How to Take Notes on a Paper (Last Update 06/03/2010)

The following procedure is a very effective way to take notes on a paper so that

1. You are sure you understand the paper at the time, and
2. You can reconstruct your reasoning at a later date if you have to go back and figure out your notes.

The following method is not intended to produce a detailed analysis of the paper -- it is designed to produce an understanding of "what they did" and "why they did it" so you can then proceed to the analysis with much greater ease and confidence. If you want advice on how to do a critical analysis, see "Paper Questions."

Basic Method:

Go through the paper. For each figure, table, or experiment described in the text, answer the following:

1. What is the question they are trying to answer?
2. What did they do to answer the question?
3. What is the answer?


1. What is the question?

The idea is to come up with a short concise statement of "Why did they do it?" Try to come up with a single sentence, which can be either a statement or a question. For example, you might write:

Q: Is the mitochondrial DNA from different cells of the same person the same?
or Q: Are restriction maps of mito. DNA same in all cells?
or Q: Can they detect any differences in mito. DNA of different cells?

Note that these questions are not exactly equivalent, but all capture the essence of the question. Also note that in a well written paper, the title of the table or figure will be very close to the question. In this case the title might be "Restriction Analysis of Mitochondrial DNA from Different Tissues."

2. What did they do?

You will need to figure this out in detail first, but once it is clear in your mind, you want to be sure to capture the essence of the procedure in a sentence or two. If the procedure is complex, or uses methods unfamiliar to you, you will need to write out a flow chart or detailed description of the procedure to get it all straight. The hard part here is to get all the details clear without losing the point. So it is a good idea to keep track of the details on a separate sheet which you can save for reference if you need it later, while you summarize the key features of the methods as briefly as possible on your main sheet. The more familiar you are with the experimental technique, the shorter your sentence can be. For example you might write:

How: They isolated mitochondrial DNA from different tissues of 5 individuals, cut up the DNA with several different restriction enzymes, ran it on gels, and visualized DNA with ethidium bromide.

Alternatively, you might write:

How: Ran gels of restricted mito DNA.

3. What is the answer to the question, or what happened?

    In simple cases, like this one, the answer can be just yes or no. ("Yes" here really means yes as far as they can tell by their method.) In more complex cases, a sentence or two may be necessary, and/or you may need to consider question 4.
    For many experiments, questions 1 to 3 are sufficient and no further questions need be raised (unless you want to do a critical analysis). Questions 1  to 3 are usually sufficient when the conclusion is obvious or follows directly from the results, and when the procedures used are standard. Both these conditions are met in the example cited above. (But see below.) When the conclusion does not follow directly from the results, you need question 4.

4. What is the conclusion?

The actual result in the case described here is that the gels look the same; the conclusion is that the DNA sequences are the same. There are occasions when this result and conclusion would need to be looked at separately, but for many purposes it would be sufficient to lump them together. Whether or not you need to bother with question 4 depends on the complexity of the experiment and the degree of analysis you are interested in.

5. What if I want to do a more critical analysis of the paper?

If you want to look more carefully at the conclusions of the paper, you need to consider whether their conclusions are justified and whether they did both the experiments and calculations correctly. These issues, and a more detailed version of questions 1 - 4 are given in "Paper Questions."

A Final Comment

Why bother to write all this down carefully? When you are reading a paper, there is a tendency to either skimp on the details, so you never figure out what happened, or if you do figure out the fine points it then becomes so clear to you what they did (and why) that you forget to write down what now seems "obvious." Then when you go back to look at the paper, you can't remember why it was obvious and you have to figure it out all over again. This method both helps you decipher the paper the first time and allows you to reconstruct easily how you deciphered it the first time, so you can do it again with ease.