NIH and the biopharmaceutical industry behind it have temporarily escaped a disaster.

In the last week of September, a draft executive order that had already been circulated within the White House and even leaked by some media outlets was suddenly put on hold.

The core content of this draft is enough to shake the entire American biomedical community. It calls for the establishment of a committee composed of political appointees with ultimate veto power over NIH's annual $48 billion research funding.

However, on September 23rd, multiple media outlets reported that the Trump administration was withdrawing the plan. Senator Appropriations Committee Chairman Susan Collins, a Republican from Maine, said she has been pressuring the White House for weeks on the executive order and is "making progress". She revealed that Trump's White House Chief of Staff, Susie Wiles, expressed concerns about the impact of this plan.

Although I have not yet received formal confirmation from White House Legislative Affairs Director James Brand, I hope this executive order will not be signed, "Collins said.
Has Trump's policy really changed its mind? Or was it just pressing the pause button?

Some very realistic results seem to have not yet turned: NIH has changed its funding decision-making approach, indirect cost policies have attempted to reduce the management and infrastructure costs that universities receive from research projects to 15%, NIH has proposed limiting the number of research projects that a single PI can simultaneously own, and the presentation of peer review results has also been redesigned.

The gloom surrounding the industry has not yet dissipated.

01. Funding Storm

According to The Washington Post, the atmosphere at the internal meeting held at the White House on September 18th was not quite right from the beginning.

NIH Director Jay Batacharia, White House Budget Office Director Russell Waters, and several other government officials sat together to discuss the feasibility of a draft executive order to expand White House funding decisions for NIH. The core objectives of the draft include reducing research funding related to Diversity, Equity, and Inclusion (DEI) and establishing a political committee with the power to veto funding.

The conflict is focused on two people. Walter accused Batacharia of still funding projects that conflict with the presidential executive order, including research involving DEI. Trump demanded that Batacharia reduce NIH funding for Harvard University, but Batacharia refused on the spot.

The meeting lasted for over an hour, and the atmosphere was tense at one point. Semafor quoted informed sources as saying that the meeting "sometimes becomes controversial".

The news was reported in the following days, quickly igniting the American political arena.

Collins said in a statement, 'Applying political scrutiny to funding that has already been selected through rigorous scientific and merit based procedures would undermine the government's long-standing principle of funding research based on scientific values and needs rather than political ideology.'.

In the view of Collins' Democratic colleague and Washington State Senator Patti Murray, whether life-saving medical research should be funded or not should be decided by NIH experts, rather than a committee composed of supporters selected by Trump and Walter. Under this draft, a political appointee can kill a cancer research or Alzheimer's trial without any scientific justification.

Perhaps surprisingly for the Trump administration, the opposition is not limited to the Democratic Party.

Pennsylvania Republican Senator Dave McCormick published a commentary in The Washington Post calling for increased funding for the NIH and clearly distancing himself from Trump's cuts. Lisa Murkowski from Alaska also stood in opposition.

Collins warned in the letter that the new committee would "undermine" congressional intentions and the pursuit of good science. She also revealed to Semafor that she has been raising concerns about the politicization of NIH funding since July and believes she is "making progress" in blocking the executive order.

On September 23rd, the situation became clear. The New York Times and Semafor reported that the White House is withdrawing its executive order plan. A source familiar with the matter told Semafor that the executive order "looks like it's already dead".

However, the White House may introduce an executive order targeting NIH funding in another form. Another insider revealed that the Trump administration plans to re-examine this issue after the midterm elections, with the goal of achieving its policy intent while avoiding the perception of "political interference in science".

A pharmaceutical industry lobbyist raised a sharper question: "Is this' dead 'or' we have no choice but to wait, so it's better not to do it before the midterm elections'
Beyond words, Trump's concessions are more like a tactical retreat.

02. The Road to Centralization

Looking back at Trump's series of actions towards NIH since his second term, we can further understand the impact of this funding restriction controversy on NIH.

