What H.R. 1 Really Codifies for Science
How a little-noticed tax and a bureaucratic cap could reshape U.S. innovation
The U.S. House of Representatives passed H.R. 1 today, the "One Big Beautiful Bill Act," a sweeping reconciliation bill intended to implement key components of the Trump administration’s fiscal agenda. Among its most controversial implications are those for science. You can read the full text of the bill here.
The Trump administration’s FY 2026 budget proposal called for aggressive cuts across the federal scientific enterprise. NIH was slated for a 40% budget reduction, with a plan to consolidate its 27 institutes into just five. The National Science Foundation (NSF) faced a proposed 55% cut, effectively terminating hundreds of research grants, particularly those focused on diversity, misinformation, and climate. NASA’s Science Mission Directorate would lose 52% of its funding, and the Goddard Institute for Space Studies was marked for closure. The National Oceanic and Atmospheric Administration (NOAA) was also targeted, with a 26% proposed reduction that included eliminating its Office of Oceanic and Atmospheric Research. The Environmental Protection Agency (EPA) faced the harshest fate: a proposed 55% cut that would shutter dozens of climate, public health, and environmental justice initiatives.
But proposals are not policy, so what did H.R. 1 actually do?
What H.R. 1 Codifies
First, it’s important to separate what’s codified in legislative text from what remains aspirational or pending through appropriations.
H.R. 1 does not legislate the deep agency-wide cuts proposed for NIH, NSF, NASA, or NOAA. Nowhere in the 1,100-page bill is there a line item mandating a 40% cut to NIH, or a provision consolidating its institutes. The same is true for NSF and NASA’s science programs. While the administration has clearly articulated its intent to slash these budgets, the bill leaves those decisions to the appropriations process.
Instead, H.R. 1 targets more immediate and politically symbolic programs, particularly those related to climate, clean energy, and environmental justice.
Among the provisions that are codified:
EPA Rescissions: H.R. 1 repeals or rescinds funding for the Greenhouse Gas Reduction Fund, the Environmental and Climate Justice Block Grant program, and funding for methane emissions reduction, diesel pollution mitigation, and Clean Air Act implementation grants.
DOE Cuts: The bill rescinds unobligated balances from multiple Department of Energy programs that fund clean energy research and deployment, including the Office of Clean Energy Demonstrations, the Office of Energy Efficiency and Renewable Energy, and tribal and transmission loan programs.
NOAA: Several NOAA programs, including facilities funding and climate resilience initiatives, see partial rescissions, though the core scientific divisions like the Office of Oceanic and Atmospheric Research are not explicitly eliminated.
A Hidden Hit to Research: Excise Tax on University Endowments
One of the less visible provisions in H.R. 1 is a dramatic expansion of the excise tax on university endowments, which threatens to further undermine the scientific enterprise, particularly at elite research institutions already facing grant cancellations.
H.R. 1 replaces the existing flat 1.4% excise tax on private universities' net investment income (which didn’t exist prior to the first Trump administration) with a tiered structure, scaling as high as 21% based on the size of a school’s endowment per student. While this provision may appear to target wealth, it will functionally target universities' research and scientific capacity.
Top research universities like Harvard, MIT, Stanford, and Yale not only hold large endowments, but they also conduct a disproportionate share of federally funded research. These institutions use endowment income to:
Backstop federal grant programs
Fund early-stage research and high-risk projects
Support graduate students, postdocs, and faculty hiring
Maintain lab infrastructure, core facilities, and research computing
At a time when federal agencies are terminating massive amounts of grants, institutions have been relying more heavily on unrestricted endowment funds to preserve research momentum. But H.R. 1’s tax shift pulls that lever away.
Take Harvard: with an endowment of over $50 billion and investment returns often exceeding $2 billion annually, a new excise tax rate of even 10% would cost the university around $200 million, a roughly $170 million increase from the previous 1.4% rate. That figure could otherwise support hundreds of researchers, fellowships, or research centers at a time when federal resources are drying up.
This is not just a revenue measure. It’s a second-order policy choice that will penalize universities for sustaining research ecosystems, precisely when the federal government is retreating from them. At elite institutions where philanthropy and endowment returns are increasingly critical to maintaining scientific continuity, the tax operates as a disincentive to reinvest in American research leadership.
A New Tool for Silent Cuts: The Cap on Programmatic Authority
While the targeted rescissions to energy and climate programs are damaging on their own, one of the more quietly consequential provisions in H.R. 1 is a clause that limits programmatic authority, but only within the Department of Education…for now. This restriction prohibits the department from issuing regulations or executive actions that would significantly increase costs, even if funding has already been appropriated by Congress.
The bill text, located in Title III, states:
“The Secretary may not issue a proposed rule, final regulation, or executive action implementing this title if the Secretary determines that the rule, regulation, or executive action—
(1) is economically significant; and
(2) would result in an increase in a subsidy cost.”— H.R. 1, Section 30061
"Economically significant" refers to any regulatory action expected to affect the economy by $100 million or more. In effect, this provision blocks the Department of Education from expanding or modifying programs, such as financial aid, institutional support, or student loan servicing, without separate congressional authorization.
While this language does not apply to agencies like NIH, NSF, or DOE, it is worth noting that this kind of statutory restriction on program flexibility reflects a broader trend. Even in just one agency, limiting agency discretion sets a precedent for how future legislation might quietly erode the autonomy of science and public service agencies more broadly. It illustrates how procedural tools can constrain federal capacity without triggering the backlash of explicit defunding.
The Danger of Delayed Damage
The Trump administration's cuts may appear softened in political messaging because many of the worst proposed reductions haven’t yet been codified. But the groundwork is being laid. H.R. 1 eliminates targeted clean energy and environmental science programs while restricting agency authority to adapt and innovate. The heavy lifting of NIH, NSF, and NASA cuts will likely appear in forthcoming appropriations bills, which now must operate within the fiscal framework established by H.R. 1.
In this sense, H.R. 1 is a down payment on a much larger demolition. It doesn’t finish the job but lays the structural blueprint and hobbles the institutions needed to resist.
The Stakes Ahead
The U.S. scientific enterprise has long been regarded as a pillar of global innovation, public health preparedness, and economic competitiveness. Weakening it, whether through blunt defunding or stealth procedural sabotage, risks America’s international standing and ability to tackle crises ranging from pandemics to climate change.
The scientific community must respond urgently and clearly. The debate over H.R. 1 is not just about which grants get funded but whether public science remains a trusted, independent force in shaping our future.
A Narrow Window for Action
It’s important to remember that H.R. 1 will not take full effect unless the Senate passes the budget cuts shaping the appropriations process. Many of the most severe reductions to NIH, NSF, and other science agencies are not yet codified—they hinge on forthcoming appropriations bills. That means there is a short window to enact change, just a few weeks, during which senators can be urged to reject these devastating cuts. Scientists, institutions, and constituents across the country must seize this moment to make clear how H.R.1 would negatively impact science and the communities that depend on it.
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