Published on February 25, 2014
How to read papers A biologist’s perspective Holly H. Ganz, UC Davis
Journals publishing papers in microbial phylogenomics • Considerations that authors make when choosing where to publish • Impact Factor • Audience • open access
Learn to read critically, so you don’t just judge a book by its cover • Don’t just assume that a paper in Science is correct. • Important to learn how to judge each paper on its own merits. • And to identify what else there is to be done. What are the unanswered questions? • This is a lot of what we learn how to do in graduate school.
Article structure • What is the format for scientiﬁc papers?
Article structure • Title • Authors and Afﬁliations • Abstract • (Author summary) • Introduction • Materials and Methods • Results • Discussion • Literature Cited • Figures and Tables • Supplementary Files
Start by reading the introduction, not the abstract • The abstract contains the authors’ summary and overall conclusions of their study. • When I write a paper, I write the abstract last. • Read it last. x
As you read the introduction, ask: What big question is being asked here?
As you read the introduction, ask: What question is being asked here? Why should we care? What is the ecology of buildings? Do buildings affect human health through the microbiome?
What is the ecology of buildings? ! Environmental selection (such as …) Dispersal of microbes from a source (such as …) Other factors (such as …)
Effects of building design on the indoor microbiome ! function, form and organization
What work has been done in this ﬁeld already? What were the limitations of prior work? What needs to be done next?
How design choices inﬂuence the biogeography of indoor bacterial communities ! What speciﬁc question(s) are the authors trying to answer? Were they testing a null hypothesis? What is it? What are they going to do? Why?
The methods section • How did they attempt to answer the speciﬁc questions? • What did they do? • How/where did they collect samples? How many? • How samples stored, DNA extracted, PCR methods, sample processing, data analysis • Be sure to read supplementary info
Methods! Where? The study site
The results section • Try to summarize the results • Focus on ﬁgures and tables • Be sure to read any supplementary results • Do they provide statistical analyses, signiﬁcance values? Do graphs have error bars? Pay attention to sample sizes. • Do the results answer the speciﬁc questions? • What do you think the results mean?
The discussion section • Do the authors refer to their questions/hypotheses? • How do they interpret their results? • Can you think of any alternative interpretations? • Do the authors identify weaknesses or limitations of their study? What do you see as limitations? • What do the authors propose to do next? • What would you do next?
Finish by reading the abstract • The abstract contains the authors’ summary and overall conclusions of their study. • Does the abstract match what was said in the paper? • Does it ﬁt with your interpretation of their results? • Can also read comments (if any) from other people in the ﬁeld.
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