Overview

Well, the proposed cuts are out. While Congress makes the ultimate decision on the budget, we have seen little appetite for the current Republican majority to oppose Trump. The topline numbers are pretty awful. The National Science Foundation (NSF) suffers a proposed cut of 55% to its overall funding. The National Institutes of Health (NIH) receive a proposed cut of 41%. The Department of Energy (DOE) is requesting a slight increase in funding (3%), though research programs on science and energy would receive decreases (14% and 37%, respectively).

So, why these cuts? What of a granular character can we say about the cuts? We have substantial detail on the NSF and DOE, though much less for the NIH. At a broad level, the NSF wants to preserve research on artificial intelligence (AI) and quantum information (QI) at present levels, and essentially to zero out virtually all programs intended to enhance diversity (with one surprising exception), research renewable energy, and research global change. The DOE wants to eliminate research on renewable energy, biofuels, and environmental studies (one particularly astonishing program there), while enhancing research on geothermal energy, and effecting relatively modest cuts to materials research (15%), high energy physics (7%), and nuclear physics (4%). The NIH cuts are laid out somewhat sketchily in the overall budget for the Department of Health and Human Services. Apart from the overall high percentage cut, consolidation of some institutes, transfer of some elsewhere in NIH, and elimination of others (such as the National Institute on Minority Health and Health Disparities) stand out.

Very broadly, it can be seen that:

1. ‘Woke’ is out. The Trump administration has done their very best to eliminate any programs that connote service to diversity, equity, and inclusion.

2. Fossil Fuels and Nuclear are in. The Trump administration wants to do all it can to hamstring alternative, sustainable energy. In terms of zero greenhouse gas emissions, only nuclear and geothermal survive.

3. Billionaire Tax Breaks über alles. The cuts at NIH and NSF are consistent with the general strategy to hack government as much as possible to offset some of the deficit busting by making Trump’s 2017 tax code permanent.

4. DOE is relatively unscathed. DOE emerges largely unscathed. My only hypothesis on this is that Chris Wright got in there relatively early and as a technical guy (oil drilling engineer from MIT) is sympathetic to most science (not renewables!). He probably resisted the DOGE team’s chainsaws and stuck up for the basic functions of DOE which mix defense and energy security.

An important question is: if the US is to again become a mecca for manufacturing, including advanced technology manufacturing, why is Trump proposing cutting the research that will lead to developing that advanced manufacturing to such a high degree? The biggest answers are cutting the budget to partially subsidize the continuing Trump tax breaks for the richest (they are set to expire this year) and attacking American universities to bring them under government control by cutting revenue streams.

National Science Foundation Cuts

The table below summarizes the cuts to programs relevant to university based funding.

What you can see is that no directorate emerges unscathed. The program for outreach to industry (Technology, Innovation, Partnerships) does somewhat better, but within that program, funding for Small Business Innovative Research (SBIR) and Small Business Technology Transfer (STTR) fare badly (57% cut). Integrative Activities fund the large interdisciplinary Science and Technology Centers (STCs), and big facilities like the Long baseline Interference Gravitational Observatory (LIGO).

The new directorate proposes a complete elimination of the previous directorates to be reformulated somehow from the ground up. Having visited NSF multiple times on panels, and been recipient of NSF grants both as an individual and as a co-investigator or advisor on large programs that cross cut between directorates, all I can say is: WTAF? Of all the bureaucracies I have encountered in the federal government, NSF is the one that I found least hampered by internecine turf wars, and as a scientific agency I found it to be the one that handled peer review with the greatest efficacy and integrity. I may not have always been happy with the outcome when I did not get funded, but apart from a few questionable reviews I generally trusted the process and the program managers.

When you look at areas for crosscutting support you see a very clear pattern.

With the exception of Artificial Intelligence and Quantum Information Science, everything else, especially Global Change Research and Clean Energy Technology is cut drastically. For an administration that says they want to bring manufacturing back to America, it is pretty hard to see why they are cutting so many manufacturing related research areas so drastically.

In the case of the Integrative Activities and large facilities, they propose cutting the Laser Interferometer Gravitational Observatory (LIGO) in two. LIGO led to a Nobel Prize for the direct observation of gravitational waves, ripples in the space-time fabric, predicted by Einstein’s General Theory of Relativity, using interferometry to monitor a huge number of low dissipation pendula moving in evacuated tubes. The observatory has been able to see and locate major events in the cosmos such as the merger of black holes. This observatory has two sites, in Hanford WA and Livingston, LA. The Trump administration wants to close one. They might as well shut the whole thing down: the deliberate choice of two sites was to perform precision localization of the gravitational wave source through different arrival times. Your ears do something similar for horizontal localization of sound via arrival time differences.

