Reading Scientific Papers
Dunn School of Pathology
Purposes of This Class
Learn some guidelines to help you assess:
Scientific content of a primary research article
Style of presentation
Encourage reflection on the way you currently read a paper
To change your habits to improve them
To read more efficiently and effectively
Levels of Engagement
A Typical Doctoral Thesis
~ 300 references
10 papers per month
Plus all those papers that don’t make it!
Why read in depth?
To check basis of your own project
Reliability of assumptions
Especially those critical to the logic of your design
Monitoring and comparing other approaches
Sensor for possibly being scooped
Assessing own lab’s approach
To study important claims in related fields
Technical or theoretical developments
To enable mature discussion with others
Develop your original viewpoint
For inspiration to write well
And what to avoid
The scientific literature
Primary research reports
News&Views, MiniReviews, Cutting Edge
What to Read? At what Level?
Test against purposes of reading
See Levels of Engagement
See Why Read in Depth
Use of Bibliographic tools
Treat big-name authors the same as little-name or no-name authors
Careful reading 1 – the question
What question is being asked?
How clearly stated?
Is it important?
Will it make an advance whichever answer is got?
Is it original?
What have others suggested as answers?
Careful reading 2 - design
How does study design address the Q?
Is it a direct or an indirect approach?
If methodology were not limiting, what would be the best way?
Is it compatible with what really happens biologically in the cell/ the animal/ the bug…
(“in vivo” versus “in plastico” versus “in silico”)
The Scientific Method
A formal set of rules for forming and testing hypotheses
Usually employed loosely and often unconsciously
Devise the good Q
For the unexpected as well as the anticipated
Create an explanatory model
That can be helpfully predictive
What is a Hypothesis?
From Greek – “Foundation, Base”
“Hypo” – not yet fully developed
“Thesis” – a placing
[what is a Hyperthesis??
Perhaps you could write one??]
An informed guess about the way a process might work
Needs logic, prior knowledge, insight, creativity
Testing a Hypothesis
It can be disproved, never proved (Popper)
Read “Pluto’s Republic”, Medawar, PB (1984)
“The Logic of Scientific Discovery” – Popper, KR (1977)
Must include controls
A Formal Theory
A system of statements and ideas that explains a group of related facts or phenomena
A set of interconnected hypotheses that
Have withstood rigorous exptl testing
Consistently resist scientists’ attempts to disprove them
Is no longer “half-baked”
Common Study Design Faults/Oversights
Seeks to confirm hypothesis by supplying an additional example
Uses absence of evidence as evidence of absence
Accepts correlation as causation
If mutant lacks a normal function, accepts that wild-type provides that function
Deletion approach should be complemented by test of adding-back wild-type
Careful Reading 3 - controls
Versions of the expt where everything is the same except for the single variable that is under test
“Negative”: omit/inactivate/vary test material
“Positive”: ensure assay system is working properly, so that lack of activity of test material is interpretable
“Restorative”: reconstitution of diminished/zero activity by re-supplying normal material
Careful Reading 4 - Reproducibility
Is it a big effect?
Do they quantify the variance associated with the observations?
Number of repetitions
May be statistically significant, but is the effect of marginal magnitude?
Do different figures in the paper show same effect?
Is the data selective?
Is M&M detailed enough to permit replication of expt?
By others “skilled in the art”?
Careful Reading 5 –
Resolution of the Question
Is the original Q answered?
What assumptions did the authors make?
Are these reasonable?
Are these reasonable?
Would you have made the same interpretation from those data?
What remains unanswered?
Are there interesting new Qs raised?
Techniques for careful reading 1
Get the gist, from Title and Abstract
Carefully read for, and Identify, the Question Q
Understand but do not accept what the authors consider the Answer to be
Use the Introduction only if necessary
It will be strongly biassed
Identify the key data Table/Figure that supplies the answer
Understand enough methodology to see how the data were obtained
Carefully read, for controls and reproducibility
Techniques for careful reading 2
Seek data that support, extend or qualify
Scrutinise other Figures or Tables
Throughout, make your own annotations
Probably on a printout/Xerox copy
Distinguish your own “Brain-On” ideas/comments (e.g. put “ME” in front of them) from notes on the authors’ text (“THEY”)
Do not merely use highlighter alone
Encourages “Brain-Off” technique
Techniques for careful reading 3
Compare your interpretation with the authors’
Carefully read for the Design
Carefully read for Conclusion
How far does it resolve the Q that was posed?
How far do you accept it?
Make your own interpretation
Minimise assumptions and dependence on other models or hypotheses – try to interpret it stand-alone
The healthy sceptic resists….
Get stuck in!
Skim, yes, but also Immerse sometimes
Be ready to sweat and fret as you interpret!
Then you must be doing the right thing
Reading and online materials
Victoria E McMillan, “Writing Papers in the Biological Sciences”. 2nd ed. Bedford Books, 1997.
Robert A Day, “How to Write and Publish a Scientific Paper” 5th ed. Oryx Press, 1998
Jan Pechenik and Bernard Lamb, “How to write about Biology”, Longman, 1994