Career Development Course for Post-docs
February 2, 2009
Critical Reading and Evaluating
Scientific & Medical Literature
Fred A. Pereira, Ph.D.
Huffington Center on Aging
Bobby R. Alford Department of Otolaryngology–Head and Neck Surgery,
Department of Molecular and Cellular Biology,
Co-Director, Graduate Program in Cell and Molecular Biology
Bioengineering Department (Rice University)
Communication
• Critical Reading and Evaluating the
Scientific and Medical Literature
• Oral Presentations Dr. Gayle Slaughter
• Posters Dr. Gayle Slaughter
• Scientific Writing I-Critical writing and
manuscript preparation Dr. Susan Marriott
• Scientific Writing II-Reviewers, revisions,
and responding to critiques Dr. Susan Marriott
The Scientific & Medical Literature
• Scientific Method
• Philosophy
• Ethics
Reading/Strategies
• Sources
• The parts & Reader
Expectations
• Strategies
–
–
–
–
Skimming
Scanning
Concept mapping
Cornell notes
Evaluating
•
•
•
•
Pitfalls / Jargon
Questions
Significance
Scientific Arguments
– Valid/Persuasive
– Statistics
– Other Biases
The Scientific Method
Ask a Question
Do Background Research
Construct Hypotheses
Rethink Hypothesis
Test with Experiments
Analyze Results / Draw Conclusions
Hypothesis is True
Hypothesis is False
or Partially True
Report /Publish Results
Philosophy of Scientific Inquiry
• A quest for knowledge and truths
• The scientific literature is a discussion
– Policed by peer review
– Textbooks, Lectures, Seminars have truths (at the time of writing!)
– Reviews, Mini-reviews and Perspectives report truths (at the time of
writing!) – Classical articles
Ethics: Definition of Research Misconduct
Research misconduct means fabrication, falsification, or plagiarism in
proposing, performing, or reviewing research, or in reporting research results.
(a) Fabrication is making up data or results and recording or reporting them.
(b) Falsification is manipulating research materials, equipment, or processes, or
changing or omitting data or results such that the research is not accurately
represented in the research record.
(c) Plagiarism is the appropriation of another person's ideas, processes, results,
or words without giving appropriate credit.
(d) Research misconduct does not include honest error or differences of opinion.
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http://ori.hhs.gov/
Houston Chronicle
October 30, 2008
• TSU professor accused of plagiarism
• Chu's proposal is an almost verbatim copy of Miller's, according to copies of
the proposals provided to the Houston Chronicle.
• Miller's [2003] grant request begins, "We propose a two-year program to
develop a prototype system designed to detect biological warfare agents
(BWAs) by probing their linear and nonlinear dielectric properties."
• Chu's begins: "We propose a three-year program to develop a prototype
system designed to detect biological warfare agents (BWAs) by probing their
linear and nonlinear dielectric properties.”
• His proposal did not mention Miller or Miller's work.
Reading: Sources for Literature
• PubMed – My NCBI – Habits
– http://www.ncbi.nlm.nih.gov/sites/entrez
– http://www.ncbi.nlm.nih.gov/sites/gquery
• HighWire Press
– http://highwire.stanford.edu
• MDAnderson Cancer Center
–
http://www3.mdanderson.org/library/online-journals/jrnls.html
• HAM/TMC (are you Registered!)
– http://ca3cx5qj7w.search.serialssolutions.com/
• Rice U.- Fondren Library
– http://ps4ps6lm2r.search.serialssolutions.com/
• Faculty of 1000
– http://www.f1000biology.com/browse/
• Science Podcasts-Nature, Science, PBS
• Faculty/Experts in field/Peers
Strategies: Parts of a scientific article:
Title
Authorship
Abstract
Introduction
Methods
Results
Discussion
References
Title/Running title
Authorship
Background
Question
Experimental Approach
Results
Answer
Significance
Modified from S. Marriott
Science 30 January 2009: Vol. 323. no. 5914, pp. 630 - 633 DOI:
10.1126/science.1166175
Survival from Hypoxia in C. elegans by Inactivation of
Aminoacyl-tRNA Synthetases
Background
Question
Approach
Results
Answer
Lori L. Anderson,1 Xianrong Mao,1 Barbara A. Scott,1 C. Michael
Crowder1,2*
Hypoxia is important in a wide range of biological processes, such
as animal hibernation and cell survival, and is particularly
relevant in many diseases. The sensitivity of cells and
organisms to hypoxic injury varies widely, but the molecular
basis for this variation is incompletely understood. Using
forward genetic screens in Caenorhabditis elegans, we isolated
a hypoxia-resistant reduction-of-function mutant of rrt-1 that
encodes an arginyl–transfer RNA (tRNA) synthetase, an
enzyme essential for protein translation. Knockdown of rrt-1,
and of most other genes encoding aminoacyl-tRNA
synthetases, rescued animals from hypoxia-induced death, and
the level of hypoxia resistance was inversely correlated with
translation rate. The unfolded protein response was induced by
hypoxia and was required for the hypoxia resistance of the
reduction-of-function mutant of rrt-1. Thus, translational
suppression produces hypoxia resistance, in part by reducing
unfolded protein toxicity.
Introduction - Background of Study
Topic Position
Purpose: To help the reader understand
and interpret the contents of the paper.
Content: Any background information and
motivations essential to understand the
specific study should be stated here.
Supporting
Sentences
Terms: Uncommon or novel terms to the
general scientific community are defined,
and prior knowledge / information are cited
here.
Stress Position
Modified from S. Marriott
Results
For studies in which the results of one experiment determine what the next
