Robert Francis Kennedy Jr. is a shining example of how the original was better. If you were not familiar with RFK Jr. and his silky-smooth voice before 2025, you probably are now. RFK Jr. is the totally normal1, 2 and not antivax3 head of the Department of Health and Human Services (HHS). You have probably read or heard that the situation for all the agencies that fall under HHS, of which there are many4, is not good, but exactly how and why everything is bad can be hard to follow and understand. Some agencies have a self-evident impact, like the CDC with public health and the FDA with food safety, but what about the NIH? Here we will try to understand the direct impacts to one specific agency, the National Institutes of Health, and the research infrastructure it supports.
Here I will mention that I have a clear stake in his. My conflict of interest is that I am currently, and for most of my adult life have been, NIH grant funded. As an employee of a university lab my salary has at times come from start-up funds and DoD grants, but the major funding source is and always has been the NIH.
Introducing the National Institutes of Health
By NIH -
http://www.media.nih.gov/imagebank/display.aspx?ID=392, Public Domain,
https://commons.wikimedia.org/w/index.php?curid=16235812
The National Institutes of Health (NIH) is the US government agency that is responsible for biomedical research and has been around in its most recognizable form since 1938 in Bethesda, MD5. Made up of 27 institutes and centers (ICs)6, the NIH funds both intramural research performed on its campuses as well as extramural research grants across the country and the globe7. ICs like the NIA (National Institute on Aging) and NIEHS (National Institute of Environmental Health Sciences) primarily fund and/or perform research in their specific research areas, while others like the NLM (National Library of Medicine) which runs PubMed, perform more research adjacent functions.
The NIH is good actually
The NIH is the global leader in biomedical research funding, to the tune of $33 billion in fiscal year 2022, dwarfing all other sources that report their investments8. It’s not like NIH keeps this money either, the majority of money spent by the NIH is grants to outside investigators81. These expenses result in contributions to 99.4% of all FDA drug approvals9 and a clear economic return: $2.56 in economic activity generated for every dollar of funding10. What would also be interesting for anyone seriously interested in geopolitical power and diplomacy is the historical leverage of science as soft power11.
Screenshot from source 8
Why fuck it up?
What would motivate a political party to kneecap a huge draw of scientific skill globally and a great source of soft power? This is all really down to the “fuck you I got mine” mentality of Russel Vought107 but a look through Project 2025 will tell you they're very focused on traditional families, abortion bad, and woke shit12. Another motivator unsurprisingly is (still) COVID and being mad about Fauci. The thin veneer of justifications can be summarized as corruption, and like most of these sorts of claims it takes a fair bit of work to unpack and understand before discarding. You can read my cursory attempt at that here but suffice to say it can be dismissed as intellectually bankrupt. Unfortunately, these arguments can be persuasive to a general public because basic research takes approximately forever to have any practical application, with all of the intermediate results being boring/weird/complicated, and scientists being notoriously poor communicators. These flaws and failures have kept us as a society from being able to meaningfully combat the truly nonpartisan proliferation of anti-science sentiments, culminating in where we are now.
Hamstringing Killing the American Scientific
juggernaut
The anti-science agenda of the Trump administration is clear to any serious observer. Scientists looking to get out (of the US), the removal of real leadership and scientists, and obvious early examples of cronyism set a precedent106-109. There is no elegant way to go through the depth and breadth of the disaster happening at the NIH and by extension effectively all research programs affiliated with American universities. The topics involved are not only the minutiae of the administration and execution of scientific research, but also the intersection with political procedure and ideology. In many ways these topics are interconnected but, nevertheless, here we will try to broadly categorize how Trump 2.0 is successfully ending American scientific progress.
Installing new Leaders
New leadership is not uncommon following presidential transitions; The NIH director is a presidentially appointed position after all. This process started back in November 2024 with the nomination of Jayanta “Jay” Bhattacharya for the position of NIH Director. Following the transition of power, however, the first new face is a longtime NIAID researcher, Matthew Memoli. Named acting director of the NIH, this is probably not based on his (lack of) experience, considering a former NIGMS director stated Memoli would not have made his “short list or long list or the list at all really". No, it’s much more likely a result of his vocal anti-vaccine mandate stance during COVID28, 29.
Memoli becomes number 2 as Bhattacharya is confirmed as the NIH director; unfortunately, it’s hard to overstate how much this guy sucks. The mere nomination by Trump is a black mark, but in that nomination the Great Barrington Declaration is unsurprisingly referenced111. For the uninitiated, the Great Barrington Declaration was an opinion of three academics that advocated for the let 'er rip approach to COVID in early October of 2020, this was roundly criticized by both scientists and the literal town of Great Barrington where the “Declaration” was written64,66, 67, 71.
