Hello fellow journalologists,
This newsletter is landing in your inbox a few days later than initially planned, for various family and technology related reasons. My apologies.
I took some time off over the Easter break, so I didn’t send a newsletter last week. This week’s edition covers the period from April 1 to April 14.
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News
F1000 and the Bill & Melinda Gates Foundation have announced plans to launch a new verified preprint platform that will enable the rapid availability of new findings and promote research integrity. VeriXiv [pronounced
very-kive] will support researchers in complying with the Gates Foundation’s
refreshed open access policy that requires all their funded research to be made available as a preprint from January 2025.
Twenty different ethics and integrity checks will assess a range of issues, including plagiarism, image manipulation, author verification and competing interests. In addition, open research transparency checks will check whether the data is available in an appropriate repository and that methods have been included to support reproducibility. Each preprint will have clear labelling so that readers know the level of verification conducted on the article, and which levels have been passed.
Taylor & Francis (press release)
JB: I covered the new B&MGF open access policy in the last newsletter. Since then, further details about the policy have been released, which you can read here. This sentence is somewhat nebulous:
All Funded Manuscripts, including any subsequent updates to key conclusions, shall be available immediately, without any embargo, under the Creative Commons Attribution 4.0 International License (CC BY 4.0) or an equivalent license.
It’s not clear to me what “including any subsequent updates to key conclusions” means. Does the author accepted manuscript (AAM) need to be published under a CC BY license too? If so, that's not spelled out specifically in the policy, as far as I can tell. There’s no mention of the Rights Retention Policy, which will be a relief to many publishers.
Ashley Farley wrote an editorial about the new policy in the International Science Council blog, which said:
While discussing policy refresh, it is crucial to note that we don’t see this as the perfect Open Access Policy, but it marks a critical step towards unlocking future potential. We recognize that there is a cost to disseminating, marketing, and preserving knowledge in the journal format but these costs remain non-transparent, continually increasing, and tied too intrinsically to journal brand. It’s been hard for me to see what value and service we get when we pay an APC. With preprints, we are alleviated from the above issues and can begin to focus on what is most critical for advancing research.
Meanwhile, Nature ran a news story that asked: Will the Gates Foundation’s preprint-centric policy help open access?. The journalist asked Johan Rooryck, executive director of cOAlition S, for comment.
The coalition has been examining the role of preprints in OA, but it’s a long way from adopting any related policy changes, Rooryck says.
A document released by the group last year discussed the issue, and the coalition is gathering feedback from the research community through a survey open until 22 April. No decisions will be made on adopting any proposal before the end of the year.
Unsurprisingly, the Howard Hughes Medical Institute told Science that they support preprinting.
Ann Michael and Dan Pollock assessed the new policy in a Scholarly Kitchen post. As they point out, a largely unanswered question is ho much the version of record and the initial preprint differ:
If researchers do work with preprints more widely, then we should be able to gather further evidence about the comparative value of preprint and VoR, and of the roles that each might play as any new system evolves.
We certainly need more insights into how manuscripts change over time. Crucially, it’s not the number of changes that are important. For example, a peer reviewer or editor who spots that a drug dose in a clinical paper should be in micrograms rather than milligrams has added immense value, even though only one letter has been changed.
Richard Sever, one of the authors of Plan U, which is very similar to the new B&MGF policy, noted:
And what of the elephant in the room, National Institutes of Health (NIH)? The recent OSTP memo requires US-government-funded articles to be made free, but does not provide additional funds. If government agencies like NIH were to decide preprints qualify, as bioRxiv and arXiv have suggested, authors would have an easy path to making articles free that doesn’t require them to find an extra $5-10K behind the couch to cover APCs.
Mandating the deposition of preprints, rather than the author-accepted manuscript, certainly makes life much easier for publishers. Posting a preprint before peer review (i.e. before the publisher has added value and incurred costs) with a CC BY license is sensible, although there’s a risk that preprints will be increasingly used to peddle misinformation to news outlets.
I suspect that the B&MGF is hoping that researchers will stop using journals and will decide, instead, to transition a paper from VeriXiv to Gates Open Research.
(Who comes up with these names? I'm tempted to create a preprint server devoted to the science of education, just so that I can call it SciXiv (skive is British slang, so this ‘joke’ won't land well with 75% of Journalology readers).
