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“If we knew what we were doing, it would not be called research, would it?” - Albert Einstein
“If we knew what we were doing, it would not be called research, would it?” - Albert Einstein
Source: Our World in Data. Link
If you are reading this: congratulations! You are lucky to have been born at the best time in history.
A few centuries ago scientific method was developed, but it has been in the last few decades that the full power of scientific knowledge has been unleashed for the benefit of mankind. A century ago, half of all children died before puberty. But not you, you are alive! Just like many of your classmates! So, congratulations on being born in the best time in history to live: the era of science! Of course, it is not a perfect era. The fact that we have quality information has brought a problem that we did not foresee, and that is that we not only live in the information era, but in the era of disinformation.
So, congratulations on wanting to contribute your time, skills, and gifts to make the world a better place. Here I have compiled some materials that I hope will help you and give you a perspective on the current scientific knowledge.
A perspective to keep in mind (click on the image)
A perspective to keep in mind (click on the image)
The Illustrated Guide to a Ph.D. Matt Might (http://matt.might.net/)
This work is licensed under the Creative Commons Attribution-NonCommercial 2.5 License.
“Science is a way of thinking much more than it is a body of knowledge.” ― Carl Sagan
Readings & Resources
Readings & Resources
General
General
Elemental knowledge
Elemental knowledge
The Demon-Haunted World: Science as a Candle in the Dark, Sagan C and Druyan A
The Basic Laws Of Human Stupidity, Carlo Cipolla
How our brain works
How our brain works
Mindset Revised And Updated: Changing The Way You think To Fulfil Your Potential, Dweck Carol
12 Cognitive Biases Explained Video and Critical thinking this
The real world
The real world
Factfulness, Ten Reasons We're Wrong About The World - And Why Things Are Better Than You Think, by Rosling
Enlightenment Now: The Case for Reason, Science, Humanism, and Progress, Steven Pinker
General
General
Dealing with data
Dealing with data
How to present data by Hans Rosling here and here and many more here
How to Make the World Add Up: Ten Rules for Thinking Differently About Numbers, Tim Hartford
The Art of Statistics, David Spiegelhalter
Advanced and Specific issues with Clinical Research
Advanced and Specific issues with Clinical Research
My educational philosophy
My educational philosophy
My research and educational philosophy
My research and educational philosophy
You discover things when you are learning
You never stop learning
The best work is work done
One should not get attached to knowledge, and should let it go without problems if there are new ones.
Is that an opinion or a fact?
The path to learning begins by recognizing that you don't know something.
The work-life balance issue is irrelevant. The important thing is to be happy.
What I expect from a doctoral student
What I expect from a doctoral student
These are the main attributes that I appreciate in a doctoral candidate:
Identifying gaps in knowledge
Willingness learn new things and to forgetting some things
Being curious
Sharing expertise
Ability to change the perspective on an issue
Ability to change opinion when considering new information
Key quotes
Key quotes
“The greatest enemy of knowledge is not ignorance, it is the illusion of knowledge.” ― Stephen Hawking.
"To play a wrong note is insignificant. To play without passion is inexcusable! ― L. Beethoven.
“Study hard what interests you the most in the most undisciplined, irreverent and original manner possible.” ― Richard Feynmann
"I have frequently been questioned, especially by women, of how I could reconcile family life with a scientific career. Well, it has not been easy." ― Marie Skłodowska Curie
Required readings and videos
Required readings and videos
General
General
Digital skills
Digital skills
How to use PubMed
Open science
Open science
Health Sciences
Health Sciences
Critical thinking Lecture, by Prof Michael Glick (video, 1hr)
Data Management
Data Management
Data Analysis
Data Analysis
Ellis SE, Leek JT. 2017. How to share data for collaboration. PeerJ Preprints 5:e3139v5
Broman KW, Woo KH. 2018. Data organization in spreadsheets. PeerJ Preprints 6:e3183v2
Data analysis: the basics, how to work with data, data visualization and tidy your data
Research study design
Research study design
A Very Short List of Common Pitfalls in Research Design, Data Analysis, and Reporting, Smeden
Basic of study design Grimes and Schulz, Levin
Waste research selected lectures here
How to read a paper, serie JADA here
Medical writing
Medical writing
Belleville G. Sit down and write your thesis! Practical and motivational tips for scientific writing. Can J Cardiol. 2019;35:945–7.
Suggested readings and videos
Suggested readings and videos
General
General
How to take notes: Cornell method
Digital skills
Digital skills
How to use PubMed
How to use GDocs here. It is particularly important not to add spaces between paragraphs. If you want to create a new page, add a page break. Learn how to use versions and add comments and actions items
Open science
Open science
Health Sciences
Health Sciences
Critical Thinking Lecture, by Prof Michael Glick (video, 1hr)
Data Management
Data Management
Data Analysis
Data Analysis
Ellis SE, Leek JT. 2017. How to share data for collaboration. PeerJ Preprints 5:e3139v5
Broman KW, Woo KH. 2018. Data organization in spreadsheets. PeerJ Preprints 6:e3183v2
Data analysis: the basics, how to work with data, data visualization and tidy your data
Best Practices for Data Visualisation + Visualization of Biomedical Data. Annual Review of Biomedical Data Science 1(1): 275–304.
