Late last week, Nature reported some details of PubPeer’s fight against a subpoena from a researcher who claims to have lost a job because of comments on the site. (Background here.) Here’s another installment of PubPeer Selections:
- “This comment is clearly unfounded.” A commenter reacts to a questions about a paper in the Journal of Pathology.
- A commenter compliments a recent paper in Cell, and the author responds with thanks and clarifications.
- “I am one of the authors and I am happy to elaborate on this comment.” Authors explain how they tried — in vain — to ensure that one of their papers made it clear that some of the material had been published elsewhere.
- The stripy nanoparticle controversy rolls on, with the publication of a revised version of a critique in PLOS ONE.
- The discussion over “DNA of a virus once thought confined to the cells of algae” that may infect humans is a good reminder that comments from PubMed Commons are mirrored at PubPeer.
Regarding the TOJET paper, a valiant attempt by the authors to be transparent about their attempts to label the partialy duplicated paper as non plagiarized by the publisher. However, two key questions arise:
1) why did the authors publish the second paper in such an obscure journal?
2) why did the authors not simply remove self-plagiarised or duplicated text BEFORE submission to TOJET? Surely, that would avoid any post-publication stresses?
Separately, “comments from PubMed Commons are mirrored at PubPeer.” But, are PubPeer comments mirrored at PubMed Commons?
Not sure why they chose that particular journal (perhaps they were invited, etc.) but it is very common in engineering/computer science fields to publish an extended version of a conference paper – which is what the first paper seems to be – in a journal, with a lot of the same text but adding new results and discussion. Usually the journal paper cites the conference paper (or multiple papers) or has a note such as the one the authors were trying to add. It’s a slightly different model I think than other fields where journal publications are the only publications and there can be _no_ shared text, etc.
Maria, thanks for the explanation. Is TOJET then a popular or common engineering/computer science publishing venue? These are scientists from Luxembourg, so why chose a Turkish journal when so many superior alternatives exist? I think the argument that field A does it this way but field B does it that way is neither convincing, nor correct. You cannot hold one set of authors up to one value and ethics system and then hold up a separate set of authors to another value and ethics system simply because that is what is “traditionally” done in that field. Different strokes for different folks does not apply to publishing ethics.
Personally, I’d never heard of that journal – I am not in the authors’ field though. Their experience with it doesn’t seem to have been great either. My point about the different fields is that journals and conferences in some fields definitely have different rules. It is acceptable for many very good journals in engineering and computer science to publish a paper which is an extended version of a conference paper. They (the journals) specifically require in that case that the journal version have “enough novelty” as far as new results with respect to any other related paper submitted for publication. This seems like what the authors did here as well. Basically, specific journals and conferences have specific rules in engineering fields which may be different than those in other fields. I don’t know how to reconcile them with practices in life sciences publishing, was just pointing out the authors seem to have played by the rules of the conference and journal they published in.
If one looks at the conference’s Web page, it states that “the best full-papers will be invited to a special issue of the SSCI-index and open access publication The Turkish Online Journal of Educational Technology (TOJET).”
Oh, that makes even more sense (the “dedicated journal” is also a common occurrence, I hadn’t made the connection). Even if the conference has no such dedicated journal, people can submit their extended conference versions to any other applicable journal, as long as the journal thinks the new version has enough novel content. Same with workshop papers which can be extended and submitted as conference papers, etc. Basically papers can definitely share a significant amount of content, as long there are new results being presented. Don’t have any experience in other fields but it sounds like that is not the case.
There’s one more question, though: Was this the special issue? It doesn’t look like it offhand (I may check the CAA2014 program later). Even if it’s not, selecting the journal for the submission makes sense.
A bit off topic…
Regarding the Cell paper, I noticed that in the long co-authors list, the first two co-authors are labeled as “co-first authors”. What does that mean if a sequential list of names is given? The first one should be considered as the “first co-first” and the second as the “second co-first”? And how should we cite such a paper with multiple first authors? “Platt, Chen et al.”? or maybe “PlattChen et al.”? or “Platt et al. & Chen et al.”?
No kidding, why try to split hairs. Anyway the last will be first, and the first last.