In January 2025, shortly after returning to the White House, Trump signed an executive order prohibiting federal funds from being used for DEI projects. This order had a profound impact on NIH, forcing the suspension or re examination of numerous projects related to health disparities and disease research in vulnerable populations.

Batacharia himself has previously conducted federally funded research on health disparities and co authored an article titled 'How We Cured NIH's DEI' in the Observer magazine. Trump and Walter clearly do not agree.

In July 2025, Walter introduced the "Multi Year Grant" policy, requiring NIH to fully allocate research funding in one go instead of distributing it in annual installments. This change may seem like a financial and technical adjustment, but the actual effect is a significant reduction in NIH's available funds and a sharp decrease in the number of new projects that can be funded.

Wisconsin Senator Tammy Baldwin pointed out at a hearing in February 2026 that the "multi-year funding" policy resulted in the NIH funding 2000 fewer projects than the previous year.

At the same time, the Trump administration also proposed a plan to cut the NIH budget by about 40%, or about $19.6 billion, and attempted to restructure 27 research institutes into 8. The two parties in Congress jointly rejected these proposals and instead approved a $415 million increase for NIH in the 2026 fiscal year. But even though the budget is preserved on paper, the flow of funds is severely hindered.

OMB's delayed approval of NIH's funding allocation has resulted in a delay of approximately 44 days in NIH's funding progress for fiscal year 2025 compared to the average pace of 2021-2024. By early July 2026, it will still be 42 days behind.

As of July, which is three-quarters of the fiscal year, NIH has only spent about half of its budget.

Batacharia's role is particularly subtle. As the director of NIH, he released new funding guidelines to comply with Trump's opposition to DEI demands. But he is also trying to maintain the scientific independence of NIH.

The conflict between Walter and Batacharia was so deep that Walter had previously refused to meet with him. By September 23rd, the two were attempting to reach a compromise with the goal of reducing political interference in funding decisions while ensuring that federal biomedical research funding remained aligned with Trump's priorities.

The problem is that the space for compromise is narrowing. The temporary funding bill passed earlier this year already includes a provision that temporarily prevents OMB from implementing its proposal to expand control over federal health funding. Congress is already using legislative means to demarcate borders.

The controversy in September is just the latest chapter in the long-term game between the White House and Congress over control of research funding.

03. Closing the business

The concerns of professionals in the biopharmaceutical industry are not unfounded, as the unpredictability of research funding has been disrupted, resulting in a series of negative impacts.

Katherine Mennick, a biomedical researcher from Cambridge, Massachusetts, has a representative experience.

In 2025, a research grant from Mennick was cancelled and subsequently joined a lawsuit filed by the American Public Health Association. After the intervention of the court, funding was restored, but the blank period of those few months completely scrapped one of her time sensitive experiments.

This impact is systematically spreading. A review in the January 2026 issue of Nature magazine pointed out that the interruption of NIH funding not only affects current research progress, but also erodes the long-term foundation of biomedical innovation in the United States.

A modeling study shows that if the NIH budget is reduced by 40% in 2026, even if the next government doubles the budget, it will still take 36 years to make up for the cumulative loss in the number of new drug approvals. More than 99% of FDA approved drugs have received funding from NIH. This means that every delay in the funding process, every cancelled project, is invisibly delaying potentially life-saving therapies in the future.

The loss of talent is equally alarming. According to STAT, in the first year of Trump's return to the White House, the White House lost over 10000 federal employees with STEM doctoral degrees, including about 1100 from NIH.

The vicious cycle of talent outflow and funding tightening is formed: senior scientists leave, young researchers cannot find mentors and projects, and the foundation of the entire scientific research ecosystem is loosening.

The CDC's situation is even more extreme, as a report by The New York Times on September 26th showed that this once leading global public health institution has become "zombie like". As of May 2026, the number of CDC employees has decreased by 30% compared to before the early layoffs in 2025. Only one of the 11 center directors remains in office. The center responsible for emerging and zoonotic diseases has lost nearly 300 employees, and the respiratory disease center has lost nearly 200 employees.

A former official described, "Imagine a city losing one-third of its firefighters and wondering why the city center is burning

The chain effect of funding interruption also affects universities.

