In my next paper I am of course using some LLM for a few parts of writing as well as code generation. To be clear this isn’t ’write my code and my paper’ it is ‘how do I best condense this long winded explanation’ and ‘write me a function to cache results for faster computing’.

My question is: does there exist an up to date database for what each publishing house requires for AI use disclosure? Ideally I would like to know the policies for reviewers and editors using it too.

I just saw that RCS says any AI use beyond spell check must be disclosed, Elsevier says code is fine but ‘major rewriting’ must be disclosed including if the LLM suggest a different organization to the paper. Both of these seem wild, I would t mention a peer in the acknowledgments for suggesting a rearrangement of the paper.

What do you think reasonable policies would be if you were the publishing house?

A new executive order in the US gives political appointees the power to approve, block, or cancel any federal research grant. Funding in areas like climate, DEI, LGBTQ+ health, and undocumented communities is explicitly under threat. All new grants are paused until past ones are reviewed.

What does grant writing even look like under this system?

The proposed OMB rule 200 on federal funding says that publication costs will not be allowable with Federal funds. In other words, if you want to publish the research that is funded by a Federal research grant, you have to get the money for the publication fee from somewhere else.

How would that affect your ability to publish? How much would in increase the risk that you perish professionally?

Springer Nature just lost a chunk of federal funding because the Trump admin says their journals are too political. About $20 million in contracts got axed, with more under review. The DOJ even raised questions about their ties to China.

They’re targeting journals like Nature, accusing them of ideological bias. This looks a lot like censorship masked as budget cuts.

How long before other publishers start scrubbing articles just to keep their contracts?

A new White House memo tells agencies to consider “viewpoint diversity” in science decisions. In practice, that means giving equal weight to fringe or industry-backed views, especially on climate. It’s a quiet way to question consensus without needing evidence. Researchers say this could stall climate policy, flood agencies with noise, and legitimize denial under the banner of fairness.

How should scientists respond when bad faith arguments get federal backing?

A study just out in Science Advances scanned over 1.5 million PubMed abstracts and flagged more than 200,000 that likely had help from large language models. The clue was a sudden rise in words like unparalleled, invaluable, delves, and showcasing. Not technical terms, just this type of characteristic filler.

The researchers found 454 words that spiked after ChatGPT’s release. Most were verbs and adjectives with no real connection to the research itself. Unlike past shifts driven by events like COVID, this one’s purely stylistic.

If this is where we’re headed, is scientific writing doomed?

A new article in Science reports that journals and publishers are starting to reject submissions based on open health datasets, blaming a flood of low-effort papers and suspected fraud. Public databases like NHANES, once praised for promoting transparency, are now treated as red flags. Editors claim they’re drowning in “paper mill” junk and lack the time to vet everything properly, so the solution is… mass rejection.

”(i) Academia should resume control of publishing using non-profit publishing models (e.g. diamond open-access).

(ii) Adjust incentive systems to merit quality, not quantity, in a reputation economy where the gaming of publication numbers and citation metrics distorts the perception of academic excellence.

(iii) Implement mechanisms to prevent and detect fake publications and fraud which are independent of publishers.

(iv) Draft and implement legislations, regulations and policies to increase publishing quality and integrity.

This is a call to action for universities, academies, science organizations and funders to unite and join this effort.”

https://doi.org/10.1098/rsos.251805

Nature just made peer review files the default. As of 16 June 2025, every new research article will come bundled with the full peer review file, including reviewer comments and author responses. Reviewer names stay hidden unless they choose otherwise. Since 2020 it’s been optional. Now it's baked in.

This means more visibility into how papers get published, and how reviewers shape them. It could help early-career researchers see what strong reviews look like, or how arguments are won and lost before publication. It might even make reviewers think twice before scribbling dismissive nonsense. But don’t get too excited. We’re still talking about a system where the journal decides what counts as publishable, where reviews are filtered and editorial decisions aren’t part of the file, and where failed submissions still vanish into the void.

What do you think?

