Finding the algorithm: An introduction to reading and understanding scientific papers

By Joseph Provost, Ph.D., Minnesota State University Moorhead and Weiyi Zhao, MPH, ASBMB

For many college students, the last half of spring semester is a time to present journal articles and assemble posters of their research to present at  local, regional or even national conferences such as the annual Experimental Biology meeting held in Boston this April.  I thought I would use today’s blog post to talk about how to read and interpret scientific manuscripts.  Natarajan_JBC_Fig1To illustrate my points, let’s use a classic paper from the Journal of Biological Chemistry (JBC, or as my post-doctorate advisor, John Exton, Associate Editor of JBC called it, “the big J”).  I choose to use the JBC because JBC papers all contain figures that are downloadable as .ppt files which are great for teaching and the format of the journal is much more student friendly than most. JBC papers, as is with articles in most biomedical journals, have a basic structure/algorithm.  Once you’ve mastered the algorithm, presenting the paper is much easier.

Natarajan_JBC_Fig2

Abstract – Notice the objective of the paper highlighted at the beginning of the abstract and the key results highlighted at the end of the abstract

Take a moment to look through a JBC article and let’s go through each section together with an eye on how to interpret the presented work.

First, let’s examine the abstract. This section of the paper is meant to provide the reader with the nuts and bolts of the paper’s results along with a strong concluding statement.  I encourage the novice reader to link the first sentence or two (which includes the main topic) with the last sentence or two (the main point of the article).  By doing this, a reader can come up with a quick and basic understanding of what the article is about.

Next is the Introduction section.  A well-written publication will use the first few paragraphs to introduce the main elements of the paper (macromolecule, cell, organism, etc.).  An intelligent reader will make sure that he/she understands the science as well as the terminology used within the article.  Skipping over confusing concepts and words will only make later sections of the paper difficult to comprehend.  Imagine if you were reading a second language.  It would be impossible to skip words you didn’t know and expect to comprehend what is written. So, when you run across something you don’t fully understand, don’t skip over the work or concept.  Write it down and Google it.  Once you’ve gotten a handle on the terminology, take a few moments to look-up the references on the main players/topics of the paper.  Most journal articles include up-to-date and relevant review articles that can help you get a feel for the background.

Introduction – This is the last paragraph of the introduction.  Circled is the gap in knowledge of the research problem and what and why the authors conducted the work.  Highlighted is the main results or findings for the paper.

Introduction – This is the last paragraph of the introduction. Circled is the gap in knowledge of the research problem and what and why the authors conducted the work. Highlighted is the main results or findings for the paper.

This is a very helpful feature to look for, and can provide real return on your time investment in terms of gaining a deeper understanding of the scientific background.  The Introduction section will also cover the limitations in our understanding of the subject being studied. The author will likely foreshadow the importance of the results the work by letting you know how their work fills in gaps in our understanding of some scientific problem or process.  The fondant (for those food channel fans) of the introduction is found in the last few sentences.  Take a close look at the end of each introduction.  These last few sentence will have a clear declarative statement telling you what the scientists have found and done.  Such statements are easy to identify once you know what to look for.  They are usually written as “in the current study, we demonstrate that…”, “the purpose of this study was…”, “our results show”, or “this study was undertaken to…”.  You’ve found the golden nugget and along with the last statement of the abstract, you should be able to hone in on exactly what the authors of the paper are trying to say.  Don’t forget these sentences are the hypothesis of the paper and each experiment that follows should be related to these critical statements.

Next, let’s examine the Experimental Procedures (materials and methods) section. Take a moment to look at each figure in the results section.  Then ask yourself if you comprehend what is described in each figure.  Much of what is written in the Experimental Procedure section will be details that are critical to repeating the experiment and understanding the results.  Important for the student reader is to understand the assay or technique used.  Less important for an undergraduate level presentation is where the material, clones, antibodies or other components originated.  Outlining the primary assays or techniques used in the paper and doing some basic background research into the purpose of such experiments will help you understand the figures and results much better.

Natarajan_JBC_Fig4

Results – Circled is the italicized header indicating the main result for the following set of experiments. Highlighted are the two statements setting up the experiment and what the results indicate

Now, let’s approach the Results section.  Many authors use an algorithm to tell their “story” in the results section.  Once you see and understand the pattern, you can quickly and efficiently drill down to the details and use this pattern to present the study in class.

The first pattern to notice is the italicized header.  This header typically informs the reader the main conclusion(s) for the upcoming set of data.  It is easy to overlook this simple statement, but don’t.  The header statement is important as it communicates the hypothesis and conclusion for the following subset of data.

The body the results section often also uses a definable pattern of writing that a sophisticated reader can make use of to better understand the rational and data in the accompanying figure(s).  The pattern starts with a statement describing some observation or experimental results used to explain why the specific experiment was conducted. The author will then tell you how she or he answered that sub-hypothesis.  Such a statement may look like this:

        “…because of x (some earlier study or data presented earlier in the paper) we asked y (a sub-hypothesis)…”  Followed by …“To answer this question (Y) we did Z (the experiment)…”

In this way the author sets the stage for the reader on a problem that needs to be investigated and why certain experiment were carried out and how they answered the question or filled the gap on knowledge.  It is often really that simple.  Results start with why an experiment was conducted, what experiment/assay/technique was conducted, what happened (results), followed by a transition to the next experiment!

Natarajan_JBC_Fig5

Discussion – This clipping of the end of the discussion section shows a “future studies” statement. Highlighted is the big picture WDIC statement. Earlier portions of this section have many specific WDIC statements.

Conclusion/Discussion:  The purpose of this section is to answer the key questions from the hypothesis, fit the findings with existing knowledge, and convince the reader/reviewer with the approach and limitations of the results.  The first paragraph or two will cover the main thrust of the results, hopefully highlighting only the key points.  This can be a good way to double check your understanding of what you’ve read up to this point.  The rest of the conclusion section should contain a series of points that demonstrate the significance of the work and whether or not there are conflicts or problems with the research.  The final paragraph will restate the logical conclusions and why the study is relevant.  To quote Brad Waller from the Chemistry Department at Grand Valley State University, “this is the WDIC (Why Do I Care) moment”.  The WDIC can sometimes  be the hardest thing for a student to find.  Look for the WDIC moment contained in each set of experiments and the big WDIC moment within the conclusion.

Reading, understanding and presenting scientific papers can be a daunting process.  The first hurdle is the vocabulary and the techniques.  Learning the algorithm used by many authors may just be the trick to help you better understand each section of the paper and allow you to see the big scientific picture.

Is this post helpful to you?  Share your techniques and strategy in the comments below.

You can read the full JBC article cited here:    http://www.jbc.org/content/283/17/11794.full

4 thoughts on “Finding the algorithm: An introduction to reading and understanding scientific papers

  1. This is amazingly helpful information! I used to disregard the experimental/materials section altogether, but now I know what to focus on.

  2. This is amazingly helpful information! I used to disregard the experimental/materials section altogether, but now I know what to focus on.

  3. Pingback: Finding the algorithm: An introduction to reading and understanding scientific papers | Gravitropic

  4. Pingback: Finding the algorithm: An introduction to reading and understanding scientific papers | Gravitropic

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