The case for open preprints in biology

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Desjardins-Proulx, Philippe; White, Ethan P.; Adamson, Joel; Ram, Karthik; Poisot, Timothée; Gravel, Dominique (2013): The case for open preprints in biology. figshare.

http://dx.doi.org/10.6084/m9.figshare.655710
Retrieved 21:31, Dec 26, 2014 (GMT)

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An article on preprints in biology. It was developed on github (https://github.com/PhDP/article_preprint) and appeared in PLOS Biology (http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001563):

Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, et al. (2013) The Case for Open Preprints in Biology. PLoS Biol 11(5): e1001563. doi:10.1371/journal.pbio.1001563

Comments (8)

  • I wish this discussed the precedence issue more. I still always have that lingering fear that if I post a preprint of my work, or blog about my work (and post is on figshare, of course!), that if I'm not quick to the trigger on getting it published, someone else can either take my work or quickly replicate my work (since I just outlined it in the preprint/blog!). AFAIK there's nothing I can do about that except complain and point to the DOI I have that shows I have precedence, but what does that get me? They're the ones with the publication.

    20/03/2013    by R. Olson

  • Thanks for the comment! I agree it can be a problem. In physics and mathematics, the arXiv publication matters more than the final publication to establish precedence because it's more fair, after all a paper can be finished/submitted earlier and still be published months later, but the arXiv version can establish exactly when the research was ready to be submitted. It's true that, since arXiv is not very well known in biology, people might overlook the arXiv paper and just look at the final publication but I don't see how it could stay that way for long, biologists are increasingly aware of public preprint servers.

    Also, I think the rise of search engines like Google Scholar, which doesn't care whether the paper is published in Nature or arXiv, is going to emphasize what matters: content. And an arXiv paper has just as much content as a formal publication.

    20/03/2013    by P. Desjardins-Proulx

  • If I can just chime in about the precedence issue: "stealing" material which is made public, and have a DOI, and is available for all to see, will probably be extremely damaging to your reputation. Especially so because it will be obvious that there was a precedent. Taking the work would be outright stealing, and IMO a good way to get blacklisted. Replicating the work before you submit (i.e. in a quick and dirty way) would just indicate a lack of ethics. I would not worry too much about that.

    By the way, papers on figshare are released with a particular licence which obliges you to attribute to the original paper: not doing so will be licence infringement, and I think that most publishers would not want to be "that guy" who published something in violation of an open access licence. The OA crowd will be all to happy to get the torches and pitchforks!

    21/03/2013    by T. Poisot

  • R., as we've discussed, I'd be more impressed by this objection if (a) people didn't present prepub work at conferences all the time in biology, and (b) if this kind of precedence stealing happened.  As it is, I'm willing to take the chance.  And it's working out, I think.

    23/03/2013    by C. Brown

  • Great paper, and coming at a great time. I have taken the liberty of providing some comments. Thanks for inviting us to do so.

    1 Introduction  

    Para 1. I think it could probably afford to include 5) no bottle-neck thus increasing likelihood of all research getting made known not just that favoured by a small subset of reviewers and 6) increasing likelihood of negative findings being published thus reducing the bottom drawer effect.

    2. The Case for Public preprints.

    The  Caption for figure 1 might say ‘inform or be integrated’ into…

    In your point about reputation in the introduction it may be worth saying that as well as allowing someone to start building a reputation sooner, the overall quality of reputations will be better as well with more diversity of reviewers/citers etc.

    One difficult point to make, but still important is the idea that there is no central ‘authority’. The ‘rich enough community’ almost makes it but the ‘quality of an idea’ which would be considered and judged by all in a community – rather than that which happens  now and only gets published  after anointment by some guru (or 2 peer reviewers) – is much better in the long run.

    ‘…publication and acceptance dates do not accurately characterize who came up with an idea first.’ I would prefer to see ‘accurately’ replaced with ‘necessarily’ but it’s a minor thing.

    3 Preprints in Biological Sciences

    Figure 2 makes the point really well.  [I still cannot understand why biologist apparently differ in their collective attitude in such a marked way.]

    The Inglefinger rule sucks in many ways in the current world. Some biologists spend weeks at a time re-writing a paper to republish with a slightly different spin thus doubling their numbers but frankly, who cares – this will come to be understood by all those peers out there and their reputation will be adjusted accordingly. [OK this para is a rant rather than a comment]

    Table 1/2 and ¾ headings /caption seem to be  mislabelled but I guess you know that.

     Table 1 caption (labelled table 2) makes a separate (but sensibly related) point rather than describe the table. Perhaps it should do both?

    5 Conclusion: 

    In the first paragraph I reckon the damage to morale (leading to imposter syndrome?), and the chronic and widespread waste of biologists time redrafting, editing and re-submitting warrant a mention too. (imagine the cumulative amount of time wasted for many biologists resubmitting a number of times for a number of papers over a career.)

    The sentence:  ‘It is the first barrier against the fraudulent and poor quality science susceptible to impede scientific progress’ reads a bit strangely. Perhaps it should read:  ‘It is the first barrier against fraudulent and poor quality science which can so impede scientific progress’

    Peer review immediately after this could also mention that limited reviewers can lead to fads or fashion in science and encourages postgrad students to follow, not lead, with new ideas.

    7. Funding:

    Probably should drop the .25 cents found at a coffee machine J

    Some claim they like a publishing bottleneck because it reduces the work they have to do finding good papers. But , like Moore’s law - its equivalent for search is improving all the time.  (see http://www.forbes.com/sites/roberthof/2013/04/29/interview-how-ray-kurzweil-plans-to-revolutionize-search-at-google/ )

    One other advantage of using online open publishing properly is immediate access (ie: train of thought) to the material cited. This can potentially improve ideas generation and also quickly allow reviewers to identify potential misinterpretations of the cited work.

    Hope some of my comments are useful. I like your approach and would love to collaborate with you guys someday! 

    01/05/2013    by A. Couch

  • Great article!

    I am willing to help spreading the word for open science and convince my colleagues to pre-publish their work in well established and known repositories. The problem lies in the heart of the evaluation system in the academic world. Scientists are afraid that their pre-published work will be criticized by people who evaluate their CV for a position or a grant. The "system" just count the same old stupid metrics that mean nothing. They only count the publications in IF journals and consider any other form of publication as beeing of low quality. For this reason, most colleagues of mine, while agreeing that the system has to change and that repositories are good for science and for themselves, they hesitate to publish something before the official peer-review process, because they are afraid that they will lose the value of their work. I believe that the reason researchers in biological sciences do not use the pre-print option that much is that they find themselves within a cruel eliitstic system of evaluation that causes stress and finally reduces the impact of science. Maybe other scientific fields are more open and their system is fair.

    01/05/2013    by A. Papageorgiou

  • Thanks for this paper. I recently contributed to a paper pre-printed on biorxiv.org (most of the collaborative work done with Google Services) - it is interesting to see how this new publishing world evolves (so fast).
    I would be interested to evaluate also f1000research and now figshare has Projects wich could allow to do similar "cloud" research like on GitHub or with Google (Docs/Groups).

    12/12/2013    by C. Rottensteiner

  • I was really glad to hear about biorXiv.  When we wrote the paper, we didn't know two preprint servers for biologists would pop up right away.  Now our paper is becoming obsolete, which was the whole point (we were making a case).

    12/12/2013    by J. Adamson

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