The Illnesses of Basic Biomedical Science, Continued: Scientific Publishing

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A life in basic research has always been uncertain but not always precarious. From the mid-1950s through the mid-1980s, it took sustained effort and some good fortune to get the grants necessary to run an academic research laboratory.  But this was also the usual outcome even with variations in funding levels from cycle to cycle.  Those who taught me were of the generation that began soon after Vannevar Bush’s vision revolutionized American science and turned it into the powerhouse it has been for the past seventy-five years.  They exaggerated when they said their review panels met to decide which applications not to fund, but not by much.  I began my career at the tail end of that era.  It was clear that in the public research university that I attended for undergraduate and, much later, graduate school, that scientists were successful if they worked hard, followed their scientific intuition, and prepared the next generation of scientists for careers in basic research and industry.

This is no longer true for the majority of basic scientists (including those in industry, who are also members of the scientific precariat).  Before the recent attack on universities and their researchers by the Current Administration, success rates at the National Institutes (NIH) were in the single digits in some institutes and overall success rates hovered near 20%. [1]  Undoubtedly, these rates will be lower going forward.

Along with the funding crisis, another critical component of our “research enterprise” in distress is the business of scientific publishing.  Some of this has been covered here before regarding peer review.  It is clear to all that scientific publishing is very ill.  Much to the chagrin of most scientists of my acquaintance, the current administration is not wrong in pointing this out.  Even if their specific criticisms miss the mark, Scientific Publishing Industry Faces Federal Scrutiny by Kathryn Palmer shows why “Long-standing criticisms of academic publishing are helping to fuel the Trump administration’s attacks on the nation’s scientific enterprise”:

For years, some members of the scientific community have raised alarm about research fraud, paper mills, a paucity of qualified peer reviewers and the high cost of academic journal subscriptions and open-access fees. Research also suggests those problems are rooted in academic incentive structures that reward scientists for publishing a high volume of papers in widely cited journals (or until virtually yesterday, “journals” that are seldom cited; most administrators can count but that is as far as it goes with the general run of the species).

“We all know there are enormous problems facing science and scientific publishing. But a lot of the scientific community is pretending there are no problems,” said Luís A. Nunes Amaral, an engineering professor at Northwestern University who co-authored a paper that identified a surge in research fraud over the past 15 years. “This attitude empowers demagogues to then come and point out issues that are real and recognizable. This gives them some sense of [legitimacy], but in reality they are not trying to improve things; they are trying to destroy them.”  (Not only demagogues but they are louder.)

Yes, indeed, on all cases.  The insularity and general political cluelessness of academic scientists is astonishing at times, but there is no real argument against Professor Amaral here.  However, the current Secretary of Health and Human Services is misguided when he says that multiple top medical journals (e.g., New England Journal of Medicine and The Lancet) are “utterly corrupt.” [2]  His claim that these journals are “controlled by the pharmaceutical industry” sounds plausible, but he misses the point correctly made by Marcia Angell, a former editor of NEJM, that it is often “no longer possible to believe much of the clinical research that is published” because of researchers’ ties to Big Pharma” (NYRB, 2009).  This is a matter separate from the business of scientific publishing.  We have covered this previously in discussions of Evidence-Based Medicine, statins, the diet-heart hypothesis, and ultra-processed foods.  However, not one part of this penetrates the carapaces of MAHA and her brother MAGA, which in any case are only tropes.

And again more recently from Dr. Angell and two former editors of NEJM in STAT:

Journals didn’t create the issue, but researchers have come to rely on support from pharmaceutical companies. They noted that journals have taken steps to mitigate industry influence, including requiring authors to disclose ties to relevant companies. (Less need to tap Big Pharma for support would solve myriad problems.)

“Kennedy is right that the dependence of medical research on pharmaceutical funding is a problem,” the former editors wrote. “But Kennedy’s actions as head of HHS—including his deep cuts to the National Institutes of Health and targeting of our best medical journals—will make that problem worse.”

Kennedy has also floated the idea of launching an in-house government journal as a solution to rooting out corruption. But Ivan Oransky, a medical researcher and cofounder of Retraction Watch, said that could also raise credibility questions.

