Faculty of 1000

Post-publication peer review

Publish or perish – a question of ethics

Posted by Callum Anderson on 15 March, 2010

I got a very strong sense of deja vu when leafing through PLoS Biol recently. I was sure I had seen something very similar to Jeffrey Shaman’s paper Absolute Humidity and the Seasonal Onset of Influenza in the Continental United States before.

A quick check on PubMed proved me right. I found the following, published two months earlier, in PLoS Curr Influenz:

Absolute Humidity and the Seasonal Onset of Influenza in the Continental US
Jeffrey Shaman,* Virginia Pitzer,† Cecile Viboud,‡ Marc Lipsitch,§ and Bryan Grenfell

PubMed ID 20066155
http://www.ncbi.nlm.nih.gov/pubmed/20066155

Because this was PLoS, I was also able to print the full paper and compare. I couldn’t find any differences whatsoever between the two papers. In fact they were exactly the same except for a reshuffling of author order and an abbreviation in the title.

A quick check back on PLoS Biol and I notice that someone else has seen the discrepancy. A comment attached to the article begins with the following

Compare, published in PLoS Currents influenza (dec 18th)
Absolute Humidity and the Seasonal Onset of Influenza in the Continental US
Jeffrey Shaman,* Virginia Pitzer,† Cecile Viboud,‡ Marc Lipsitch,§ and Bryan Grenfell

PubMed ID 20066155

with (and not cited, if I am not mistaken)

Absolute Humidity and the Seasonal Onset of Influenza in the Continental United States (23 february 2010)

Jeffrey Shaman1*, Virginia E. Pitzer2,3,4, Cécile Viboud2, Bryan T. Grenfell2,4,5, Marc Lipsitch6,7,8

When this poster commented, only one of the articles was listed in PubMed. A search for “Absolute humidity” on PubMed today however yielded the following results [click it to get full size]

A PLoS spokesperson had answered the comment in less than 3 hours (perhaps they anticipated something being said). Their official line was as follows

PLoS Biology is fully aware of the authors’ submission to PLoS Currents referenced above. PLoS Currents is a website for immediate, open communication and discussion of new scientific data, analyses, and ideas in a critical research area. The work is screened by experts, but is not subject to in-depth peer review…

Our policy until now (February, 2010) has been to allow resubmission of PLoS Currents content to another PLoS journal. However, the decision to include Currents in PubMed (and PubMed Central) has caused us to reconsider the status of content communicated via Currents, relative to other journals.

I am certainly not convinced by this argument. Having personal experience of getting journals into PubMed, it is not something that happens immediately; the typical process is eight to twelve weeks and PLoS Curr Influenz was already accepted by PubMed in 2009. The accepted date on the re-submitted paper in PLoS Biol was January 20, 2010.

And even worse still, the received date of the paper by PLoS Biol was September 10, 2009. PLoS Curr Influenz did not even accept the duplicate paper until December 18, 2009.

The dates simply don’t add up, a journal doesn’t just email PubMed and expect to show content the next day, and feigning innocence just makes PLoS look at worst deceitful and at very best incompetent. If PLoS was aware that the paper had been submitted to both journals, and was aware that PLoS Curr Influenz would be listed on PubMed, they should have made a full disclosure on the paper subsequently published in PLoS Biol.

Now, I am very much in favour of rapid communication journals, I think they represent an excellent platform to publish cutting edge research, but a distinction between these and traditionally peer-reviewed journals must be drawn somewhere. Should a publication like this really be submitting content to PubMed when their editorial policy allows re-submission in other PLoS journals? PLoS have been having their cake and eating it for a long time now. In a world where publication stats are frequently used as a method of judging the worth of a researcher, are the authors here benefiting twice from the same paper? And PubMed has a very clear policy on duplicate articles, which PLoS should know about.

So why didn’t they do it? Why didn’t they tell PubMed that they would be knowingly supplying duplicate articles? Well I do have a theory [snip-snip – F1000 Lawyers]… But it would be much better to see what you think.

