I lamented in the comments of Steve Novella’s post this week how, every time I sit down to write my weekly SBM post, I swear I will to try to write about something else—anything else, like homeopathy, cancer quackery…anything!—but inevitably something will have happened that compels me to write yet again about the current administration, in particular our Secretary of Health and Human Services Robert F. Kennedy Jr., and some new assault on science-based medicine, public health, and vaccination programs. It was tempting to write one more post about Dr. Vinay’s Prasad‘s troubled (and very brief) tenure as the FDA’s Director of the Center for Biologics Evaluation and Research CBER), his downfall and forced resignation, and, over the weekend, his seemingly miraculous reinstatement as CBER Director, but then there was this story in Nature on Friday:
US President Donald Trump issued an expansive executive order (EO) yesterday that would centralize power and upend the process that the US government has used for decades to award research grants. If implemented, political appointees — not career civil servants, including scientists — would have control over grants, from their initial solicitation to their final review. The order is the latest move by the Trump administration to assert control over US science.
The new EO, titled “Improving Oversight of Federal Grantmaking”, orders each US agency head to designate an appointee to develop a grant-review process that will “advance the President’s policy priorities”. Those review processes must not fund grants that advance “anti-American values”, but prioritize funding for institutions committed to achieving Trump’s plan for ‘gold-standard science’. (That plan, issued in May, calls for the US government to promote “transparent, rigorous, and impactful” science, but has been criticized for its potential to increase political interference in research.)
Impacts might be felt immediately: the latest order directs US agencies, such as the National Institutes of Health (NIH), to halt new funding opportunities, which are calls for researchers to submit applications for grants on certain scientific topics. They will be paused until agencies put their new review processes in place.
You might recall that during the pandemic, the lament among contrarian scientists and doctors was that any criticism of what they said or professional consequences that came about due to their promoting dangerous misinformation represented not normal consequences for their words and behavior, but rather their being “canceled,” “repressed,” or even “persecuted.” You might remember the wailing and gnashing of teeth as these COVID-19 contrarians lamented that their “freedom of speech” was somehow being “suppressed” and science hopelessly politicized by The Left. In particular, our new NIH director, Dr. Jay Bhattacharya, long complained bitterly that his “freedom of speech” and “inquiry” were being somehow violated when someone like Dr. Anthony Fauci correctly perceived the document that he’d co-authored in October 2020, The Great Barrington Declaration, as a scientifically unsupportable call for a “let ‘er rip” approach to the pandemic in a futile bid to reach “natural herd immunity” in 3-6 months that never would have worked (and didn’t work, despite the revisionist history of Dr. Bhattacharya and his supporters claiming it did). You might even remember that Dr. Bhattacharya has proclaimed loud and long that he wants nothing more than “free speech” and “open debate” about science.
To that, I will say: With these people, every accusation was a confession of what they wanted to do if they were ever to attain power. Moreover, in response to the contrived, self-proclaimed victimhood of such people, I like to answer with a quote from Robert Evans, who does the Behind the Bastards podcast:
Yes. It sucks actually being oppressed, but pretending to be a victim of censorship is great because you get all of the benefits of being a victim. You get that sympathy, you get to feel like a hero, you get to make grand speeches about how you won’t be silenced.
But you don’t actually have to face any consequences for any of your shitty behavior, right?
Right, except in this case Jay Bhattacharya, Marty Makary, RFK Jr., et al are facing the consequence of now being firmly in control of all non-military federal health and biomedical science programs.
In fact, none of these “silenced” or “canceled” free speech warriors were really “silenced” or “canceled.” Moreover, as you will see, with these people, every accusation during the pandemic was in reality a confession of what they wanted to do if they ever achieved power. They claimed that science was being politicized, but, as this EO is the latest indication, now that they’re in power they’re politicizing US science more than any other administration, Republican or Democratic, has ever done before. This is just the latest, though, given that this administration immediately started canceling grants that funded science that it did not like, again, something no administration has ever done before.
Remember, every accusation was (and is) a confession. I will be repeating that mantra throughout this post.