However, that transition will only occur if Gates Open Research is able to amplify the authors’ message. In recent years publishers have focused much of their efforts on improving the author experience. F1000 / Taylor & Francis needs to adopt a different tactic and invest in driving usage of the content published in Gates Open Research, as well as developing it as a brand. Otherwise, researchers will continue to publish in traditional journals for years to come and the version of record will often remain behind a subscription barrier.
The chief editors of three major scientific journals have been asked to testify before a House of Representatives subcommittee on whether their journals have an “inappropriate relationship with government”.
The invitation from Republican representative Brad Wenstrup (pictured), chairman of the Select Subcommittee on the Coronavirus Pandemic, relates to a hearing taking place on 16 April.
It “seeks to examine any potential inappropriate influence exerted by the federal government over research publications related to Covid-19 and ensure that the federal government is not granted undue access to the scientific review process during a future health crisis”, according to the subcommittee webpage controlled by Wenstrup.
Wenstrup has invited the editors-in-chief of Science, Nature and The Lancet, respectively Holden Thorp, Magdalena Skipper and Richard Horton.
Research Professional News (Craig Nicholson)
JB: You can read the letters each editor received here. A few hours ago the website U.S. Right To Know published a summary of yesterday’s meeting.
Thorp emphasized that the peer review process at Science had tempered the claims in the papers and generally criticized how the media covers preprints as sensational.
“At the end of the process, they were edited under my supervision to ensure that the language was consistent with the extent to which the evidence presented was supportive, but not dispositive, of a natural origin,” Thorp said in his prepared testimony. “We made these changes because we felt that lab origin was still a possibility.”
His new statements contrast with the prominent public statements of the virologist authors — both before and after peer review — that their papers were nothing short of conclusive.
Central to Pickering and Kgotleng’s critique is that neither the Netflix documentary nor a book published in October mention that the findings were preliminary and subject to review. This, they say, runs counter to the spirit in which the preprint publishing system was introduced. Nor, they write, have Berger or his co-authors revised the original manuscripts to address the reviewers’ comments.
“This is not just a muddle of dates or a slip of the tongue at a stressful press interview by a media-shy academic. This appears to be a deliberate and well-planned exploitation of a new publishing model to shortcut the usual scientific process of academic publishing,” Pickering and Kgotleng write
“Palaeoanthropology is not a field that needs urgent research and rapid breakthroughs. Given the huge and wide public interest in human evolution and our origins, this research field benefits from much slower, measured and careful research,” they say, adding that there is “no demonstrable need to peddle an unreviewed narrative to the public”.
Research Professional News (Linda Nordling)
JB: This is old news in many ways. I covered the eLife paper and Netflix documentary in issue 38 of this newsletter.
In the arXiv study, a team led by Weixin Liang, a computer scientist at Stanford University in California, developed a technique to search for AI-written text by identifying adjectives that are used more often by AI than by humans.
By comparing the use of adjectives in a total of more than 146,000 peer reviews submitted to the same conferences before and after the release of ChatGPT, the analysis found that the frequency of certain positive adjectives, such as ‘commendable’, ‘innovative’, ‘meticulous’, ‘intricate’, ‘notable’ and ‘versatile’, had increased significantly since the chatbot’s use became mainstream. The study flagged the 100 most disproportionately used adjectives.
Reviews that gave a lower rating to conference proceedings or were submitted close to the deadline, and those whose authors were least likely to respond to rebuttals from authors, were most likely to contain these adjectives, and therefore most likely to have been written by chatbots at least to some extent, the study found.
Nature (Dalmeet Singh Chawla)
Other news stories
ResearchGate and Wiley's Journal Home partnership expands to 700 journals
ResearchGate and Extrica announce Journal Home partnership for open access journals
ResearchGate and Optica Publishing Group announce new Journal Home partnership
Exclusive: official investigation reveals how superconductivity physicist faked blockbuster results
Changes to Scopus Open Access (OA) document tagging
Early Career Professionals in Scholarly Publishing Tell All
Silverchair Expands Product & Strategic Partnerships
Embattled researcher Didier Raoult earns more than 100 expressions of concern and another retraction
Developing a US National PID Strategy Report Released
Molecular Connections Launches Conversational Search Platforms - Powered by LLM
Paperpal Preflight for Whitepaper
A key chemistry journal disappeared from the web. Others are at risk
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Opinion
There is an emotional toll of working in forensic scientometrics. The thrill of investigating crimes against truth may fascinate and enthrall many, but this comes with the emotional complement of delving into the deception of a field you trusted. People you believed in. Knowledge you believed in.