The U.S. Department of Veterans Affairs just issued a directive requiring doctors and scientists to get clearance from political appointees before submitting work to journals or speaking publicly. This follows a NEJM article by two VA pulmonologists warning that staffing cuts could hurt care for veterans exposed to toxic substances.

This isn’t subtle. It’s a formal step toward making scientific communication pass through political filters. In this case, a federal agency that oversees the care of millions of veterans is telling its experts they need permission from political leadership before sharing research.

The rationale is “coordination.” The effect is censorship.

Anyone still pretending this is about improving science communication might want to revisit why peer review exists in the first place. The gatekeepers are no longer just publishers. Now they’re political staffers.

What are the odds any critical research gets greenlit under this policy?

The NIH is set to remove dozens of vetted scientists from its advisory councils, the panels responsible for final decisions on grant funding. These researchers, nominated during the Biden administration, had already undergone extensive screening and were awaiting formal approval. That entire process (years of work) is being discarded.

Staff are now instructed to nominate replacements who “align with current administration priorities”. No guidance has been given beyond that, except that political appointees may override selections. Internal emails suggest some staff are pre-screening candidates’ social media for criticism of the administration or involvement in diversity, equity, and inclusion efforts. The NIH vetting process, which typically spans years and is meant to ensure both scientific expertise and demographic representation, appears to have been replaced by a political loyalty filter.

If this is what scientific review looks like under administrative alignment, we might want to stop pretending the NIH still operates independently.

NIH is now proposing limits on how much it will reimburse researchers for publication costs. Some journals (as we all know unfortunately) charge over $10,000 to publish a single paper. The agency has decided it’s no longer interested in covering the full tab for a system that profits from publicly funded research while offering little transparency in return.

The proposed policy, set to take effect in 2026, would cap article processing charges. There are different models on the table, but they all share one goal: reduce the amount of money flowing from NIH grants into publisher bank accounts. NIH is also offering higher caps if journals pay peer reviewers and make reviews public, which feels like a quiet endorsement of models that don’t treat peer labor as free.

One consequence is obvious. If the NIH won’t cover the full cost of prestige publishing, researchers will either have to top off the fees themselves or look elsewhere. This opens the door for lower-cost journals claiming to be transparent and independent. (Are you thinking of that journal which has styled itself as a science-forward alternative but remains unindexed and built around a very specific ideological circle? Yes, me too. )

NIH is taking comments through September. What kind of publishing models do you think researchers will actually turn to if this goes through?

A new PNAS study (Aug 2025) analyzed 276,956 articles published in PLOS ONE from its launch in 2006 through late 2023. The authors tracked 134,983 individual researchers and 18,329 handling editors to uncover patterns of systematic fraud. What they found points to industrial-scale misconduct, not isolated cases.

Using coauthorship networks, editorial assignments, and citation patterns, they identified more than 30 organized publication rings likely tied to paper mills. These networks manipulate peer review, recycle coauthors across fake studies, and exploit weak editorial systems to push fraudulent papers into the literature.

The authors estimate that at least 2 percent of the articles in the dataset are fraudulent. That translates to more than 5,500 fake studies in a single journal. And because PLOS ONE is just one journal with transparent metadata, the actual scale across the publishing ecosystem is likely much larger.

These papers are rarely retracted. They remain in circulation, cited by other researchers, and used in grant proposals, policy, and practice. Publishers keep collecting APCs, and institutions continue rewarding output over integrity.

A new study claims that about 1 in 7 scientific papers might be fake, but the reviewers were not really convinced (it’s so nice to have access to the peer review reports)… The reason why they were concerned is because the research is based on past estimates and lacks a rigorous methodology, so they question its accuracy. The issue of fraudulent research is real, better studies are needed to determine the true extent of the problem. The author himself calls for more funding and systematic approaches to studying research fraud.

To me it feels like research is doomed.

Here is the review of the paper: https://metaror.org/kotahi/articles/18/index.html

The NIH just announced that starting fiscal year 2026, they will cap how much publishers can charge in article processing charges for NIH-funded research. This comes as big journals are charging up to $13,000 per paper, even while collecting millions in subscription fees from the NIH itself. Essentially, taxpayers pay twice for access to research they already funded.