It starts with a bogus rationale
I’m just going to emphasize again that this EO is bad. Very bad. At this point, I’m half-tempted to riff on the passage from The Hitchhiker’s Guide to the Galaxy about how big space is, in order to emphasize how bad this EO is, but I’ll leave that to Douglas Adams fans. Basically, this EO, if fully implemented, would for the first time put political appointees entirely in charge of the grant making process and completely subordinate career staff and peer review to political appointees. Don’t believe me? I will quote extensively from the preamble to the EO:
By the authority vested in me as President by the Constitution and the laws of the United States of America, and to improve the process of Federal grantmaking while ending offensive waste of tax dollars, it is hereby ordered:
Section 1. Purpose. Every tax dollar the Government spends should improve American lives or advance American interests. This often does not happen. Federal grants have funded drag shows in Ecuador, trained doctoral candidates in critical race theory, and developed transgender-sexual-education programs. In 2024, one study claimed that more than one-quarter of new National Science Foundation (NSF) grants went to diversity, equity, and inclusion and other far-left initiatives. These NSF grants included those to educators that promoted Marxism, class warfare propaganda, and other anti-American ideologies in the classroom, masked as rigorous and thoughtful investigation.
Let’s just say that the rationale used here is based on some rather questionable sources. One notes that nowhere does this EO actually provide references for these claims, although one can’t help but note that the usual non-science-based right wing hostility to transgender medicine is there. A bit of Googling quickly revealed that the basis of the claim that one-quarter of new NSF grants went to “DEI” programs was not as “study” at all, but a highly politicized report by U.S. Senate Commerce Committee Ranking Member Ted Cruz (R-Texas). As for funding “drag shows in Ecuador,” it is true that a small USAID grant ($20,600) was awarded to Centro Ecuatoriano Norteamericano (CEN) in 2022 as part a public diplomacy program. Whatever the policy merits or lack thereof that you might perceive in such a grant, whose purpose was, according to the State Department, to “promote tolerance” and “provide new opportunities for LGBTQI+ Ecuadorians to express themselves freely and safely,” I can’t help but note the obvious overgeneralization (not to mention, a bit of a bait-and-switch). Basically, the administration is generalizing a tiny grant that was not a peer-reviewed science grant as representative of huge swaths of federal science grants. Moreover, USAID has been essentially disbanded, and this was a tiny grant. Again, even if you don’t think federal dollars should be spent on such programs, you must realize how deceptive the rationale for this EO is.
Need more? How about this:
The harm imposed by problematic Federal grants does not stop at propagating absurd ideologies. An unsafe lab in Wuhan, China — likely the source of the COVID-19 pandemic — engaged in gain-of-function research funded by the National Institutes of Health. The NSF gave millions to develop AI-powered social media censorship tools — a direct assault on free speech. Taxpayer-funded grants have also gone to non-governmental organizations that provided free services to illegal immigrants, worsening the border crisis and compromising our safety, and to organizations that actively worked against American interests abroad.
First of all, notice the lie that accepts a version of the “lab leak” conspiracy theory as though it were established historical and scientific truth. It is not. It remains, despite years of advocates trying to put scientific varnish on a nasty conspiracy theory, nothing more than a conspiracy theory. As for “AI-powered social media censorship tools,” one notes that the previous administration was desperate to slow the spread of pandemic misinformation of the sort spread by those now in charge of the entirety of the non-military US medical, public health, and biomedical research infrastructure, which had been turbocharged by social media algorithms. So what’s their answer? To abandon all attempts at controlling misinformation and then engaging in a vast censorship effort of their own. As for that part about “illegal immigrants,” that has nothing to do with scientific research and is just another bait-and-switch in which grant-making policies that have nothing to do with science are used as a pretext to bring scientific grant-making under the political control of the administration, thus conflating grants given to further political policies with NIH grants that have traditionally been based on finding the best science through peer review.
True, it does add:
Nothing in this order shall be construed to discourage or prevent the use of peer review methods to evaluate proposals for discretionary awards or otherwise inform agency decision making, provided that peer review recommendations remain advisory and are not ministerially ratified, routinely deferred to, or otherwise treated as de facto binding by senior appointees or their designees. Further, nothing in this order shall be construed to create any rights to any particular level of review or consideration for any funding applicant except as consistent with applicable law.