Converting data into information
Converting data into information
Learning to use a statistical program: Ten simple rules for teaching yourself R
Books
Vu & Harrington 2020. Introductory statistics for the life and biomedical sciences (free book here, print version ISBN-10: 1943450129). Also recommended (optional):
Kirkwood, B., Sterne, J., 2003. Essential Medical Statistics ISBN-10: 0865428719
Norman GR, Streiner DL. Pdq Statistics 3rd Edition. ISBN-10: 1550092073
Wickham and Grolemund. R for Data Science free book https://r4ds.had.co.nz/ or ISBN-10: 1491910399
Research study design
Research study design
Basic of study design Grimes and Schulz, Levin
Waste research selected lectures here
How to read a paper, serie JADA here
The history of dental research: J Dent Res Centennial anniversary here
Book: Browner, W.S., Newman, T.B., Cummings, S.R., Grady, D.G., 2022. Designing Clinical Research. Lippincott Williams & Wilkins.
Book: Clinical: Schulz, K., Grimes, D.A., 2018. Essential concepts in clinical research: Randomised controlled trials and observational epidemiology, 2nd ed. Elsevier Health Sciences, London, England. (also available in The Lancet series)
Book: Fletcher, G.S., 2019. Clinical Epidemiology: The Essentials. Wolters Kluwer.
Book: Westreich, D., 2019. Epidemiology by Design: A Causal Approach to the Health Sciences. Oxford University Press.
Book: Moher, D 2014. Guidelines for Reporting Health Research: A User’s Manual. Wiley. (very recommended)
Medical writing
Medical writing
Belleville G. Sit down and write your thesis! Practical and motivational tips for scientific writing. Can J Cardiol. 2019;35:945–7.
Schwab S, Janiaud P, Dayan M, Amrhein V, Panczak R, Palagi PM, et al. Ten simple rules in good research practice for early career researchers. 2021.
Assel M, Sjoberg D, Elders A, Wang X, Huo D, Botchway A, et al. Guidelines for reporting of statistics for clinical research in urology. BJU Int. 2019;123:401–10.
Vickers AJ, Assel MJ, Sjoberg DD, Qin R, Zhao Z, Koyama T, et al. Guidelines for Reporting of Figures and Tables for Clinical Research in Urology. Eur Urol. 2020. https://doi.org/10.1016/j.eururo.2020.04.048.
Productivity tips
Productivity tips
Skills required for biomedical research
Skills required for biomedical research
Time management skills: ideally Time block as Reclaim and Carl Newport's Deep Work
How to search: Internet search beyond the first page of results and how to write good questions
Understand the nature of research in dentistry serie JADA
How to read the medical literature serie JADA
Scientific writing: Scientific writing, this and you should buy this book: Moher, D 2014. Guidelines for Reporting Health Research: A User’s Manual. Wiley and how to write a grant application. Also how to use to use Google Docs here (yes, again!)
Presentations Oral presentations skills
Basic Data Analisis: introductory guide for students and self-paced course
How to name things: video
Data Management: Research Data Management and Sharing, 10 mistakes in DM and more information in the RDM toolkit. Also from UNC a nice guide
Open science: course and paper 10 rules to implement open and reproducible research
Desirable
Desirable
Data science tools: tidyverse in R, Learn R and books about R. Suggested lecture: Lawlor et al. Ten simple rules for teaching yourself R..
Data visualization here, here. Books recommended Healy or Wilke. Choose the correct viz.
Statistics:
EXPLORATORY DATA ANALYSYS, plus inference via frequentist or bayesian approach
Understand regression since every analysis is some kind of linear modelling
Institutional information
Institutional information
"The excitement of learning separates youth from old age. As long as you're learning, you're not old." Rosalyn Yalow
Some quotes for inspiration
Some quotes for inspiration
"I was taught that the way of progress was neither swift nor easy." ― Marie Curie, '
"There are two possible outcomes: if the result confirms the hypothesis, then you've made a measurement. If the result is contrary to the hypothesis, then you've made a discovery." ― E. Fermi (1901 - 1954)
“An experiment is a question which science poses to Nature, and a measurement is the recording of Nature’s answer.” ― Max Planck
“What we know is a drop, what we don’t know is an ocean.” ― Isaac Newton
“In questions of science, the authority of a thousand is not worth the humble reasoning of a single individual.” ― Galileo Galilei
“The greatest enemy of knowledge is not ignorance, it is the illusion of knowledge.” ― Stephen Hawking
“What I love about science is that as you learn, you don’t really get answers. You just get better questions.” ― John Green
“The scientist is not a person who gives the right answers, he’s one who asks the right questions.” ― Claude Levi-Strauss
“Science is what we understand well enough to explain to a computer; art is everything else.” ― Donald E. Knuth
"If you know you are on the right track, if you have this inner knowledge, then nobody can turn you off... no matter what they say." ― Barbara McClintock
Summary
Summary
The illiterate of the future are not those who can't read or write but those who cannot learn, unlearn, and relearn
Alvin Toffler
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