“I’m not quite sure what creating a journal accomplishes. It’s just another journal that will have to compete with other journals,” he said. “The other question is, will it be fair and balanced? Will it be interested in what’s true and getting good science out there or only in science that [Kennedy] believes is worthwhile? That’s a real fear given a lot of his pronouncements and what he’s trying to do.”

Which brings us to three other principals in this argument, Jay Bhattacharya, the current Director of the National Institutes of Health and Martin Kulldorf, the current chair of ACIP, the Advisory Committee on Immunization Practices of the Centers for Disease Control and Prevention (CDC). [3]  Drs. Bhattacharya and Kulldorf along with Dr. Marty Makary (wait for the remainder table or use your local library), the current commissioner of the Food and Drug Administration (FDA), have launched their very own scientific journal:

The Journal of the Academy of Public Health…is linked to the right-wing news site RealClearPolitics…as a counter to mainstream journals. During the pandemic, Bhattacharya and Kulldorff co-authored the Great Barrington Declaration, which called on public health officials to scale back stay-at-home recommendations aimed at mitigating the spread of disease and received widespread criticism from NIH officials at the time.  Critics worry that the new journal may become a platform for some of the dubious research pushed by the Trump administration.

These critics are right to worry.  Only members of the new Academy of Public Health (not to be confused with the American Public Health Association, founded in 1872) can publish papers in The Journal of the Academy of Public Health.  There is nothing unusual with the establishment of a new scientific society and its cognate journal.  This has happened regularly since the Royal Society first met on 28 November 1660 in the company of, among others, Sir Christopher Wren (St. Paul’s Cathedral) and Robert Boyle (Boyle’s Law).  Philosophical Transactions of the Royal Society was first published in 1665.  But legitimate concerns have been raised about the Academy of Public Health and its journal:

A new journal co-founded by President Donald Trump’s pick to direct the National Institutes of Health (NIH) says it will “promote open and transparent scientific discourse” but is drawing controversy within mere days of its launch.

The Journal of the Academy of Public Health (JAPH), announced on Wednesday, is the brainchild of NIH nominee Jay Bhattacharya, a physician (Bhattacharya has an MD but has never been a physician) and economist at Stanford University, and Martin Kulldorff, a former Harvard University biostatistician who became known for his opposition to lockdowns, child vaccination, and other public health measures during the COVID-19 pandemic. Its editorial board also includes Trump’s pick to lead the Food and Drug Administration, Johns Hopkins University surgeon Martin Makary, who also opposed vaccine mandates.

The journal, which has already published eight articles on topics including COVID-19 vaccine trials and mask mandates, eschews several aspects of traditional publishing. It lacks a subscription paywall, posts peer reviews alongside published articles, and pays reviewers for their work. But other researchers have criticized the journal’s exclusivity and lack of quality control. Only members of a newly formed body, the Academy of Public Health, can submit articles, and all submitted articles are published. Skeptics worry the publication will be used to sow doubt about scientific consensus on matters such as vaccine efficacy and safety.

The lack of a paywall is very good, and the transparency of peer review will be the standard eventually.  If every reviewer of every scientific manuscript and grant proposal were required to defend his or her work in public, the quality of scientific papers and funded research proposals would improve.  An added benefit would be that the best research would get published and supported, no matter from where or from whom it comes.  The entire edifice of for-profit scientific publication is dependent on editors and reviewers working for free, except for recognition by the journal for having contributed to its existence.  However, this recognition does not buy the lab coffee.  Neoliberal wage theft happens everywhere.  More interesting, though, is the membership of the Academy of Public Health:

According to the academy’s guidelines, public health researchers can become members through invitation or nomination from other members. New members are accepted based on whether they are “good scientists,” Kulldorff says, something the academy establishes “either by knowing it already from our own experience as scientists, or by reading what they have published” and checking for sound methods and interpretation. Kulldorff says he doesn’t know how many members the academy currently has, but (adjunct) Stanford physician scientist (and pharma executive) George Tidmarsh, an author on one of the eight papers, said membership was “growing rapidly by the hour, and it will continue to grow indefinitely.” [4]