Somehow, this does not reassure me, as it the EO is saying to do what federal agencies that award scientific grants do: Routinely defer to study section reviews and scores and treat them for the most part as de facto binding by political appointees and their designees, which is how grants should be reviewed. That’s how the NIH has emphasized funding the highest quality science. Is the current system perfect? Of course not. Does it sometimes fund science that isn’t the greatest? Obviously yes. Is what is being proposed more likely to decrease the problem of funding science that might not be the greatest? That’s not just a “No,” but an “Oh, hell no!”
While one can read this EO in a way that doesn’t sound too horrible (with difficulty), to me such a view is whistling past the graveyard of US science. This EO is basically the formalization of what I’ve been calling the science and medical policies of this administration: Lysenkoism 2.0. You remember Trofim Lysenko, don’t you? He promoted a sort of Lamarckian version of genetics that aligned with his belief in Communist ideology but, alas, did not actually align with the real science of genetics and, because Josef Stalin liked him and his “science,” became so powerful that his view of genetics predominated in the Soviet Union for three decades, leaving famines in its wake. As I’ve argued, RFK Jr.’s “make America healthy again” (MAHA) movement is pure Lysenkoism; i.e,, science whose underpinning is ideology rather than, you know, actual science. The only difference now is that, in contrast to the one Trofim Lysenko running Soviet agricultural science, we now have many Lysenkos running many areas of our federal health and medicine infrastructure, and they do not limit themselves to one area of science.
What’s happening at HHS goes far beyond the fears that I expressed when I first saw proposals for how to “reform” the NIH peer review process, as it subordinates peer review to the political, making it purely advisory, to be ignored completely if political appointees don’t like the research proposed. Let’s start by reviewing how peer review has traditionally worked in grant-making. I will use the NIH as the prototype, if only because, unlike the case for the NIH, I have never applied for or garnered a National Science Foundation grant, nor have I sat on a study section to participate in peer review of NSF grant applications. Thus, I know a lot more about NIH grants and the peer review process used at the NIH than I do the NSF, as I have directly experienced it as an applicant, grant holder, and peer reviewer.
How the NIH actually reviews grant applications vs. President Trump’s executive order
I know I’ve written about this before, but I think it’s good to go over this process again every now and then when it’s appropriate to the topic. At the very least, it’s useful to compare and contrast how the NIH decides which grant applications are funded now, compared to how the Trump administration appears to want such decisions to be made.
I’ll start by reiterating that approximately 80% of NIH funding goes to funding extramural research grants (extramural=laboratories and research sites that are not part of the NIH, mostly universities and private research institutes). Contrary to the conspiracist vision of Anthony Fauci—or any other Institute director at NIH, or even the NIH director him or herself —personally viewing every grant application and deciding who gets those sweet, sweet NIH dollars and who does not, there is a long-defined, rigorous, and codified process used by the NIH to evaluate grants applications. (Here’s another area where every accusation was a confession, as you will see, given that the Trump administration seems to want to convert the NIH grant process into political patronage, with his underling Jay Bhattacharya, doling out the Godfather’s favors in the form of grant money.)
The process begins with the submission of a grant to the NIH. The NIH has a number of granting mechanisms designed for different purposes. For example, the R21 grant is designed for preliminary work, often the “higher risk” studies that the brave mavericks demand, and doesn’t require a lot of preliminary data. (The claim that it can require no preliminary data, however, is generally nonsense. You need at least some data.) R21s can fund up to two years and cannot be renewed.
In contrast, the granddaddy of them all, the “gold standard” grant for an individual investigator, small groups of co-investigators, or collaborators, is the R01, which can be funded for up to five years (it’s also one of the only grant mechanisms where the investigator can propose basically anything, rather than having to address a particular topic or question). At the end of that time, the investigator can apply for a competitive renewal, which can extend the grant for up to another five years, and so on ad infinitum. There are a number of other grant mechanisms, which include training grants for graduate students, center grants (e.g., for cancer centers), larger multi-investigator grants, and more targeted grants—Wikipedia has a nice list here—but in general all of them are scored by groups of scientists with the relevant expertise in a review group called a study section, of which there are dozens in the NIH arranged by topic into Review Branches at the Center for Scientific Review. Many of these study sections are permanent, but the NIH can and does set up temporary study sections for topics of special interest at the time.
NIH grants generally undergo two levels of review, first the study section and then advisory councils. To guide the reviews, the NIH has five criteria that it uses to evaluate grant applications:
- Significance
- Investigator(s)
- Innovation
- Approach
- Environment
Other considerations include “Additional Review Criteria”:
As applicable for the project proposed, reviewers will evaluate the following additional items while determining scientific and technical merit and in providing an overall impact score, but will not give separate scores for these items.