Andrew Harnik/Getty Images from source 97
Unsurprisingly Bhattacharya is real big on “free speech” in the context of COVID, but maybe we can look past that, is Bhattacharya qualified for the job? Well, he is technically a physician-scientist in that he is an MD-PhD but has never practiced medicine or done any post-med school clinical training61. His education aside from the MD is three economics degrees (BA, MA, PhD) from Stanford, and while he has an impressively lengthy publication list62,63, he also lists many commentaries and op-eds that are nakedly pandering to the anti-lockdown crowd. He was the corresponding author (most senior author) on a 2020 pre-print paper (it was eventually published in 2021) that looked at seroprevalence (the level of infection of a population) of COVID in Santa Clara, that got a ton of attention for all the flaws it had50,70, 72 and notable outlets like Zero Hedge and The Epoch Times liked to reference it. This might give you an indication of how things are going to go.
The Matt and Jay Show
Memoli was appointed on January 24th, followed by Bhattacharya’s confirmation58 on March 25th, but make no mistake that both men entirely cosign all the actions that have preceded their ascendancy. What we are seeing now is likely the biggest disaster in American Science. Before January, I think most scientists or researchers would not have hesitated to tell you their critiques of the NIH, but in my opinion all previous issues become indistinguishable from background noise when compared to the scope of what is happening now. It is cliché, but this is a cancer that has started at the NIH and will quickly metastasize nationwide
NIH Necrosis
Necrosis is when cells in tissue die prematurely; this often happens inside large cancerous tumors because of lack of nutrients. Necrotic tumors frequently indicate aggressive cancers, metastasis and poor survival.
Under Memoli and Bhattacharya, the rot at the NIH has been quickly obvious. Longtime leaders leave or are pushed out, staff are removed illegally and barriers are put in place to make it difficult to retain talent. Large NIH-lead programs are cancelled while redundant offices are created, and research is funded as quid pro quo while HHS and DOGE propose massive budget cuts.
Travel and hiring freezes are instituted, and NIH research is quickly disrupted with supplies unable to be ordered17.
Significant departures from the NIH include Francis Collins, the Director from 2009-2021, who had a lab at NHGRI53, Eric Green, the director of NHGRI54, and Lawrence Tabak, the number 2 guy at the NIH since 2010. Tabak decided to leave rather than take the meaningless advisory role assigned to him by HHS36, 37, and was shortly followed out by Michael Lauer, the Deputy Director for Extramural Research38, who seems to have been fired after directing grant managers to start issuing grants again39-41.
It isn’t just big names though, probationary workers, which include promoted and reassigned workers, start getting illegal form letter terminations from OPM on Valentine’s Day42-47, while employees hired under Title 42 which allows payment above the federal pay scale have their renewals put on hold51, 52 and external scientists that evaluate internal NIH research proposals and performance are removed55.
Major reductions in force (RIFs) start on April 1st, with the expectation that 1,200 people will be cut74, and 4 institute directors (NIAID, NIMHD, NINR, NHGRI) are also removed75. RIFs have an entire procedure outlined by OPM which were most likely not followed here. Many of those RIF’d include communications and procurement workers, and allegedly the FOIA office at the Office of the Director49. It goes without saying that any abrupt workforce change will cause disruptions, but the reductions here are wide-ranging. How does an agency function without proper IT staffing? How long can research continue with only the supplies on hand? Who do all these people let go contact when the HR people are gone?
Getting rid of good workers isn’t enough for this administration, good long-term programs are on the chopping block too. The Safe to Sleep campaign, which has been around since 1994 and mostly been about bringing awareness to and preventing SIDS92, loses the support of the NIH93. The Diabetes Prevention Program (DPP) a big study on diabetes started in 200156 with an outcomes study with long-term follow-ups is discontinued57. This is probably related to Trump’s vindictive grant cancellations at Columbia.
There does seem to be room in the budget for Bhattacharya to establish a new (redundant) office at the NIH to reduce animal use in research94, as if researchers don’t already use as few animals as possible,
Even with all the staff reductions the NIH is still a target for budget cuts. DOGE asks them to cut a paltry $2.6 billion from their internal spending, this amounts to 35% of their funding79-81 and the HHS draft budget leaks showing a proposed reduction from the 27 ICs to 8 as well as a >40% cut to the entire NIH budget82, 83,100.
