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Retraction Watch

Tracking retractions as a window into the scientific process

Doing the right thing: Authors retract protein paper after finding experimental errors

with 11 comments

embo reportsA group of researchers in the Netherlands has retracted a paper once they realized that the findings weren’t reproducible and that there had been an error in the experiments.

Here’s the notice for “Ubiquitin‐specific protease 4 is inhibited by its ubiquitin‐like domain,” by MP Luna‐Vargas, AC Faesen, WJ van Dijk, M Rape, A Fish, and TK Sixma:

The above article from EMBO reports, published online on 18 March 2011, has been retracted by agreement between the authors and the journal Chief Editor, Howy Jacobs.

The authors have decided to retract this paper because, upon further analysis, the lower Km for the USP4 catalytic domain, which is crucial for the conclusions of the study, could not be reproduced under the described conditions. Additionally, the authors realized that an error was made in the binding experiment, leading to the report of an erroneously high affinity for the Ubl domain and Ubl‐insert. Because of these problems, the main conclusion of this work is no longer valid and the authors regret any problems this may have caused. An institutional pre‐investigation came to the conclusion that there are no grounds to suspect intentional misconduct. The authors would like to emphasize that the USP4 crystal structure, the ubiquitin binding data and the kinetic analysis of the minimal catalytic domain D1D2 are not in question.

The paper has been cited 18 times, according to Thomson Scientific’s Web of Knowledge.

We hadn’t seen the term “pre-investigation” before. (It did remind us of Ivan’s TEDMED talk about pre-conditions, including one that we all have and that is universally fatal.) Corresponding author Titia Sixma tells us:

It’s standard procedure at NKI for any retraction to see if there is any reason to suspect issues with integrity. The committee analyzed our efforts at reproduction, the original data and computer files and interviewed the authors; if they had concluded there was any doubt about integrity a more in depth analysis would have followed.

In fact I was very grateful for this, because in the process a likely cause for the erroneous binding assay result was found, which relieved my own lingering doubts.  The errors are very unfortunate and should not have happened, and I feel very badly about this. We felt it was important to do the retraction as the errors really invaldiate the main conclusion of the paper, even though a substantial part of the paper is still valid (as indicated in the retraction notice).

Kudos — another example of doing the right thing.

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Written by Ivan Oransky

January 10, 2014 at 12:30 pm

11 Responses

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  1. I am not sure Retraction Watch should be dividing people into those that “do the right thing” and those that don’t. You aren’t really in a position to make these judgements and you can’t really know what the steps or events that took place that lead up to this retraction.
    Perhaps this group has “done the right thing”, perhaps they didn’t. We can’t really tell.

    littlegreyrabbit

    January 10, 2014 at 12:44 pm

    • One may only comment, or judge, if one is an insider with knowledge of all the backgrounds? If that were the proper attitude, then one should hardly ever voice an opinion about anything, and furthermore it would be rewarding the people that try to cover things up. In sharp contrast, evidence-based “name and shame” does provide an incentive to us all to honestly try to Do The Right Thing, and since it is proven almost daily that this incentive is needed I welcome it warmly.
      The best one can do is inform oneself properly, form a balanced opinion, give the arguments behind it, and should it later prove to be the case that one was wrong then admit that fair and square. RW seems to do fine on all fronts so far.

      Dave Langers

      January 10, 2014 at 5:31 pm

      • “The best one can do is inform oneself properly”

        Indeed, but when your blog encompasses terrorism, plant biology, xray crystallography, economics, psychology, epidemiology, organic chemistry and nuclear physics – then informing yourself properly is an unrealistic expectation.
        Most of the retractions that appear here I am an unqualified to judge, but the few which I do have the expertise to make an assessment, their judgements often appear to be flawed or at least potentially flawed.
        RW provides a service: it collates retractions and tries to obtain on the record comments from editors and corresponding authors. That is useful, but it doesn’t form the basis of passing judgement – either favorable or unfavorable.

        littlegreyrabbit

        January 11, 2014 at 10:46 am

        • IMHO, the problem lies not with the one voicing a substantiated opinion, but it is the one who attributes excessive authority to it.
          The same happens with impact factors, by the way: ISI collates citation data, and there is nothing wrong with that; however, the fact that these numbers are attributed excessive value to in unsuitable ways by funders and universities is bad. (There are problems with ISI’s lack of transparancy too in this case, but that is not the reason why IFs are the problem they are.)
          Let us not make a similar mistake: just use RW as a source of information, pointers to interesting stories, insightful discussions of backgrounds, collection of other sources, motivated reasonings, and judgements that all are welcome to disagree with. As with any source of info, critically value the available arguments behind an opinion more than the opinion itself.
          That being said, who *would* qualify to give judgement? The author, employer, peers, funder, editor, publisher, media, court of law, …? These may be informed parties, sometimes, but they all tend to have biases or interests that prevent them from casting a perfect verdict too. Yet I hope that all of these parties keep voicing their opinion with their arguments for everyone to sift through for themselves.