- Study Timeline (specific to applications involving clinical trials)
- Protections for Human Subjects
- Inclusion of Women, Minorities, and Children
- Vertebrate Animals
- Biohazards
- Resubmission
- Renewal
- Revision
Additional Review Considerations. As applicable for the project proposed, reviewers will consider each of the following items, but will not give scores for these items and should not consider them in providing an overall impact score.
- Applications from Foreign Organizations
- Select Agent
- Resource Sharing Plans
- Authentication of Key Biological and/or Chemical Resources
- Budget and Period Support
Grants undergo anonymous peer review, and usually each application is reviewed by three or four reviewers, with one of them being a statistician where appropriate (which is usually). Those assigned to do the detailed reviews score each of the above areas from 1-9. In this case low scores are better, denoting high impact/priority. Reviewers also assign an overall impact score to the grant application. During the study section meeting, the study section member assigned as primary reviewer starts the discussion with a summary of the grant application, the score assigned to it, and why that score was assigned. Then the others who evaluated each grant application do the same, after which the whole study section discusses the application. At the end, every member assigns an overall impact score to the grant under discussion before moving on to the next application. After the study section meeting, all the impact scores are used to calculate a final overall Priority Score assigned to the grant application. Also, the membership rosters of the study sections are public knowledge.
Although I’ve never served as a permanent member of an NIH study section, on a number of occasions I have served as an ad hoc member for specific expertise. (Ad hoc members generally serve for only one or a handful of grant review cycles, rather than being assigned for multi-year stints.) As such, I can only comment on the dynamics of study sections in which I’ve participated. One thing that I’ve noticed is that it only takes one highly negative review from a reviewer who is outspoken to tank an application. I’ve also noted that someone who really likes a grant application can sway others to score it higher, but the effect seems a bit weaker than “negative campaigning,” which seems more effective in getting others to lower their scores.
When an individual grant application hits the NIH, it will be assigned to a study section. Investigators can influence this process by suggesting study sections, and, unsurprisingly, some study sections have reputations for being harsher than others. Once a grant is assigned to a study section, that study section’s Scientific Review Officer (SRO) will read it, decide if it’s appropriate for the study section, and assign reviewers:
Assignment of Applications to Specific Reviewers: The SRO assigns applications to particular reviewers by matching the science in the application to the reviewer’s expertise. Assignment considerations include: reviewer knowledge about, and interest in, the goals of the project; expertise in the techniques proposed; reviewer workload; and real or perceived conflicts of interest. The SRO encourages reviewers to let him/her know of any concerns that they have about their assignments. This would include conflicts of interest, concerns about the appropriateness of the assignment, or the need for additional expertise.
The SRO also recruits scientists to serve on the study section, thusly:
Identifying and Recruiting Reviewers: Possibly the most important role of the SRO is to ensure that the reviewers present at the study section meeting have all the needed expertise to evaluate the applications under review.
In choosing regular members for study sections, it is essential that the SRO recognizes current trends in the field and ensures that the membership reflects where the field is now and where it is going. It is also critical that the expertise of each nominee complements that of the other members and strengthens the study section as a whole.
As you can see, the SRO is a big deal.
The SRO also runs the study section meeting, collates the reviews, takes notes, and from those notes and the overall reviews produces a Summary Statement that includes the overall Priority Score assigned (with a percentile measurement denoting the percentage of grant applications that were scored higher than the applicant’s), comments about the discussion at the study section, and the original “raw” reviews from each study section member who reviewed the grant. Note that now generally only grants that score in the top one-third to one-half receive overall Priority Scores and Summary Statements, because any grant with higher (and therefore worse) scores are so unlikely to be funded as to make it not worth the SRO’s effort to put the documents together. These investigators do, however, still receive the reviews carried out by individual study section members. SROs also handle appeals from applicants who question whether their review was fair or whether one or more of the reviewers had the requisite expertise.
Now, imagine if SROs were to be political appointees whom the administration could hire or fire at will and/or have to report directly to political appointees. That is one consequence that I can foresee if this EO stands.
