Writing scientific papers

Sun 1 March 2015 5 min read

(Updated 2016-03-12 to re-add the links)

I am probably the last person you would want to consult on tips to write a scientific publication. I’m slow, I procrastinate, my English is not the best, much work lies on the cutting room floor - skeletons of half assembled papers. Still, ‘that which we are, we are’, though my skills are lacking I’m very interested in improving, and certainly enjoy reading a well written paper.

It is an unfortunate fact that the quality of scientific writing is decreasing as a function of time. Some of this can be explained by the laudable continuing expansion of scienitific research across the world resulting in a greater number of authors writing English as an additional language. I believe the major reason stems from the unrelenting pressure to publish. Many more papers are written, yet there are still only the same number of days in the year. With these publication metrics deciding so much of our future careers (and thus lives), there is also enormous pressure to ‘glam up’ work and oversell, as well as to ‘salami slice’ and represent work that belongs together in one paper in many.

It used to be that scientists would work continuously on a problem, and then publish when a ‘breakthrough’ had been made. To be honest I think we would have a better scientific corpus if this was still the case - careful work on a hard problem for a few years until we gain some traction, then write it up for the benefit of anyone who could take it elsewhere.

(Along these lines, Ross McKenzie has a recent blog post ‘In praise of modest goals’.)

So the first thing to do when writing is to overcome the cynicism! When I get particular disaffected I return to Simon Peyton Jones’ talk on how to write a great research paper . His enthusiasm and motivation is infectious. I am a worm. A worm with a infectious mind virus, and that is good.

Sabine Hossenfelder wrote a useful blog post on How to write your first scientific paper, this covers the construction and sectioning of a physics paper.

I’ve personally found the Penguin Writer’s Manual very useful for the nitty gritty of ‘that’ vs ‘which’. I’ve also read Strunk and White (The elements of style), though I’m not sure how much I took from it. The economist style guide (available online) is also very useful as a reference. (2016 update: Steven Pinker’s ‘The Sense of Style’ is fantastic. Dispels a lot of prescriptive myths, but also teaches how to analyse your sentences and identify clumsy phrases.)

I much prefer to write with Latex. Sometimes I first go via Markdown (a lightweight markup language that looks a lot like how you would naturally format a text email), so I don’t need to bother with thinking about the Latex commands when forming a text, and then convert to Latex (with pandoc) for inclusions of figures & all the revisions that incur thereafter. The whole project I put within a ‘git’ repository and so have version control, effectively offsite backup (to Github / Bitbucket). To get the diffs to work well with the files, it’s easiest to add a newline after the end of every sentence (I usually hard-break my lines at 80 chars as I write in Vim).

I have contributed to papers in Microsoft Word (usually originating with collaborators). It works OK, and the track changes / comment tool can be really useful, though a distressing number of collaborators seem to send you back a ‘clean’ document with the tracking dropped. Whether that’s due to ignorance of the tools, compatibility with different versions of Word, or an attempt to bury any information about which of your changes they reverted, I do not know. Certainly it makes me respect them less both academically and professionally. It is most incredibly frustrating to be editing a sentence, not sure whether you’re applying the same change again, undoing an important correction or what.

I typically plot data in GNUPLOT or XMGRACE, sometimes also in Python’s Matplotlib (though this is much less deterministic - the output depends on the specific version you have installed, and it can be extremely frustrating to reproduce a tweaked diagram). I’ve found some useful websites on tips + tricks for plotting, useful beyond an immediate answer to resolving a problem.

Writing scientific papers

Useful general resources

Colour

Writing

Plotting

Git / Latex / Markdown

Ambient music for headphones in noisy offices

Jarvist Moore Frost

Electronic structure theory

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