The Jist: July 28 to August 8
Get the gist of recent news stories, written by journalists, that cover topics related to scholarly communication.
Hello fellow journalologists,
Welcome to another edition of The Jist, a newsletter that summarises how news outlets have been covering scholarly communication.
‘A waste of time for all of us’: caught in the crossfire of the peer-review wars
Review mills not only threaten to sully the academic record with irrelevant references and compromise the quality of peer review, but are a bane to authors such as Börsch, who are finding themselves caught in the crossfire between review mills, the sleuths that hunt them and the journals scrambling to undo the damage. Understanding review mills requires a deep look at the systemic forces that drive fake reviews and the pressures faced by authors and journals to publish studies as quickly as possible.
Nature (Katarina Zimmer)
JB: This news feature about peer review mills focuses on the authors whose papers have been fraudulently assessed by peer review mills. Unlike many news stories, which repeat the same tired tropes, this one provides genuine insight. It’s well worth spending some time with.
For me the take home message is that peer review reports should be published to provide an auditable paper trail (see next story)
Also, editors (and publishing staff) need to do a better job of checking the papers that peer reviewers want authors to cite.
The story concludes:
Wholly preventing the issue, however, would require funders, institutions and publishers to address the pressures on scientists that lead them to duplicate reviews and to try to game the citation system.
How long? How long must we sing this song?1
Papers with open peer-review reports are less likely to be retracted
Papers with publicly available peer-review reports are less likely to be retracted than are those without public reports, a study has found. The authors say this could, in some cases, reflect greater confidence among researchers who choose to make the review process transparent.
Nature (Dalmeet Singh Chawla)
JB: At the risk of being pedantic, ‘open peer review’ and ‘transparent peer review’ are two different things. In both cases the peer review reports are published. However, under ‘open peer review’ the names of the reviewers are always disclosed (they need to agree to this before taking on the assignment), whereas in transparent peer review the referees can choose to opt in to having their name published in their public peer review report.
Based on my reading of the PLOS policy page, they operate transparent peer review not open peer review. And so the title of this news story — and the references to ‘open peer review’ throughout — is inaccurate.
This sounds like a reasonable hypothesis to explain the observation:
… researchers who are confident in their work and who broadly embrace open-science practices might be more likely to choose open peer review. As a result, the decision to opt for open peer review could itself serve as an indicator of article quality.
This is worth noting:
Barnett sees the 40% opt-in rate for the PLOS papers as suggesting a lack of widespread support for open peer review. He notes that the study included only papers from open-access journals, and suspects that the rate of authors opting out would be higher at paywalled titles. All primary research articles submitted to Nature, which publishes Nature Index editorial content, automatically undergo transparent peer review.
AI agents are checking the scientific literature — and spotting decades-old errors
Many researchers already dedicate their time to spotting errors in papers and use tools to check certain facets of papers. But one advantage of using AI is the speed at which it can scan scientific databases and literature compared to humans, says James Zou, a computer scientist at Stanford University, California. “The biggest difference is to be able to do this at a scale that was not possible before.”
In a study posted on the preprint server arXiv, Zou and his colleagues used an ‘AI checker’ to scan papers published at NeurIPS — a prestigious annual AI research conference — for errors. Their tool found that errors in papers rose from 3.8 in 2021 to 5.9 in 2025 — an increase of 55%.
Nature (Chris Stokel-Walker)
RFK Jr. questions another publisher on expression of concern for a vaccine paper
The U.S. Secretary for Health and Human Services is once again questioning a publisher on an editorial action regarding a paper on vaccination.
Published in Sage Open Medicine in 2020, the article looks at health outcomes in vaccinated versus unvaccinated children. Its authors are Brian Hooker and Neil Z. Miller, both longtime vaccine critics.
Retraction Watch (Kate Travis)
JB: I feel for the managing editor who received this missive. Their heart must have sank when they read it.
RFK Jr. now has his own cooking show, which presumably means he’s angling to become a chef in The Scholarly Kitchen.
Jack Grove: I was reported to police over the Jason Arday case. I was just doing my job
I was shocked to hear it was from the Metropolitan Police, asking me to call them back. Why? Nothing remarkable had happened to me in the previous year. When I rang back the officer explained a complaint had been made against me regarding the University of Cambridge professor Jason Arday, but the matter was now closed.
But it was important, the officer explained, that I not contact him again, because it was affecting his mental health.
However, I hadn’t emailed Arday in four months – my last direct email had been in September, offering formal right of reply to allegations that he had plagiarised his PhD.
Times Higher Education (Jack Grove)
JB: The Jason Arday plagiarism case was front page news in the UK national newspapers this week, but I first heard about it when I read Retraction Watch’s story News outlet killed story on plagiarism allegations after Cambridge prof hired law firm. The news outlet in question was Times Higher Education and Jack Grove was the reporter, whose journalism beat includes academic publishing.
