Posted by: Kay at Suicyte | May 31, 2007

Early access blues

One part of my job is staying informed on the latest developments in my field of expertise. Being a bioinformatician with a focus on protein function prediction, I could switch biological topics without too much effort – at least I don’t have to worry about setting up new assay systems, buying new antibodies, making new constructs, and so on. This flexibility is an advantage for me, as compared to experimentalists. Unfortunately, this flexibility also applies to my competitors, and I’d rather not count the number of occasions where I have been scooped by somebody who was working on a completely unrelated topic yesterday. Or last month, at least.

Thus, it is of crucial importance to have access to the latest literature, otherwise I would clearly lose a competitive edge. I am sure this will apply to most other researches, no matter what topic they are working on. One of the uglier consequences is that I hardly read proper papers anymore, but mostly ‘early access’ or ‘advance access’ or ‘immediate early’ or ‘in press’ or ‘preprint’ versions of papers. Most journals do this – the name varies – but the idea is the same: soon after acceptance, the author’s version or some slightly reformatted version of the manuscript is made available online. As with most journals, the editorial process is based on electronic manuscripts anyway, this early-publication process requires only minimal effort from the publisher and can be done blazingly fast.

No mistaking – I do like the early access idea very much. I would like it even better if my competitors did not have this option (ok, ok, just an idea) but this not an option. What I don’t like is the fact that these preliminary versions are often so ugly. I am not talking about fonts and stylesheets here, but rather on annoyances like 80 page manuscript with figures and figure legends separated by 20 pages, not to mention that both of them are 60 pages away from the place where the figure is referenced in the text. Even if you don’t read early access papers, you will have encountered these manuscripts as a reviewer.

Well, there are some journals doing it differently: Nature and PNAS don’t use these ‘alpha-test’ versions of the accepted papers for early publication but rather publish ‘release candidate’ versions that look like the final paper but without page numbers. Typically, only PDF versions are provided for early-access papers, but this is ok – I always print out the PDFs and read them on paper; I cannot get used to reading stuff off the screen. Looking up things is ok, but for reading an entire article I need a paper copy.

The journal Bioinformatics provides early access PDFs that look nice but are huge files often more than 10 times the size of the final version. Many other journals that I read frequently subscribe to the ‘ugly manucript’ option: the BMC journals, JBC, MBC, and many others. Science has found an intermediate solution: they do some reformatting and so avoid the 80 page monster papers, but their early access articles look ugly nevertheless: all the figures are at the bottom and the legends are someplace else.

Is all of this necessary? I don’t know. It is understandable that journals want to be fast, and there is no way of being faster than just publishing the version received from the authors. Several journals make these ‘author versions’ available without charge, while one has to pay for the final typeset version. I don’t have any objections. What I am not sure about is whether it is nowadays still necessary to force the authors to submit ‘ugly manuscripts’. There certainly was a good reason in former times, when manuscripts were sent to the journal on paper (3 copies with glossy photoprints), the peer review was still done by human beings, and for typesetting everything had to be keyed in by journal staff. Ok, the middle bit was supposed to be a joke. At that time, it was probably reasonable to ask for double-spaced manuscript pages with ridiculous margins on the left and right (for accommodating the correction marks) and with figures and figure legends separated from the main text, as they were typeset in a different way.

Many things have changed since then – we have online submission systems, peer review is done by soulless machines (at least the one for my last paper), and typesetting is no longer done by re-keying in the whole manuscript text. Shouldn’t it be possible to allow the authors to submit their manuscript in a more readable format? I am thinking of single-spaced pages in a pleasant font, with figures inserted at the proper position in the text, and with the figure legends right where they belong! It probably wouldn’t even be necessary to require such a manuscript style, but it should at least be allowed.

I am quite optimistic that many authors would like the idea, as their manuscript would look nicer and more appealing to the reviewers. As a frequent reviewer (at times, I can be a soulless machine myself) I would also prefer to read manuscripts with a basic layout. And finally, as a reader of early-access papers, I would clearly love this idea.

As usual, there are certainly some disadvantages to my proposal. At the moment, I cannot think of any, but I am sure you will point them out. But please – don’t make me use LaTeX templates….



  1. I can really relate to this :). I even sometimes bookmark/download the early online version to have a quick look but wait for the final version to read it properly.

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