Once members, researchers can publish “any of their public health research” in the journal, as well as contribute perspectives and reviews of papers in other journals, according to the submission guidelines. “If somebody’s a good scientist, we think they should have academic freedom to publish what they think is important,” Kulldorff says. He notes that the Proceedings of the National Academy of Sciences (PNAS) used to allow members of that academy to forgo peer review. (This approach has since faced strong criticism, and PNAS has adjusted some of its policies over the years to increase oversight of submitted articles–this parenthetical insert is in the original)

Reviewers will be paid $500 out of the $2000 submission fee for each article.  Aside from the payment to reviewers, the Journal of the Academy of Public Health appears to be not much different from any other garden variety open-access online journal of uncertain provenance that publishes preferred science, from a member of this new scientific society whose members are “good scientists.”  Whatever the definition of peer review used here, a journal that publishes all submitted manuscripts (albeit alongside their reviews) cannot be considered a peer-reviewed journal in any meaningful sense. [5]  “Jay and Martin and Martin’s New Journal” is exceedingly unlikely to become our new source for “gold-standard science” (a topic for further discussion at another time).  The same is true for an in-house NIH journal.

For this to end, scientists themselves will be required to pay serious attention to the serious problems with the business of scientific publication, which pervade the entire scientific landscape.  And then we must revise the standards by which our peers are evaluated.  What was once “publish or perish” has become “publish and perish anyway, while ignoring the temptations to take shortcuts that lead inevitably to the abyss.”  This is no way to run the research enterprise that has accounted for most of the Nobel Prizes awarded over the past seventy-five years.  The era of peak predatory publication that has enshittified basic science beyond all recognition seems to be waning.  Or so I wish.  It will be a pity if this development is accompanied by the destruction of American science in the name of making it agree with the “priorities” of the Current Administration.

Finally, I continue to remind my largely oblivious scientific colleagues that Pogo was correct, “We have met the enemy and he is us.”  We must get our disordered house put back together, and then we can figure out a way forward.  The strictly performative “trust the science” trope from the usual suspects was like fingernails on the blackboard five years ago and will get us only where MAHA, with its “wearables-for-everyone” desideratum is going, too.  Nowhere, or worse.

Notes

[1] Twenty-five years ago success rates approached 30%.  This was probably close to an optimum.  The rule of thumb for at least 50 years is that to have a healthy research ecosystem, one-third of applications should get funded in the first round of review, another one-third should get funded after revision, while one-third will remain hopeless for the duration.  This has also been my experience in reviewing grant applications for numerous private and public funding agencies.  Most review panel members leave a meeting sick at heart that two-thirds of worthy applications will not get funded.  The discoveries not made in this parlous environment are probably more significant than those that attract broad public attention.

[2] This does not mean these journals are flawless by any means.  The Lancet published Andrew Wakefield’s paper on the spurious link of the childhood MMR vaccine with autism.  The Lancet was subsequently slow in retracting the paper, long after its damage had been done.  The Wikipedia entry is consistent with the long-form work of Brian Deer in which he exposes the unfortunate influence of Andrew Wakefield from the very beginning.

[3] Martin Kulldorf’s leadership of ACIP was a topic in a recent Coffee Break.

[4] As best as can be determined from the journal website on 6 October 2025, the only online issue of The Journal of the Academy of Public Health is from February 2025, with four research articles, three perspectives, one external article review, and one article on the history of public health.  Jay Bhattacharya and Martin Kulldorf are the authors of the history article: The Covid Vaccine Trials: Failures in Design and Interpretation.  Neither reviewer is likely to have been considered disinterested by the editors of other journals, which is not standard procedure.

[5] As noted above, PNAS at one time allowed members to publish without significant peer review, but that policy has been changed because members abused the privilege (e.g., at least one paper disputing HIV as the infectious agent responsible for AIDS if I remember correctly).  Prior to 1995, all manuscripts considered by PNAS were either submitted by members or communicated by members on behalf of nonmember authors.  Since then, nonmembers, (i.e., the vast majority of scientists) may submit a manuscript that is edited by a member and reviewed by outside peer reviewers.  This is based on my experience, which included one of the first PNAS papers published by this mechanism in 1995, and as a previous peer reviewer for PNAS.