How to read a scientific research paper

First, skim a paper quickly to get an overview of the purpose, approach, and conclusions.

Next, read the paper carefully. Below is a list of questions that will be useful in evaluating primary literature:

Introduction: summarizes the background for the current study, and introduces the purpose of the current study.

• What is the overall purpose of the research?
• What is the hypothesis of the paper and the ways this will be tested?
• How does the research fit into the context of its field? Is this work attempting to settle a controversy? show the validity of a new technique? open up a new field of inquiry?
• Do you agree that this is an important research question? Do you agree with the authors’ rationale for studying the question in this way?

Methods: provide details of the experimental design or sampling approach, laboratory methods, and data analysis. You should try to get a clear picture of what was done at each step. What was actually measured? If necessary, make an outline or diagram of the procedures. Take notes about any questions you may have, and bring them to the discussion.

• Were the measurements or methods appropriate for the questions this work was addressing?
• Researchers often need to use indicators or indirect approaches because they cannot measure something directly - this is particularly common in microbial ecology. Were the measures in this study appropriate for the variables that the researchers wanted to examine?
• Was the sample collection or experimental design adequate to give us a representative view of the community under study?

Results: figures and tables are the "meat" of research papers. Examine the figures carefully, and interpret the data for yourself. Do not just read the results and accept the authors' interpretation.

• Carefully assess the figures. What do you think each figure means? Do you agree with the authors' interpretation? Did they draw conclusions that are not supported by the data?
• What is the major finding presented in this paper?
• Were enough of the data presented so that you feel you can judge for yourself how the experiment turned out?
• Did you see patterns or trends in the data that the author did not mention? Were there problems that were not addressed?

Discussion: contains the conclusions that the author would like to draw from the data, and relates these conclusions to findings from other studies. This section will also discuss the importance of the results for the general field of study. You should be able to describe the conclusions in your own words.

• Consider what conclusions you would draw from the data. Do you agree with the conclusions that the authors presented?
• Are these conclusions over-generalized or appropriately careful?
• Are there other factors that could have influenced, or accounted for, the results?
• What are some unanswered questions in this area of research?
• What is the next step in this research? What further experiments would you recommend to continue the research or to answer remaining questions?

Reflection and criticism: It is useful to keep track of your questions as you go along, returning to see whether they have been answered. After you understand the article and can summarize it, then you can start to evaluate the importance of this work and the quality of the study.

A review article has been assigned with every primary literature article to provide some context for the microbial ecology study.

Discussion leaders will provide a primer related to each week's community ecology concept to allow you to evaluate each paper in a community ecology context. Consider the following questions:

• Is the microbial ecology literature a good example of the ecology concept under discussion?
• Are ecology concepts misused or applied incorrectly in the reading?
• How well does the ecology concept apply to microbial communities? Do microbes "play by the rules"?