The Landscape of American Scientific Research: A Year in Review

Approximately a year ago, optimism surrounded the realm of American scientific research. However, in February, the Trump administration executed significant staff reductions within federal science agencies, limiting grant access for universities and undermining funding for research overhead. Targeting prestigious universities for accusations of anti-Semitism, the administration retracted grants on matters deemed relevant to diversity, equity, and inclusion. Proposed budgets for key agencies, including NASA and the National Science Foundation (NSF), indicated sweeping financial cuts.

This turmoil led many to believe that the scientific community was under siege. Post-World War II, the federal model of outsourcing research to academic institutions seemed to be unraveling.

Holden Thorpe, editor of Science Journal, noted, “That partnership is now breaking down,” calling some of these cuts “an unexpected and immediate blow” and a “betrayal of the partnerships that have enabled American innovation and progress.”

Yet, as we reflect on the past year, those dire predictions have not materialized. Legal challenges and a recent Congressional rejection of many proposed cuts have preserved essential funding.

A coalition of scientific, educational, and civil liberties organizations, including the ACLU, APHA, and AAU, successfully contested some of the Trump administration’s pivotal policy shifts, safeguarding billions in scientific funding. As a result, funding packages negotiated in Congress over the past few weeks have largely maintained federal funding for scientific agencies similar to last year.

The House echoed the Senate’s decision on Tuesday, passing a funding package that included modest increases for National Institutes of Health (NIH) research while rejecting Trump’s proposal for a more than 40% funding cut. Trump signed the bill that evening.

Joan Padron Carney, chief government relations officer at the American Association for the Advancement of Science, stated, “Congress has effectively rejected the president’s very deep cuts.” Given recent trends, she added, “While flat funding may not have seemed like a victory before, considering the circumstances of the past year, we are quite satisfied.”

It’s crucial to acknowledge that the scientific sector hasn’t completely evaded the adverse impacts of the administration. Both the National Oceanic and Atmospheric Administration (NOAA) and NASA have experienced substantial job losses, NIH leadership underwent significant changes, and there have been reductions in essential climate reports and weather services.

Padron-Carney acknowledged that the Trump administration would likely persist in its initiatives to defund science on topics it disapproves of. She noted that a presidential order mandates many grants to obtain approval from senior political appointees.

Despite these challenges, Padron-Carney remarked, “Science is holding up as best it can,” particularly after a year that felt precarious.

The White House did not respond to inquiries regarding Congressional decisions on science funding, although it commended the bill prior to its passage.

“The Administration appreciates that Congress is proceeding with the spending process in a manner that avoids an extensive omnibus package while adhering to a fiscally responsible agreement that prioritizes essential investments,” stated the White House Office of Management and Budget.

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A significant concern within the scientific community revolves around disrupting grant flows to universities and research institutes, especially from the NIH, the primary agency responsible for biomedical and life sciences research funding.

The Trump administration’s attempts to assert control over government agencies led to substantial delays, cancellations, and a halt in thousands of grants. Additionally, the administration’s move to limit indirect costs universities could charge to NIH created uproar, with a proposed 15% cap estimated to save the government $4 billion annually. Universities and states contested this cap, claiming it violated Congressional guidelines and NIH policies.

Substantial legal victories eventually facilitated the reinstated flow of funds.

Last month, an appeals court upheld a ruling that the Trump administration couldn’t impose caps on indirect research spending. Furthermore, in December, the ACLU reached a partial settlement when it filed a lawsuit challenging the NIH’s alleged “ideological purge” on research grants. This settlement mandated the NIH to resume reviewing specific stalled grants, while other aspects related to the diversity, equity, and inclusion lawsuit are still pending.

Olga Axelrod, ACLU attorney involved in subsidy litigation, described the lawsuit as an essential check, affirming, “However, public health research remains under threat.”

The NIH opted not to comment on the lawsuit proceedings.

A surge in lawsuits contesting the Trump administration’s restrictions on grant funding continues, with appeals pending. The Georgetown University’s Health Policy and Law Initiative has tracked 39 related funding complaints this past year, a significant increase from zero last year.

