Hypocrisy inside open access journals
Update 2: Peter Binfield writes in the comments below that PLoS One has begun accepting LaTeX. Hooray!
Update: someone pointed me to the Topaz project, which looks promising!
I am currently preparing an article for submission to an open access journal (PLoS One, to be specific). I have just learned that PLoS One, like many other journals, requires all articles to be submitted in either .doc or .rtf format. But why do I care? My article was originally written in the open-source LaTeX system and intended as a conference contribution. The article deals heavily in math and statistics and makes use of LaTeX’s excellent equation typesetting abilities. As far as I can tell, it’s no simple matter to convert a LaTeX document with equations to M$ Word format.
How can it be that the leaders of the open-access journal movement require submissions in a closed and proprietary format? Didn’t the open-access journal movement draw at least some of its inspiration from the free software movement that predated it by at least 10 years? I presume the answer to this question lies at least partially with the proprietary nature of publishing and typesetting systems in common use at publishing houses. The good people at PLoS probably made a decision to purchase existing proprietary publishing software for their operation rather than investing in an alternative that supports open standards. And sadly, they now probably view change as too expensive.
To their credit, the topical PLoS journals do accept papers written with open-source software such as LaTeX, but that policy has only been in place recently. The editorial office converts LaTeX submissions on a case-by-case basis. Last year I published a paper authored in LaTeX in PLoS Genetics. While I was very happy that I didn’t have to do the conversion myself, I think that the PLoS approach (and that of other journals) essentially amounts to applying band-aids to a broken publishing system. It is not a good long term solution.
We need a scientific publishing system that is founded on open document standards and open source software. Viable alternatives such as OpenOffice exist, yet I can not rely on OpenOffice to save complex equations in Microsoft Word documents (it works fine in the native OpenOffice format). PLoS should lead the way in revolutionizing scientific publishing, and they should start on the inside by developing a publication process based on open standards. After five years of PLoS, why are we still without a viable open-source platform for scientific publishing?
In the meantime, I have to carefully consider whether it’s a more effective use of my time to painstakingly convert my document to Word and support the status quo, or whether I should instead spend that time adding content that would make my article appropriate for a journal that will accept LaTeX. Reformatting documents is mind-numbing, while submitting elsewhere might actually involve some interesting work.
February 13th, 2009 at 2:08 am
Have you tried latex2rtf?
February 13th, 2009 at 12:02 pm
Aaron – the good news is that PLoS ONE is on the verge of accepting LaTeX files as standard (literally in the next few weeks). If anyone would like to submit in LaTeX right now then they can form part of a ‘test group’ of authors. In this case, they can contact me directly.
Pete Binfield
Managing Editor, PLoS ONE, pbinfield at plos [.] org
February 13th, 2009 at 3:01 pm
@Ian: Yes, I did try latex2rtf, in fact I tried all the options listed on the PLoS page for converting latex to Microsoft-friendly formats. Of the bunch, latex2rtf did the most admirable job. If I absolutely had to convert the document myself, I would definitely use that software as a starting point. Unfortunately, latex2rtf stumbled over several of the equations. They do not appear at all when the document is opened in OpenOffice 3.0. I also have MS Word XP running in wine, but the equations turn up with LaTeX commands still embedded, and when I launch the Equation Editor the equation disappears entirely?! Nor do the equations appear in OS X’s TextEdit, but maybe that’s not surprising. I had Office 2007 running in wine at one point and recall that at least some equations did appear but weren’t editable — wine balked at loading the equation editor. Could it be that if I used Office 2007 on Windows that everything would just work? I’ve been trying to exterminate all Microsoftware from my laptop, but maybe that’s too ambitious…
@Peter: That’s great news about PLoS One beta testing LaTeX submission, yes, I would like to be part of that group. I never expected anyone from PLoS to read this post, much less respond, so maybe I can ask you more directly: is there any hope of having a scientific publishing platform that is based on well-supported open document format standards? Such a system could do the entire publishing industry a huge favor by helping them move away from closed-proprietary software, cutting costs and improving operability, and most importantly, enabling me to avoid microsoft entirely :^) I do think LaTeX support at PLoS One would be great, but it’s not a good general solution… By its very nature, TeX is inherently difficult to support because its command language is not well specified and zillions of variants and extensions exist. That’s where the cooperatively developed XML-based standards come in.
February 13th, 2009 at 5:29 pm
Jonathan Eisen just pointed me to some comments about this post on his friendfeed (http://friendfeed.com/treeoflife). Somebody there points out the Topaz project (http://www.topazproject.org/). I had not come across Topaz before, but it looks like they’re well on their way to addressing exactly the issues I raised above. So cool! That really made my Friday.
February 16th, 2009 at 3:47 am
[...] Hypocrisy inside open access journals (The secret microbe) [...]
March 16th, 2009 at 4:22 pm
As an update, PLoS ONE is now open for LaTeX submissions
http://www.plos.org/cms/node/451
Pete Binfield,
Managing Editor, PLoS ONE
October 28th, 2009 at 6:36 pm
As many of you, I am very sympathetic to PLoS and its open-access policy but cannot understand the choice of a Word-based option, specially for its mathematically oriented journals. Although it’s certainly good news that they now accept LaTeX submissions, we are still left with all the typographical imperfections derived from the suboptimal format all the manuscripts end up being converted to. Unnatural spacings in mathematical expressions, ugly mathematical fonts, or weird kernings are a sad and pervasive proof that PLoS made a poor choice.
Possibly unrelated to the previous point: can anyone tell me the advantages of accepting only figures in tiff format (bitmap format)? Judging from the pixelation visible in the figures of too many articles, quality cannot be the reason behind this restriction.
Sorry for the rant.