The threats to forensic scientometricians are alarming – including revealing personal information like home addresses (doxxing) in an attempt to intimidate the individuals. Real or threatened lawsuits target people and organizations striving to do the right thing, even those without institutional support. Moreover, lawsuits against publishers aim to prevent retractions, and both individuals and institutions face the burden of lawfare– the exploitation of legal systems and institutions to undermine, discredit, or exhaust an adversary.
The Scholarly Kitchen (Leslie McIntosh)
JB: You can read the full paper, available as a preprint, here.
“Keystone” is a network analysis built on OpenAlex that I’ve been running in one form or another since shortly after the Papermill Alarm was released in 2022. We analyse the relationships between papers, individuals, institutions and other signals to learn about the papermill problem. Last year, Keystone went through some substantial development. It is now integrated into the Papermill Alarm and is already in use by a number of publishers.
I’ve spent a lot of time with Keystone and I’m seeing some interesting things.
- We can tell which researchers are most likely to be running papermill operations.
- Some Keystone-authors’ papers are real. This puts an interesting spin on investigations. That ‘KYA’ [Know Your Author] principle applies: an author only needs to have one verified fake in their history for me to be concerned about all of their output.
Medium (Adam Day)
The second is to play through all of the potential consequences. This is something our industry isn’t very good at and we’re today living with the consequences of our failures in this area. I include my own organization in this – back when PLOS was launched and focused in the biomedical sciences where large grants were common, charging authors a fee to publish seemed fair and reasonable if it meant that anyone could read and reuse the paper. But we failed to anticipate how successful APCs would become, how commercial publishers would exploit this space, and how inequitable they would become. In a similar vein, there is a risk under the “refreshed” Gates Foundation policy that, without established alternatives, their grantees will revert to publishing their research behind paywalls. That’s why the work PLOS is doing with the working group we established with cOAlition S and Jisc is important to facilitate discussions with relevant stakeholders to try to drive change across the industry.
The Scholarly Kitchen (Alison Mudditt)
JB: I always enjoy reading Alison’s well argued opinion pieces. It would be fair to say that many observers warned, right from the outset, that an APC economy could cause problems. If a publisher’s primary goal is commercial, then it will adopt strategies to maximise a return for its investors: ‘publish more papers and make more money’ was always going to create problems, although few anticipated how quickly new entrants would be able to grow, by focusing on rapid publication and by commissioning content for special issues at scale.
We begin our reflection on transformation with perhaps one of the most unremarked on, yet most pervasive changes in research – the switch between initials and full first names in the author records. As we will see, the shift from the formal to the familiar has been in flux from the start of scholarly publishing, however – particularly in the last 80 years – we can trace the influence of countries, fields of research, publishers and journal submission technology, funders and scholarly knowledge graphs on author name behaviours. In more recent history, we can observe that the shift towards full names has also been gendered, particularly in medicine, with men shifting towards full names earlier than women.
TL;DR (Simon Porter and Daniel Hook)
JB: This is the first in a series of articles about Research Transformation. You can read the introduction to the series here. This particular article, which looks at how names have been listed in research papers over the course of decades, is absolutely fascinating. The authors conclude with this challenge:
The transformation away from name formalism of course does not stop at author bylines. Name formalism is also embraced in reference formats. It could be argued that even within a paper, this formalism suppresses the diversity signal in the research that we encounter. Reference styles were defined in a different era with physical space constraints. Is it time to reconsider these conventions?
Within contribution statements that use the CRediT taxonomy, initials are also commonly employed to refer to authors. Here, this convention also creates disambiguation issues when two authors share the same surname and first initials. Here too, as the digital structure of a paper continues to evolve, we should be careful not to unquestioningly embed the naming conventions of a different era into our evolving metadata standards.
