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The landscape of basic research has always been characterized by uncertainty, but it was not always fraught with peril. Between the mid-1950s and the mid-1980s, obtaining grants necessary to operate an academic lab required sustained effort and a bit of luck. Regardless of fluctuations in funding levels, a measure of success was typical. The mentors I had were part of a generation that flourished after Vannevar Bush’s vision transformed American science into a formidable force over the last seventy-five years. While they claimed that review panels aimed primarily to determine which applications not to fund, the reality was a bit more nuanced. My own career began at the tail end of that prosperous epoch, and it was evident at the public research university I attended for both undergraduate and graduate studies that hard work, scientific intuition, and mentoring the next generation were pathways to success in the scientific field.
Sadly, this is no longer the case for most basic scientists, including those in industry, who are part of the scientific precariat. Before recent government actions targeted universities and their researchers, the success rates at the National Institutes of Health (NIH) were alarmingly low, sometimes in the single digits at specific institutes, with overall rates hovering around 20%. [1] These figures are expected to decline even further in the future.
In addition to the funding crisis, the realm of scientific publishing is in distress, a topic we’ve previously explored regarding peer review. It’s an open secret that scientific publishing is deeply troubled. Despite the current administration’s criticisms often missing their target, they aren’t entirely incorrect. The article Scientific Publishing Industry Faces Federal Scrutiny by Kathryn Palmer illustrates how “Long-standing criticisms of academic publishing are helping to fuel the Trump administration’s attacks on the nation’s scientific enterprise”:
For years, members of the scientific community have voiced concerns about research fraud, paper mills, a shortage of qualified peer reviewers, and the high expenses associated with academic journal subscriptions and open-access fees. Research indicates these issues stem from academic incentive structures that favor scientists who publish a large quantity of papers in widely cited journals (or, until very recently, in “journals” that see little citation; while administrators may be able to count, their understanding rarely extends beyond that).
“We all know there are enormous problems facing science and scientific publishing. But much of the scientific community is in denial,” stated Luís A. Nunes Amaral, a professor at Northwestern University and a co-author of a paper highlighting a surge in research fraud over the past fifteen years. “This attitude empowers demagogues to point out real and tangible issues, providing them with a sense of legitimacy; however, their true aim is not to improve the situation but to dismantle it.”
Indeed, Professor Amaral’s observations resonate. The insularity and political naivety among academic scientists can be staggering. Nonetheless, the present Secretary of Health and Human Services overstates the case when he alleges that leading medical journals (like New England Journal of Medicine and The Lancet) are “utterly corrupt.” [2] His claim that these publications are “controlled by the pharmaceutical industry” may have some merit, but it overlooks the significant point made by Marcia Angell, a former editor of NEJM, who noted that it’s often “no longer feasible to trust much of the clinical research published” due to researchers’ connections to Big Pharma” (NYRB, 2009). This issue is distinct from the operations of scientific publishing itself, which we’ve analyzed in discussions on Evidence-Based Medicine, statins, the diet-heart hypothesis, and ultra-processed foods. Regrettably, such realities often fall on deaf ears within the corridors of power.
Recently, Dr. Angell and two former editors from NEJM remarked in STAT:
While it is not the journals that created the challenge, researchers have increasingly depended on financial backing from pharmaceutical companies. They pointed out that journals have attempted to minimize industry influence by mandating authors disclose ties to relevant companies. (A reduction in dependence on Big Pharma could resolve numerous issues.)
“Kennedy has accurately identified the problematic nature of medical research’s reliance on pharmaceutical funding,” the former editors stated. “However, his actions as HHS head—deep cuts to NIH funding and targeting our top medical journals—will only exacerbate the issue.”
Kennedy has even suggested creating an in-house government journal to root out corruption. Yet, Ivan Oransky, a medical researcher and cofounder of Retraction Watch, cautioned that this could also raise concerns about credibility.
“I’m not sure what launching a government journal would achieve. It’s merely another journal that would need to compete with existing ones,” he noted. “Moreover, will it uphold fairness and objectivity? Will it publish genuine science or only the research that [Kennedy] deems valuable? This raises legitimate fears considering his past statements and intentions.”
Amid this dialogue, we observe the involvement of three significant figures: Jay Bhattacharya, the current Director of the National Institutes of Health, Martin Kulldorf, chair of the Advisory Committee on Immunization Practices (ACIP) at the CDC, and Dr. Marty Makary, the present commissioner of the FDA. [3] They have launched their own journal:
The Journal of the Academy of Public Health is associated with the right-wing news site RealClearPolitics and aims to counter mainstream journals. During the pandemic, Bhattacharya and Kulldorf co-authored the Great Barrington Declaration, advocating for the reduction of stay-at-home mandates, which attracted substantial criticism from NIH officials back then. Critics worry that this new journal could serve as a platform for questionable research endorsed by the Trump administration.
These concerns are valid. Only members of the new Academy of Public Health (not to be confused with the American Public Health Association, which was established in 1872) are eligible to publish in The Journal of the Academy of Public Health. Although establishing a new scientific society and related journal is common—dating back to the Royal Society’s initial gatherings on November 28, 1660, involving figures like Sir Christopher Wren and Robert Boyle—serious concerns have been raised about the Academy and its journal:
The Journal of the Academy of Public Health (JAPH), launched recently, states it will “promote open and transparent scientific discourse,” yet it has faced controversy almost immediately.
