Writing Your First (or next) Paper: Part II

This is part two of a four part series on writing your first paper. For the first part in the series, click here.

You have been pounding away at your project, probably for a year… or two… or three… Anyhow, you now have a collection of figures that seem to tell quite a nice story, and now it’s time to write the first draft. There has been a lot written on the mechanics of scientific writing, and even if you haven’t read that material, you have read a lot of papers. So rather than giving you a section-by-section breakdown on paper writing, I’m going to outline my process for generating the first draft of my manuscripts.

Create an outline
Opinions differ on this point, but I personally like starting things off with an outline. This allows me to map out the order in which I introduce material, describe the experiments, and list the key points that I want to make about each without getting wrapped up in phrasing and transitions. I do the whole thing – Introduction through Discussion including the Experimental Procedures. Usually at this stage I can see problems that might arise in the presentation and fix them without deleting sentences I spent hours crafting. It also serves as my ‘map’ while writing to keep me focused and aware of where I’m going in the narrative.

After finishing a reasonably detailed outline, it would be a good idea to give it to your mentor along with the figures (complete with legends) to look over. Hopefully, your mentor can give this some serious consideration, and afterward meet with you and discuss it. If there are large, sweeping changes to the order of the experiments, or if he or she envisioned a different focus of the work than the one you’ve put forward, then the changes can be made here where the time investment in the prose is still minimal.

Determine the destination
You may have discussed this with your mentor before now, but if you haven’t, then the meeting where you discuss the outline would be the best time to talk about what journal you will be sending it to. This becomes most critical at the top of the pile – the manuscript you write for Nature will be radically different from the one you write for Cell. Other journals may not have such extremes in the structure, but may have other content requirements that should be kept in mind. For example, a primarily biochemical paper intended for The Journal of Biological Chemistry will likely have to have more emphasis on biological relevance than if the same manuscript were being sent to Biochemistry.

Just spit it out
Now you have the outline with your mentor’s tentative stamp of approval and a solid idea about where it should go, it’s time to start fleshing it all out into a paper. My next piece of advice is to be careful how much time you spend getting the wording just perfect on any particular section. If you are having a tough time saying something just right, then take your best stab at it and leave behind an e-note saying “I’m not certain I’m happy with this yet.”

On one occasion I spent three days writing and re-writing just one paragraph that I thought was essential to the paper. In the first round of edits, my mentor eliminated the whole thing. That was three wasted days, and in the end the paragraph wasn’t as necessary as I was convinced it was at the time. When you find yourself at a loss for just the right words, do your best in a reasonable period of time, mark it, and move on. The statement may not be as necessary as you think or your mentor may have just the right turn of phrase needed to make the point.

Let it rest
You just finished writing the first draft! You even referenced it! Now, if time allows, close the file and don’t open it again for a week. You need time for your mind to ‘reset’ on the subject so you can read what you wrote again with fresh eyes. Besides, you probably should go re-read the papers you referenced again, just to make sure they said everything you thought they said when you cited them. If you haven’t written the Experimental Procedures yet, this is also a good time for that.

Once you have let the manuscript rest, come back to it and read it again, slowly. Does it ‘sound’ like the published papers you’ve been reading? (In other words, did you get the tone right?) Make sure the narrative flows, fix the typos, and correct any wrong words (there, they’re, and their…). Of course, if you find any larger issues with the science, fix those as well.

Phone a friend
If you have a senior labmate with some publication experience that can be bribed with either cookies or beer, then have him or her read the manuscript over quickly and get some feedback. Now may not be the time for multiple opinions – I would ask just one person that you trust and respect as long as it doesn’t offend anybody else. Stress that you aren’t looking for line-editing, just general impressions of your writing style and the storyline. Once you get their feedback, try to incorporate it.

Now you have your first draft. It’s time to give it to your mentor. The next step – surviving the editing process.