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UPDATE: Be sure to read the comments below, and my response

As a newly-minted PhD student, I was talking with a friend about writing papers.  “Use LaTeX”, he said.  I thought he meant the rubbery material commonly found in lab gloves.  But apparently not.  LaTeX (pronounced “lay-tech”) is typesetting software that he used for writing papers.

Eager to be on the cutting edge of scholarship, I spent a few days learning how LaTeX worked, how to insert symbols, figures, and tables.  I even produced my thesis proposal with it.  But my supervisor used Word exclusively, and I had no compelling reason to use LaTeX over Word, so I switched back.

Fast-forward a few years.  Now, everyone should be using markdown in a plain text editor, doing statistics in R, uploading versions to github or figshare, and managing citations with JabRef, BibTex or Mendeley.  Apparently, Word, Excel, Endnote, and SPSS are things of the past.  Special sessions at the 2013 Ecological Society of America meeting seem to be the nail in the proverbial coffin.  Some are even calling these new tools essential pieces of software for students.

There is a movement afoot to move the process of writing science out of Microsoft Word, and into other “better” formats like LaTeX, or Markdown with the argument that “researchers shouldn’t waste time on formatting, just the text of what they’re writing”.  They can then keep version control using something like GitHub, and invite collaborators to do the same.  This also keeps science open, since scientists aren’t beholden to a proprietary file format.

But in my mind, there are two arguments: the practical (A is tangibly better than B), and the philosophical (A is better than B because of ethical, moral, or philosophical reasons).  These are both important discussions to have, but in this post, I’m going to focus on the first.

Learning Curve

I’ve used Word for my typing needs since about 1997 (prior to which, I used Clarisworks, and WordPerfect, two functionally similar programs).  I know how to easily insert commonly used non-Roman letter symbols (like β), and most of my work (>95%) doesn’t extend beyond simple mathematical symbols or diacritical marks (like ±, Σ, or é).  I use minimal formatting in Word (bold, italics, line numbers, maybe changing the font size of the title), and after almost 20 years, I’ve gotten pretty good at Ctrl-B (or, in the last 10 years, command-B).

Coauthor inertia

The vast majority of my work is collaborative to some degree.  Whether it’s a supervisor or boss, or a larger group of other researchers, someone’s going to read, comment on, revise, and critique any paper I write before it goes to the journal.  Word is ubiquitous, while these other methods are not.  And like me, my coauthors are most familiar with Word, and use its Track Changes feature to make suggestions, comment on text, and insert their own edits.

Reference integration

This is really the deal-breaker for me.  Since 2005, I’ve used Endnote to manage my reference papers, and I use the “Cite While You Write” feature in every paper.  Basically, this means I can write something like “Birds have feathers, and can fly (Gill 2007)”, and Endnote will drop the full citation (in the specified format) in the Literature Cited section.  How cool is that?  It also makes reformatting for different journals relatively easy.  Yes, there are other types of programs that can do that for you (e.g., BibTex), but there’s a learning curve, and many hours updating citation keys so that there aren’t 4 “Jones2007”s.

Cost & Access

Word (and to a lesser extent, Endnote) are readily available at most research organizations, or are relatively cheaply obtained (let’s say a maximum of $200).  If you want to keep your projects private, GitHub will run you $7/month (or about $200 over 2 years), while the rest are free.  Word and Endnote are perpetual licenses.  True, universities and research organizations pay for these, but it’s unlikely that will change since the programs are used by non-academic staff, too.

Academic hipsters

The following was just tweeted from the 2013 ESA conference

The implication, whether intended or not, is that those of us still using Word aren’t doing reproducible research.

Now before folks get their open sources all in a knot, I’m not just being a Luddite.  I use R regularly.  I’ve also used LaTeX for one manuscript.  I’m not advocating against using any of these tools if they’re the right tools for the job.  What I’m saying is don’t use them for the sake of using them–a form of what I could call academic hipsterism.

Case in point.

My experiences with other early-career researchers, collaborators, supervisors, and grad students is that 99% of them will keep their data in Excel, write the manuscript in Word, and some will integrate references using Endnote (important point: the same applies to non-Microsoft products like Apple’s Pages and Numbers, OpenOffice etc.).

And for a good chunk of the statistical analyses I do, or that are in papers I read, review, and co-author, it doesn’t matter if they were done in R, or SPSS, or SAS, or Minitab, or JMP, or many other common statistical programs.

Are there issues with all these pieces of software? Yes. Are there issues with any piece of software? Yes.  Has a manuscript in ecology/zoology been rejected because the authors used a particular program to compose their text? I don’t think so.

Jeremy Fox at Dynamic Ecology wrote about how he keeps on top of the literature.  His point was that his system works for him, and yes, there are other systems out there.  The interface that I set up on my computer between Word and Endnote when I started my MSc aeons ago still works for me.  It also works with my coauthors, all of whom use Word as a primary text editor for manuscripts, and it works for journals, all of which accept submissions in Word format, or the easily-generated PDF.

Are tools like markdown, LaTeX, and github useful? To some, they are.  But they’re not yet useful to me. If they look useful to you, check them out – they just may be. But don’t feel beholden to adopt the latest software trend.

30 years ago, John Weins wrote in The Auk on the perils of word processors:

John Wiens on the perils of using word processors in an editorial in The Auk, 1983

John Wiens on the perils of using word processors in an editorial in The Auk, 1983

Has word processing improved how science is disseminated? Of course.  Perhaps we could say the same for the current crop of new tools in manuscript writing and statistics. But not for me, at least not yet.

I’m not saying these new pieces of software are terrible and useless.  I’m saying that I’m not inclined to use them because I don’t see how they are materially better than my current system.  Sometimes, it seems like the argument from the non-Word proponents is that “our way is better than yours in every case” (see the quote tweets above), which isn’t the case.

For what it’s worth, I’m going to have a lengthy skype chat with Andrew MacDonald later this month about the advantages of Markdown, and integrating it with BibTex.  I might even try it.  I’ll let you all know how it goes.

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As a quick note, I’m off to the Society of Canadian Ornithologists meeting in Winnipeg, and won’t be as quick to approve new commenters, or respond to comments. Thanks for your patience. -AB

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