In the article quoted above, Jack explains what happened to him. It’s a shocking story. It’s worth noting that Police admit they were wrong to warn THE reporter off Jason Arday contact.
Journalists need to be able ask questions, even if they make the interviewee feel uncomfortable.
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Federal lawsuit accuses four major publishers of extorting article processing charges
Publishers’ fees vary, but APCs for open access can range from hundreds of dollars for small journals up to thousands, with some topping $10,000 per paper. The real costs of processing such articles are between $200 and $1,000, Alperin claims in the complaint. The U.S. government requires papers based on federally funded research be freely available. The lawsuit alleges the publishers address this mandate by “extorting” APCs and copyright transfers from “unknowing” PIs who have an “understandable desire to publish in prestigious venues to advance in their careers.”
Retraction Watch (Alicia Gallegos)
JB: Recent evidence suggests that publishers incur costs much larger than those stated in this quote. I made the mistake of reading the lawsuit in full. Ugh.
Major scholarly publishers report ‘strong’ financial results
On 5 August, Springer Nature reported half-year underlying revenue and adjusted operating profit growth of 6.2 per cent and 7.7 per cent respectively for the whole company, and of 7.2 per cent and 8.2 per cent for its research segment. Total revenue and adjusted operating profit rose to €940 million and €246m, with figures for the research segment of €748m and €229m.
…
Two weeks earlier, Relx, which is a more diversified company, reported half-year underlying revenue and adjusted operating profit growth of 7 per cent and 9 per cent respectively for the whole company, and 6 per cent and 8 per cent for its scientific, technical and medical section, which includes scholarly publisher Elsevier. Total revenue and adjusted operating profit reached £4.87 billion (€5.68bn) and £1.73bn, while STM figures hit £1.23bn and £491m.
Research Professional News (Isaac Barbosa)
NUJ issues notice of ballot at The Lancet over pay
Members at The Lancet NUJ [National Union of Journalists] Chapel have overwhelmingly rejected the company’s latest pay offer, with the union now having sent notice to ballot for industrial action. Management presented two offers to our members, both of which were structured as a two-year pay deal. More than three-quarters (78%) voted against the first offer and 87% rejected the second on a turnout of 92%. Despite the chapel’s willingness to broaden negotiations beyond pay, the employer declined to engage. The rejected offers followed an extensive period of negotiations with management, culminating in a final meeting attended by both the NUJ General Secretary and the Advisory, Conciliation and Arbitration Service (Acas).
National Union of Journalists
JB: This is the latest in a series of pay disputes initiated by salaried journal editors. You may remember that back in 2023 the US employees of PLOS formed a union and created a collective bargaining unit. Then, a year later, UK NUJ members working on the Nature Portfolio of journals voted to go on strike in a dispute over pay.
In the previous story we learned that Elsevier’s revenues increased by 6% in the first half of this year while operating profits increased by 8% (i.e. costs, including salary overheads, increased by less than revenues).
Businesses need to balance the needs of three key stakeholders: customers, shareholders and staff. Editors working on selective journals create value for shareholders and it’s not unreasonable to expect to be treated fairly by employers (I have no view on whether the Lancet staff’s demands are reasonable, but they clearly feel undervalued based on the results of the ballot).
Do AI Scientists Need a New Research Paper Format?
One is the “storytelling tax.” Once we write everything into a paper, 80 percent of the information about the work is lost. We only write down the last 20 percent. All the process, a lot of important decision-making, the failures, the attempts that didn’t work out, they are all gone. In my work, I might spend a lot of time on fine-tuning a small component, maybe just a parameter or several lines of code to make the system perform better. Yet none of that is shown in my final paper. Someone can read the paper, think the work is great, but they won’t learn what is actually the trick that makes it perform better on a certain workload. So many side branches get left out in creating the story of how the work was done.
IEEE Spectrum (David Berreby interviews Jiachen Liu)
JB: Mark Hahnel makes a similar argument in his essay Whoever writes the paper, the tools have to be trustworthy.
Most of what a lab knows is not in its papers. It is in the three approaches you already tried that did not work, which will never appear in any published record anywhere. It is in the reason you chose this cohort and not that one, and the argument you had with your collaborator about it. Michael Polanyi called this tacit knowledge, and Hayek’s argument about why central planning fails is the same argument: the knowledge that matters is local, provisional, held privately by the people who acquired it through doing the work, and it does not survive being aggregated into one place. Life science researchers have an enormous context window.
At various points in my career I’ve attended brainstorming sessions about ‘the article of the future’, which often felt like exercises in science fiction. However, I can see some fields embracing a different approach to IMRAD formatted papers. Change is coming.
Exclusive: the science papers that patents cite the most
Patent citations are one way to examine how academic research flows into commercial innovation. So, with an eye to getting a sense of the most industrially influential work, Nature has charted the scholarly papers that patents cite the most.
