A very brief introduction to reading scientific papers and
preparing for 4th year seminars.
Anthony Poole (von Haast 466, anthony.poole@canterbury.ac.nz)
1. Ask yourself what type of paper you’re reading:
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It could be a paper reporting primary data, or the description of a new phenomenon
It could be an analysis of existing data (e.g. a computational analysis) or a metaanalysis of numerous data published on a particular subject (e.g. comparing data for
various cancer treatments)
It could be a mathematical model or a simulation with relevance to how a particular
biological phenomenon may operate
It could be a factual review, describing and summarizing the incremental advances in
a field that have occurred over the last year or two
It could be a paper advocating a novel viewpoint or presenting a substantial new
hypothesis, and may for example be controversial
Different types of papers have very different organization, and even use different
language. The general structure for a paper reporting a primary analysis or experimental
observations is as follows (though the order can vary, some sections get amalgamated,
and sometimes there are no headers to say where one section ends and the next starts):
Abstract
Introduction
Materials & Methods
Results
Discussion
Conclusion
As well as reporting specific results, primary papers also incorporate elements of review
(e.g., the introduction) and opinion (discussion section). Because different styles of
language are used, you should be able to recognize them even if you aren’t too familiar
with the research topic.
Perhaps among the hardest papers to read are those published in Nature and Science,
because they are short and do not usually have subheadings. Consequently, you may find
yourself having to read other papers in order to make sense of them.
2. Reading about a subject you are not familiar with:
If the reported work is in a field that you don’t yet know much about, sometimes the
paper feels as if it is written in a foreign language.
• For topics you are not familiar with, it is usually necessary to read the paper
more than once.
• You may need to go back to textbooks or find other papers in order to check
basic facts (such as methods, technical terms, the basic biology of a system).
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You may need to read additional papers referenced in the paper itself.
If the paper is a review, you may wish to go back to the primary literature to read
about key experimental or theoretical results that have shaped current opinion.
If you are reading a paper that reports new results, you may wish to read a few
reviews to get an overview of the field and to make sense of what is being
reported.
It may also help to read earlier experimental results that lead up to the current
study.
3. Reading critically:
As well as doing background and supplementary reading so one can decode a paper,
one also has to learn to read critically. If you talk to established scientists you will find
that they spend a lot of time discussing, debating and disagreeing, and will often have
very critical things to say about published work, even when it is published in the best
journals.
Some things to keep in mind while reading:
• Do you think that the data is of sufficiently high quality to be reported?
• Do you agree with the experimental design and data analyses?
• Do you agree with the results reported?
• Do you agree with the way the results are reported?
• Do you agree with the interpretation being presented?
• Is the scientific literature being accurately represented?
The first three are primarily concerned with the methods used to gather data, whether
the data are relevant to the particular problem being posed, and whether the results are
valid (e.g. are they of a sufficiently high standard?). The next two are concerned with the
wording, and the conclusions being drawn from the data. These can be quite separate
things, and the key thing to learn is to read between the lines. In much the same way as
journalists or newspaper columnists can use tricks to get you to accept a particular point
of view, so too can scientists. Some statements may be backed up with a reference to
another paper, and some are not. In the latter case, you have to decide whether you think
a statement being made (e.g. a primary conclusion in a paper) is supported based on the
data being presented. In the former, you should check to see whether the reference really
does back up that statement — scientific papers frequently carry inaccurate citations (i.e.,
a paper is cited to back up a particular statement, but in fact that paper does not back that
statement up). This is one reason why it is important to go back and check references
when you are reading material that is unfamiliar to you.
If you are reading literature from fields with which you are unfamiliar, in addition to
reading around the topic, you should take notes and write down any questions that
come to you while you’re reading. This is important because sometimes it is hard to
follow an argument or a series of experiments without jotting them down yourself. This
can be because the work is very complex, but it can also be the case that the paper is
poorly written, or so full of jargon that you need to do some translating to make sense of
what is being said or what has been demonstrated. It also helps to be able to pick out
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experiments or analyses where you do not understand the methods, so you can go and
look these up yourself. Doing this will help you evaluate the significance of the results.
Some people like to do this in the form of bullet points or notes, some like to write out a
glossary of terms they don’t understand, and some like to draw a diagram that details the
work being presented. Find whatever works for you, or for a given paper, and use that;
there is no ‘best’ way to do this.
