Retraction Watch

Tracking retractions as a window into the scientific process

Retracted retraction leaves Genomics paper intact — but authors wonder if anyone will know

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Last March, the journal Genomics retracted a paper, “Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches,” for reasons that don’t really fit into a tight lede sentence. Let’s just say that at times the problems involved both questions of authorship and the validity of the research. More on all that in a moment.

Meanwhile, things change. Now the journal, an Elsevier title, is un-retracting (that can’t be a real word, can it?) the retraction. You’d think that would please the authors, and it does to an extent. But they also wonder, legitimately, whether the original retraction will refuse to relinquish its grip on the resurrected article and consign it to database oblivion.

First, some background. The paper in question — which has been cited six times, according to Thomson Scientific’s Web of Knowledge — comes from the lab of Sally Camper, head of the human genetics program at the University of Michigan. The first author had been, but is no longer, Nicola Solomon, an Australian scientist who came to Camper as a post-doc in the mid-aughts.

Solomon might not be too keen on federal officials in her adopted country, because she eventually found herself the subject of an investigation by the Office of Research Integrity (ORI). Earlier this month, ORI released its final determination, complete with its talk of multiyear sanctions (two, in this case) on various aspects of conducting federally-funded research.

Here’s a taste of what the inquiry found:

[Solomon] did not perform DNA sequencing on 202 cDNA clones of homeobox genes to confirm their identity and integrity. Through multiple revision of the manuscript, the Respondent did not discuss this with the corresponding author or question and correct the corresponding author’s addition of text indicating that the clones had been fully sequenced and were full length or longer (as indicated in Table 3) when compared to NCBI Mus musculus Unigene. This text supported the use of the Cap-Trapper technique to produce full length clones for the discovery of new genes without polymerase chain reaction (PCR).

Both the Respondent and the U.S. Public Health Service (PHS) are desirous of concluding this matter without further expenditure of time and other resources and have entered into a Voluntary Settlement Agreement to resolve this matter. This settlement is not an admission of liability on the part of the Respondent.

What does all that mean? Two things. Solomon said she did some genetics work but didn’t. And, it sounds as though the ORI decided they’d pushed the case as far as they could afford to, and got the scientific misconduct equivalent of a plea bargain without any admission of guilt. ORI typically sanctions researchers for three years, although we’ve seen other cases in which they’ve given out two-year sentences.

Camper said she first recognized a possible problem with Solomon’s research during the process of making changes that reviewers for Genomics had requested on the manuscript. By that time, Solomon had already left Camper’s lab for the University of Southern California — she’s no longer there, either — so Camper asked another researcher to help satisfy the reviewers. That scientist — Michelle Brinkmeier, the second author manuscript, who had initiated the project before Solomon joined the lab — could not replicate Solomon’s work, which was supposed to have been sequencing clones that had been provided by a lab in Japan.

Upon resubmitting the corrected manuscript, Camper informed Genomics that she would be removing Solomon as a co-author — putting her into the acknowledgments section instead — and adding Brinkmeier in her place. That change — and Solomon’s hostile reaction to it — explains the rather confusing retraction notice that appeared in March of this year, nearly two years after the paper was published:

This article has been retracted at the request of the Editor-in-Chief. A co-author, who was indentified [sic] as a co-author during the submission process, had their identity removed from the author by-line during the revision process by another co-author, without any documentation that this removed co-author had received notification and/or consented. This runs contrary to Committee on Publishing Ethics (COPE) position on good publishing practice in regard to changes in authorship (see http://publicationethics.org). This decision does not in any way reflect on the scientific findings presented in the article.

Why the long delay? The editor of the journal, John Quackenbush, referred us to Elsevier. A company spokesman told us that the person who lodged the complaint didn’t learn about the change in authorship until long after the paper was published.

Genomics decided it had to pull the article, with what strikes us as an odd caveat: If Camper could demonstrate, among other things, that she had properly notified Solomon and the editors of the authorship change, they would consider restoring the paper. The journal also wanted to wait until the investigation into Solomon’s conduct was complete — which again raises the question of why the retraction happened when it did. Was the de-retraction (is that better?) was meant to time with the release of the ORI report? Seems plausible, but then couldn’t the whole switcheroo been avoided entirely?