Nature (Richard Van Noorden, Heidi Ledford & Edward Chen)
JB: This extract interested me:
When Nature examined only the papers from the 2010s onwards that are most mentioned in patents, a few papers related to artificial intelligence appear, including the most highly-cited twenty-first-century paper in scholarly journals. It is a report by researchers at tech giant Microsoft about ‘deep residual learning’ networks. Overall, however, AI- and software-related studies are conspicuous by their absence in the lists.
Which publisher hosts this paper? If you read my analysis of IEEE last week, you’ll be able to take an educated guess.
It’s not clear if there’s any overlap between this story and the next one.
Just over 400 U.S. patents contain citations to retracted scientific papers
Of the 401 patents that cite retracted papers, Kim conducted a further audit of 39 high-impact filings — defined by how many citations the patent itself has received, among other reasons. Nearly half (19) relied substantially on the retracted papers they cited.
…
Rules for amending patents when mistakes or errors are found differ in different jurisdictions, noted Freilich, who has previously called for new mechanisms to retract patents. The United States has no process to formally retract patents, she said, but if a patent contains inaccurate information, a judge may choose to invalidate it in court, which would mean it can’t be enforced against other patents.
Retraction Watch (Dalmeet Singh Chawla)
James Bond, not Bond James: why scientific publishing must respect name order
Yao Ming is not the same as Ming Yao, just as James Bond is not Bond James. Beyond the order of names, it is important to recognize that cultures in many regions do not have family names at all. Yet many journals, conferences and citation systems still insist inadvertently on separating humanity into rigid given-name and family-name order, often enforcing conventions that do not reflect cultural realities. For example, online submission systems often require author names in a fixed order that must exactly match the manuscript files. These systems can create invisible hurdles and frustration for authors seeking to present their names in culturally appropriate ways.
Nature (Rachakonda Sreekar)
JB: This topic has been discussed at length, but is becoming increasingly important now that so much of the literature is written by researchers working in Asia. Unique identifiers are likely the answer.
ICYMI: recently in Journalology
Clarivate removes hold on mega-journal Heliyon after internal audit, 650+ retractions
Clarivate has lifted its hold on Heliyon after the journal’s internal audit led to over 1,000 retractions, expressions of concern and corrections. As a result, the journal will receive an impact factor in the coming cycle, a Clarivate spokesperson said.
Clarivate decided in September 2024 new content from Heliyon would not be indexed in its Web of Science due to concerns about quality. The journal told us at the time it was “investigating,” and since then, it has retracted over 650 articles.
Retraction Watch (Avery Orrall)
JB: I covered this story at the end of June in issue 150. Come on Retraction Watch — keep up!
Can we stop AI from flooding scientific journals?
“We’ve been talking about not measuring quantity over quality for decades,” [David] Resnik says. “It hasn’t happened.” Meanwhile, it’s everybody’s problem, he adds. “Funders and funding agencies need to take responsibility, and Institutions need to develop better AI policies. And then of course, researchers should be responsible and disclose too. We need to slow down,” he says. “Publish less and let peer reviewers do their job.”
The barrier to fraud has never been lower. When fabricating a paper required months of effort and specialized skill, the cost was high enough to deter most people. When it requires an afternoon and a chatbot, the cost-benefit calculus changes entirely.
C&EN (Ananya Palivela)
JB: The answer to this question is almost certainly ‘no’. Perhaps it’s a small consolation that other sectors are also struggling. The lead story in the UK edition of The Economist this week is How AI is breaking the British state.
Citizens frustrated by the poor deal they get from the authorities are turning to artificial intelligence to file objections and appeals, and claim their dues. The resulting deluge of complaints, and demands, will overwhelm bureaucracies built for the age of the post and the telephone. Too little is being done to prevent the state from drowning.
I haven’t heard editors or publishers complaining about an increase in appeals against editorial reject decisions. Is that happening? Please hit [reply] and let me know.
Scientists using LLMs will ‘do more, less well’, modelling study predicts
Scientists who use large language models (LLMs) to help them with their research will spend less time refining their work and instead jump quickly to fresh projects, according to a modelling study.
Adoption of LLMs will cause scientists to “do more, less well — rather than the same amount, better”, write the authors. But they say that such artificial-intelligence tools do not bear all of the blame for that outcome.
The results reflect a flawed incentive system in science that prioritizes quantity over quality, says study co-author Carl Bergstrom, a biologist at the University of Washington in Seattle. Scientists are incentivized to churn out papers, he says, and LLMs help them to reach ever-growing quotas. “LLMs are rarely the problem themselves,” says Bergstrom. “LLMs hold up a mirror to problems that we already have.” The study was posted on the arXiv preprint repository on 19 July and has not yet been peer reviewed.
Nature (Kaia Glickman)
JB: Yes, the root cause of the problem is the academic incentive structure. How long? How long must we sing this song?
The northern hemisphere summer months are meant to create a slow news cycle, but there was no sign of that happening in July. Perhaps August will be quieter.
Until next time,
James
With apologies to Bono.