          Dave Langers

          January 11, 2014 at 7:16 pm

          • I think all four comments above (Dave and littlegreyrabbit) are right to some extent. RW currently serves as the MOST important site on the entire web about retractions (at least in English). That in itself is telling. Given this importance, there should be some room for flexibility, and tolerance. Of course stories might not be perfect, but that is why they are open to the public. For further discussion and scrutiny, by whoever is willing to provide it. The greatest power of RW is not so much the perfection of the blog, but rather the massive awareness it is creating. Awareness is one of the most important factors for change. So, even though readers and bloggers, or even RW owners are not experts in ecology or radiology, that’s not the point. They collate information from various sources, provide a catchy title and present the facts as accurately as possible.

            To draw another parallel, look at Jeff Beall’s blog on “predatory” open access publishers (www.scholarlyoa.com) . One could say, by the same measure, that Mr. Beall – who does not hold a PhD but only an MA, is not trained to provide comment on issues such as ethics, fraud, veterinary science or astrophysics, or hundreds of specialist topics that appear in the journals of open access publishers he is critiquing. After all, he is a librarian. One could even say that he is not qualified to judge the predatory nature of such journals. But, placing these valid critiques aside, what one can definitely say that is absolutely essential about Mr. Beall’s site is that it raises awareness. And that ingredient, as for RW, is essential. By raising awareness, bringing the issue to young and old, new and seasoned scientists, you eventually find some sparks. Those sparks are the important elements of our communities that will start the fire. Fire = exploration of the literature, critical analysis of it, and reporting of the errors and fraud within it. Thus fire is post-publication peer review (PPPR).

            As far as I have seen, always, whenever errors have appeared on RW, a strikethrough has correctly appeared, and almost always an apology. It doesn’t get more perfect than that. So, kudo’s to Adam and Ivan for this tremendous effort. Praise aside, it is then incumbent upon all of us, now that we have this powerful tool called RW, to draw on our own expertise and to conduct free, passionate and focused post-publication peer review to examine the literature that is within the scope of our understanding. Of course, we also need comments by generalists, too, because they sometimes add much-needed humor, or alternative perspectives. RW is the true modern public forum, and should remain open to all opinions, expert or not. Science is integrated into a wider society, and to assume that somehow scientists are this marble tower of intellect separated from the surrounding society is dangerous. RW is flexible, and tolerant, that I have learnt by experience. So, use the tool smartly, because one never knows when it could disappear. In fact, I have always advocated that we need more lawyers, copyright specialists, and actual publishers’ representatives commenting on this blog. We even need members of the general public who are interested in such issues to comment. RW is currently the premier site of issues related to retractions.

            JATdS

            January 12, 2014 at 1:14 am

  2. Everyone can make (all kinds of) a mistake, even the people with highest integrity.
    Doing the right think is about What happens AFTER the mistake has been discovered?
    Then, there are two main categories:
    (i) people who Do the right thing, i.e. acknowledge the mistake and make whatever is necessary to put the records straight; and
    (ii) people who refuse (for whatever reason) to Do the right thing.
    All fraudsters make different kinds of mistakes intentionally with the only goal to deceive the public and to get more public money in the form of grants. In most cases they stubbornly refuse to Do the right thing. Regrettably, in many cases their institutions and/or editors/publishers also refuse to Do the right thing, and often even do the wrong thing, i.e. actively do cover the “mistake” up, in spite of trumpeting around the world that they have Policies & Frameworks to Do the right thing.
    One should always distinguish between the above mentioned two categories.

    YouKnowBestOfAll

    January 10, 2014 at 4:24 pm

    • Agreed, fully! I really do look forward to Doing the Right Thing in the [s.c.] field of ‘climate science’. There you have loads and loads of ‘retractables’. Not holding my breath to see such happen, though… :(
      Brgds from Sweden/TJ

      thojak

      January 11, 2014 at 2:12 am

  3. The paper is still listed on her professional website. She should do the right thing and have it removed, or marked.

    http://xtal.nki.nl/Titia_group/Titia_group/Publications.html

    Declan McManus

    January 10, 2014 at 4:33 pm

    • The only thing I can see is a link to pubmed. Maybe it has been modified since your post. I guess it can take time to pubmed to change the records but I don’t think one should blame the authors for that. And the retraction notice is the first paper (as the most recent I guess) mentioned in the pubmed list.

      Deillevid

      January 12, 2014 at 4:09 am

      • A few days ago, a full list of papers was listed year by year like on a printed cv. Now there is indeed only the pubmed link and an otherwise empty page.
        In any case, someone seems to have felt a need to work on that site. I guess Declan’s point is addressed.

        Dave Langers

        January 12, 2014 at 6:42 pm

  4. There would not be a category “Doing the right thing” if it was more common. As I noted in a post entitled “Getting Science Right Side Up” a while back, only a small number of retractions catalogued here fall into this category. If science was operating according to what is says on the box, then most retractions would be for this reason and then the category would not exist. So the category only exists because it is the exception and it is useful to draw attention to that fact.

    ferniglab

    January 13, 2014 at 12:10 pm


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