The Slant of the Lectures
  • 1.6. Computing, Platforms, and Software Freedom
• 2. Nuance and the Avoidance of Platitudes
  • 2.1. How To See More of the Painting
  • 2.2. Platitudes
    • 2.2.1. The Platitude Sickness: Taking Out the Trash of Corporate Speak
    • 2.2.2. Another Rant Against Platitudes
    • 2.2.3. Mark’s Personal Experience
• 3. Propaganda and Special Interest Groups
  • 3.1. The National Association of Manufacturers
  • 3.2. The American Liberty League
  • 3.3. The Return of NAM
  • 3.4. The Global Climate Coalition
  • 3.5. Green-washing and Recycling
  • 3.6. Works Cited
• 4. Scientific Fraud
  • 4.1. William Summerlin
  • 4.2. Andrew Wakefield
  • 4.3. Diederick Stapel
  • 4.4. Works Cited
• 5. Reading Effectively
  • 5.1. Lesson ideas for this chapter
  • 5.2. Reading to Understand Vs. Reading to Critique
    • 5.2.1. Understanding with Grace
    • 5.2.2. Critiquing with Wanton Abandon
    • 5.2.3. Notes Are Your Best Friend
  • 5.3. Reading non-fiction versus reading fiction
  • 5.4. Handling Jargon
    • 5.4.1. Suspension of Not-getting-it-ness
    • 5.4.2. The Dream of Full Understanding?
    • 5.4.3. Remembering this when you are the writer
  • 5.5. An Exercise
  • 5.6. Building Connections
  • 5.7. Where Is This Source Coming From?
  • 5.8. Building Blocks: Prefixes and Suffixes
    • 5.8.1. Latin Prefixes
    • 5.8.2. Greek Prefixes
    • 5.8.3. Latin Suffixes
    • 5.8.4. Greek Suffixes
• 6. Data Visualization
  • 6.1. The Big Picture
  • 6.2. The Data can Lead you Astray
  • 6.3. Data Visualization Software
  • 6.4. The !Kung of the Kalahari Desert (Bubble Chart)
  • 6.5. A Fingerprint of a Soccer Player’s Effectiveness (Radar Chart)
  • 6.6. Foreigners Living in Milan (Bumpchart)
  • 6.7. A Treemap of Orchestra Hierarchies
• 7. Research Step by Step
  • 7.1. How do we get to our research question?
  • 7.2. Finding some early sources
  • 7.3. Traditional Library Research, Step by Step
  • 7.4. Noticing Trends
  • 7.5. Getting Quantitative
• 8. Cognitive Errors and Selection Effects
  • 8.1. Cognitive Biases
    • 8.1.1. Selection Effects and the “Hidden Prior”
    • 8.1.2. Causation Versus Correlation
    • 8.1.3. Confirmation Biases
  • 8.2. What kind of mind set avoids these cognitive problems?
  • 8.3. Implicit Bias and Underrepresentation
    • 8.3.1. Implicit Bias
    • 8.3.2. Underrepresented and Underserved Groups
  • 8.4. Groupthink and red team exercises
• 9. Workshop skills
  • 9.1. The Ballad of Jack Thompson
  • 9.2. Keeping Research Tidy
    • 9.2.1. Citations
    • 9.2.2. Source Management Software
    • 9.2.3. Adding Sources
    • 9.2.4. Annotating Sources
  • 9.3. Time management
    • 9.3.1. Planners
    • 9.3.2. Knowing Your Work Style
  • 9.4. Communication and Collaboration
    • 9.4.1. Collaboration with peers
    • 9.4.2. Collaboration with mentors
    • 9.4.3. Effective use of email
    • 9.4.4. A good start is not enough
• 10. Products - written and verbal
  • 10.1. The Written
    • 10.1.1. The thing being shown
    • 10.1.2. Legal writing
    • 10.1.3. Nominalizations and “zombie nouns”
    • 10.1.4. Academic/business writing
  • 10.2. The Presented
    • 10.2.1. Problems to Overcome
    • 10.2.2. The Solution - a reasonable baseline
• 11. Academic awareness
  • 11.1. What is an academic field
  • 11.2. A tour of academic fields
  • 11.3. Well-informed career choices
• 12. Relevant Ethics
  • 12.1. The Big Picture of What We Do