The journal is the brainchild of NIH nominee Jay Bhattacharya, an MD and economist from Stanford, and Martin Kulldorff, known for his opposition to lockdowns and vaccination during the COVID-19 pandemic. Its editorial board includes Martin Makary, the FDA head who also resisted vaccine mandates.
Though the journal has already published eight articles on subjects like COVID-19 vaccine trials and mask mandates, it diverges from traditional publishing norms. It lacks a subscription paywall, displays peer reviews alongside published articles, and compensates reviewers for their efforts. However, critics have expressed apprehension regarding the journal’s exclusivity and quality control, as only members of the Academy can submit articles, and all submissions are published. Skeptics worry it might propagate doubts about scientific consensus on vital issues such as vaccine safety and efficacy.
The absence of a paywall is commendable, and the transparency of peer reviews may eventually set a new standard. If all reviewers were held accountable for their evaluations, the quality of scientific papers and research funding would undoubtedly improve. This change would ensure that top-quality research receives the support it deserves, irrespective of its source. The profit-driven model of scientific publishing thrives on unpaid labor, relying heavily on editors and reviewers who are only rewarded with recognition. This acknowledgment, however, does not cover basic expenses—an example of pervasive neoliberal wage theft. A compelling aspect is the Academy of Public Health’s membership:
According to the academy’s guidelines, public health researchers may join through invitation or nomination from current members. New members are selected based on their status as “good scientists,” as determined by the existing members’ firsthand knowledge or through their publications and methodological soundness. While Kulldorff claims he’s unaware of the academy’s current membership count, adjunct Stanford physician and pharma executive George Tidmarsh, involved in one of the published papers, stated that membership is “growing rapidly by the hour and will continue to expand indefinitely.” [4]
Academy members can publish any relevant public health research and submit perspectives or articles for other journals as well, per the submission guidelines. “If someone is a good scientist, they should have the freedom to publish what they find significant,” Kulldorff explains. He recalls that the Proceedings of the National Academy of Sciences (PNAS) previously allowed members to publish without peer review, a privilege that faced backlash and has since been reformed.
Reviewers are compensated $500 from the $2000 submission fee for each article. Aside from this payment, the Journal of the Academy of Public Health bears resemblance to other open-access journals of questionable standing, publishing favorable research from its society’s members deemed “good scientists.” However, a journal that publishes all submitted articles (even those alongside their reviews) cannot genuinely uphold the principles of peer review. [5] “Jay, Martin, and Martin’s New Journal” are unlikely to emerge as reliable sources of “gold-standard science,” a subject for future exploration. The same skepticism extends to the proposed in-house NIH journal.
It is imperative for scientists to recognize the critical issues plaguing the scientific publishing industry, which affects the broader scientific landscape. We must also reevaluate how we assess our peers. The previous mantra of “publish or perish” has morphed into a grim reality of “publish and perish regardless, while succumbing to the allure of shortcuts leading to inevitable failure.” This approach is unsustainable for the research sector responsible for the majority of Nobel Prizes awarded over the last seventy-five years. Though the peak of predatory publication may be waning, it would be tragic if this evolution coincided with the dismantling of American science to align with the “priorities” of the current administration.
In conclusion, I find it crucial to remind my largely oblivious colleagues that Pogo was right: “We have met the enemy and he is us.” It is essential that we reorganize our chaotic scientific community before we can plot a way forward. Embracing the performative stance of “trust the science” pushes us towards irrelevance and disaster.
Notes
[1] Twenty-five years ago, success rates soared around 30%, which was likely near optimal. For a sustained research ecosystem, a rule of thumb has been that one-third of applications ought to receive funding on the initial review, another one-third after revisions, while the final third remain uninvited for consideration. This aligns with my experiences reviewing grant applications across multiple funding bodies. Most reviewers leave meetings disheartened that only a third of eligible applications are funded. The discoveries that elude this precarious scenario are probably more consequential than the ones that gain public attention.
[2] While these journals certainly have their flaws, The Lancet did publish Andrew Wakefield’s fraudulent paper linking the childhood MMR vaccine to autism, a claim that was later retracted long after considerable damage was done. The associated Wikipedia entry aligns with the in-depth investigations by Brian Deer, who outlines Wakefield’s influence.
[3] Martin Kulldorf’s leadership of ACIP was a topic discussed in a recent Coffee Break.
[4] According to the journal’s website as of October 6, 2025, the only available issue of The Journal of the Academy of Public Health is from February 2025, featuring four research articles, three perspectives, one external review, and a historical article. Bhattacharya and Kulldorff authored the history piece: The Covid Vaccine Trials: Failures in Design and Interpretation. The reviewers are unlikely to have been perceived as independent by the editors of other journals, which would contradict standard protocols.
[5] Historically, PNAS did allow members to publish without significant peer review, a policy later revised due to misuse; one example includes a paper disputing HIV as the basis of AIDS. Before 1995, all manuscripts considered by PNAS were either submitted by members or communicated by members on behalf of non-member authors. Since then, non-members—who comprise the majority of scientists—have been permitted to submit manuscripts, which are edited by a member and reviewed by outside experts. My own experience includes contributing one of the first papers published via this mechanism in 1995 when I was a peer reviewer for PNAS.
