A scientific paper with a variety of highlights and notes on it

How to read a scientific paper

When I started my PhD, I was quite intimidated by the prospect of reading scientific papers. I had read some literature during my master’s research, but for my doctorate, I felt I needed to develop a much better system for reading papers and retaining what I read. Over the last few years, I’ve honed my scientific paper reading skills and thought I’d share my own system. I’ll be covering how to find literature in next week’s post (edit: here is that post), so here I’ll just be focusing on what I do once I have a paper that I’ve chosen to read.

Reading a scientific paper is a bit of an art and it’s something that requires practice. It can be quite hard, especially if you’re entering a new field. There will be loads of new jargon that you need to learn- I certainly found myself looking up terms every other sentence when I started my doctorate. But the good news is that over time you’ll become more and more familiar with the terms, theory, and methods commonly used in your field which makes reading and comprehending things much easier.

I use the three-pass method for reading papers. It was mentioned in a doctoral college workshop I attended early on in my programme and I’ve used it ever since. This is a useful way to filter out papers that are not completely relevant to your study and it gives you some structure to follow. As well as this, I have a list of ‘questions for critical engagement’ which come into play during the second pass and help me engage with what I’m reading.

The first pass

The first pass is pretty straight forward and should take a few minutes. I use this for any paper whose title has caught my eye. This step consists of:

  • Scanning the title, abstract, and introduction
  • Looking at the figures and captions
  • Noting the section headings to get an overview of the content of the paper
  • Scanning the conclusion
  • Checking the bibliography for papers you have already read

After doing this, I can decide whether it’s worth my while reading the paper in more depth. Part of the skill of reading papers is in being able to identify when a paper isn’t relevant enough so you don’t waste precious research time on it when you could be reading something much more pertinent. I still record the papers I do a first pass on as I might want to come back to them at a later date when I’ve moved onto a slightly different research question.

During the first pass, I note down details of the paper in a spreadsheet or database (excel or Notion work well for this). The aim of this is to set it up so that it’s easy to retrieve the paper at a later date. I also identify tags that will help me gather papers into categories when I come to writing a literature review. These tags consist of key terms, materials, standard methods, theory, etc. that are covered in the paper:

A Notion database called 'Literature Tracker' showing the key terms added for each paper
My ‘literature tracker’- tags can be seen in the ‘key terms’ column

I’ll be covering the literature synthesis and review process in more detail next week so keep an eye out for that if you’re interested in learning more details about my literature databases.

The second pass

The second pass is where the main bulk of my reading happens. This is where I’m trying to get a good understanding of the paper and how it relates to my own research. I like to print off papers as reading from a screen tends to make my visual stress worse and I find that I absorb information better when reading a paper copy, but you can do whatever you find most convenient. There are loads of programs that allow you to highlight and make notes on digital files these days if that’s what you prefer to use. I like to read the paper using a highlighting system to pick out various aspects of the work. My highlighter key consists of these categories:

🟥Objectives and findings
🟧Key terms/acronyms
🟨Past work & theoretical background
🟦Materials, experimental parameters & equations used
🟪Future work & implications
🟩References to check

As well as highlighting things in the text, I’ll write anything that comes to mind in the margins and I’ll add new key terms and acronyms to a big document I have that acts like a bit of a dictionary/encyclopedia for my PhD.

Once I’ve gone through the paper with my highlighters, I then fill out my literature matrix. This consists of writing a very brief summary of the paper and then noting down the objective, key results, the theory used, materials, methods, conclusions, future work suggested, and my critiques. I usually do this in bullet point format so it’s easy to read when I return to these notes at a later date. I then answer a series of questions about the paper:

Questions for critical engagement:

  • What was the research question/problem?
  • Is this title of possible value to my study?
  • If so, why do I think so?
  • What is the author of this paper attempting to persuade me of, and am I persuaded?
  • If not, why not?
  • Which part of this paper is of most interest to me and why that part?
  • Why have they chosen this approach or theoretical framework?
  • Do I agree with the author’s reasoning for this?
  • What does the author think are the implications of their findings?
  • Do I agree with the author’s reasoning for this?
  • What does this paper contribute to my own thoughts on my own research?

By doing this, I think about how the paper relates to my research and can then decide whether it is a ‘core’ paper for me. If it is, I’ll note down to do a third pass.

The third pass

I don’t get to this stage with many papers, but for the most seminal works in my field and studies that are very closely linked to my research, a third pass ensures that I fully understand prior work. To do this pass, you basically have to reimplement the paper. It forces you to think about how you would approach the same study. I usually do this by drawing out a paper outline and bullet pointing what I would do if I were carrying out the same work. This helps you identify where the authors were particularly innovative and where they are lacking. For example, I like to analyse the assumptions the authors have made in the study and ensure that their experimental and analytical techniques are sound. This often involves reading the supplementary material too.

What to do when you don’t understand a scientific paper

This happens more often than you might think so don’t worry if you find it hard to understand something that you’re reading. It may just be that it’s a poorly written paper (there are lots of those out there) or that you have a gap in your knowledge that you need to fill.

When this happens to me, I do a bit of research around the topic (usually using textbooks as they don’t assume as much knowledge as a lot of papers do) and I’ll also ask colleagues what their thoughts are on the paper. My supervisor and I have a little journal club meeting from time to time and I’ll often pick something I don’t quite get to cover in these so that I can discuss it with him and see what his take is on it. Reading around the subject and reaching out for help to discuss things with colleagues is all part of becoming a self-directed learner, which I spoke about a bit in last week’s post.

The other thing to do is just put the paper to one side for now. I did this a lot early on in my PhD and it’s a nice feeling returning to something you couldn’t get your head around to begin with, but now it makes more sense because you have a better understanding of the field. I always try to remember that as a researcher, it’s part of my job to read literature. The more I read, the better I become as a researcher because I know what makes a good study and a bad one which shapes how I do my own work.

I hope you found this post useful and happy reading!

If you like my work, I’d love your support!

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