The second level of review occurs through committees formed at each Institute and Center (IC) at the NIH called Advisory Councils:
The Advisory Council/Board of the potential awarding Institute/Center performs the second level of review (See Advisory Councils or Boards). Advisory Councils/Boards are composed of scientists from the extramural research community and public representatives (NIH Federal Advisory Committee Information). Members are chosen by the respective IC and are approved by the Department of Health and Human Services. For certain committees, members are appointed by the President of the United States.
Unsurprisingly, the Trump administration recently moved to dismiss new advisory council members appointed by the previous administration and instructed NIH directors to nominate new members who will be aligned with the priorities of the Trump administration, nominations that can be overruled by political appointees, apparently not caring about this:
The researchers up for dismissal, who are based at academic institutions across the country, were all nominated during the administration of Trump’s predecessor, Joe Biden, through a process that has been used for decades, but had not yet taken up their positions. The move will leave advisory councils at most of the NIH’s institutes understaffed, leaving them without a breadth of expertise in making final decisions about which research projects the agency funds.
The move throws away all the effort put into vetting those reviewers, says Eric Green, who was director of the NIH’s National Human Genome Research Institute (NHGRI) for more than 15 years, until March, when his tenure was not renewed. The NHGRI had 7 advisory council members vetted under Biden who have been awaiting final approval, Green says. Without them, the institute’s panel will have only 6 out of its potential 18 members. It’s unclear how long it will take to install new members. In the meantime, “to have it be that small is atrocious — you want these advisory groups to be robust because they’re taking the final look at everything going to be funded”, Green adds.
In other words, the Trump administration is politicizing US science, and Dr. Bhattacharya, for all his complaints about the politicization of science and being in favor of “free speech,” will be the useful idiot who oversees this process. Once again, every accusation was a confession of what they wanted to do.
Now here’s the part where the conspiracy might come in:
Recommendation Process
- NIH program staff members examine applications and consider the overall impact scores given during the peer review process, percentile rankings (if applicable) and the summary statements in light of the Institute/Center’s priorities.
- Program staff provide a grant-funding plan to the Advisory Board/Council. Council members have access to applications and summary statements pending funding for that IC in that council round.
- Council members conduct a Special Council Review of grant applications from investigators who currently receive $1 million or more in direct costs of NIH funding to support Research Project Grants (see NOT-OD-12-140). This additional review is to determine if additional funds should be provided to already well-supported investigators and does not represent a cap on NIH funding.
- The Advisory Council/Board also considers the Institute/Center’s goals and needs and advises the Institute/Center director concerning funding decisions.
- The Institute/Center director makes final funding decisions based on staff and Advisory Council/Board advice
It’s that last part that the conspiracy theorists harp on. In theory, an Institute director could override all the peer review to fund a grant, but in practice, thankfully, it almost never happens. Why? Because the NIH set up this process in order to minimize the possibility direct involvement of its leaders in picking and choosing grant awardees based on personal whim. The whole system exists to try to ensure as much as possible that grant selection is based on scientific merit, and few other considerations. What President Trump’s EO seems to be doing is to set up, at minimum, institute directors to feel free to override peer review and fund grants with poor scores or refuse to fund grants with high scores, all based on political considerations, or, as the EO puts it, to fund proposals that are “consistent with agency priorities and the national interest” and that ” demonstrably advance the President’s policy priorities.”
Repeat again after me: Every accusation was a confession.
To sum it all up, at the NIH the system is set up to minimize the possibility of personal and political biases playing a major role in funding decisions. Going along with the theme of this post, I will note that this is not new. Often the people who were most prone even decades ago to characterizing NIH funding decisions as the personal doling out of funding by directors are the same ones who have no compunction about trying to shut down research they don’t like themselves—and have been for a long time.
Add to this efforts by the NIH to minimize reputational bias, in which, all things being equal, more highly ranked universities and researchers are more likely to be funded than researchers with a lower reputation or at a university with a lower reputation, and the system is complex, full of safeguards, and designed to work as close to a meritocracy as possible. It is imperfect, of course, and often doesn’t achieve that goal, but you can’t convince me that anything in this EO will reform the system to make it closer to a meritocracy, rather than closer to a kakistocracy.
