Wednesday, December 24, 2014

Do preprints count for anything? Not according to Elife & G3 & some authors ..



Well, just got pointed to this paper: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms | eLife by Martial Marbouty, Axel Cournac, Jean-François Flot, Hervé Marie-Nelly, Julien Mozziconacci, Romain Koszul.  Seems potentially really interesting.

It is similar in concept and in many aspects to a paper we published in PeerJ earlier in the year (see Beitel et al., 2014 Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. (2014) Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415 http://dx.doi.org/10.7717/peerj.415.

Yet despite the similarities to our paper and to another paper that was formally published around the time of ours, this new paper does not mention these other pieces of work any where in the introduction as having any type of "prior work" relevance.  Instead, they wait until late in their discussion:
Taking advantage of chromatin conformation capture data to address genomic questions is a dynamic field: while this paper was under review, two studies were released that also aimed at exploiting the physical contacts between DNA molecules to deconvolve genomes from controlled mixes of microorganisms (Beitel et al., 2014; Burton et al., 2014).
Clearly, what they are trying to do here is to claim that since they paper was submitted before these other two (including ours) was published, that they should get some sort of "priority" for their work.  Let's look at that in more detail.  Their paper was received May 9, 2014.  Our paper was published online May 27 and the other related paper by Burton et al. was published online May 22.  In general, if a paper on what your paper is about comes out just after you submit your paper, while your paper is still in review, the common, normal thing to be asked to do is to rewrite your paper to deal with the fact that you were, in essence, scooped.  But that does not really appear to be the case here.  They are treating this in a way as "oh look, some new papers came out at the last minute and we have commented on them."  The last minute would be in this case, 6 months before this new paper was accepted.  Seems like a long time to treat this as "ooh - a new paper came up that we will add a few comments about".

But - one could quibble about the ethics and policies of dealing with papers that were published after one submitted one's own paper.  From my experience, I have always had to do major rewrites to deal with such papers.  But maybe E-Life has different policies.  Who knows.  But that is where things get really annoying here.  This is because it was May 27 when our FINAL paper came out online at PeerJ. However, the preprint of the paper was published on February 27, more than two months before their paper was even submitted.  So does this mean that the authors of this new paper do not believe that preprints exist?  It is pretty clear on the web site for our paper that there is a preprint that was published earlier.  Given what they were working on - something directly related to what our preprint/paper was about, one would assume they would have seen it with a few simple Google searches.  Or a reviewer might have pointed them to it.  Maybe not.  I do not know.  But either way, our preprint was published long before their paper was submitted and therefore I believe they should have discussed it in more detail.

Is this a sign that some people believe preprints are nothing more than rumors?  I hope not.  Preprints are a great way to share research prior to the delays that can happen in peer review.  And in my opinion, preprints should count as prior research and be cited as such.  I note - the Burton group in their paper in G3 also did not reference our preprint in what I consider to be a reasonable manner.  They add some comments in their acknowledgements
While this manuscript was in preparation, a preprint describing a related method appeared in PeerJ PrePrints (Beitel et al. 2014a). Note added in proof: this preprint was subsequently published (Beitel et al. 2014b). 
Given that our preprint was published before their paper was submitted too, I believe that they also should have made more reference to it in their paper.   But again, I can only guess that both the Burton and the Marbouty group just do not see preprints as being respectable scientific objects.  That is a bad precedent to set and I think the wrong one too.  And it is a shame.  A preprint is a publication.  No - it is not peer reviewed.  But that does not mean it should not be considered part of the scientific literature in some way.  I note - this new paper from the Marbouty group seems really interesting.  Not sure I want to dig into it any deeper if they are going to play games with the timing of submission vs. published "papers" as part of how they are positioning themselves to be viewed as doing something novel.

8 comments:

  1. Hi Jonathan,

    I noticed the omission as well! I do have some sympathy with people who don't know how to deal with preprints, but the almost complete omission of any discussion of your published, peer-reviewed paper is quite a bit stranger. Regardless, I think the best thing for science would have been for them to embrace the preprint, discuss it in some detail, and compare and contrast their results with yours. The other thought I have is this: do people who argue for precedence really think that this kind of interaction is going to lead in positive directions for their future work? It seems a bit shortsighted.

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  2. I think citing preprints is a grey area. Certainly there are some folks that would never cite something that isn't peer reviewed , which i may not agree with, i can see the logic to. As an example, where should preprints reside relative to other non-peer reviewed things like presentations/posters/datasets that effectively never get cited. Like if i wanted to use some data that Jonathan presented in a seminar as support for my argument, its hard to imagine that passing muster. Some people would say the same for preprints. The more visibility/discussion preprints get the more people will get comfortable with using them, and how to place them in the right context.

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    1. Dave

      I think one should cite EVERYTHING that either had an impact on the work being reported or is relevant as prior related work. That would include presentations, posters, letters, books, Tweets and preprints. Obviously it would be hard to completely survey the scope of all information all the time. But if it is out there and if it is "published" and if it is relevant it should be referenced.

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  3. something similar happened recently when I reviewed an article for Microbial Cell Factories. It was a recombineering technique article. The authors failed to cite several previously published articles on the same subject - whilst claiming that their work was the original/novel - first ever example! Moreover, it turned out, after a bit of research, that their MCF method was a tiny tweak on a method they had published previously! Perhaps people think that there are so many articles/journals around now that no-one will notice??

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  4. Tweets Jonathan, really? As if there isn’t enough drivel to sieve through out there, now I have to bother with incomprehensible, misspelled shorthand? That sounds like a complete nightmare. (Pardon the tone, my mood seems to be affected by working this late in the year)
    I do think there’s merit in the conversation, however, the way you phrased it, it strikes me as being rather petty. Sure, they read your pre-print. Some phd student somewhere broke down crying. Her years of toil have just gone out the window, blown out of the water by what you might call “similar work” that went for the “fast” (or at least fastER) route into the open.
    And your objection is that you didn’t get enough credit for having scooped them? Who in their right mind would do that? Sure, it would be lovely to do, in some imaginary lala land where our lives don’t depend on not doing it (by us here I mean the lowly phd student; I’m sure you can afford to uphold a higher standard). Don’t you think this first to publish thing is completely mental? Unless you think they wrote their paper after reading yours, you must give them that they had the idea and did the work and thus are separate originators of the same nugget of knowledge (and they mentioned that you also came up with it, but do that every so subtly, cause otherwise they’re not getting published). They only had the poor judgment of going through pesky peer review, silly them.
    Can you see how a claim could be made for this pre-print thing being a bit of a cheat? You don’t have to polish your figures, the text can still be a bit poor but the idea is out there. Shaves plenty of time off of an actual submission and you get to take all the credit. I’m not saying you did this, but if we go for all this being fair game, can you see people doing it? It won’t be apocalyptic or anything, but would create a bigger mess.

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  5. You say "Clearly, what they are trying to do here is to claim that since they paper was submitted before these other two (including ours) was published, that they should get some sort of "priority" for their work."

    I do not agree: they claim that, although other work has priority, their work should not be seen as a copycat since their paper was submitted before the other two were released.

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  6. Fair point. But again, our paper was released before theirs was submitted. I think they could have just said "just before our paper was submitted ..." and it would be clear their work was not a copycat.

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