experiment will be, the story consists of a repeated four-part pattern:
• Subheading
• Question/Topic position
• Experiments
• Results
• Answer/Stress position
Modified from S. Marriott
Results Continued
• Transition/Background
• Question/ Topic position
• Experiments
• Results
• Answer
• Interpretation/Transition
• Stress position
S. Marriott
www.biosciencewriters.com
The Discussion
A Discussion has three parts:
The beginning states the answer to the question and provides evidence to support the answer.
Does not begin with a summary of the results.
Does not begin by repeating the Introduction or writing a new Introduction.
The middle explains the answer, thus indicating how the answer fits in with previous work.
The end states recommendations, applications, implications, or speculations, thus
indicating the importance of the answer.
Generalities:
The discussion includes alternative explanations of results.
Topic sentences tell the overall story of the study – found at the beginning of every
paragraph, either alone or in combination with transition words, phrases, or clauses,
repeated key terms, and other techniques of continuity.
The answer should be clearly identifiable at both the beginning and the end of a Discussion.
In each paragraph, supporting sentences should be organized to support the topic sentence.
Does / should not include tangential topics.
Modified from S. Marriott
Reader Expectations
•
Every unit of text, no matter the size, serves a single function or
makes a single point.
•
Topic position: Old information - the information that begins a
sentence establishes a perspective for viewing the sentence as a
unit.
–
•
Provides linkage (looking backward) and context (looking forward).
Supporting sentences: knowledge to support the topic position.
–
Subject - Verb Separation: Readers expect a grammatical subject to be followed
immediately by the verb.
–
Anything of length that intervenes between subject and verb is read as an interruption, and
therefore as something of lesser importance.
•
Stress position: New information - saved the best for last.
–
Readers naturally emphasize the material that arrives at the end of a sentence.
–
Commas and semicolons are used to create units of thought in long sentences.
Modified from George D. Gopen and Judith A. Swan, Scientific American
1990
“If the reader is to grasp what the writer means,
the writer must understand what the reader needs”
• Readers do not simply read; they interpret. All sentences are
infinitely interpretable, given an infinite number of interpreters.
• As the complexity of the context increases moderately, the
possibility of misinterpretation or non-interpretation increases
dramatically.
• Being conscious of these locations, we can better control the
degrees of recognition and emphasis a reader will give to the
various pieces of information being presented.
George D. Gopen and Judith A. Swan, Scientific American 1990
Strategies – Skimming an article
• Title (Not always true/justified – quality of journal)
• ISI citation index: Journal Citation Reports & Citation Index
• http://admin-apps.isiknowledge.com/JCR/JCR?SID=S266COIkpLd1pCKFmJd
• http://apps.isiknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSear
ch&SID=S266COIkpLd1pCKFmJd&preferencesSaved=
• Abstract (Not always informative/justified – journal type)
• Figures/Legends (Results)
• Discussion
• Introduction
• Methods
Strategies – Scanning for Information
1. What was the major purpose of the study? (Intro)
2. What source/organism(s) was studied? (Intro/Methods)
– Is it the same one you would study?
3. What variables were studied? (Intro/Results/Figures)
– Are they the same ones you would use?
4. Did any conditions differ between other studies and this one?
(Methods/Results)
5. What were the major results of the study? (Results/Figures)
– Pay special attention to figures and the author’s description of them.
6. Determine what the author considers the major contribution
of the study. (Abstract/Discussion)
Strategies – Concept Mapping
• to generate ideas (brain storming, etc.)
• to design a complex structure (long texts, hypermedia, large web
sites, etc.)
• to communicate complex ideas
• to aid learning by explicitly integrating new and old knowledge
• to assess understanding or diagnose misunderstanding
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http://users.edte.utwente.nl/lanzing/cm_home.htm
Strategies: Cornell Notes
1/4
3/4
•write
questions
•notes
•draw graphs
•record
important
QuickTime™
and a info.
•keywords
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•Summary
•conclusions
• Promotes active learning – Each
major point on the right ought to
have a question or keyword on the
left.
• Left column: write questions and
keywords that relate to the
information recorded on the right
• Right column: make notes, draw
graphs and record the important
information from the lecture or
reading
Evaluation – Pitfalls
Some literature is better than others!
Some authors are smarter than others, some are right more often – sometimes
these are not the same people – Opinion Leaders
It is an art of storytelling – most often not chronological.
Some articles are driven by special interests (tenure/promotion/business).
Data are plentiful but truth is elusive!
Be skeptical but not cynical.
Demand excellence – be critical but be fair.
Find balance between believing everything and believing nothing.
Intimidation
Scientific Jargon – Get a review
Use medical dictionary – e.g. http://www.thefreedictionary.com/
Consult technical literature – e.g.
http://www.ambion.com/techlib/resources/RNAi/index.html
Scientific Jargon:
the Mysterious Language of Science and Medicine

