New paper on faster X effect in Drosophila – sort of…

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We have found evidence for faster X hypothesis on the level of gene expression in Drosophila embryos. Since March we are battling to publish it and besides the usual stuff from reviewers the situation got complicated by the fact that another group has their paper accepted on the same subject in the same journal where we are being reviewed. Scoop alert.

Well, Casey Bergman, as usual, had an excellent idea to place the manuscript on the arXiv archive. So here it is :

Melek A. KayseriliDave T. GerrardPavel TomancakAlex T. Kalinka An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis

Population genetics is actually very well represented in the arXiv with a lot of labs posting their pre-prints there (including Casey).

More generally, it got me thinking why haven't we done this back in March and in fact why don't we always place the manuscript on archives at the time of submission. Such paper is ready for prime-time. Its written the way you want it, before the combination of editor and reviewer comments molds it into something else (which is not always better). By placing it on the archives you establish a precedence for your discovery. People can actually use your data to inform their follow up experiments, its easy to share with collaborators and competitors (just send them a link) etc. Check out Casey's blog entry which drove this home for me.

You may object that in biology this is inviting others to scoop you. Yes, most biologists are paranoid to even write something in an abstract at a conference, not to mention publishing an entire paper in an non-peer reviewed archive. But upon reflection I disagree with that position. When your paper is so finished that you are willing to try it at a journal, it means you are going to publish it somewhere relatively soon. Lets say within a year, if there is particularly strong opposition. Its really unlikely that someone will catch up with you at this point. And if so your precedence is established. The archives like arXiv give you an opportunity to update the paper, for example everytime you rewrite it to resubmit or when you have the final journal-accepted version. This means that whatever the reviewer have made you do to your baby (I mean paper), its out there for everyone to see!

The main argument against archiving is the worry that some journals will consider it prior publication that will disqualify your submission.

Check out this excellent website on journal policies : SHERPA/RoMEO

In fact, most journals including Nature, Science and of course PLoS allow you to archive your manuscript BEFORE you submit (PLoS is among the so called 'green journals' which actually enables archiving at any stage before, during or after review). Ok, if you want your paper to ultimately come out in Cell press, don't put it on archives before it is accepted or take this as another reason to boycott Elsevier.

Have I missed something? Feel free to comment. I propose that JEDI's start doing pre-print archiving to continue the reform of publishing for better transparency and accessibility of research results.




  1. Eduardo Moreno

    September 13, 2012

    I agree, I think prepublication is a good tool, and I have used it in the past also, mainly the Nature Precedings (RIP). I think it could make a good topic to discuss in Lisbon.

  2. Fer Casares

    September 20, 2012

    What do you think go FAC1000 research ( I had been thinking to launch a similar thing myself! Quick publication, data availability, open peer-reviewing and impact measured by how much your paper is cited.

    • Pavel Tomancak

      September 21, 2012

      I guess it depends whether the F1000 people will really review the submissions systematically and in an unbiased manner. Otherwise there is the danger that the reviews will be endorsements from friends or attacks from enemies.

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