Protein structure retracted after investigation into “highly improbable features,” journal calls it fraud
In 2010, a group of
crystallographers immunologists and allergy researchers at the University of Salzburg published a paper in the Journal of Immunology claiming to have derived the structure of a birch pollen allergen.
That structure, however, caught the attention of Bernhard Rupp, an eminent crystallographer. In January of this year, Rupp submitted a paper to Acta Crystallographica Section F pointing out problems with it, which prompted the editors of the crystallography journal to contact the authors of the original paper a month later. Those authors, it turns out, agreed with Rupp, they write in a response to his paper published in the April 2012 issue of Acta Crystallographica Section F:
This manuscript presents strong evidence that the diffraction data of Bet v 1d (PDB code 3k78 ; published in the J. Immunol. paper) are not derived from a diffraction experiment and that the model of 3k78 contains some highly improbable features.
That, in turn, prompted the University of Salzburg to ask the Austrian Agency for Research Integrity (OeAWI) to investigate whether the “highly improbable features” were due to fraud
…on the part of author Robert Schwarzenbacher, the co-author solely responsible for the Bet v 1d structure and the crystallographic section of the J. Immunol. paper.
A report of that investigation is being prepared, according to the authors, but in the meantime, Schwarzenbacher confessed:
Author Schwarzenbacher admits to the allegations of data fabrication and deeply apologizes to the co-authors and the scientific community for all the problems this has caused.
But did he? The authors add:
Note added in proof: subsequent to the acceptance of this article for publication, author Schwarzenbacher withdrew his admission of the allegations.
Fatima Ferreira, who assumed responsibility as corresponding author of the paper when former corresponding author Gernot Achatz passed away last year, tells Retraction Watch:
I really have no explanation for that. We had elaborated the response and author Schwarzenbacher agreed to the text as it has been published now. However, later on, he contacted the Workers Union and the Union sent us a letter where he withdrew his confession. This is the reason for the note added in proof.
We’ve reached out to Schwarzenebacher and others involved in the case to find out more details, and will update with anything we learn.
In the meantime, the authors asked the Protein Data Bank to retract the 3k78 entry, which happened in February. The Journal of Immunology paper — which has been cited 11 times, according to Thomson Scientific’s Web of Knowledge, has not been retracted, however:
The main body of the J. Immunol. publication concerns the immunological study and the retraction of the crystallographic section does not affect the major conclusions. The Editors of J. Immunol. have been informed about the problem with the structure 3k78 . Co-authors Zaborsky, Brunner, Wallner, Himly, Karl, Ferreira and Achatz were in no way involved in the generation of the crystallographic data.
Ferreira tells us:
I think the crystallographic data should be retracted, since it was fabricated. However, the immunological data is solid. The conclusions in the paper can still hold without the crystallographic data.
My group has produced and characterized the recombinant allergen, which was used for the immunological experiments. The same batch was given to Schwarzenbacher for the crystallization, which obviously was never done.
(This raises a related question: What’s the right place to publish critiques of papers? You’d think it would be the journal in which the original paper was published, but we often hear from scientists who tell us that journals decline to publish their critiques because they lack space. That happened to a group that submitted a critique to Science recently who ended up publishing it in PLoS Genetics, we learned on Twitter. And Keith Baggerly and Kevin Coombes, who did much of the heavy lifting to bring down the Anil Potti oeuvre, ended up publishing much of their analysis in the Annals of Applied Statistics. We’ll probably come back to this issue, so we welcome all feedback.)
For their part, in an editorial titled “Another case of fraud in structural biology,” the editors of Acta Crystallographica Section F mince no words. They bemoan the fact that this is “another instance of scientific misconduct in the literature of macromolecular crystallography,” referring to an episode that forced about a dozen retractions:
The second painful insult, disclosed in this issue, was also the act of a single individual. While it seems to be limited to one structure, one journal, one institution and fewer colleagues, and may or may not attract the same amount of attention as the first, it is no less painful, no less disappointing.
The editors are clearly frustrated:
What motivates these hoaxes? It seems clear that the pressures on scientists early in their careers are so severe that a few are compelled to risk their careers in order to further them. The dilemma is perhaps more fathomable when one considers the publication and citation metrics academic departments now use to evaluate staff, the difficulties crystallographers face in attracting funds early in their careers, and the seemingly inexorable march toward commoditization of the crystallographic product. Can this be changed any time soon?
Where scientific publication is the concern, however, their impact will only be fully effective if all relevant journals follow the path of IUCr Journals and require that validation reports as well as coordinates and structure factors be made available for peer review upon submission. It is equally important that all relevant journals include at least one expert crystallographer among the referees for all submissions that describe crystallographic structure determinations, even if those structures are but one aspect of the paper.
That will take effort, they note:
In the current case, however, validation by re-refinement and electron-density evaluation seems to have been the key. To do this on a routine basis will put an extra burden on crystallographers who serve as referees, making development of tools to ease that burden another worthwhile contribution.
Fraud will be tough to beat, they acknowledge:
It is important to note, however, that in neither of these cases was a single frame of data collected. Not one. This alone demands a redoubled effort to produce a universal system for deposition and storage of original diffraction images.
Update, 11:30 a.m. Eastern, 4/2/12: First line edited to clarify that most of the people in the group were immunologists and allergy researchers. Schwarzenbacher was the only crystallographer on the paper.
Please see our update including the news of Schwarzenbacher’s firing.