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24 Responses to “Publish or perish – a question of ethics”

  1. Jim said

    I don’t agree with PLoS’s decision on this….and I would point out that if you moderate these comments and we start supplying theories (which I have), your F1000 lawyers may still be concerned.

    In any case, I would have no problem with people submitting manuscripts to Currents and being indexed IF they were not able to re-submit to one of the other PLoS journals without presenting something wholly new, and building upon the earlier paper.

    Alternatively I would have no problem with duplicate papers, so long as only ONE is indexed via PubMed.

    Getting two PubMed citations for effectively one paper is deeply unethical. Most research evaluation exercises don’t scrutinise the text of individual papers, thus duplicates could be passed off as distinct papers.

    In discussions about duplicate papers on other blogs, I think there was a consensus that duplicate papers could be justified only if the duplicate is submitted to a journal that operates in a different language, and is marketed only in that language.

  2. Kevin said

    Full explanation from the PLoS Currents FAQ:

    If I publish results in PLoS Currents: Influenza, will I be able to publish the work in another journal?

    “Our policy until now (February, 2010) has been to allow resubmission of PLoS Currents content to another PLoS journal. However, the decision to include Currents in PubMed (and PubMed Central) has caused us to reconsider the status of content communicated via Currents, relative to other journals. Some authors have used Currents to communicate drafts of almost final manuscripts (essentially preprints), and revised versions of the same articles have subsequently appeared in another journal. Indexing of both articles in PubMed could therefore lead to the unintended appearance of dual publication and misunderstanding about the relative status of the two articles. We are also aware that some journals (even before Currents was indexed by PubMed) considered publication in Currents to constitute ‘prior publication’.

    We have therefore revised our policy for Currents. For the articles already made available in Currents, and which might appear later in other journals in essentially the same form, we will work with PubMed to try and provide a link between related versions. Going forward, we feel that the Currents system is now sufficiently robust, via archiving in PMC and indexing in PubMed, that it would not be appropriate to resubmit the same content to another journal. PLoS Currents is therefore a channel for extremely rapid publication of new results – the work is screened by experts, citable and permanently archived”

    • Callum Anderson said

      Hi Kevin,

      I am not sure if you are defending PLoS here or not, but I will try to answer your point as best I can.

      In my opinion PLoS are simply paying lip service, appeasing the lawyers so to speak. The point I want to draw you to is where they say

      we will work with PubMed to try and provide a link between related versions

      The most recent article was published on February 26th and PLoS claim they were aware of the duplicate. As of March 15, 2010, no link between the articles has been made. And as I pointed out in my post, PubMed has a very clear policy on this. Why have they not notified PubMed of the duplicate?

  3. Bob O'H said

    Hm, why don’t they just push pre-print servers?

    My theory is lack of omniscience – they simply didn’t think this through. PLoS has form on this – publishing the Ida paper without checking that the name would be officially recognised, for example.

  4. NO DISCERNIBLE ETHICS PROBLEM HERE

    This is a tempest in a teapot. The PLoS Currents series is clearly not a refereed journal, but a venue for posting unrefereed preprints to solicit commentary and to publicize new, not-yet-refereed findings.

    There is nothing wrong with the fact — indeed it is highly desirable — that these posted preprints go on to be submitted to refereed journals (and if they get through the peer-review process without changing a word, good for them — though I doubt that happens often, if the refereed journal is one with high quality standards!).

    There is no problem about “multiple versions,” though it’s a good idea to start setting up the links and coordinations among multiple versions that will simplify the user’s life and get scholarship practice in the online/OA era up to speed (e.g., valrec).

    Researchers do, and always did, have the responsibility of ascertaining the track-record for quality standards of the journal (and author!) whose contents they are using, citing and trying to build upon.

    • Callum Anderson said

      I think you may be over intellectualising the debate Stevan, but I will answer you as best I can. In my opinion PLoS is established and large enough now to be treated in the same way as any other publisher. We can’t keep making excuses for OA just because the intention of the movement is ‘good’. It is not enough to

      get scholarship practice in the online/OA era up to speed

      The practices should already be there, and if not, shortcomings should be acknowledged. If PLoS says they will tell PubMed when they are submitting duplicate content, I fully expect them to do just that.