Camper describes the process with evident frustration, and we’re sympathetic. Camper told us that she explained to the editors that Solomon’s research had been expunged from the final version of the article. Therefore, authorship shouldn’t really be a question. Indeed, as readers of this blog are well aware, journals are quick to retract articles for including authors who didn’t play a role in a manuscript — they shouldn’t be in the business of doing the same to groups that try to weed out noncontributors.

To that point, Camper and her colleagues conducted their experiments again and are now confident in the science behind the paper as it now appears.

Others in the lab repeated all of the work before we resubmitted. I can stand behind all the work in the paper. Everything in that paper has been checked and double-checked.

The same cannot be said, however, for another paper of Solomon’s. In 2007, the Journal of Medical Genetics published a letter on which she was lead author that called do-over on a 2004 article she’d written as part of her doctoral work.

Here’s said letter, which in a bit of serendipity came out just as Camper was learning about the problems with Solomon’s work in her lab:

In our previous article,1we used array‐comparative genomic hybridisation (CGH) analysis to identify Xq26–q27 duplications in families with X‐linked hypopituitarism (XH). The array‐CGH assay was validated using affected male genomic DNA from two previously characterised XH families that carry Xq26–q27 duplications2,3 (fig 1B,C) and by interphase fluorescence in situ hybridisation (FISH) analysis (fig 2). Array‐CGH analysis of three novel XH families, A, B and C (fig 3), indicated that each of these contained a different Xq26–q27 duplication (fig 1D–G).

Recently, we repeated these array‐CGH experiments using a more extensive X chromosome array containing over 2000 bacterial artificial chromosome (BAC) clones.4 As expected, duplications were identified in males from the two previously characterised XH families.2,3 However, we have been unable to detect Xq26–q27 duplications in affected males from families A, B and C. Furthermore, repeated quantitative real‐time PCR experiments performed by an independent collaborator in a blinded assay detected SOX3 duplication in affected males from control families,2,3 but not in affected males from families A, B and C. On the basis of these new data, we now cannot replicate the observation of duplications in families A, B and C families that was published in our paper.

Meanwhile, Genomics and Elsevier will be posting the following notice next week, we’re told:

An allegation was made concerning a problem with co-authorship that upon receipt of further information appears to have been non-problematic, and therefore the retraction notice, which was in place for March 2011 through September 2011 has been lifted.

For Camper, the experiencing has been wrenching.

I have people depending on me for leading a research team. This is my first experience with this kind of thing and it’s been very difficult. I feel like the people who are getting hurt the most here are my lab and my colleagues.

As a footnote, Camper didn’t cut Solomon loose completely. The acknowledgments section of the newly restored article states:

We thank A.H. Mortensen, M.A. Potok, and N.M. Solomon for their contributions to this work.

Written by amarcus41

October 26th, 2011 at 9:30 am

Comments
  • DrugMonkey October 26, 2011 at 10:47 am

    Interesting bit of brushback for those of you that clamor for more-rapid retractions, less waiting for internal investigations and more initiative from journals/editors, eh?

  • klaus October 26, 2011 at 11:29 am

    It appears to me that personal conflicts have caused this mess. Scientific fraud is reprehensible in all forms. But, taking all of the credit away from someone who contributed majorly (design of experiments etc.) to a project seems to me to be more a matter of Camper punishing Solomon, rather than best scientific practice. Good luck to all involved!

  • juliod October 26, 2011 at 5:02 pm

    This example is not sitting right with me. Particularly your statement “Solomon said she did some genetics work but didn’t.” The ORI report most definitely doesn’t state that. What the report says it that Solomon didn’t “…correct the corresponding author’s addition of text indicating that the clones had been fully sequenced…”

    It seems to me that if they had evidence, the report would have found Solomon to have fabricated data or misrepresented data to her PI. Instead they seem to be dancing lightly in order to avoid calling attention to the fact that the PI is the one who wrote the false statement into the manuscript.

    There is a great difference between conscious fraud and failing to challenge a PI on the wording of a manuscript.