  • 12.2. Respect and Codes of Conduct
    • 12.2.1. Workplace Behavior
  • 12.3. Plagiarism: Don’t Do It.
    • 12.3.1. What is Plagiarism?
    • 12.3.2. Putting Yourself in Their Shoes
    • 12.3.3. Scary Campfire Stories
    • 12.3.4. The Beauty of Citations: Sharing is Caring
  • 12.4. Established Ethical Guidelines in Certain Fields
• 13. The research project cemetary
• 14. Thought-provoking books and media
  • 14.1. Books: non-fiction
    • 14.1.1. History
    • 14.1.2. Politics
    • 14.1.3. Art
    • 14.1.4. Miscellaneous
    • 14.1.5. Computer science, AI, math
    • 14.1.6. Psychology
    • 14.1.7. Writing and literary criticism
    • 14.1.8. Philosophy
    • 14.1.9. Medicine and epidemiology
  • 14.2. Articles, article collections, blogs
  • 14.3. Audio/visual
    • 14.3.1. Lectures
    • 14.3.2. Interviews
    • 14.3.3. Podcasts
  • 14.4. … And what about fiction?
• 15. Research examples
  • 15.1. Things to have handy before you do research
  • 15.2. Worked examples
    • 15.2.1. Taxation, disposable income, quality of life
    • 15.2.2. The King Henry I Eclipse
    • 15.2.3. The fivethirtyeight data sets and examples
    • 15.2.4. President Biden’s comment on the Marijuana suspension of Richardson
  • 15.3. Partially worked examples
    • 15.3.1. Poverty, scarcity mindset, efefective altruism, moral ambition
  • 15.4. Unworked examples
    • 15.4.1. Malcolm Caldwell and Pol Pot
    • 15.4.2. Julia Galef’s hidden prior experiment
    • 15.4.3. Instant messaging and privacy
    • 15.4.4. Texas mask mandate mystery
    • 15.4.5. Seychelles Islands vaccine mystery
• 16. Sample syllabuses
  • 16.1. Bruno and Galassi 2025
    • 16.1.1. Week 1, 2025
    • 16.1.2. Week 2, 2025
    • 16.1.3. Week 2 - Tuesday colloqium - Amanda Ziemann
    • 16.1.4. Week 2 - Wednesday tutorial - Andrea Bruno
    • 16.1.5. Week 2 - Wednesday career path talk - Ariana Taylor
    • 16.1.6. Week 2 - Thursday tutorial - Mark Galassi
    • 16.1.7. Week 2 - Thursday colloqium - Joanne Mudge
    • 16.1.8. Week 3, 2025
  • 16.2. Hyperaccelerated Research Skills Academy 2025
    • 16.2.1. Tutorial 1 - Nuance and the Avoidance of Platitudes
    • 16.2.2. Tutorial 2 - Giving Talks
    • 16.2.3. Tutorial 3 - Written Communication
    • 16.2.4. Tutorial 4 - Work together on examples
  • 16.3. Galassi and Reeder 2024
    • 16.3.1. Week 1
    • 16.3.2. Week 2
  • 16.4. Higginson, Kerelis, Galassi 2023
    • 16.4.1. Lesson 1: The History of Critical Thinking
    • 16.4.2. Lesson 2: Keeping Research Tidy
    • 16.4.3. Lesson 3: Good Writing: What it is, How to recognize it, and How to do it
    • 16.4.4. Lesson 4: Progress
    • 16.4.5. Lesson 5: Measurement, Method, and Parsimony
    • 16.4.6. Lesson 6: Cultivating Curiosity
    • 16.4.7. Lesson 7: Epistemology, Hermeneutics, and Pragmatism
    • 16.4.8. Lesson 8: Introduction to Absurdism
    • 16.4.9. Lesson 9: Energy and Thermodynamics!!
    • 16.4.10. Lesson 10: Poetry and the space between life and death
    • 16.4.11. Lesson 11: The Surrealist Art Movement and Imagination
    • 16.4.12. Lesson 12: Gender and Queer Theory Primer
• 17. Appendix: List of articles for discussion
  • 17.1. Media bias diagram
  • 17.2. Pushing at an open door
  • 17.3. Selection effects
  • 17.4. Taxation policy
  • 17.5. Rennaissance Capital
• 18. Appendix: How to build this book
  • 18.1. Installing the Sphinx tools
  • 18.2. Building the book