Bhattacharya is a failure in his role as NIH director by not being an advocate for this agency. He says that the proposed 40% NIH budget cut is totally chill or whatever, because it’s part of the negotiation process. And he’s totally pro-academic freedom (free speech), because NIH not funding specific research doesn’t mean they’re saying you can’t do that research91. Did I mention this guy sucks?
Remember Memoli? The now Deputy Director of the NIH is getting $500 million to try making a universal flu vaccine using tech from the 70s110. This is an absurd amount of funding for one project, and “is clearly someone taking advantage of the system”108. So as long as you are aligned ideologically with the Trump administration and are useful you might get something in return. This usefulness doesn’t extend to the Clinical Center, the NIH Research hospital, which is limping along because of Trump policies105 or the National Cancer Institute104. Science is not a person to be manipulated, but a process of discovery, and as such it doesn’t serve the Trump administration unless they can specifically pick and choose to fund only what, and who, they want.
Metastasis
Cancer cells can detach from the main tumor, enter the bloodstream and spread throughout the body, creating secondary tumors and often dramatically reducing survivability.
A result of RIFs/firings, loss of communications
staff/offices and centralizing of communications going forward. image
source
https://www.reddit.com/r/NIH/comments/1kxtupk/this_really_sucks/
The rot rapidly radiated out of the NIH almost immediately following the inauguration of Donald Trump. The HHS-wide communications freeze was probably the worst part; it prevented meetings of study sections and advisory councils, the first and second levels of the arduous grant review process13, 14. The HHS memo instituting the communications pause importantly prohibits publication to the Federal Register where public notices of study section meetings need to be published before they are allowed to happen, this continues through February with directions coming “from the White House, most likely OMB and Vought"15, 16, 48.
No registrations, no meetings. No meetings, no new grants.
Next existing grants are targeted.
The OMB (Office of Management and Budget) releases a memo18 freezing all federal grants. In the memo is “pausing disbursement”, which means not sending funds for grants already awarded. Additionally, grants start getting terminated. This is historically, very rare, "reserved only for gross misconduct, poor performance or fraud"20. This is all in service of the President’s Executive Order21, so anything “DEI” is the first target; while the NIH also starts putting a list together of grants that fight “misinformation or disinformation”, likely targets for cancelation73.
Shocking no one who was listening, “DEI” grant programs are discontinued including a prestigious diversity related grant program started in 198931; not a surprise but is nonetheless sad.
In response to the OMB memo freezing all federal funding, two separate lawsuits are immediately filed against the administration in Rhode Island and in the District of Columbia followed immediately by an administrative stay of the OMB memo, but unfortunately compliance with the memo has already started22-24. The next day the administration rescinds the memo directing the freeze of funding, but not the freeze itself19, 25, 26. They’re being cute.
The first TRO is issued for the OMB memo27; this is quickly followed by a second TRO.
The grant fuckery continues, if a university has funds frozen by the administration, they won’t get any new grants86; and absolutely no grants to universities with “DEI” programs87-89. More bureaucratic hurdles to grant funding are introduced. One rumor quickly confirmed to be true is the ending of foreign subawards. This will prevent NIH funding going to institutions outside the United States, which will hamper international collaborative research and clinical trials98 .Separately, DOGE introduces Defend the Spend, a new innovative efficient roadblock where for every drawdown of funds, the institution must justify spending90. This essentially means for institutions already awarded funding, they have to do an additional step of justification whenever they need to actually access those funds.
source:
https://www.reddit.com/r/NIH/comments/1kqiz7y/jay_bhattacharya_town_hall_the_tie_grows_a_little/
Did I mention that Jayanta Bhattacharya sucks?
Bhattacharya is interviewed by Science and does a little bit of lying, a little bit of victim blaming97. All the restrictions coming from the NIH are “panicked overreaction” to directives they’re given. He not only said that the story about ending foreign subawards was “false” (it wasn’t99), but had the balls to chastise the reporter for “reporting rumors” going on to say that “the leaks don’t actually reflect what’s happening. Don’t write about rumors“. This was literally the morning of the day of the foreign subaward announcement.
All my homies hate Jayanta Bhattacharya.
In April at least NIH grant meetings can start again84, oh wait DOGE can apparently control grant awarding because they control grants.gov now85.
There is an announcement of a 15% cap on indirect costs for research grants32. This on its own would devastate scientific progress in America.