      OA can survive and even thrive on an even playing field, but dissemination of mistakes and subsequent learning is an important part of improving practice.

  5. If I am not mistaken, everything that is submitted to PubMed Central automatically shows up in PubMed. If anything, then this is a policy problem / question for the PubMed Central board, on whether or not they want to allow “rapid communications” in PMC. If they do, they should probably treat them as pre-prints / author manuscripts and not generate a duplicate PubMed entry, for them. I think it is unfair to criticize PLoS here – rather, NLM needs to adapt certain processes and policies.

    • Callum Anderson said

      Yes, you are correct in noting that anything deposited to PMC shows up in PubMed. All publishers know this too.

      On a completely unrelated note, it is much, much easier to get a journal into PMC than into PubMed.

  6. 1) The duplicate publication is certainly a source of concern, and I hope the authors (or PLoS) retracts one of the pair (most probably the Currents version),

    2) What really disturbs me is:
    “In fact they were exactly the same except for a reshuffling of author order and an abbreviation in the title.”
    I have not checked the two papers yet, but this statement is so disturbing for two reasons:
    a- there needs to be a clear explanation for why the last authors were swapped (even if on basis of equal contribution)
    b- if there was no change since December 18 till January 20, 2010 (the date of acceptance), does this mean that there was no significant peer review? or does it simply mean that the authors wanted to publish an “online early” version in Currents till the final Biology version comes out? This still needs to be clarified. What happened between Dec 18 and Jan 20?

  7. Ideally, I’d like to see clearly which papers have been peer reviewed and which haven’t. However, there are several journals on PubMed which are not peer-reviewed, so PubMed can’t really be the place to look up people’s publication record. PubMed also mixes reviews and original publications – with the option to screen each one out. All that would be necessary is to have filters (maybe at myNCBI?) for each publication category?

    There will be more new publication forms in the future, so this will not be the last time this issue comes up. As long as both publications are marked as different types of publications, I don’t see a problem with this. We should have more categories of publications – it has long bothered me that “short communications” are not clearly marked as such in databases: they look just like regular papers, unduly inflating someone’s publication record. Why should a “short communications” paper be equally weighted as a regular, fully controlled, multi-year study?

    I hope this example showed that one might just as well frame this not as a case of duplicate publication, but rather as one of inadequate categorization.

    Bjoern

    • Yes, there is a problem with PubMed of course. PubMed lists any article in Science and Nature–except ads; even letters-to-the-editor are indexed. To my knowledge, all journal editorials get indexed in PubMed, even if it they’re about what the editor thinks of the US president, or the Oscar winners! Surprisingly, Science Translational Medicine, for example, has not been indexed yet! This is also true about ISI of course. ISI Web of Science indexes some conference abstracts (e.g. in BMC Supplements) and counts their citations, while many peer-reviewed journals are excluded from that “Impact Factor” heaven!

      However, the paper in question in this blog post is not a “short communication,” and the question to be answered is why the authors deposited it in PLoS Currents while after it was submitted but before it was accepted in PLoS Biology? The timing is intriguing, but the entire thing can be fixed easily, I assume.

  8. Bob O'H said

    Hm. the underlying issue is whether we have a formal scientific literature. I blogged about this last year. But before you all run off and read that, I didn’t address this point.

    Clearly there’s a feeling that PubMed has a role in defining what is part of the formal literature (for those of us outside medical science, Web of Science fills the same shoes). In that case, they need to be careful about what they let in.

    Pre-prints are part of the grey literature, and will raise problems like this (it’s really no difference to the problem raised by publication in conference abstracts). Perhaps there is a demand for a system that will allow this literature to be recognised, but not as formally.

    Bjorn – WoS has a tag for article type, so you can filter by that. it shouldn’t be difficult for PubMed to do that too. perhaps it does.

  9. Name academic said

    . It was possible for many academics to discover the duplication. But, what about those who plagiarize and duplicate older papers, and what about those who translate foreign papers and claim to have done the research themselves. And can someone think of ideas piracy committed by reviewers in the peer review worldIs there anendto this dillema? Can journals take research more seriously instead of perceiving it as a lucrative business?

