doing the right thing – Page 2

Contamination leads to swift retraction for Science paper on the origins of Omicron in Africa

The authors of a paper that proposed the Omicron variant of SARS-Cov-2 had evolved in Western Africa months before it was first detected in South Africa have retracted their study after discovering contamination in their samples, as several scientists had suggested on Twitter was the case.

The article, “Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa,” was published in Science on December 1 by a team led by Jan Felix Drexler of Charité – Universitätsmedizin Berlin.

Soon after publication, many geneticists expressed skepticism on social media about the study, including questioning whether the results came from contamination during the sequencing process.

Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation and the KwaZulu-Natal Research Innovation and Sequencing Platform at the University of KwaZulu-Natal in South Africa, tweeted on December 4 about “weaknesses” in the study, including that “the quality of the sequences seems problematic”:

‘A display of extreme academic integrity’: A grad student who found a key error praises the original author

Last week, we wrote about the story of Paul Lodder, a graduate student at the University of Amsterdam who had been trying without success to replicate the findings of a 2020 paper in Scientific Reports by Rubén Herzog, of the Universidad de Valparaíso in Chile. The paper would end up retracted. At the time, Lodder had not had a chance to respond to our questions about the case. We’re pleased to share his comments as a guest post.

I’ve had a big passion for research into the therapeutic potential of psychedelics ever since I had started my undergraduate in biomedical sciences at Amsterdam University College. I am currently a MSc Artificial Intelligence student and about a year ago, in preparation for a computational neuroscience course, I wanted to expand on the model used by Rubén.

I sent him an e-mail explaining the situation, and requesting some parameters that weren’t detailed in the paper so that I could start running the simulations myself. Rubén responded very quickly and was immediately very helpful with getting me started with running the simulations.

Now that I was able to run the model properly, I wanted to start off with being able to reproduce the paper’s analysis results before looking into expanding. Using the methodology described in the paper, I re-implemented the steps needed to compute the entropy. And indeed, this is where I got some different results as presented in the paper.

A grad student finds a ‘typo’ in a psychedelic study’s script that leads to a retraction

Sometime after it was published, Paul Lodder, a graduate student at the University of Amsterdam, had been trying without success to replicate the findings of a 2020 paper in Scientific Reports.

The original article was written by a group led by Rubén Herzog, of the Universidad de Valparaíso in Chile. Titled “A mechanistic model of the neural entropy increase elicited by psychedelic drugs,” the paper purported to help illuminate what happens in the brain under the influence of substances like LSD.

But the findings of the study wouldn’t replicate. And unlike some researchers who might blow off criticism of their work, or blame the replicators for the failure, Herzog sent Lodder the scripts his team had used.

Lodder found the problem quickly. As Herzog related to Retraction Watch, Lodder (whose schedule has been challenging the past few weeks as we’ve played phone tag) [See update on this post.]:

Doing the right thing: Harvard researchers retract Cell paper after work contradicts finding

The authors of a 2020 paper in Cell are earning plaudits after they retracted the study following the publication of an article last year that contradicted their earlier findings.

The paper, “Allosteric Activators of Protein Phosphatase 2A Display Broad Antitumor Activity Mediated by Dephosphorylation of MYBL2,” purported to show that a particular compound could be useful in animal studies because it did not have some of the off-target activity of other compounds. It has been cited 45 times, according to Clarivate’s Web of Science.

But as the retraction notice says, a paper published last year in The EMBO Journal by Jakob Nilsson and Gianmatteo Vit of the University of Copenhagen and colleagues found that wasn’t true:

‘A terrifying experience’: A team of researchers does the right thing when they find an error

Mitch Brown was preparing last August to launch a follow-up study to a 2021 paper on coalitions when he found something in his computer coding that sent his stomach to his shoes.

As Brown, an experimental psychologist at the University of Arkansas, recalled for us:

Doing the right thing: Neuroscientist announces retractions in ‘the most difficult tweet ever’

A group of neuroscientists in Germany and Hungary is calling for the retraction of two of their recent papers after discovering a fatal error in the research.

Myriam Sander, a memory researcher at the Max Planck Institute for Human Development in Berlin, took to social media on Wednesday to alert her followers to the decision. In what Sander called the “most difficult tweet ever,” she wrote:

Second time’s the charm: The author who requested a retraction twice

As Jason Isbell sings, doing the right thing is the hardest thing to do. But sometimes it’s even harder than it needs to be. Ask Cory Xian.

When Xian, a bone researcher at the University of South Australia, in Adelaide, and his colleagues found an error in their 2018 paper in the Journal of Bone and Mineral Research — a top journal for the field — they notified the editors and asked for a retraction. But the journal demurred, instead issuing a correction for the article, titled “Release of CXCL12 From Apoptotic Skeletal Cells Contributes to Bone Growth Defects Following Dexamethasone Therapy in Rats.”

The correction states that “incorrect photos had been accidentally and mistakenly used by a staff person as representative photos”.

Xian, the senior author of the article, told us:

Doing the right thing: Co-authors of researcher who covered up data fakery retract paper

A group of researchers in Canada who’d collaborated with a one-time rising star in the bone field have retracted a 2014 article after determining that the data were unreliable.

They did so even though the paper was not a focus of the investigations into the work of Abida Sophina “Sophie” Jamal, whose once sparkling career in endocrinology crumbled after an investigation found that she had fabricated data and took elaborate steps to cover her deception — from doctoring patient records to changing the temperature of a freezer at a government blood facility to damage samples that might reveal the fraud.

‘Please don’t be afraid to talk about your errors and to correct them.’

A “systematic error” in a mental health database has led to the retraction of a 2017 paper on how people with psychosis process facial expressions.

Joana Grave, a PhD student at the University of Aveiro, in Portugal, and her colleagues published their article, “The effects of perceptual load in processing emotional facial expression in psychotic disorders,” in Psychiatry Research, an Elsevier title.

According to the abstract of the paper:

‘In hindsight the mistake was quite stupid’: Authors retract paper on stroke

File this under “doing the right thing:” A group of stroke researchers in Germany have retracted a paper they published earlier this year after finding an error in their work shortly after publication that doomed the findings.

Julian Klingbeil, of the Department of Neurology at the University of Leipzig Medical Center, and his colleagues had been looking at how the location of lesions in the brain left behind by cerebral strokes were associated with the onset of depression after the attacks. According to the study, “Association of Lesion Location and Depressive Symptoms Poststroke”:

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