bibliography.rst

Indices and tables

• Index

• Module Index

• Search Page

Bibliography

[1]

Screening for autism spectrum disorder. URL: https://www.cdc.gov/autism/diagnosis/index.html.

[2]

Routine measles, mumps, and rubella vaccination. Jan 2021. URL: https://www.cdc.gov/vaccines/vpd/mmr/hcp/recommendations.html.

[3]

M.R. Banaji and A.G. Greenwald. Blindspot: Hidden Biases of Good People. Bantam Books, 2016. ISBN 9780345528438. URL: https://books.google.com/books?id=z6WvDAAAQBAJ.

[4]

John J Berger. Climate Myths: The Campaign against Climate Science. Northbrae books, 2013.

[5]

Yudhijit Bhattacharjee. The mind of a con man. The New York Times, 2013. URL: https://www.nytimes.com/2013/04/28/magazine/diederik-stapels-audacious-academic-fraud.html.

[6]

Jane Brody. Inquiry at Cancer Center Finds Fraud in Research. The New York Times, 1974. URL: https://www.nytimes.com/1974/05/25/archives/article-5-no-title-fraud-is-charged-at-cancer-center-premature.html.

[7]

Brian Deer. Andrew wakefield: the fraud investigation. URL: https://briandeer.com/mmr/lancet-summary.htm.

[8]

Diane D. Edwards Erika W. Davies. Case study 1, William Summerlin - Promoting Responsible Scientific Research - NCBI Bookshelf — ncbi.nlm.nih.gov. URL: \url{https://www.ncbi.nlm.nih.gov/books/NBK519803/box/box001/?report=objectonly}.

[9]

Maggie Farley. Showdown at global warming summit. Los Angeles Times, 1997. URL: https://web.archive.org/web/20160118234039/http://articles.latimes.com/1997/dec/07/news/mn-61743/2.

[10]

Julia Galef. The Scout Mindset: Why Some People See Things Clearly and Others Don't. Penguin, 2021.

[11]

Siegfried S Hecker. Retargeting the weapons laboratories. Issues in Science and Technology, 10(3):44–51, 1994.

[12]

Natalie Kita and Julie Scott. Skin grafts treat burns, wounds, and are used for reconstruction. 2024. URL: https://www.verywellhealth.com/skin-grafts-in-reconstructive-surgery-2710284.

[13]

Andy L. The Society of Homeopaths, Richard Barr and MMR &#x2013; The Quackometer Blog — quackometer.net. URL: \url{https://www.quackometer.net/blog/2010/10/the-society-of-homeopaths-richard-barr-and-mmr.html#google_vignette}.

[14]

Andreas Lundh, Joel Lexchin, Barbara Mintzes, Jeppe B Schroll, and Lisa Bero. Industry sponsorship and research outcome: systematic review with meta-analysis. Intensive care medicine, 44(10):1603–1612, 2018. URL: https://link.springer.com/article/10.1007/s00134-018-5293-7.

[15]

Noel Maurer and Carlos Yu. What roosevelt took: the economic impact of the panama canal, 1903-37. Harvard Business School, Working papers, pages 06–041, 2006.

[16]

Michele Mauri, Tommaso Elli, Giorgio Caviglia, Giorgio Uboldi, and Matteo Azzi. Rawgraphs: a visualisation platform to create open outputs. In Proceedings of the 12th biannual conference on Italian SIGCHI chapter, 1–5. 2017.

[17]

Alison McCook, Ivan Oransky, Shannon Palus, Ross Keith, and Adam Marcus. Diederik stapel. Sep 2016. URL: https://retractionwatch.com/category/by-author/diederik-stapel/.

[18]

Naomi Oreskes and Erik M Conway. The big myth: How American business taught us to loathe government and love the free market. Bloomsbury Publishing USA, 2023.

[19]

Frederick Rudolph. The american liberty league, 1934-1940. The American Historical Review, 56(1):19–33, 1950.

[20]

Diederik A Stapel and Siegwart Lindenberg. Coping with chaos: how disordered contexts promote stereotyping and discrimination. Science, 332(6026):251–253, 2011. URL: https://www.science.org/doi/abs/10.1126/science.1201068.

[21]

Albert Kleckner Steigerwalt Jr. The National Association of Manufacturers: organization and policies, 1895-1914. University of Michigan, 1952.

[22]

William T Summerlin. Allogeneic transplantation of organ cultures of adult human skin. Clinical Immunology and Immunopathology, 1(3):372–384, 1973. URL: https://www.sciencedirect.com/science/article/abs/pii/0090122973900548.

[23]

tomislavhorvat. URL: https://tomislavhorvat.com/mission-statement-examples/.

[24]

Andrew J Wakefield, Simon H Murch, Andrew Anthony, John Linnell, David M Casson, Mohsin Malik, Mark Berelowitz, Amar P Dhillon, Michael A Thomson, Peter Harvey, and others. Retracted: ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. The lancet, 351(9103):637–641, 1998. URL: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(97)11096-0/fulltext.

[25]

United States Environmental Protection Agency. Facts and figures about materials waste adn recycling. 2024. URL: https://www.epa.gov/facts-and-figures-about-materials-waste-and-recycling/plastics-material-specific-data.

Copyright (C)  2022-2025  Mark Galassi, Andrea Bruno, Karina
Higginson, Juno Kerelis

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