  10. Dr. J-B said

    While this may be perceived as an issue associated with the policies of PLoS, it is more of a problem associated with the evolving policies of Medline. There was a time when a listing in Medline was a reflection of the scientific rigor of a journal, a reflection that it had been published for approximately 2 years. Unfortunately, with the advent of PubMed and PubMedCentral, and the presence of public access advocates within the leadership of NLM, we are seeing accommodations being made to encourage OA journals like PLoS Current based on their willingness to deposit into PMC. It probably doesn’t hurt that the conceptual founder of E-Biomed, which evolved into PLoS, worked closely with the government’s because supporter of PMC.

  11. I was closely involved in the launch of PLoS Currents Influenza last August, so I’d like to clarify a few points if I can.

    The goal of launching PLoS Currents Influenza was and is to experiment with a potentially very powerful channel for research communication. Motivated by the H1N1 flu pandemic, we wanted to provide a channel to allow very rapid communication of new results, which would also be citable and archived.

    Authors write their content using Google Knol, submit it to a group of moderators for rapid screening, and so long as any major flaws aren’t found, the work appears immediately in the PLoS Currents Influenza site. The process is very fast and very cheap (there are currently no charges to authors), and we felt that a channel like this could work well for other topics and fields as well.

    When we launched PLoS Currents Influenza, it was not archived in PubMed Central or indexed in PubMed or in any other ‘formal’ indexing services. As pointed out, it takes a while for that to happen. We therefore felt that it was appropriate for content communicated rapidly through PLoS Currents to be
    submitted later to a ‘formal’ journal, such as a PLoS Journal.

    However, when the decision was made by the NLM to include PLoS Currents Influenza in PubMed Central and therefore in PubMed, we realized that the perception of the ‘status’ of the PLoS Currents Influenza content would change. When PLoS Currents content started appearing in PMC and PubMed in December, we therefore reconsidered our policy, and towards the end of February indicated that we no longer felt it was appropriate to resubmit content published in PLoS Currents to another journal.

    We have tried to explain why we have changed our policy in the FAQ that was highlighted above by Kevin. But further questions have been raised and I’d like to respond to these. First, PubMed and PMC are fully aware of the ‘duplicated’ articles, and we are working with them to figure out a way to provide a clear link between them. Second, by changing our policy such that PLoS Currents Influenza content is now considered ‘formal’, the problem going forward is eliminated. The discussion that’s occurred on this posting demonstrates very clearly why we needed to adjust the policy in this way.

    PLoS Currents is still a very new channel for research communication, and we feel there’s much interesting experimentation to be done, and much to be learnt.

    Mark Patterson (Director of Publishing, PLoS)

    • Callum Anderson said

      Thanks for posting here Mark, it is good to see a clear picture of the work behind the scenes(which we have all been pontificating about here).

      After speaking to you, I agree that PLoS Currents found itself in a difficult position, somewhere between grey and formal – and the problem was exacerbated by the time-scales which provided a veritable goldmine for those with an eye for conspiracy!

      I am confident that PLoS is doing the right thing here by bringing rapid commentaries into the formal literature, and I look forward to seeing a link between the papers appearing on PubMed in the future.

    • rpg said

      Thanks for the comment, Mark (and for taking the time to call Callum!) Nice to see you’re on top of it.

    • Jim said

      Right, well this makes a lot more sense 😉

    • Namnezia said

      Why not remove articles from PLoS currents (which is a preprint server) once they have been accepted elsewhere in final form?

    • Bob O'H said

      Thanks for the clarification. But by re-positioning PLoS Currents Influenza as part of the formal literature, don’t you lose the appeal as a way of rapidly disseminating information? Anything ‘big’ will be published elsewhere, so will be held back.

      I know, you’re damned if you do, damned if you don’t. Could PLoS Currents Influenza be linked to a pre-print server (e.g. Nature Precedings), so that both sorts of content are available?

  12. […] Publish or perish – a question of ethics […]

  13. […] been doing a bit of art ourselves. Here’s the Wordle of Callum’s blog post the other day […]

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