Ivan Oransky

Nature earns ire over lack of code availability for Google DeepMind protein folding paper

A group of researchers is taking Nature to task for publishing a paper earlier this month about Google DeepMind’s protein folding prediction program without requiring the authors publish the code behind the work.

Roland Dunbrack, of Fox Chase Cancer Center in Philadelphia, peer-reviewed the paper but was “not given access to code during the review,” the authors of a letter submitted today, May 14, to Nature – including Dunbrack – write, “despite repeated requests.”

A Nature podcast said AlphaFold3 – unlike AlphaFold2 – “can accurately predict protein-molecule complexes containing DNA, RNA and more. Although the new version is restricted to non-commercial use, researchers are excited by its greater range of predictive abilities and the prospect of speedier drug discovery.”

Professor, former dean earns nearly 100 expressions of concern for citation manipulation

A professor at King Abdullah University of Science and Technology in Saudi Arabia who once served as a dean at the Stevens Institute of Technology in the United States, has received expressions of concern on 93 of his conference proceedings for what a publisher said were irrelevant self-citations and “artificially inflating the number of citations.”

The notes by the Institute of Electrical and Electronics Engineers (IEEE) on the work of Yehia Massoud, a professor of electrical and computer engineering, take two forms. One reads:

Weekend reads: Editor under scrutiny resigns; bullshitting scientists; questionable practices in expanding disciplines

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The week at Retraction Watch featured:

Our list of retracted or withdrawn COVID-19 papers is up past 400. There are more than 48,000 retractions in The Retraction Watch Database — which is now part of Crossref. The Retraction Watch Hijacked Journal Checker now contains more than 250 titles. And have you seen our leaderboard of authors with the most retractions lately — or our list of top 10 most highly cited retracted papers? What about The Retraction Watch Mass Resignations List — or our list of nearly 100 papers with evidence they were written by ChatGPT?

Here’s what was happening elsewhere (some of these items may be paywalled, metered access, or require free registration to read):

Concussion researcher McCrory up to 17 retractions

More than two years after retracting an article by one of its former editors in chief for plagiarism, the British Journal of Sports Medicine has retracted six more pieces by the editor, Paul McCrory, a noted concussion researcher in Australia.

The retractions join 11 more of McCrory’s works, including 10 from BJSM and one from Current Sports Medicine Reports.The BJSM, published by The BMJ, is also correcting two additional articles by McCrory.

Troubles for McCrory – for decades “the world’s foremost doctor shaping the concussion protocols that are used by sports leagues and organizations globally,” according to the New York Times – began in 2021 when Steve Haake, a professor at Sheffield Hallam University in the UK, told the BJSM McCrory had plagiarized a 2000 article by Haake in Physics World. (It would not be the only time the work was plagiarized.)

Weekend reads: Medical residents’ publish or perish problem; Alzheimer’s and predatory journals; brain biopsies set off alarm bells

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The week at Retraction Watch featured:

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Weekend reads: Superconductivity researcher’s lawsuit dismissed; no grounds for prosecuting Elisabeth Bik; a rector candidate who boosted his metrics

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The week at Retraction Watch featured:

Here’s what was happening elsewhere (some of these items may be paywalled, metered access, or require free registration to read):

Send lawyers, Einstein and Maugham: Authors object to PLOS ONE retraction

Here’s a tale of a paper retracted because other articles published years later seemed to plagiarize it – and its unhappy authors, whose behavior the journal says hints at paper mill activity.

On January 16 of this year, Maria Zalm, a senior editor at PLOS ONE and team manager for publication ethics, asked the authors of a 2015 paper to respond to concerns about their work – which had been flagged on PubPeer the previous November – by February 6, according to an email seen by Retraction Watch. After some apparent back and forth, Zalm wrote to the authors on March 6 to say the journal had decided to retract the article.

Weekend reads: Deans out following Retraction Watch reporting; making sense of retractions; why one university is having grants withheld

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The week at Retraction Watch featured:

Dean in Indonesia resigns following Retraction Watch report

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Dean in Indonesia resigns following Retraction Watch report

Kumba Digdowiseiso, the dean of the economics and business faculty at Universitas Nasional in Jakarta, Indonesia, resigned on Thursday after a firestorm of criticism over the past week.

The move, reported widely in the Indonesian media, came eight days after Retraction Watch reported that researchers at Universiti Malaysia Terengganu alleged that Digdowiseiso had added dozens of their colleagues’ names to papers without their permission.

“This resignation is a form of my academic responsibility to the Chancellor of Unas and the academic community so as not to burden the campus in carrying out investigations into the problems I am facing,” Digdowiseiso told Kompas yesterday.

Weekend reads: A decade after the STAP scandal; more allegations about Francesca Gino; the disappearing journal

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The week at Retraction Watch featured:

Here’s what was happening elsewhere (some of these items may be paywalled, metered access, or require free registration to read):

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