But, but, but… supporters of Trump might say, pointing to this part of the EO:
Even for projects receiving Federal funds that serve an ostensibly beneficial purpose, the Government has paid insufficient attention to their efficacy. For example, a significant proportion of the results of federally funded scientific research projects cannot be reproduced by external researchers. Even at Harvard and Stanford, once considered among America’s most prestigious universities, senior researchers have resigned following accusations of data falsification. A substantial portion of many Federal grants for university-led research goes not to scientific project applicants or groundbreaking research, but to university facilities and administrative costs.
Yes, President Trump went there, but you can be sure that a concern about the “reproducibility crisis” is not why this rationale has been added. It’s barely mentioned after this, with only one bullent point in the EO addressing it:
To the extent institutional affiliation is considered in making discretionary awards, agencies should prioritize an institution’s commitment to rigorous, reproducible scholarship over its historical reputation or perceived prestige. As to science grants, agencies should prioritize institutions that have demonstrated success in implementing Gold Standard Science.
As we have discussed, Gold Standard Science is a buzzword that this administration came up with and that its useful idiot appointees, from Dr. Marty Makary to Dr. Jay Bhattacharya to Dr. Mehmet Oz to everyone else involved in the dismantling of US federal scientific infrastructure parrots as though it means anything. It certainly doesn’t mean what it sounds like it means; i.e., actual “gold standard science.” As for the reference to the “replication crisis” or “reproducibility crisis,” I have long argued that it’s not a “crisis,” but a problem that is often overblown in order to cast doubt upon science that is supported by strong evidence and experimentation. Don’t misinterpret us; we don’t deny that it’s a problem and that more effort should be devoted to ensuring reproducibility of scientific findings, findings that are the result particularly taxpayer-funded scientific research. It’s just that we see through the transparent attempt by this administration to weaponize problems with replication in the service of dismantling and politicizing US science under the guise of only being about “gold standard science” (which I refuse to capitalize the way everyone in the Trump administration does).
We are witnessing the destruction of the NIH, NSF, and US federal science
Back in November, a couple of weeks after Donald Trump won the Presidential election and soon after RFK Jr. was named his nominee to head HHS, I predicted that we would get here, that what RFK Jr. wanted to do was to “replace directors, managers, and scientists whom he doesn’t like with political loyalists.” I don’t claim any great insight or ability to see the future; it’s just that Trump, RFK Jr., and all their sycophants, toadies, and lackeys had been making it crystal clear exactly what they intended to do for many months before the election. Now, nine months after the election, the Trump administration is doing exactly what I predicted. Again, this is not a surprise, given that the entire infrastructure of debate bros, COVID-19 contrarians, climate science denialists, antivaxxers, and wellness grifters who had glommed onto Donald Trump’s campaign had been signaling that they wanted to do exactly this for a long time before, even as they lamented to high heaven that their speech was being “suppressed,” that they were being “canceled,” and even that they were being “persecuted,” likening themselves to, of course, Galileo and Semmelweis.
In reality, they were not for free speech or scientific freedom at all. They were just unhappy that they were not in power and therefore were not able to suppress speech and science that they didn’t like. Now that they are in power, they’re going farther and faster than any administration has ever done to defund grants supporting science they don’t like, to require grants to align themselves with the priorities of the President, and to suppress dissent. Indeed, recently I was asked to be an ad hoc reviewer for an NIH study section. Not wanting to get the SRO in trouble for having appointed me, given how much Jay Bhattacharya dislikes me—he’s called me a “threat to science”—I pointed the SRO to the article by Paul Thacker portraying Dr. Bhattacharya as “silenced” and “persecuted” for being the brave maverick COVID-19 contrarian. I never heard back, and that’s OK. Again, I didn’t want to get anyone in trouble, as much as I love being on NIH study sections.
To conclude once again, every accusation from antivaxxers and the opponents of public health during the pandemic was a confession, and we’re now seeing this administration do exactly what its useful idiots had been accusing scientists, physicians, and “progressives” of doing. I only wonder if the administration’s useful idiots have figured out yet that they are, in fact, nothing more than the useful idiots chosen to be the face of the dismantling of US support for rigorous science in favor of turning federal grant programs for medicine and science into grift and patronage to be doled out as rewards to political loyalists. They probably don’t, at least not yet, but sooner or later they will.
Lysenkoism 2.0 is here, and I fear that I will not live long enough to see the damage that’s already been done repaired, if it is ever repaired at all.