In programs that broaden participation from underrepresented groups, virtually everything is zeroed out. Exceptions are: Excellence in Research Program at Historically Black Colleges and Universities (HBCUs)-20% cut; Undergrad Programs at HBCUs - no cut; Tribal Colleges and Universities Program - 57% cut. Support for research at Hispanic serving institutions is proposed to be zeroed out. I know a fair amount about the Centers for Research Excellence in Science and Technology, available only for universities with a majority of students who are a minority, having been advising the excellent Center for Cellular and Biomolecular Machines for 8 years at University of California, Merced. The proposal is to eliminate this program.

A number of states with lower research participation have benefited from the EPSCoR program for promoting geographic diversity in research. This has disproportionately benefited “red state” universities. The proposed budget will cut this by 57%.

There is no explicit mention made of programs like the Career Awards for young scientists or the Physics Frontier Centers. It is possible these will survive within the reduced funding environment in some form.

The NSF will maintain the lower 15% indirect cost rate implemented by DOGE.

Department of Energy Cuts

The key division within DOE that awards to universities in condensed matter physics, energy related research, high energy physics, and nuclear physics, is the Office of Science. That is proposed to receive an overall 14% cut. Here are details about individual programs in that Office. It seems possible that physics, at least, is being viewed as more belonging to DOE than to NSF. 

 In the Office of Energy Efficiency and Renewable Energy, research on Solar, wind, renewable-to-grid integration, and fuel cells (hydrogen) are being zeroed out.  There are steep (>90%) reductions in vehicle research, bioenergy, and building efficiency, and about 70% cuts in manufacturing, decarbonization. Hydropower research is cut by more than 50%, and advanced geothermal research is grown by 25%. 

Atmospheric radiation detection is also being zeroed out in the Office of Science.  This is not measuring nuclear radiation, but rather is the collection of data about capture and reflection of solar electromagnetic radiation (light) in the atmosphere. It is critical to understanding energy budgets and changes in the earth’s atmosphere-ocean system, and so seems to be an ideological victim of the Trump crew’s anathema to global change.

The DOE will maintain the lower 15% indirect cost rate instituted by DOGE.

National Institutes of Health Cuts

As mentioned above, the proposed NIH cuts are not as specific as the proposed NSF and DOE cuts. There is not a line item explanation of how each institute will be cut since some will be moved out of the NIH, and some will be consolidated, per the chart below, taken from the budget document.

Several institutes will be eliminated:

• The National Institutes for Nursing Research (no explanation given).

• The National Center for Complementary and Integrative Health (no explanation given).

• The Fogarty International Center (no explanation given).

• The National Institute on Minority Health and Health Disparities (no explanation given).

The NIH will maintain the lower 15% indirect cost rate implemented by DOGE. Their rationale has an interesting phrasing: “In FY 2026, the budget will continue the policy to cap indirect cost rates at 15 percent, ensuring that the United States taxpayer is funding only necessary project costs, not extraneous salaries or flashy new buildings at wealthy universities.”

Epilogue: Why these cuts?

The cuts at NIH and NSF are consistent with the broad goal of Trump and Republicans to cut government wherever they can in order to subsidize the continuation of the Trump tax breaks set to expire this year. As the Congressional Budget Office has summarized, you cannot cut discretionary spending enough to offset the revenue shortfall generated by these tax breaks for the wealthiest Americans; the CBO estimates show that even with draconian cuts that will take health care from 11M Americans and devastate US research in the current House version of the budget, the deficit will balloon by $2.4T over 10 years. Within that budget cutting framework, there is a clear emphasis on cutting programs interpreted as supporting diversity, equity, and inclusion, alternative (non-fossil fuel) sustainable energy, and climate change research.

The latter programs are also cut within the Department of Energy, but somewhat mysteriously the DOE has emerged with far less scathing cuts. My lead hypothesis on this is that DOGE did not get into DOE before Secretary Chris Wright did, and he has provided protection against the cutting, with the exception of alternative energy and climate change research.

The cuts are also part of the Rufo/Project 2025 scheme to bring universities under government control. By cutting revenue streams they can force change on universities. For R1 elite universities, these federal budget cuts are disastrous.

These cuts are clearly short sighted. The NSF budget projects funding success rates at 6-7%. That was already the case with big center grants. Individual PIs will have an even greater challenge supporting research. Red states will get hammered just as badly as blue states. If the economic growth engine driven by science was a V8 engine, methaphorically speaking, the Trump administration is suggesting we can live on just about 3 or 4 cylinders firing right now. How that will contribute to his envisioned manufacturing renaissance is beyond me.