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Science has retracted a 13-year-old paper, five years after data sleuth Elisabeth Bik first raised questions about issues with the images in the article.
The paper, “Secondary siRNAs result from unprimed RNA synthesis and form a distinct class,” appeared in 2007 and was written by a group of researchers in the Netherlands and Switzerland. The senior author of the study was Ronald Plasterk, founder of Frame Cancer Therapeutics in Amsterdam and once a minister in the Dutch government. The article has been cited at least 300 times, according to Clarivate Analytics Web of Science.
It also drew Bik’s attention. In 2015, she posted — as Peer 1 — on PubPeer about her concerns with one of the figures in the paper. Other commenters joined in, including to point out similarities between images in the Science paper and two other articles from members of the group.
Bik said the paper:
appeared to contain duplicated bands in the RNA blots shown in Figure 2D. The bottom part of two lanes in two different panels looked remarkably similar. It was not a simple re-probing of the same blot, because the marker lanes look very different. Closer inspection of the similarities revealed a possible sharp horizontal transition just above the bands of interest, which suggested the bands might have originated from somewhere else, and might have been copied into the photo.
I found additional problems in two supplemental figures, Figure S1C and Figure S3C. In both figure panels, lanes appeared to be visible multiple times.
Bik said the article did not wind up in the dataset of her 2016 paper in mBio on image problems in the literature because she and her co-authors, Ferric Fang and Arturo Casadevall, couldn’t agree on whether the images were indeed suspect. However, she
still believed the paper contained inappropriate duplications, so I reported it to Science in April 2015, together with 10 other Science papers with similar image problems. I asked the journal several times for an update, but had not heard back from them yet with an answer about this specific paper.
Unfortunately, Bik said, such lack of action is not unique, in her experience reporting issues to journals. In March of this year, Bik tweeted a thread of cases of “very problematic images where the journal either only did a correction or where they did nothing,” including the Science paper:
In that tweet, I did not specifically link to the Sijen paper or PubPeer post, nor did I mention the name of the senior author, since he is such a well-known person in the Netherlands, and I was hesitant to call him out. But I did mention that the paper was from the lab of a “former Dutch scientist/politician”, and some people quickly figured out whom I meant. Pepijn van Erp, a Dutch scientist and skeptic (skeptical about pseudoscience) then wrote an article about the case (in Dutch) on March 13, a couple of days after my tweet. And on March 20th the Hubrecht Institute even answered to my tweet saying that they would start an investigation:
Therefore, this appears to be another case in which reporting problematic papers through the regular channels was not very effective, while Tweeting about them might finally result in some action.
Bik notes:
Plasterk has several other papers with PubPeer posts raising concerns about image reuse across different figures or different papers. It would be good if the Hubrecht Institute investigated those cases as well, to see what happened there.
Plasterk told us:
My former institute, the Hubrecht Institute, informed me earlier this year of a PubPeer posting. When I saw the posting I concluded that it seemed indeed there was something wrong with the negative control lanes in a figure, and I contacted the other authors. The first author went to the archives of the Hubrecht to search for the original autoradiograms, but could not find them. We informed the editor of Science. While the conclusions of the paper have since been repeated and confirmed by us and others, we retract the paper, because of the absence of a correct negative control in that figure.
According to the retraction notice:
The authors of the 2007 Science Report “Secondary siRNAs result from unprimed RNA synthesis and form a distinct class” have been made aware of duplications in Fig. 2D and supplementary figures S1C and S3C. They attempted to find the original data from 2007, but all authors have left the Hubrecht Institute, where the work was performed, and the data could not be located. Although other data in the paper was consistent with the conclusions supported by Fig. 2D and figs. S1C and S3C, all data was taken into account in the review of the paper, and the loss of these figures weakens the conclusions. Therefore, in the spirit of full transparency, the authors have decided to retract the paper.
Holden Thorp, the editor-in-chief of Science, told us:
The possible problems were discussed in the past before my arrival at Science. The more recent posts by Bik gave more detail that allowed us to reach agreement with the authors on how to proceed.
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“Holden Thorp, the editor-in-chief of Science, told us: The possible problems were discussed in the past before my arrival at Science. The more recent posts by Bik gave more detail that allowed us to reach agreement with the authors on how to proceed.”
Dear Thorp: Did you or your colleagues ask for more detail from *Dr.* Bik or (more likely) did you/they ignore these concerns until enough external pressure had accumulated? If the latter, this is why research sleuths seem so cynical about journal ethics… and why some of us bug you on social media. COPE guidelines need to be updated so editors acknowledge receipt of a notification of concern.
To the best of my knowledge, Science never asked me to clarify my findings, which were the same as posted on PubPeer. It also sounds as if the journal never did anything with my 2015 allegations at all. Because Plasterk said he only learned about the concerns earlier this year, it appears that the journal did not contact him nor the Hubrecht lab back in 2015. I asked the journal for an update on this and other cases in 2017 but they did not provide me with any. The way that Science handled (or rather, did not handle) this case appears to be in sharp contrast with COPE guidelines.
Given the many contribution you, Elizabeth, have made to ensure the integrity of the research record, I feel that some/many of us will be profoundly disappointed if Science does not provide _you_ with an adequate explanation for what happened in this case.
i started to worry about where science is heading. We are all scientists, we work on evidence we have and we write papers based on what we get. When “evidence” is shown on duplications, why there should be hesitation? What are the repercussions? the paper was published in 2007 – first author got a career boost because of a science paper – probably became a PI somewhere for 13 years now (it is indeed true – i just searched, see below). Life is made, career is made. Everything goes on. Please don’t take other honest students/scientists opportunities for your ambitious approach to publish a career best paper! I suffered as well – i have/had colleagues whose papers are still on pubpeer but are successfully getting big grants from funding agencies, as if nothing has happened, i lost my grants and lab..
“….has been team leader and senior scientific researcher at the NFI in The Hague since 2007. Her earlier activities included acting as postgraduate researcher at the Hubrecht Institute for Developmental Biology & Stem Cell Research and at the VUmc Genetics Department at Amsterdam UMC. ….. has played a leading role in the development, validation and implementation of various investigation methods.” -UvA website (September 3, 2020)