Anatomy of a retraction: When cleaning up the literature takes six years

In 2018, a biochemist in Scotland became aware of image irregularities in two of his papers through comments on PubPeer, each in a different journal. The researcher, Dario Alessi, a professor at the University of Dundee, said he alerted his home institution immediately.

In July and October 2024, the papers were retracted.

Emails obtained by Retraction Watch through a public records request show what happened in the intervening six years: Consecutive investigations by Dundee and a funder, then delays as the journals juggled conflicting narratives. In the meantime, the papers continued racking up citations.

Alessi said he came across comments on Pubpeer in April 2018 “suggesting irregularities” in one of his publications. The comments raised concerns about two of his 2005 papers: “Role of the PDK1–PKB–GSK3 pathway in regulating glycogen synthase and glucose uptake in the heart” published in FEBS Letters, and “Deficiency of PDK1 in liver results in glucose intolerance, impairment of insulin-regulated gene expression and liver failure” published in Biochemical Journal (BJ).

In January 2019, following a preliminary investigation, the research integrity group at Dundee’s School of Life Sciences recommended a formal investigation, according to emails Inke Nathke, the interim dean and top research integrity officer at the School of Life Sciences, sent to the journals. 

The group came to the conclusion there were “additional issues beyond those flagged on PubPeer at the time,” Alessi told us. 

Since Alessi was also affiliated with the UK-based Medical Research Council (MRC), they undertook the second investigation. But appointing the investigation panel took two years – during which the COVID-19 pandemic happened. The panel began its work in July 2021 and in December 2022 determined the two papers be retracted. 

Six months later, Nathke contacted the journals with the results of both investigations.

She waited four months for a response. In an October 2023 email to Nathke, a BJ representative wrote that their office “has been contacted separately by the co-corresponding author on this publication … who has appealed the proposed retraction.” (The name of the researcher was redacted by the University of Dundee before they provided us the emails.)

We emailed both corresponding authors of the BJ paper, Calum Sutherland and Alfonso Mora, asking if they appealed the retraction. Sutherland, also a researcher at Dundee, responded, simply: “Not me, sorry.” 

In an email to Retraction Watch, Nathke referred to “an appeal by the first author.” In both papers, the first author is Mora, a researcher at Centro Nacional de Investigaciones Cardiovasculares and Organ Crosstalk in Metabolic Diseases Group in Madrid, Spain, according to a recent publication. He did not respond to our request for comment. 

The complaining author, presumably Mora, “did not think the MRC investigation was fair,” according to the Portland Press Editorial Office, which  publishes  BJ. Lapses in communication and disagreement over the text of the retraction notice  — which remained unchanged, despite the co-author’s objections — delayed the retraction. 

Aside from complaints from Mora, BJ investigated the existence of the PubPeer comments Alessi said caused concern in 2018. No PubPeer comments on either the BJ or FEBS papers date before 2024; however, Alessi’s other works have received comments going back to 2017. 

Emails between BJ and Nathke reference Mora’s objections to the retraction, which we have  not seen. Nathke wrote in the October 2023 email, in response to the appeal: “my view is that whether something has or has not appeared on PubPeer is not relevant. What is relevant is that issues discovered with data in the publication remain questionable.” 

Nathke told us: “With regards to the PubPeer alert that you cannot find, there are two possible reasons. I think some problems were discovered by the research integrity group in [the School of Life Sciences] when they started investigating, which were not on PubPeer, and (I do not know this) but it is possible that the MRC may have received independent report(s) directly.”

The Portland Press representative blamed the delay on the lack of comments posted about the paper on PubPeer,” and “the issues that were raised to us that were investigated were due to direct emails from the University of Dundee rather than via PubPeer.” 

Whether or not PubPeer comments on the papers existed at the time, they do now. The BJ paper has two comments published October 2024, after the paper had already been retracted, pointing out that the images were “Much more similar than expected.”

The FEBS Letters paper also has comments from October 2024, underneath the announcement of the retraction. One says: “Much more similar than expected after vertical resizing.” Several simply contain links to announcements of the awards and grants Alessi has received in the past few years. 

Alessi didn’t respond to our questions about the PubPeer comments. 

In December 2023, Nathke wrote in an email to the BJ editorial team that Alessi “kindly shared with me your update about taking the retraction forward.”

It still took more than six months. On July 25, 2024, after several follow-up emails from Nathke, a staff member at the journal said the retraction was “just in the process of being published.” 

The next day, the retraction notice appeared, stating: 

This article is being retracted from the Biochemical Journal at the request of the authors. The authors willingly supported independent investigations, which have confirmed concerns regarding image duplications in Figures 3B and 5B in the original publication. The authors apologise for the inconvenience caused. The Editorial Board agrees with the decision to retract.

As for the seven-month delay after agreement that the retraction would move forward: “Unfortunately, this delay was caused by unforeseen changes in staffing arrangements,” the Portland Press Editorial Office told us in an email. 

Meanwhile, at FEBS Letters, things were quiet. 

In June 2023, soon after Nathke sent her initial email requesting the retraction, an “Image Integrity Analyst” was assigned. “This may take some time to look into,” an unnamed editorial assistant said in an email obtained through a public records request. 

After over a year of the journal not responding and Nathke’s repeated follow-up emails, a representative for the publication said they had “initiated an investigation, but recently had some staffing changes so things may have gotten side-tracked.” 

The paper was finally retracted in October 2024, “by agreement between the authors; the journal Editor-in-Chief, Michael Brunner; FEBS Press; and John Wiley and Sons Ltd.,” according to the statement. 

The journal was contacted by a representative of the research integrity group at the authors’ institute, since an institutional investigation revealed inappropriate splicing and duplication of image sections within Fig. 2A, B and Fig. 3A. Consequently, the conclusions of the paper are substantially compromised, and the institute has recommended the paper to be retracted. The editors of the journal agree with the retraction based on the institutional investigation.

When we asked for clarification regarding staffing issues, a representative from the editorial office told us the retraction “was indeed delayed, due to internal miscommunication during a time of staff turnover. Nevertheless, the article has been retracted, and we feel that the matter is now closed.”

This case is hardly the first time we’ve seen a protracted retraction. Last year, for example, we covered the University of Maryland’s mission to retract a researcher’s faked data, and in 2020, philosophy professor Michael Dougherty detailed his “two year drama” to get a plagiarized paper retracted.

In the six years it took for the papers to be retracted, the paper in FEBS Letters was cited 19 times and the BJ paper 14 times, according to Clarivate’s Web of Science. They have been cited 78 times and 71 times in total, respectively.

The retraction “took longer than anticipated due to the involvement of multiple institutions (UoD, MRC, Journals) and an appeal by the first author,” Nathke told us, but she still defended the journals: “I would like to emphasise that in my experience over the last year, journals are responding and take action very quickly.”

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