It has long been known….. I didn’t look up the original reference.

A definite trend is evident…..These data are practically meaningless.

While it has not been possible to provide definite answers to the questions….. An
unsuccessful experiment, but I still hope to get it published.

Three of the samples were chosen for a detailed study….. The other results didn't
make any sense!

Typical results are shown….. This is the prettiest graph I could muster.

These results will be in a subsequent report….. I might get around to this sometime,
if pushed / funded.

The most reliable results are obtained by Jones….. He was my graduate student; his
Thesis depended on this.

Correct within an order of magnitude ... Wrong!
Modified from Dyrk Schingman, Oregon State
What is a logical argument?
An argument is a set of statements consisting of premises and a
conclusion; normally the premises give evidence for the conclusion.
Premise: If you overslept, you’ll be late. You aren’t late. Therefore:
1.
You did oversleep.
2.
You didn’t oversleep.
3.
You’re late.
4.
None of these follows.
Premise: If you overslept, you’ll be late. You didn’t oversleep. Therefore:
1.
You’re late.
2.
You aren’t late.
3.
You did oversleep.
4.
None of these follows.
Modified from Introduction to Logic,
Harry Gensler, 2001
Valid and Sound Arguments
• An argument is valid if it would be contradictory to have the premises all true
and conclusion false.
• An argument is sound if it is valid and has every premise true.
Valid and true premises!
If you’re reading this, you aren’t illiterate.
You’re reading this.
You aren’t illiterate.
First premise false!
All scientists are millionaires.
Joe is a scientist.
 Joe is a millionaire.
Conclusion doesn’t follow!
All millionaires eat well.
Joe eats well.
 Joe is a millionaire.
When we try to prove a conclusion, we try to give sound arguments. We must
make sure of two things: our premises are true, and our conclusion follows from
our premises.
Modified from Introduction to Logic,
Harry Gensler, 2001
Evaluation – Questions asked, answered and if a persuasive
scientific argument is made – Significance
•
Defined the specific problem of research.
–
Cited reviews and articles in high impact journals.
•
Indicated the importance and the hypothesis.
•
Placed the problem in the intellectual context of field.
•
Gave reasons and detailed the experimental methods.
•
Detailed accomplished and expected results (Statistics).
•
Clearly identified the potential unique contribution (Significance).
•
Suggested possible theoretical or practical relevance of findings (Biases vs
Implications).
•
Did they answer the question? Was the right question asked?
The Scientific & Medical Literature
• Scientific Method
• Philosophy
• Ethics
Reading/Strategies
• Sources
• The parts & Reader
Expectations
• Strategies
–
–
–
–
Skimming
Scanning
Concept mapping
Cornell notes
Evaluating
•
•
•
•
Pitfalls / Jargon
Questions
Significance
Scientific Arguments
– Valid/Persuasive
– Statistics
– Other Biases