Who are the indirect costs of NIH research? We talked to 3

Pamela Canaday loves her job. For the last 20 years, she has been supporting biomedical research labs at Oregon Health & Science University in Portland by running flow cytometry, a test that helps researchers figure out what kinds of cells are in a sample. A self-described “machine junkie,” Canaday says she was born for the job, and that there is nothing else she would rather do. Her title on her LinkedIn profile reads “Flow Cytometry Nerd.”

So when Canaday got word of proposed cuts to funding from the National Institutes of Health, and heard that positions like hers may get caught in the crosshairs, she says she was “worried, concerned, terrified.”

The world’s largest public funder of biomedical research initially said it planned to slash grantees’ budgets starting February 10, raising fears that many jobs — and the science they support — may be in jeopardy. In fiscal year 2023, NIH doled out more than $35 billion in grants to recipients at universities, medical centers and other institutions. 

Those budget cuts were set to begin three days after NIH announced a cap on “indirect costs” for new and existing grants that’s equivalent to 15 percent of the money it awards for direct costs like lab equipment and paying researchers. These funds, also called facilities and administrative costs, cover operating expenses that can’t be tied to specific projects, such as Wi-Fi networks, waste disposal, access to scientific journals and administrative labor. Around $9 billion went to such costs in fiscal year 2023. 

A federal judge has paused NIH’s payment-cutting policy after several lawsuits were filed by states, universities and organizations that serve research institutions. A hearing is scheduled for two of the cases for February 21. 

But real, vital jobs hang in the balance of efforts to swiftly and severely limit indirect costs — jobs that often go under the radar. 

To better understand the potential impact of NIH’s proposed budget cuts, Science News spoke with Canaday, senior systems engineer Nate Klingenstein of Johns Hopkins University and pre-award administrator Blake Cowing of Emory University in Atlanta. All three do work that transcends specific research projects. 

Helping scientists focus on their research 

For almost 15 years, Cowing has been helping scientists compile research proposals to submit to funding agencies, including NIH. “Any number of mistakes can jeopardize that research project,” he says.

Cowing supports scientists at Emory by letting them focus on their research rather than getting bogged down by paperwork. It’s a highly specialized, detail-oriented job. In addition to understanding what the researchers want to accomplish through their projects, Cowing must be well-versed in each funding agency’s guidelines, from formatting to paperwork requirements. “An entire application is typically over 100 pages,” he says. 

He’s actively working on 15 proposals. Those include research on congenital heart defects, artificial intelligence’s potential applications in medicine and mRNA technologies that could prevent and treat diseases.

Indirect costs, Cowing says, are very much real costs that support research. They go toward paying for not only building space and utilities, but also the people who work in regulations and compliance, administration, legal and IT. These costs are considered indirect because they’re spread out over so many projects. 

For more than 50 years, research institutions have negotiated individual indirect cost rates with the federal government. These typically range between 30 and 70 percent of each grant’s direct costs, which are added on top of funds that pay for items like lab supplies. That means around 25 to 40 percent of a grant’s total budget goes to indirect costs, which can translate to tens of millions of dollars annually to a university. 

“Even with universities getting the full rate that they’ve negotiated, they’re still operating [research activities] at a loss,” Cowing says. So capping the indirect cost rate at 15 percent “would have a very big impact.” 

Cowing worries about potential budget cuts leading to layoffs in cities where many residents are employed by local universities. “It would just be a huge impact on those economies.… Countrywide, the implications are pretty stark for a very sudden cut of this magnitude,” he says. It “would probably lead to layoffs and a higher unemployment rate.”  

While NIH’s sudden announcement first struck Cowing with disbelief, it also led to fears about his own career’s safety. “If it were to disappear, I’m not sure where I would pivot to next,” he says. 

Lives rely on essential IT services 

Klingenstein has lost sleep since the push for cuts first surfaced. He immediately stayed up all night analyzing Johns Hopkins’ financial reports and, using his salary as a baseline, calculated that NIH’s payment reduction would equal a 30 percent layoff across the institution.

At Johns Hopkins and its affiliated health system, Klingenstein is part of a tiny team that manages login services for computer applications, including the system doctors use to prescribe drugs that could cause physical or mental dependence. He and his colleagues maintain around 2,000 applications and integrate new ones, ensuring they’re compliant with privacy protection laws such as HIPAA. 

“We always have someone on call on our team, just to ensure there are no interruptions, because there are literally lives at stake,” Klingenstein says. “If the login service is down, a clinician is unable to get into a workstation or into an application that’s necessary to provide urgent care to patients.”

Cutting Klingenstein’s job wouldn’t mean just thwarting crucial health care services. It could slow medical advances, too. For instance, Johns Hopkins is joining the Undiagnosed Diseases Network, a collaboration among several research institutions to treat patients with mysterious diseases. Klingenstein will soon integrate a secure connection to the network so Johns Hopkins doctors can access and share data. “It is one of my bigger concerns that [budget cuts] will lead to further siloing of science and even less collaboration between universities,” Klingenstein says. 

Furthermore, replacing or reducing his team due to cost-saving measures would prove challenging. “We have been doing integrated login for 20 years and there is a great deal of institutional knowledge and Hopkins-specific implementation,” Klingenstein says. “We have developed many bespoke systems explicitly designed for the unique needs of a health care system fused with a … research university.”

It often takes years or decades before scientific research can be applied to people’s lives, Klingenstein says. But those incremental steps — and the indirect costs they incur — are necessary to advance science. 

“While indirect costs and staff may be totally invisible, and while the discoveries of our researchers may not be immediately appreciated, the ultimate benefit to society is incredible,” he says.

A Flow Cytometry Nerd worries

Core labs, like the one Canaday works in, are labs that provide institution-wide access to expensive equipment that smaller labs on campus may not be able to afford on their own. The basic research that uses flow cytometry has led to treatments for cancer and other diseases. 

“I’ve never thought of my job as something that is not essential for basic research,” says Canaday, who stresses that she is expressing her own opinions and not those of Oregon Health & Science University. “If the flow cytometry core, or any other shared resource lab, can no longer help labs do their analysis … then research is going to come screeching to a halt.”

Canaday’s day starts with running quality control on the flow cytometry machines, which range from the size of a microwave to that of a refrigerator. The machines line cells up one by one — like a line of kindergarteners on their way to the park — and scan them with lasers that help detect fluorescent markers added to the cells. The machines then spit out data that scientists can use to identify which cells are in their samples.

Like any complicated machine, flow cytometers need occasional maintenance. That’s when Canaday gets to play doctor.

“The most exciting thing is when we get to align the lasers, and then we get to open up the instruments and put on our special safety glasses, take out our tools and try to align the lasers so that they’re hitting the cells in the optimal manner,” she says.

Indirect costs support core labs at Oregon Health & Science University and other academic institutions around the country. Canaday says that although someone can be minimally trained to operate the instruments within months, learning how to do advanced troubleshooting and to help scientists plan their experiments takes years.

“You could probably hire somebody else for half of what I’m getting paid, but they wouldn’t be able to provide the same services,” Canaday says.

She emphasizes that a variety of people — from people in IT to those who maintain facilities — contribute toward driving research forward.

“There are a lot of people, both administrative and lab people, who work together to make research possible,” Canaday says. “And if we can’t have a good support team … then research isn’t going to be able to happen.”