It is also a good idea to read each paper several times, particularly if you feel you
don’t understand the paper. Usually a lot more becomes clear on the second or third
reading. Once you understand a paper, you should be able to write a short summary (e.g.
a paragraph or two, or a series of bullet points) detailing:
• what the topic is
• what question or hypothesis is being addressed
• what methods were used and why, what results were gathered and why these results
are of interest (or even why you think they’re not relevant).
• whether the results and the interpretation are compatible
• whether the results are too preliminary or irrelevant
• whether they are confirmatory of a particular viewpoint
• whether additional work might be required to back up a particular interpretation (and
if so, what would be required)
You should also be able to include your own interpretation of the work: do you agree
with the authors’ claims, or do you disagree, and why your opinion is as it is.
4. Be prepared for discussion sessions:
If you have written summaries of the papers you read, and jotted down your own
opinions, you will soon start to feel in command of the papers you read, and you will
have plenty to discuss as a result. An important aim of discussion sessions at 4th year is
for you to ask questions of your lecturers, based on what you’ve read. Such questions can
range from simple requests for clarification on a method, the presentation of a result or
the interpretation of a graph to questions concerning the validity, significance or
implications of a study. You will also develop the capacity to compare and contrast
studies and even methods; all essential skills for your future career.
If you turn up to a discussion session under-prepared, it will feel like pulling teeth,
and you will just sit there feeling it is confusing and perhaps even a waste of time. That’s
disappointing for a lecturer, but of greater concern, you’re missing out on making the
most of valuable contact time with scientists who are able to help you get to where you
want to be.
The aim is not for us to tell you what to focus on, or what questions you should be
answering, the aim is for you to bring your own agenda to the discussions. It is very easy
for us to tell you what to think, but then you’re not actually thinking. So come to your
lectures armed with a list of specific questions!
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Exercise:
When I was a postgraduate student, one of my lecturers said that by the end of 4th year we
should all be able to pick up the latest issue of Nature or Science and read pretty much
any article in there. 4th year can be daunting because you constantly have to read papers
on topics you feel you know next to nothing about. Here is a secret that at most only a
few of your lecturers will admit to: we lecturers often feel the same way.
At the School of Biological Sciences, we run a fortnightly Journal Club where we
discuss papers taken from all fields of biology – often we do not feel qualified to
comment on the technical details, but we can always think of some things to discuss after
having read the papers. And we have learnt quite a few tricks on how to decipher what’s
going on in a paper. Here are two ways you can make reading a complicated and
condensed paper a bit easier – first, we will look at the structure, then we will see how
reading additional material can make the task of understanding that little bit easier.
As an exercise, read the below paper from our Journal Club. Don’t worry if it’s a
field you are completely unfamiliar with. All we are going to do is to try to place
subheadings into the paper.
Schuster et al. (2010) Complete Khoisan and Bantu genomes from southern
Africa. Nature 463:943-947.
This was presented on 5 March 2010 and you can locate it by going to:
http://www.biol.canterbury.ac.nz/
Click on the link to ‘Journal Club’ (last item under ‘About’). Next, click on [Previous
Papers] on the right-hand side. Download all three files (PDF, Supp Info, News Article).
1. Read the PDF of the paper. (Schuster et al.)
Don’t worry if you don’t understand everything – we won’t be going into specifics!
Highlight sentences or sections that you think fit into the following standard
subheadings:
• Introduction
• Results
• Discussion
• Conclusions
Next, look at the paragraph p945 beginning: ‘Of the 14,495…’ You will see that there is
a lot of information packed into that paragraph, and it mentions things like ‘lactase
persistence’ the ‘SLC24A5 allele’ and the ‘Duffy null allele’.
• From the text contained in the paragraph, try and summarise what these mean.
2. Next, have a look at the supplementary information file. (Big, isn’t it?)
• Locate the sections of text from the supplementary information that relate to the
above terms. See if you can find out what a SNP is.
• After you have read these sections, try to explain what these are once more.
3. Finally, read the news article by Heidi Ledford.
• Now that you have read this, try once more to explain the text contained in the
paragraph from p945.
• Do you feel like you have a better idea what the authors are trying to say in this
paragraph now?
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