How to Read Primary Literature

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BSEN 416/816		Fall 2014
How to Read Primary Literature Articles
The main purpose of a primary literature article (aka scientific article, research article, journal article, scientific paper, research paper…) is to report new results, usually experimental, and to relate these results to previous knowledge in the field. Papers are one of the most important ways that scientists communicate with one another.
Before reading a paper, you should understand the standard format of an article and what information can be found in each section. Typically, a research article will begin with a Title, followed by a list of Authors and their Affiliations. The main body of the article contains an Abstract, Introduction, Methods, Results, Discussion, Acknowledgements, and References. Sometimes the sections may have slightly different names or be combined (e.g. Materials and Methods instead of Methods; Results and Discussion combined, etc). Also, the Introduction may be called Background, or given no subheading title. Each section within a paper serves a specific purpose:
ABSTRACT: Summary of the key points of the paper, including the purpose of the study (why was the research done?), hypothesis, methods, results and discussion (why are results important?). 
INTRODUCTION: Presents the background knowledge necessary for the reader to understand why the findings of the paper are an advance on the knowledge in the field. Typically, the Introduction surveys relevant background and then focuses more specifically on a particular aspect (context of study), usually describing a finding or set of findings that led directly to the work described in the paper. If the authors are testing a hypothesis, the source of that hypothesis is spelled out, findings are given with which it is consistent, and one or more predictions are given. In many papers, one or several major conclusions of the paper are presented at the end of this section, so that the reader knows the major answers to the questions just posed. 
METHODS: Describes the materials used in the experiments and the methods by which the experiments were carried out. In principle, this description should be detailed enough to allow other researchers to replicate the work. In practice, these descriptions are often highly compressed, and they often refer back to previous papers by the authors.
RESULTS: Data is summarized in this section, and relationships among variables and/or differences among groups are reported. Typically, data are presented in the form of images, figures and tables, all with legends to give details of the particular experiment or experiments shown there. 
DISCUSSION: Data in the paper are interpreted in narrative form and findings of the paper are related to other findings in the field. This serves to show how the findings contribute to knowledge, or correct the errors of previous work. 
ACKNOWLEDGEMENTS: Various contributions of other workers are recognized, as well as funding sources and conflicts of interest.
REFERENCES: Listing of the sources cited in the article such as books and papers. 
Most articles follow the above format, but there are exceptions. As mentioned above, occasionally the Results and Discussion are combined. In some journals, the Materials and Methods follow the Discussion. The formats for two widely-read journals, Science and Nature, differ markedly from the above outline. In both journals, there are no discrete sections, except for a short abstract and a reference list. In Science, the abstract is self-contained; in Nature, the abstract also serves as a brief introduction to the paper. Experimental details are usually given either in endnotes (for Science) or Figure and Table legends and a short Methods section (in Nature). In addition, an increasingly common practice is to put a substantial fraction of the less-important material, and much of the methodology, into Supplemental Data that can only be accessed online.
Now that you are familiar with the general format of a scientific paper, you are ready to read one. The worst way to assimilate a research paper is to read it word for word, first to last page, as if it were a textbook. This approach is a waste of time, because 1) perhaps as few as 1 in 4 articles that find their way into your hands should be committed to your brain, and 2) is deadly boring. Before reading one word of an article, ask yourself: What am I looking for in this article? Knowing what I do about the subject, what gaps need to be filled, what knowledge needs to be expanded, and what controversial points need to be corroborated? Generate expectations of a journal article before you read it. This will help your analysis of the work in front of you, plus keep you more interested in the material. With that in mind, follow these steps:
Read and digest the title. It should summarize the article and help you to clarify your expectations of the paper.
Read the authors' names. Where and with whom are they working? What is their expertise? Names may mean little at first, but as you become familiar with a scientific subject or topic you will recognize “key players” in the field and determine those individuals with whom you agree and those whom you question. Look in particular at the first and last authors.
Read the abstract carefully and try to understand it (though it may be the densest prose you will ever encounter). Abstracts are as difficult to read as they are to write, because an entire publication must be summarized in only about 200 words. Never rely on an abstract solely to draw conclusions about the paper or cite an article after having read only the abstract!
Skim the paper quickly and study the figures, illustrations, and tables, including the legends. You may need to consult the Methods and Results section to clarify figures and understand the experimental design. 
Read the Introduction to understand the field and past work, as well as where this current paper "fits into the puzzle". You should be able to determine the authors’ objectives and hypothesis (typically last paragraph of the Introduction). If you are very familiar with the field, the Introduction can be skimmed or even skipped.
Read the Results section. The logical flow of most papers goes straight from the Introduction to Results; accordingly, the paper should be read in that way as well, skipping Materials and Methods and referring back to this section as needed to clarify what was actually done. A reader familiar with the field who is interested in a particular point given in the Abstract often skips directly to the relevant section of the Results, and from there to the Discussion for interpretation of the findings. 
Now read the Discussion. This is perhaps the most important section, because it is here that the results are explained. The authors should (at least try to) explain "why" they saw what they saw and how that fits with body of knowledge in the field. However, be critical when you read the discussion, as they are often littered with unsubstantiated speculation, timidity, over- and understatement. It is the responsibility of the reader (you) to interpret the data, thus one could argue that the Results section is actually more important.
Finally, read the whole paper, first page to last page. Reread for the greatest comprehension. 
Evaluate the paper. Once you understand the paper and can summarize it, you should be able to both criticize and praise several points of the paper. You should be able to reach your own conclusions, as well as determine the questions and conclusions that the authors address, and critically assess whether their evidence actually supports their conclusions. 
Adapted from:
Franzoi, S.L. and Ratlif-Crain, J. (2003). Guide to reading research articles. In Instructor's manual to accompany social psychology. 3rd ed. (pp.29-30).  Boston: McGraw-Hill. 
Little, J.W. and Parker, R. (2007). How to read a scientificpaper. www.biochem.arizona.edu/classes.bioc568/bioc568.htm. University of Arizona.
 
ten tips to guide reading of the primary literature:
Focus on methods and results. Try not to be influenced by the way the study is presented, but rather focus your analysis on the experimental design, techniques, and data. 
Be a skeptic. Ask yourself how strongly the authors' interpretations and conclusions are supported by the evidence. 
Be fair. Scientific research is difficult, and scientists operate under many constraints. Don't expect studies to be perfect. 
Read non-linearly. Exploit the format of research articles to quickly access the information you need. Don't feel compelled to read every line start to finish. Skim the paper to understand its overall approach. Refer to previous sections as necessary. 
Consider the big picture. Assess where the study fits into the cycle of science, and how it relates to previous research. 
Consult other sources. Writers of research articles assume their audience has basic knowledge of the area. Consult secondary sources to get the needed background. 
Take your time. Research articles condense entire studies into a few printed pages. It probably took the authors years to conceive, perform, and publish their work. Be patient and persistent when reading articles. 
Accept uncertainty. Research articles deal with emerging knowledge and controversial issues. Don't expect to find absolute answers to every question. Each paper is a step in an ongoing process. 
Expect to be challenged. If you're not an expert in an area, there might be aspects of a paper you can't understand fully. That's OK, you can still learn from those parts of a paper that you can comprehend. 
Relax and enjoy. Perhaps this is the hardest advice to follow, especially when you're confronted with a complicated paper. But try to approach an article like a puzzle. It's going to take time and effort to make progress, but there's real satisfaction in doing so.
From: Gillen, C.M. (2007). Reading primary literature: a practical guide to evaluating research articles in biology. (pg 44). San Francisco: Benjamin Cummings. 
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