Late last week, word started leaking that the National Institutes of Health (NIH) had reached an agreement with the Department of Defense that would see part of the NIH's budget used to fund research at the Department of Defense. So, on the Friday just prior to a US holiday weekend, the Department of Defense released a copy of the agreement and confirmed that it had been signed roughly a month earlier. The move is striking for a number of reasons, ranging from the existing budget disparities between the two parties involved to the fact that the money would be used for projects that the current NIH leadership has explicitly rejected.

The agreement itself sets up a system where the NIH would transfer money to the Department of Defense to fund staff and projects that would "support the advanced development of medical countermeasures against pandemic influenza, chemical, biological, radiological, and nuclear (CBRN) threats, and emerging infectious diseases." The money would come out of the budget for the NIH's National Institute of Allergy and Infectious Diseases, or NIAID, to which Congress has allocated $6.6 billion in 2026. The agreement is set to run for a decade.

Left unspecified is just how much of the NIAID budget will be spent on Defense projects. Reporting by Nature suggests that the Department of Defense was looking for up to a third of its total budget but was being told to settle for about 10 percent. There's obviously an enormous disparity between the budgets of these two agencies, given that the 2026 Defense budget is roughly $1 trillion. That budget is under considerable strain, however, due to the open-ended nature of the conflict with Iran. The deal has also been announced at a time when the NIH has been struggling to issue sufficient grants to use the money that Congress allocated to it.

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On Tuesday, the House of Representatives passed a stopgap measure that would continue funding the US government through early December. While the measure still requires the signature of President Trump, it's widely expected that he will act to avoid a government shutdown immediately before the midterm elections.

This is a normal part of how the US government has operated in recent years, as it's often difficult to build the political support needed to pass a full year's budget in advance. In fact, dissent within the House's Republican caucus prevented them from agreeing on their own measure to keep the government open; instead, the House simply adopted a version of the spending bill that had previously passed the Senate.

From the perspective of scientists and their supporters, that adoption turned out to be a very good thing, because the Senate's budget bill, passed in early August, contains a provision that blocks the Office of Management and Budget (OMB) from implementing new rules that would give political appointees full control over what science is funded and allow them to cancel any grant at any time. The proposed rule has been widely decried as catastrophic for science, and it faced widespread opposition from scientific and health-focused organizations.

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