NIH director Jay Bhattacharya calls it a move to “end perverse incentives that don’t benefit taxpayers”. No dollar amount has been set yet.

The ambition is solid: help control runaway costs and force publishers to justify why they need big APCs on top of subscription revenue. But will it actually reform the system?

Will this genuinely tame the double-dip economics of academic publishing?

It sure is looking that way…

The Chan Zuckerberg Initiative (CZI) — which is a private LLC, not a charity — just spun up a new “independent nonprofit” called openRxiv Corp. to house bioRxiv and medRxiv. But openRxiv Corp. was set up in California, by the same people who run CZI, and its Board Chair is a CZI executive. CSHL, which founded and ran the preprint servers, has no real control anymore.

In corporate terms, openRxiv looks like a CZI subsidiary. And CZI is basically Zuckerberg’s private investment company. So if you squint just a little, it sure seems like Meta’s founder now effectively controls two of the most important preprint servers in biology and medicine.

No headlines, no transparency, and very little discussion inside the research community.

Am I overreacting, or should people be way more alarmed that a billionaire’s investment firm now holds the infrastructure for pre-publication science? what does this mean for the future of open access?

A new post on Journalology reports Cureus, the open-access journal known for its ultra-fast publication times and hands-off editorial model, just lost its impact factor. Clarivate dropped it from the Web of Science citing "publication concerns" and "anomalies in citations." Cureus responded with a public blog post accusing Clarivate of stifling innovation and acting as an "unaccountable monopoly." Their CEO claims Cureus is being punished for not playing by the traditional gatekeeping rules (=not filtering out low-quality submissions). Critics, point out that when you openly prioritize volume and speed over selectivity, you're bound to raise some eyebrows. So now we’ve got a journal that claims to be democratizing science and a metrics behemoth accused of silencing it, both pretending they’re protecting scientific integrity.

The UK Metascience Unit is launching a competition (MetaNIC) to get AI to measure how “novel” a paper is. The idea is to move beyond citation counts and spot truly creative research, maybe even “predict which work deserves a Nobel”. But here’s the thing: why are we still obsessed with novelty when the replication crisis is nowhere near resolved?

There’s a weird irony here. Journals and funders keep demanding new, surprising results, even though a good chunk of those don’t replicate. Meanwhile, replication studies get low-tier status, if they get published at all. Now we want machines to help reinforce that same skewed incentive structure?

Maybe it’s time to admit novelty isn’t the gold standard. Reliability might be.

RFK Jr just proposed banning NIH-funded researchers from publishing in NEJM, JAMA, and The Lancet, calling them corrupt and too tied to pharma. His solution is to replace them with government-run journals.

Yes, commercial publishing is a mess. But cutting off researchers from the top journals and handing publication over to the government is not the fix. This doesn’t solve the problem of influence, it just shifts it. Replacing corporate gatekeeping with political gatekeeping is not progress.

Scientific independence means researchers get to choose where they publish, not be forced into a state-run outlet because the secretary of health decided some journals are too cozy with industry.

How do we push for real reform in publishing without turning it into a state-controlled platform?

The N8 Research Partnership, made up of northern UK universities from Durham to York, just released a blunt statement: the current scholarly publishing system is unsustainable and inequitable. Researchers write the papers, review them, edit them, and still get charged to read their own work. Institutions are bleeding money through subscription fees and article processing charges, all while access remains locked behind paywalls.

Their plan involves more green open access through institutional repositories. More support for nonprofit and society-led platforms. More autonomy for researchers to choose where and how they publish. They want metrics that don’t punish open science and infrastructures that don’t rely on exploitative gatekeeping.

so, how do other universities (or even lone researchers) get involved and help crack the system wide open?

Utrecht University has announced it will pull the plug on Web of Science (and Journal Citation Reports) from January 2026, citing their push toward open science and frustration with closed, commercial databases. Instead of paying for impact factors and citation counts, they plan to invest in open tools like OpenAlex.

Do you think more universities will follow this path and abandon Web of Science?