The Trump administration introduced a proposal to cap indirect costs on National Institutes of Health grants at 15% on Feb. 8, igniting widespread concern among scientists, universities and policymakers.
The decision, which was blocked by a federal judge on Feb. 10, would significantly reduce funding for essential infrastructure that sustains research on diseases such as cancer, Alzheimer’s disease and cardiovascular conditions. While the administration argues the change redirects funds toward direct research, opponents warn of devastating consequences for scientific progress and institutional stability.
Since World War II, the United States government has partnered with research institutions to drive biomedical innovation. Instead of building state-run research facilities, the government-funded, university-based research covers direct costs like salaries, equipment and experiments, and indirect costs, such as facility maintenance, utilities, and compliance requirements.
Institutions negotiate these indirect cost rates with the NIH, elite universities like Harvard University receiving up to 69% in indirect funding. This long-standing model has made the U.S. a global leader in medical advancements.
The Trump administration’s plan would drastically reduce these reimbursements, forcing universities to cover more of their research infrastructure costs. Johns Hopkins University would lose approximately $200 million annually, while Michigan State University warned that construction of a $330 million research center might be abandoned. The Association of American Universities emphasized smaller institutions, already struggling with financial constraints, could be forced to close their research operations altogether.
Researchers are particularly alarmed by the practical implications of the funding cuts. NIH grant recipient Rick Huganir, a neuroscientist at Johns Hopkins, described the policy as an existential threat to his decades-long work on intellectual disability treatments. Other scientists working on cancer, maternal health and infectious diseases share similar concerns, arguing the loss of infrastructure funding could slow or halt crucial discoveries.
The policy has faced fierce legal challenges. A coalition of 22 state attorneys general sued the NIH, leading to a temporary restraining order that paused implementation. The plaintiffs argue the funding cap defies congressional mandates and disrupts ongoing projects. The Trump administration, however, insists the move ensures transparency and efficiency, aligning NIH funding practices with private foundations that provide lower indirect cost rates.
Politically, opposition to the policy has come from both sides of the aisle. Republican senators Susan Collins (R-ME) and Katie Britt (R-AL) criticized the move, emphasizing its potential harm to biomedical research in their home states. Meanwhile, Democratic Sen. Patty Murray (D-WA), condemned the cuts as reckless and counterproductive to American innovation.
Beyond immediate financial constraints, experts warn of long-term consequences for U.S. scientific leadership.
The World Trade Center Health Program, which supports Sept. 11 first responders suffering from cancer and respiratory diseases, was briefly affected by the administration’s broader cuts to public health research funding. While the Center for Disease Control reinstated some funding, concerns persist that erratic policymaking could undermine trust in government support for science.
Researchers fear that these cuts could accelerate a “brain drain” of talent, with top scientists and graduate students seeking more stable funding environments in Europe and Asia. Deborah Stine, founder of the Science and Technology Policy Academy, cautioned that without sustained federal investment, the U.S. risks falling behind in critical fields like neuroscience and climate research.
Another major concern for scientists is the impact of NIH cuts on emerging fields of biomedical research, such as gene therapy and personalized medicine. These fields rely on long-term investment in infrastructure, technology and expert personnel — all of which could suffer under the proposed funding cuts.
Delays in research could also impact the development of treatments for rare diseases, which already struggle to attract sufficient funding from private sources. Moreover, international competition in biomedical research has recently intensified, with China and the European Union significantly increasing investments in scientific innovation.
If the funding cap is upheld, universities and research institutions will face difficult trade-offs, potentially scaling back projects and laying off staff. Universities are already adjusting to the financial uncertainty caused by the proposed NIH funding cuts.
Columbia University’s medical school paused hiring and restricted spending on travel, procurement and capital projects to mitigate potential financial losses. The institution stands to lose approximately $111 million under the cap, while universities across New York face a collective loss of $850 million.
Similarly, the University of Kentucky warned its research on heart disease, Alzheimer’s and opioid use disorder could suffer without sufficient funding. Faculty layoffs, halted clinical trials and reduced available research assistant programs are among the consequences institutions fear if the funding cap is upheld.
Some universities are considering tuition hikes or reallocating endowment funds to sustain their research initiatives. However, experts caution that public universities, which rely more heavily on federal funding, may struggle to compete with wealthier institutions with alternative financial resources.
As legal challenges continue, institutions remain in limbo, uncertain of how to plan for future research while facing the possibility of drastic budget constraints. If the proposal is overturned, the decision could reaffirm the federal commitment to supporting a robust research ecosystem.
Regardless of the final ruling, the debate highlights the fragile nature of research funding and the critical role government policies play in shaping scientific progress. The long-term effects of these decisions will shape the trajectory of American scientific progress for years to come, influencing research institutions and public health, economic growth and the nation’s standing in the global scientific community.
As institutions, policymakers and the public grapple with these changes, the question remains: Can the U.S. maintain its position as a global leader in medical innovation, or will funding constraints compromise its scientific future?
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