What Happens When Science Stops

For a time last month, science in the US stopped.

On January 22, the Trump administration instructed federal health and science agencies, including the National Institutes of Health (NIH), National Science Foundation (NSF), and Centers for Disease Control and Prevention (CDC), to halt external communications, meetings, and travel. It also ordered a freeze on federal grants and canceled a series of grant reviews that allow government research funding to be dispersed to scientists nationwide, preventing the start of new research.

Two weeks later, the administration lifted some of those freezes and the research community was still in turmoil. 

On Friday, February 7, the administration announced more funding cuts, this time capping “indirect costs” at 15% of a grant total — the money that goes to research institutions to cover overhead like facilities, equipment, hazardous waste, and more.

Now, legal fights. Rulings and reversals. As of February 12, the NIH appears poised to unfreeze grant funds and withdraw the indirect cost cuts, and, according to an internal NIH memo, will now “effectuate the administration’s goals over time.”

Aside from emotion, uncertainty, and suspicion among boots-on-the-ground researchers nationwide … what’s real?

“Scientists feel like they are just blowing in the wind right now,” said Jason Shepherd, PhD, a professor of neurobiology at the University of Utah. “It’s whiplash.”

The NIH is in the Trump administration’s crosshairs. Given the breadth of research funding that comes from government sources, that means science in the US isn’t what it was a month ago, and no one knows what it will be 4 years from now. 

Still, while many disagree with the Trump administration’s abrupt and heavy-handed approach, some researchers believe there is room for reform in the grant system at the NIH.

The question: When you’re talking about $48 billion, is this the best way to fix it?

Indirect Costs Having Their Moment

The NIH funds over 5src,srcsrcsrc grants, supporting a research community of at least 3srcsrc,srcsrcsrc scientists in over 25srcsrc universities, medical schools, and other institutions. About 8src% of the NIH’s $48 billion budget goes toward funding these grants. Typically, about 3src% of each grant goes to the research institution to cover “indirect” overhead costs, according to the NIH. 

The sticking point: Some universities take 5src% or more.

The NIH defines two categories of indirect costs: “facilities,” which covers physical plant and even debt associated with it; and “administration,” covering anything from accounting to personnel not directly involved with the research.

According to the University of Pennsylvania — which takes 62.5% to cover things like construction of specialized labs, utilities costs, technical equipment, and regulatory compliance — “government funding covers only about half of these infrastructure costs.” If they were limited to 15% for indirect costs, as the Trump administration proposed, they would lose about $24src million a year.

Stanford University estimates its potential loss at $16src million.

“The bottom line is that the 15% indirects would dramatically cut research activities at universities,” Shepherd said. “The sudden change and the flat rate means no one could plan for it and mitigate the impact. We can only hope that change, when it happens, at the NIH will be more thoughtful and all stakeholders are included in the discussion.”

Capping indirect costs is not a new idea.

In 1994, the US government imposed a 26% cap on universities’ administrative cost rate for federally funded research grants following several cases where universities misapplied grant funds, using them for purposes beyond the scope of the original award. But the cap lasted for only 1 year.

There is some sense that the indirect costs allowed in NIH grants have become overinflated. Other organizations, such as the Gates Foundation, cap indirect costs at 1src%.

“Although I think there are legitimate reasons to think that indirect costs at many universities are on the high side and could be budgeted differently, the way the administration went about this policy — slashing the rate so dramatically and making it apply retroactively — is going to lead to job losses and huge hits to scientific progress,” said Darby Saxbe, PhD, a researcher and psychology professor at the University of Southern California.

As of February 1src, the Trump administration’s indirect cost cap has been blocked in 22 states that sued, arguing that it would be disastrous for current studies. The lawsuit said, “Without relief from NIH’s action, these institutions’ cutting-edge work to cure and treat human disease will grind to a halt.”

Starts, Stops, Rulings, Reversals All Cause Damage

It’s not unprecedented for new administrations to temporarily restrict public communication the way it happened in January. 

President George W. Bush’s administration implemented a cap on attendance at scientific meetings, which in some cases meant staff canceled trips. This cap on attendance at scientific meetings was continued by the Obama administration.

However, the decision to halt grant review and funding was “an unprecedented move that has created chaos and anxiety,” said Shepherd. Initially, he thought the freezes, if left in place, “could collapse the US research and innovation enterprise.”

For some, a freeze is ongoing, as the NIH isn’t the only federal department funding research. The US Agency for International Development (USAID) funds clinical studies and all have stopped, leaving researchers and participants in limbo.

