Reading Primary Literature 101

One of the goals of much popular science writing is to keep the public in touch with research as it happens.  Most people have read science text books, read popular science publications like Scientific American or see summaries in the news. A less known world of science publishing is that of primary literature, the journals scientists publish in to share the details of their work with their peers and students. These journals require that all material be reviewed by other researchers to be sure it was done responsibly and their experiments demonstrate precisely what they are claiming. Of these some of the most highly regarded are Science, Nature and, in my field, Cell. These journals have some material, usually reviews, summaries and blogs that are free to the public but most of the content requires a subscription to view. An increasing number of journals are publishing in an open acces format so that everyone can read the details of scientific work as it is done. The of these the Public Library of Science (PLoS) publications are perhaps the best known. To introduce you to the world of primary literature I will be reviewing articles published in PLoS. This will include providing background information, describing methods, summarizing conclusions and offering criticism.

Let's start by looking at the anatomy of a journal article!

Take a looks at this cellular neuroscience article by Casper C. Hoogenraad et al published in PLoS Biology. If you scroll through it quickly you will see it is divided into these sections: Abstract, Summary, Introduction, Results, Discussion and Methods. This is fairly typical though not all have the Summary, some combine the Results and Discussion section and the Methods section is often before the Results.

Abstract: This is short synopsis of the article giving a brief description of the questions addressed, the methods used and the conclusions drawn from the work.  Reading this is like looking a the back cover of a book and getting all the spoilers of the main plot in just a few sentences. This will tell you want the important points are.

Summary: Similar to the Abstract but usually less technical. Here the authors can introduce suggestions of significance and give perspective on how their work contributes to or alters the current body of knowledge.

Introduction:  This section contain little original information and sets the tone for the rest of the article. Here the authors introduce relevant background information and indicate where gaps in our knowledge exist. Within the text there are citations, these apear as numbered hyperlinks in the article we are looking at. Citations are references to previously published articles on similar topics that set the stage for the work being presented. Authors will show the limitations of this previous work and introduce the new information they have to contribute. This is particularly useful for readers who are not well acquainted with the field. This usually culminates in the stating of the authors primary question, their hypothesis and how their work addresses these.

Results: This is where the real fun begins! Having given you some idea of the state of the field and what they have found, the authors have to explain what they did to address their questions. Combined with figures seen throughout the paper, the results are by far the most important part of any paper. Authors should establish that their methods do not perturb the system they are observing and that they are able to observe relevant events in the first place. This will indicate that the premises for later experiments make sense. Latter parts of the results will show how they uncovered new information and outline how each experiment is connected to the others. In the text they discuss the rational and implications of each expriment, in the in the figures they present exactly what they looked at to draw the conclusions. You can roughly judge from their examples if you concur with their conclusions, but formal quantifications are a must to show there are consistent trends.

Discussion: This is often the easiest to read part of a paper. The authors will step through what they have shown and generally propose a model of how they think it is all working. You shouldn't take this like you would a text book, it is more like an opinionated insertion of their conclusions into contemporary thought. Reading this area can help clarify what some of the details of the results might have muddled. This is really the where they can stress their take home and argue for the importance of their work. If you weren't already thinking along these lines by the time you finished the results, be careful! Here an idea is being pitched to you, but careful review of the results and Methods is needed before you go along with it.

Methods: This is often the second most important part of a paper for active researchers. We need to be able to replicate eachothers' work and the methods are a guide to doing so. Often methods used by one group are used by many others. There are often subtleties to experimental work which can have a huge effect on how an experiment turns out. I will be discussing particular methods as they come up.


So there you have it, the basic structure of primary scientific literature. Perhaps less friendly than articles seen in popular publication but filled with information you can't get anywhere else. Understanding the actual reports researchers make about their work will let you judge what we can conclude from the work for yourself, rather than relying on a reporter or opinionated blogger to tell you how things are going!

Welcome to Cytophilia

Cytophilia translates to 'lover of cells' or 'one having a high affinity for cells' as a PhD student in cellular neuroscience this serves my life well.  Please check back soon for reviews of recent science news, book reviews and summaries of current important literature in cell biology, neuroscience and my other favorite fileds! With this blog I hope to contribute to the body of scientists trying to make our work approachable and exciting for everyone.  If you have ever wondered how research gets done, what makes for a solid study and what the implications of new research might be, I'm going to try to provide some answers for you!