Sylvain, in many developed countries, the position of the author gives different points, which then counts for tenure, grants etc. Thus, first vs second position is a big deal for them. However, it is impossible to physically merge two names in one, so the only viable way of indicating that two authors share the same pole place on a paper is with this notice. I do agree that the way such papers should be referenced is flawed for such cases.
It’s simply an awkward version of a “these authors contributed equally” footnote.
Citation style is a purely syntactic matter, not a semantic one.
As a mathematician who has only in the last decade become involved in publishing/presenting (with a CS co-author) at robotics conferences, I found it very surprising that “extended conference versions” are the norm there—but they are. I don’t know about the hardest-core engineering ones. I do know about a bunch of the more theoretical IEEE mega-conferences, as well as the smaller Workshop on Algorithmic Foundations of Robotics and Robotics: Science and Systems (at all of which I’m pretty sure that engineers of one sort or another make up a large plurality of the participants).
Die Theorie liefert viel, aber dem Geheimnis des Alten bringt sie uns kaum näher. Jedenfalls bin ich überzeugt, daß der nicht würfelt!
It is heartening to learn about PubPeer’s decision to challenge Prof. Sarkar’s subpoena. It should be quite obvious to anyone who has accessed the comments on Retraction Watch, particularly the image analyses painstakingly put together by Scrutineer, and the original comments on PubPeer itself, that the concerns raised by PubPeer reviewers are quite justified; they are legitimate queries that question the science conducted by the scientists in Prof. Sarkar’s or his collaborators’ labs; none go for personal character assassinations as Prof. Sarkar alleges. For those of us cancer researchers who have had the misfortune of witnessing a loved one suffer and die from cancer, or currently have loved ones suffering and dying from cancer (the primary reason why we became/become cancer researchers) questioning what was going on in Prof. Sarkar’s lab is no joke – it is a very serious matter – particularly when federal funds are involved, and clinical trials are being conducted. It is the tax payers who fund research, and Congress and Senate who earmark funding to NCI through NIH in the hope that the cancer research community will do their best to find potential cure/s for cancer that the pharmaceutical industry can take up for drug development, or clinicians can advocate for treatment or therapy. Also, it is the cancer patients among the same tax payers who offer themselves as guinea-pigs to test the drugs or medical procedures/treatments that are developed, in the hope for a potential cure. Yes, when you take all these things into account, questioning the science, in any form or manner, is completely legitimate. It is the duty of the likes of Prof. Sarkar to answer the questions (or depart from cancer research) instead of trying to intimidate and silence PubPeer or the scientists through lawsuits.
Why can not all DOIs be read by PubPeer? This is seriously hindering PPPR reports from being effectively linked and posted. Some DOIs are listed on the DOI site and at CrossCheck, but cannot be “read” by PubPeer, leading to a “null” entry, with zero comments. Perhaps some RW reader that uses PubPeer, or even a PubPeer rep could provide an explanation why this is, and how we can work around this firewall. If necessary, I can provide some examples to show what I mean.
Oh JATdS I am happy you finally decided to embrace PubPeer! I like using Pubpeer, but indeed the system is still far from ideal; full of glitches, etc. Still I think it is the reference now for PPPR, and such things can be improved. Now, on DOIs, I remember having had an issue with this once before, but cannot remember how it got fixed. In principle you can add any paper with a DOI, and “obscure” papers that have not been added automatically to their database will start by showing between quotation marks. However some may not show correctly, I think. Best way is to directly contact administration; they are not exactly super nice (I picture they are very stressed postdocs) but they answer you quickly. I think they fixed my issue without telling me, and it started working after I queried them — try that and good luck. And remember: “with great power, comes great responsibility”!.. Fair use will yield you good (long-term) feedback, bad use may lead to trouble and exposition.
Thanks CR. BY the way, your made a mistake with your incorrect second language claim. There are definately trolls at PubPeer. So, indeed, PubPeer has a long way to go. The DOIs is a technical probem, but criticism of anonymous commentators at PubPeer rather than on the comments themselves will be the thorn in PubPeer’s side. Oh, and let me make this clear. I have not embraced PubPeer. Finally, “exposition” = exposure.
Sorry I did not know you were born from an English speaking country. Thanks for pointing out! I think PubPeer is on the right track, you shall see your comments will be read by many. Good luck!