As stated in the Publishers Association’s letter, publishers across the industry are aware of the use of “vast amounts of copyright-protected works without the authorisation of the right holder in the training, development, and operation of AI models”. The risk for publishers and, fundamentally, for research authors is the potential power of AI technologies to absorb, retain and re-use knowledge. Against these risks, publishers are balancing the need to adapt – and quickly – to this new world, with the need to ensure that published material is neither overlooked as a critical source of knowledge nor simply taken without appropriate authorisation, remuneration and attribution.
Times Higher Education (David Clark)
JB: Just imagine what the backlash would have been if the Elsevier CEO had written this instead. University presses, and not-for-profits more broadly, are understandably concerned about the potential effect of AI to reduce the financial resilience of their publishing programmes.
Other opinion articles
Three ways ChatGPT helps me in my academic writing
‘Without these tools, I’d be lost’: how generative AI aids in accessibility
Artificial Intelligence: What the Future Holds for Multilingual Authors and Editing Professionals
Response from ALPSP to ICO’s Second Generative AI Consultation
Kitchen Essentials: An Interview with Tracey Armstrong of CCC
Chefs de Cuisine: Perspectives from Publishing's Top Table - Susan King
Kitchen Essentials: An Interview with Tasha Mellins-Cohen of COUNTER
Peer review demystified: part 2
Social science impact demands faster publishing and more reproducibility (paywall)
Publishing negative results is good for science
Journal Club
Authorship credit distribution conflicts seem to intensify later on in one’s career, this time in the form of “peer conflicts”. Specifically, the results suggest that roughly one-half of the participants in this study have experienced a conflict with their peers. These conflicts seem to escalate with age and experience with older, more experienced, and more productive participants reporting higher conflict rates compared to their counterparts. Conflict prevalence with one’s peers seems to be high despite some non-consistent moderators such as gender, workload, and geography
Scientometrics (Elizaveta Savchenko and Ariel Rosenfeld)
This study draws on a longitudinal dataset of 277 UK learned societies covering the period 2015-2023 to provide evidence-based insights into the changing landscape of society publishing. It identifies a rapid decline in the number of self-published societies and an increasingly complex outsourcing landscape. New publishing partnerships are emerging with university presses and other not-for-profit entities rather than commercial publishers, while all but the largest UK societies have seen their publishing revenues decline in real terms since 2015. In general, UK learned society publishers are seeing their influence wane as market conditions favour publishing models focussed on quantity rather than quality.
Research Consuting preprint on Zenodo (Rob Johnson and Elle Malcolmson)
JB: OK, so this isn’t a journal article in its strictest sense, but it’s likely to be of interest to many readers of this newsletter.
And finally...
Many academics don’t fully understand and appreciate the work that publishers do. This article (Scientific publishers not adding value) caught my eye this week. Here's an excerpt:
For one of my papers — a paper on studying mental health problems as systems, not syndromes — the copy editor insisted that key terms required different spelling: “mental-health problems”, “mental-health practitioner”, “mental-health problems”, “mental-health systems” and so on. I kept reverting these changes multiple times, and left comments, but the copy editor kept returning them to their silly hyphenated versions. I honestly may have let this one go if the title of the paper wouldn’t have read ..
Studying Mental-Health Problems as Systems, not Syndromes
I tried a number of arguments, including that in this very same journal, and other journals of the same publisher, mental health is spelled correctly. The response was that the existence of mistakes isn’t reason to change the rule. This was only resolved once I sent a pretty strongly worded email with over 10 screenshots from large mental health organizations about “mental health”, including NIH, NIMH, NHS, Mayo clinic, WebMD, The Wellcome Trust, and so on.
We shouldn’t mock this author for being unaware of how to use compound modifiers, but it’s reasonable to ask why the copy editor didn’t explain why they were adding the hyphens (correctly). Publishers need to do a better job of explaining the value they add and why the changes they make are important.
If you’re not sure what a compound modifier is, here’s an explanation from The Guardian:
The general rule is to use hyphens only when it is a matter of necessity. Where an adverb can also be an adjective, such as hard, the hyphen is required to avoid ambiguity – it's not a hard, pressed person, but a hard-pressed one; an ill-prepared report, rather than an ill, prepared one. A hyphen is also needed to distinguish between the different meanings of such phrases as "black-cab driver" and "black cab-driver".
Until next time,
James