Indirect costs in research are all costs that are not directly research related (obviously). Things like utilities and maintenance of buildings. Indirect costs are negotiated between institutions and the NIH, for my institution it is 53%
It's important to point out that indirect costs are calculated in addition to direct costs. If an institution has a negotiated IDC rate of 30%, and a PI at that institution is awarded a grant for $1 million, the actual amount awarded would be $1.3 million. The administration is either lying or stupid or both here. The argument is that reducing the IDC rate increases funds to researchers but this is obviously a lie. For that hypothetical PI getting a $1 million grant, the total award would just be $150,000 less to the institution.
In response to the 15% indirect cap thankfully a (say it with me) lawsuit is filed, and a TRO is basically immediately granted to block the indirect cost cap33-35, this is followed by a permanent injunction which is of course immediately appealed77, 78.
In line with trying to starve out science, NIH disabled the automatic no-cost extension “temporarily”101, 102. A no-cost extension is required when a project will continue past the initial proposed end date, but does not require any additional funding. Now this will trigger a manual review103, basically so NIH can filter out things it doesn’t like.
Prognosis
It’s bad what do you want me to say? The small consolations in all of this are the States and, now that Harvard finally grew a spine96, institutions have filed lawsuits against the administration. Unfortunately, law and science are both slow moving processes and the negative consequences of these actions are already apparent, though they will likely continue for decades. In the past we have had smart, thoughtful, articulate leadership at HHS and NIH, but now that is unfortunately not the case. While some had said that Bhattacharya was the “least bad” option to head the NIH, others have seen the unfortunate writing on the wall30. Bhattacharya is a weak and cowardly leader who views the role of NIH director as a burden and does not have the respect of the scientists that work under him76, 95. Like many “free speech” advocates, he is only really concerned with speech he agrees with, going so far to start a new scientific journal69 where only people in the associated “Academy”68 can publish, and to join that Academy you need to be nominated or invited by a current member. This is the obvious incubation of a misinformation generating echo chamber and Jayanta has shown previously that he has no problem pushing conspiracies and pseudoscience on various substack platforms60. At an AEI sponsored symposium59 in 2024, Bhattacharya spoke about the reform needed in public health, pointing to desired increased transparency, decentralization, and depoliticization. There are of course lies. Under Bhattacharya the NIH has become increasingly opaque with power concentrated by political figures for political purposes. My personal hope is that enough of the general public cares about science and can be activated politically to move congress and eventually the next president to correct the mistakes made and get science in America on life support.
Supplementary Information
Project 2025 claims of corruption at NIH
This starts with a WaPo story from 2018 about a large study on alcohol consumption, the preliminary talks for which probably violated NIH policy, there were hearings on this (1, 2).
Then it's of course COVID + corruption
1. NIH being on the Moderna patent is a conflict of interest (COI).
Claiming this is corrupt/a COI and pointing to a CBS news story that is basically saying the opposite, with the watchdog group cited in the story literally arguing that NIH scientists should be on the patent (3, 4). Wild to claim that the work done by NIH scientists should never be credited to them though patents.
2. NIH conducted Moderna clinical trials internally instead of funding grants for external clinical trials and this is a COI.
The (literal antivax advocacy group) source they cite says that "NIAID used taxpayer dollars to sponsor, assume responsibility for, and perform the first clinical trial of this vaccine" (5). A cursory look at the clinical trial information will show you that it was performed at 3 sites: NIH, Kaiser Permanente Washington Health Research Institute, and Emory University (6). So, on its face the claim is incorrect as it was collaborative to begin with.
3. NIH has a monopoly on directing research, this is corrupt.
The implication is that there are a few people directing where all research funding goes. For the uninformed this sounds like all grants are reviewed by the same people, they are not. To oversimplify: grant review panels are called study sections, and they are organized by general scientific area (review branch), study sections are more specific, and you can find the members and affiliations for each study section at the CSR website (7). For example, the Basic Cancer Immunobiology study section has 32 members for the most recent review dates and is in the Basic and Translational Cancer Review Branch. There are 205 standing study sections if i counted correctly.
4. Bonus meme: NIH foundation should be decommissioned
They are here referring to the Foundation for the NIH (FNIH) is a 501(c)(3) that allows private fundraising for the NIH and had about $65 million in revenue vs about $77 million in expenses, about 90% of which went to research programs (8). Relative to the total funding of the NIH, this amounts to a rounding error, in fiscal 2022 that would be 0.2% of all NIH funding, so what does that matter? If you can say that money distributed from the FNIH is controlled inappropriately, by extension the uninformed will understand that money distributed from the NIH is controlled inappropriately, which is obviously false.