“It’s especially worrisome for early-career researchers who depend on these grants to launch their careers,” said Shepherd. “These are scientists trying to cure cancer, Alzheimer’s disease, heart disease.” 

Any pause on study sections — the process by which groups of expert scientists review grant applications to ensure that federal funding goes to the most promising research — leaves a mark.

Monica Bertagnolli, MD, previous director of the National Institutes of Health, wrote on LinkedIn, “[P]reventing NIH from issuing research funding by stopping ongoing grant proposal reviews and the work of congressionally mandated advisory committees required for final funding approval, even temporarily, can have a devastating effect on our nation’s longer term research productivity and success.” 

Even now that some of the grant review process has been restored, the chaos and anxiety remain.

Did You Get Your Money?

Saxbe, at USC, is entering the final year of a 5-year study on the long-term effects of the pandemic on maternal and infant health. Her research follows women who had babies in the early phase of the pandemic.

The year-5 money from her NIH grant was due to land on February 1. She confirmed that the money was dispersed early, before the new administration took over.

She’s not sure what would have happened to her research had the money not arrived. Like Shepherd, she is concerned for younger researchers. Trainees could be especially impacted by any pauses, as their positions could depend on having funding lined up.

Not that submitting a grant is a guarantee of funding; only between 7% and 2src% of grants submitted to the NIH are funded. Every grant is reviewed by three expert reviewers, explained Saxbe. 

“We write critiques, and then grants that score in the top half of all the reviewed grants are then discussed in the study section meeting. That’s usually a day-long meeting,” she said. After that discussion, the grants are re-scored and the best go on for further review of budget and ethics by NIH staff. 

The reason the process is so rigorous, Saxbe believes, is to guard against criticism. More than a decade ago, “shrimp on a treadmill” made the news because some said it was evidence of the NSF wasting money on silly science.

Critics say that process could be improved. “Millions of human hours are spent each year writing NIH grants that are unfunded. The greatest waste of scientific capital is writing unsuccessful NIH grants,” Vinay Prasad, MD, a hematologist-oncologist and epidemiology and biostatistics professor at University of California San Francisco, and potential candidate for surgeon general under the Trump administration, said in a YouTube video.

“As someone whose research is supported by the NIH, I do think there is opportunity to improve some of the bureaucracy,” Mike Donnino, MD, a professor of emergency medicine at Harvard Medical School, posted on X.

Saxbe agrees. “I think that’s probably true, that it’s a lot of time and energy that goes into applying for grants that you know ultimately are not successful. I would love to see really smart proposals for how to address that.” 

But she pointed out that if changes to the process are made quickly — and without warning like last month — it will mean grants that researchers have already spent countless hours writing won’t match up with the new criteria. “It’s hard to change the way we’re reviewing grants midstream, once people have already written and submitted them,” she noted.

Bottom line, Saxbe said, “The freezing and pausing and delays are creating chaos and confusion, not actually improving scientific review.”

Suffering — and Speculating — in Silence

Saxbe wasn’t the only researcher we contacted for this story. We contacted 1src others who had grant funds due to disperse on February 1, to confirm that they got their money. Only one responded — her funding arrived — and only Saxbe went on the record.

The possibility of jeopardizing a researcher’s or university’s federal funding keeps a lot of people from talking about it publicly, willingly or unwillingly. The replies we received went like this: “My institution said I cannot speak.” “We are getting a strong message to not comment.” “I don’t have anything to say at this time.”

One MD researcher agreed to an interview for this story and withdrew at the last minute under direction from her university.

What happens next is unclear, but Shepherd warns this is just the beginning. 

“There will be domino effects,” he said. “The bans on study section meetings and release of funds have been lifted, although NSF employees have all been asked to resign or have been given this option. [Last] week some NIH council meetings were canceled abruptly because they could not be open to the public. Certain grant mechanisms have been wiped out — R15s that were DEI related. So nothing is normal and we are all still very concerned.”

Until some dust settles — and no one can even confirm that it will — everyone involved is stuck in a news-of-the-day/no comment limbo.

“Communication still seems to be the main issue,” Shepherd says. “We don’t have any word on future plans. I assume much of this will be resolved once the HHS director and NIH director are appointed.” (Robert F. Kennedy, Jr, was confirmed HHS secretary on February 13.) 

He is quick to add: “But we don’t know what their priorities are at this point.”