Reading Papers: getting the most out of a scientific article

Does anyone remember back in high school and college when you had to write a research paper and it felt like a crazy, daunting task because you had to find all those peer-reviewed articles to support your writing? I remember digging through Google Scholar and trying to find as many papers that seemed to be on topic for my research paper, but not really knowing what to do with that information, much less how to find the information I needed. Fast forward to my first year as an undergraduate research assistant where the grad students in the lab gave me some papers to read that had been published by the lab so that I could catch up on the kind of research the lab has already done. Now as a graduate student, where you have to keep up to date on the most recent research and also have a thorough understanding of the historical work on your particular research topic, I’ve managed to find a system of reading scientific papers efficiently and critically so I can interpret their findings for myself and keep up with the field. So without further ado, here is my breakdown for reading scientific papers (which can also be applied to peer reviewed papers in other fields, not just biomedical sciences).

Let’s start with a little bit of background on what a peer reviewed, scientific article really is. What does it mean for a paper to be peer-reviewed? In every field there is a collection of scientific journals that publish the work of different labs. When you submit an article it goes through an extensive review process where 2-3 other scientists/specialists in the field will receive your manuscript and deliver criticism on the methods used in the experiments, the interpretation, or the analysis. The reviewers assemble all of their comments and criticism and then it is sent back to you (the author(s) of the paper). Usually, the reviewers suggest additional experiments to do that they believe would improve the paper or changes in the structure of the paper that would make it easier to read. Basically, the overall goal is to improve the paper. This process can go back and forth multiple times and I’m grateful to say that in my experience, though it can be painful and difficult to take all the criticism and do all the experiments/analysis the reviewers request, my papers have come out even better thanks to the feedback of reviewers.

Now, on to the anatomy of a scientific paper. The first section of a paper is called the abstract. This is a brief synopsis of the entire paper including a few lines of significance (why we care about their work), the experimental method used, the results, and a conclusion. The entire paper follows the same structure of the abstract, just with a lot more details. The first part gives you the background on the particular topic that the paper will be addressing. The background usually contains information about what has already been done in the field, including the previous work of the lab. In addition, there’s usually a connection to some sort of translatable aspect of the research or clinical relevance, which in short ties the research to a given disease that the findings could be applied towards. The methods generally come next (though some journals put their experimental methods at the end of the paper). In the methods section you can find the details about how the authors conducted their experiments which is especially important for trying to replicate experiments (or reproduce a similar finding). The results put the findings from the experiments in the context of the questions the authors are trying to address. Now you know how they did their experiments and the outcome of their experiments. The last section is called the discussion, which can be a little bit of a free-for-all. In the discussion, the authors can speculate about their findings and how they can be used in the future or what it may mean for a particular physiological process. The authors can also use the discussion to compare their findings to work that has been done in the past and point out how the findings are similar or different. The discussion is a place where you can point back to the big picture of your work in terms of a particular disease pathology, behavior, or medical/technological application.

Now that we know the critical parts of the paper, here is my list of tips for getting the most information out of reading a scientific paper using a paper I read recently as an example (the paper is cited and linked at the bottom of this post):

  • If you’re not familiar with the field, start with the background and start identifying key features. Scientists like to use a lot of acronyms and also genes and proteins can have funny names. It always helps me to look up the names of whatever I’m not familiar with. Don’t know that acronym? Look it up - that way you know what it does and why the authors care about it. Do the authors mention a particular protein, but you’re not sure what it does? Just do a basic search and write down the information you find. For example, maybe the authors talk about a protein that’s called a transcription factor. But what is a transcription factor? If you do a quick and dirty Google search, a transcription factor is: “a protein that turns a specific gene ‘on’ or ‘off’ by binding to nearby DNA,” meaning it can regulate gene expression. Write that in the margin of your paper or make a note somewhere that’s easily visible while you’re reading the rest of the article. I like to have everything in context when I’m reading so that I can also see the bigger picture while I’m reading.

  • What question are they asking/What is the gap in knowledge that they are trying to fill? Oftentimes we think of hypothesis testing when we think of scientific research, but authors don’t always outright state their hypotheses. So then how do you know what they authors are really trying to figure out and test? Look for phrases like, "Though we know x,y,z, how x,y,z contributes to ___ is unclear.” This identifies a gap in the knowledge of the field that needs to be filled and this is most likely what the author will be addressing with his or her experiments.

Soh et al., 2018.

Soh et al., 2018.


  • What are their findings - look at the figures. Figures in a paper can seem kind of daunting, but there’s always a handy little figure legend underneath that explains what each panel of the figure is showing. Walk step-by-step through each figure panel. If it’s a graph, what is on the x-axis? What is on the y-axis? Don’t remember how they did the experiment? Revisit the methods briefly then make a note beside the figure to remind yourself how they got that data. When you take the figures at face value, you can form your own interpretation of the data without the potential bias of what the authors states they find in their data.

Soh et al., 2018.

Soh et al., 2018.

  • Highlight the major conclusions at the end of each results section. If you highlight the main findings for each section you can easily compare the stated conclusion to the data the figure is actually showing and tie the paper together. By doing this, you can more easily come back to the main points and it can help you understand the overall scope of the paper a little better. Also, you can go back and forth between the conclusions and the figures to compare the data to the claims being made by the authors and interpret their findings for yourself.

  • Write notes separately as you read. There is evidence that writing things down or taking notes by hand is linked to better retention of information. As I read through a paper I like to write down the big statements or even draw different pathways to help myself understand and remember. Lots of physiological processes are complex and have many different factors that influence the outcome, so drawing it step by step, where I can fill in different factors that play a part of the process, helps me understand more how it all works and later apply that knowledge when designing my own experiments or coming up with a new theory to test.

References:

Transcription factors:

https://www.khanacademy.org/science/biology/gene-regulation/gene-regulation-in-eukaryotes/a/eukaryotic-transcription-factors

Example paper:

Soh, H., et al. (2018) Deletion of KCNQ2/3 potassium channels from PV+ interneurons leads to homeostatic potentiation of excitatory transmission. eLife. DOI: 10.7554/eLife.38617

Handwritten Notes:

https://www.pbs.org/wgbh/nova/article/taking-notes-by-hand-could-improve-memory-wt/


Bree Watkins