Katie Keith, the initiative’s director, expressed that “It’s exploded,” noting mixed results thus far.

In one instance, a judge ruled against the Trump administration after it cut Harvard University’s funding by $2.2 million. Conversely, another case saw a judge dismiss a lawsuit where faculty aimed to restore nearly $400 million in grants to Columbia University. Notably, Columbia had to pay the government a $200 million settlement after allegations of anti-discrimination violations.

By the end of the fiscal year 2025, NIH expenditures reached typical levels. This marked a substantial shift from earlier in the year, when it seemed improbable NIH would fully utilize the $36 billion allocated by Congress for external grants.

“NIH was significantly lagging,” remarked Jeremy Berg, a professor of computational and systems biology at the University of Pittsburgh who monitors NIH spending.

However, after Congress urged NIH to expedite spending, the funds began to flow, mitigating risks to vital research.

To adapt, the NIH has adjusted its usual practice of funding projects annually, now distributing funds across the entire grant period (typically 4-5 years).

“This essentially serves as an accounting measure,” stated Berg, adding that the number of new projects funded in 2025 had dwindled by about 5% to 10%.

Nonetheless, financial resources continued to flow into research institutions nationwide.

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The scientific community has increasingly turned to Congress as an ally amid funding disputes.

In its budget proposal last spring, the Trump administration expressed strong opposition to scientific funding, suggesting significant cuts to various agencies. Proposals indicated the NSF would face a reduction of nearly 57%, NASA around 24%, and the NIH exceeding 40%. Overall, the proposal outlined almost a 36% cut in non-defense scientific research and development funding, as noted by AAAS.

Nevertheless, Congress largely opposed President Trump’s recommendations, maintaining scientific funding within negotiated spending bills. The NIH’s budget was established at $48.7 billion, reflecting a $415 million increase over 2025. According to Senate Vice Chairman Patty Murray, approximately 75% of this allocation supports external research grants. Moreover, NASA’s budget faced only a 1.6% reduction, and NSF experienced a 3.4% cut.

Congress also enhanced NIH funding for cancer research by $128 million, Alzheimer’s research by $100 million, and added $15 million to ALS research initiatives.

Additionally, legislative measures were introduced to prevent future attempts to limit indirect research spending.

The law mandates NIH to provide monthly reports to Congress on grant awards, terminations, and cancellations, allowing for better tracking of expenditures.

“This illustrates continued bipartisan support for the federal government’s crucial role in bolstering research,” noted Toby Smith, senior vice president for government relations and public policy at the Association of American Universities.

Nonetheless, questions linger about the NIH’s functionality with a reduced workforce and the extent of political influence from the Trump administration. Approximately half of the directorships at the NIH’s 27 institutes and centers remain unfilled.

“We’ve secured Congress’s support for funding. However, can they effectively execute it? Will adequate staffing be available?” queried Smith.

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Even if major funding disruptions are averted this year, the uncertainties stemming from the first year of the second Trump administration could resonate throughout the scientific community for years to come.

A recent report in Science Magazine revealed that over 10,000 professionals holding Ph.D.s have departed from the federal government. Moreover, a study published in JAMA Internal Medicine indicated that funding interruptions affected clinical trials involving 74,000 participants. Additionally, the influx of young scientists training at U.S. universities is dwindling.

At the University of Washington, a leading public institution for biomedical research that heavily relies on NIH funding, there have been hiring freezes, travel restrictions, and furloughs implemented. The influx of new doctoral students entering the medical school has decreased by one-third, primarily due to uncertainty regarding continued funding for principal investigators.

Shelly Sakiyama Elbert, associate dean for research and graduate education at the University of California School of Medicine, expressed, “Some nights, I find it hard to sleep, pondering how to secure funding for my lab.”

The only constant in 2025, she emphasized, has been the feeling of “whiplash.”

Elbert also highlighted a decline in faculty positions and a 5% drop in doctoral student applications at universities.

“This uncertainty only hampers scientific progress,” she concluded.