How to write a scientific paper (part 1)

[I've updated this post by request to include a more in-depth description of the competitive eating analogy, which was promising but sadly lacking in the first version. Thanks Nat]

I’ve written or participated in writing a bunch of scientific papers, book chapters, and conference papers and figured out a thing or two about the process. The process of writing a paper is difficult and in a lot of ways a labor of love.

Writing a paper (or a proposal, or a thesis) is like eating. But not just your sit-down-at-the-Sunday-dinner-table-eating; it’s like competitive eating. The goal is to see how much you can write, revise, smooth, shape, revise again, update, write, revise again, until you feel like you’re going to vomit (figuratively speaking, most of the time)- and then, guess what? You get to continue with the same. At a normal meal you start out hungry. You sit down at the table and help yourself, then pleasantly enjoy eating, growing slowly less and less hungry as you eat more. When you’re full, or sometimes slightly later than that, you stop, push back from the table, burp, then go about your business satisfied with a full stomach. Not so in competitive eating, nor in paper writing. The goals are completely different. You are not eating to feel full- you’re eating to win godamnit. And likewise, you’re not writing just until you don’t feel the urge to write anymore- you’re writing until you damn well finish that stupid paper. Cram it down until you’re finished. It actually is a skill worth having to be able to revisit writing a paper long after you’ve lost the appetite for it.

It’s also similar to the process of moving (like from one residence to another). The moving analogy is that after you’ve finished the first 90% of a paper, you find that you only have 50% more to go, then after you finish 90% of THAT, you find that you only have 50% more to go. It can get ugly, but it’s generally the case that the easiest lifting (moving the couches and beds and other big items) gets done first, goes the fastest, and sometimes you have a bunch of friends helping out. It’s after that part gets finished that the real work starts. And always it takes one person who drives the paper- there’s got to be someone who takes ownership (hopefully the first, or in some cases, the last, author- but not always) and drives the stupid thing to completion, staying after everyone else has left to sweep out the corners and make everything look beautiful.

First, writing a scientific paper is telling a story. Don’t get me wrong- this is non-fiction, and it all should be TRUE as far as you can determine- but it is a story nonetheless. If you organize a paper like a protocol (do step 1, then do step 2, etc.) or present it in the linear way most studies actually occur (we started out to show this, but then we found this other interesting thing, and then we went back and tested it, but that failed so we did something else) then you will lose your audience’s attention. And your primary (as in first, and in some ways most important) audience is the reviewers who act as gatekeepers for your paper to get seen by a larger scientific audience. If your audience loses interest or can’t follow the story or gets frustrated- it’s generally game over. Reviewers might, if you’re lucky, tell you that the overall flow is confusing, or that you should clarify parts or the whole, but it’s equally likely that they’ll lose interest and will simply turn in a poor review that entirely misses your (incredibly important) point.

So my point is that the story that you tell can be in an order other than which it was actually executed. I have clear memories of my graduate advisor taking a bunch of immunoblots that my wife (who was a research tech in the same lab) and I had generated over the course of about a year, laying them out on the bench, and starting to move them around in order as he figured out the story. I was taken aback- I remember thinking, “but that’s NOT the way we did it!” But, of course, he had the big picture in mind and knew how these things could fit in to a story worth telling. It’s important to note that this is not the same as making up a hypothesis to fit the results post hoc. Each of the chunks of results is, itself, an experiment with a hypothesis that was set a priori and tested with the experiment.

Anyway, I like to think of the paper writing process as modular, similar to the way my graduate advisor, and then my post-doc advisor after that, shuffled around bits and pieces of evidence to make a complete picture. Each of those pieces was a module. A bit of science that was executed in a very similar way. Each of those pieces had a beginning, the hypothesis, a middle, the experiment, and an end, the interpretation of the results and placement in the larger context. Each could be moved around, but the order determines how the story flows. These modular pieces fit nicely into the discussion of the scientific method I posted earlier.

Here’s my modular template. This works reasonably well to lay out an initial outline. If you’re having trouble figuring out a paper, it’s not a bad idea to compose a bunch of these modules, print them out, and then physically move them around on a table. It helps make connections that are not apparent from a more static document. For those who’ve written a lot of papers (this holds for proposals as well) this will come as no great revelation but I hope it’s helpful for those who aren’t as experienced.

Manuscript Modular Template

Introduction/Background

  • Statement of problem and significance
  • Background information that leads to the overarching hypothesis
  • Previous approaches
  • Statement of overarching hypothesis
  • Summary of results

Module x: Title

  • Input: What question does the previous module raise that should be answered? This piece obviously has to be in the context of the order that you’ve put these modules so can’t be written ahead of time.
  • Hypothesis: What is the question being asked? What does this experiment test?
  • Method/experiment: How was the question addressed? What were the steps in this experiment?
  • Results/analysis: What were the results and how do they address the hypothesis?
  • Output: What question(s) does this result raise? This will link to the next section and you probably shouldn’t duplicate it with Input section of the next module.

Discussion/Conclusions

Generally this section is a bit more customized to the implications of the study. I think it can follow some general guidelines, but there will be things that have to be given more weight, considerations about data and data processing, caveats of the study, and discussions of the biological importance of the finding in a larger picture view of the overall problem.

4 thoughts on “How to write a scientific paper (part 1)

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