MIT's federal research funding has decreased by about 20% this year, while Johns Hopkins University - a hub for cultivating a large number of biomedical scientists - has seen a nearly 45% decrease in federal funding. In 2024, international students will account for nearly 40% of doctoral students in the fields of science and engineering, and the Trump administration's restrictions on international student visas are further narrowing this talent pipeline.

More broadly speaking, this destructive nature will to some extent accelerate the outflow of innovative resources and reshape the position of other countries such as China in the global pharmaceutical market landscape.

According to Grant Witness tracking data, since Trump returned to the White House, over 5700 NIH grants have been frozen or cancelled, with a total value of approximately $15 billion, of which about 4500 were later restored through litigation or administrative procedures. More macro level data shows that the Trump administration has reduced or frozen a total of $177 billion in federal appropriations nationwide, covering all 50 states and the District of Columbia.

04. Have you changed your mind?

Based on current information from various sources, the Trump administration has pressed the pause button under pressure from Congress, but has not abandoned its strategic goals.

A key variable is December 11th, which is the expiration date of the current government's temporary funding bill. If the White House insists on advancing the executive order, it may not even be able to get Congress to pass a temporary appropriations bill. A source familiar with the matter told Semafor, 'If they issue an executive order before December 11th, they won't think about a temporary funding bill.'.

This means that Trump's retreat at the timing is not a coincidence, he is a pragmatic choice in the face of the risk of government shutdown.

But suspension does not mean termination. According to Semafor, the White House's executive order on NIH funding may make a comeback in a different way. This indicates that the White House's strategic intent has not changed, only tactics and timing have changed.

Congress is already taking action. The bipartisan members of the Senate Appropriations Committee are drafting wording to include it in a spending bill to prevent White House intervention in the NIH funding process.

The temporary funding bill passed earlier this year already includes a provision that temporarily prevents OMB from implementing its proposal to expand control over federal health funding. That is to say, even if the Trump administration attempts to push forward in the form of another executive order or OMB rule in the future, Congress can once again counter it through legislative means.

This game of control over NIH funding has essentially become a power boundary struggle between the White House and Congress.

Obviously, the Trump administration's attitude towards science has not fundamentally changed.

On October 8th, Trump announced a STEM education program worth over $100 million aimed at cultivating domestic research talents in the United States. Michael Krazios, Director of the White House Office of Science and Technology Policy, stated that this investment will "ensure that the United States continues to lead the world in discovery.

However, on the same day, the Department of Homeland Security proposed a fee of $70000 for foreign students seeking graduate work visas, with an additional $30000 for STEM field extensions. On one hand, we are cultivating local talents, while on the other hand, we are closing the door to prevent foreign talents from entering; On one hand, it supports science, while on the other hand, it narrows the funding channels for scientific research.

The negotiations between Batacharia and Walter are still ongoing. Even if a compromise is reached, the core logic remains that federal research funding must be aligned with the president's political priorities. There is a fundamental tension between this and NIH's decades long tradition of funding based on scientific value and peer review.

Collins told Semafor on September 24th that if the executive order is ultimately issued, she will "continue to work in the Appropriations Committee to prevent it implementation".

The withdrawal of the funding order has given NIH and the biopharmaceutical industry a breathing space, but no one knows when the next shock will come. The only certainty may be that the US federal research funding system is undergoing its most profound political transformation in history, and the cost of this transformation will be paid for by decades of scientific innovation and public health.

Reference material:
1.Exclusive / Trump administration backing off NIH grant order amid pushback
2.White House Backtracks on Plan to Exert New Control Over N.I.H. Grants
3.Trump administration has cut or frozen $177 billion in grants across every state, analysis shows
4.‘Zombified’ C.D.C., Hobbled by Cuts, Struggles to Fulfill Scientific Mission
5.Trump Makes $100 Million Push to Train American Scientists
6. Trump's 100 Days: The Cost of Attacking the Pharmaceutical Industry; Same freehand brushwork
7.FDA， The aftershocks continue; Same freehand brushwork