    I also suspect that personality conflict is lying behind this issue rather than scientific misconduct.

    Also, Genomics should not have allowed a change of authors without consent or investigation. And I don’t think having someone else repeat work is sufficient to allow removal of an author who would otherwise qualify for inclusion.

  • Conrad T Seitz MD October 26, 2011 at 5:15 pm

    A slight semantic quibble. One can say “retracted a retraction” (for example) and it is not necessary to add a prefix when saying this… really, it’s proper English to me, although it certainly sounds funny to do it with prefixes: I can’t resist repeating “un-retracted” or “dis-retracted.”
    It helps to keep a sense of humor when reporting sad stories like this, as @klaus has stated. It seems likely that Solomon will not publish again.

  • Sierra Rayne October 27, 2011 at 10:43 am

    Agree with DrugMonkey, klaus, and juliod. Get the feeling Solomon might be getting scapegoated on this one. It appears to be a potentially disfunctional research group anyway if you make a substantial contribution to the work and the corresponding authors feels it in any way reasonable to leave you off the author list.

  • Pinko Punko October 28, 2011 at 2:02 am

    Pay attention to the experiments- if you are claiming that your method allows capture of full-length cDNA clones, clones isolated would have to be validated. Hypothetically, if this is the lead author’s project- the sin is of omission but not of the PI.

    DM’s statement is of a different category of others, and I wouldn’t say there is evidence of agreement of DM with some of the other commenters.

    It does seem like the PI decided that since all the experiments of the original lead author had to be re-performed or performed in the first place, this negates that individual’s contributions. I guess we’d need to know more, wouldn’t we?

  • chirality November 4, 2011 at 7:45 am

    “un-retracting (that can’t be a real word, can it?) the retraction.”
    if you un-retract the retraction, you still leave the paper retracted. To reinstate the paper, one needs to either retract the retraction or un-retract the paper. Just saying.

    • True Scientific Genius August 18, 2013 at 2:26 pm

      Haha very true. You know that Solomon is the chief scientific writer at City of Hope National Medical Center now?

  • Miguel November 23, 2011 at 9:53 am

    This is really unfair to Solomon and i agree with Juliod, it feels like Solomon has been made the scapegoat.
    It doesn’t feels right that as written in the report, the corresponding author Camper wrote the incorrect text, but Solomon is being punished for something that she didn’t write. If the “Respondent did not discuss this with the corresponding author or question and correct the corresponding author’s addition of text” is the issue, then surely both should be punished the same (at least). Camper more so for writing it to begin with, it states through “multiple revisions”, so perhaps the origanal version (vs1) did not have the text, in vs2 Camper adds the text but is not corrected. Why add it without checking the data, simply asking did you do it and not checking the data, that you put your name to, lacks scientific rigour in its self. How many other papers from the Camper group have written on ‘trust’ but not checking the data?????

    It’s not the best advert for the Camper lab… but it shows that if you’ve got a little power in academia and can start a witch hunt behinds someones back and not get burnt your self, you’ve made it!

  • genetics January 5, 2012 at 4:57 am

    Found this a little late here….

    Regarding the genomics paper issue, everything has been said.

    But a true scandal is the “correspondence” the Australian group around Solomon was allowed to publish in J Med Genet in 2007. This is essentially a retraction that they just not called a retraction. The main message of their 2004 J Med Genet paper was, that they identified a microduplication Xq by using a custom made BAC-Array-CGH in three out of three new families with X-linked hypopituitarism. The “correspondence” reports that they were not able to reproduce this duplication in any of the three newly characterized families. Sure, there are more points in the paper than this, however it was clearly one of the core points of the paper, expecially considering it is a medical genetics journal. The error could have been easily detected in the first place by the authors. They used two families with previously identified duplications (found by two other groups) to confirm that their Array works. In these control-cases, they used interphase-FISH as an additional method. Strangely, they didn’t use that to confirm their findings in the three new families. I really wonder how they got through peer-review without confirming their results with an independent method. But thats another story.

    Anyway, instead of scraping a paper off their publication record, the authors got another publication!

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