A new court filing Tuesday shed some light on an unusual wrinkle in the U.S. government’s fight with Harvard University.

Harvard previously claimed the U.S. Department of Defense had terminated a $3.4 million grant for important research into biological threats, despite pleas from an official to maintain the grant for national security purposes — but then asked for work to continue and paid the grant anyway^[1].

A Defense Department official issued a court statement this week saying the grant — supporting research for the “AMPHORA” program^[2], which stands for Assured Microbial Preservation in Harsh or Remote Areas — wasn’t canceled after all. That’s even though it was included in a list of terminated Harvard grants released in May.

Efstathia Fragogiannis is director of the contracts management office with the Defense Advanced Research Projects Agency ( DARPA) in the Department of Defense.

Fragogiannis wrote that in the days following a May 12 letter to Harvard announcing the cancellation of that grant and many others, DARPA officials sought and received an exemption for the grant for reasons of national security.

“On May 21, 2025, May 22, 2025, and June 27, 2025, DARPA informed Harvard via email that the agreement remains active and that it should continue to perform work on the AMPHORA project,” Fragogiannis wrote. “As such, Harvard has continued to perform work pursuant to that agreement, for which DARPA has paid, including the July 8, 2025, payment for work performed from May 1 to 31.”

Harvard had claimed the request for continued work and the payment it received were evidence that “reinforces” its court argument that “the government’s categorical terminations of research funding were arbitrary and capricious.”

Harvard had said in a court filing they inquired with the federal government^[3] about whether the AMPHORA grant is in fact still active, but they haven’t received a response.

In a filing released Tuesday, the government argued that “Harvard’s grants were ultimately terminated because of Harvard’s categorical refusal to respond to the Government’s concerns” over antisemitism.

A Harvard University spokesperson did not immediately respond to a request for comment.

The court filings come as part of an ongoing lawsuit^[4] in which Harvard disputes cancellation of billions of dollars of funding by the U.S. government.

It’s one of two lawsuits the university has against the Trump administration, the other relating to its ability to accept foreign students^[5].

©2025 Advance Local Media LLC. Visit masslive.com^[6]. Distributed by Tribune Content Agency, LLC.^[7]

A retired Army^[1] officer and conservative commentator who could not be approved for a Pentagon job during the first Trump administration because of past Islamaphobic and conspiratorial statements has been confirmed by the Senate to be the Pentagon's personnel chief in the second Trump administration.

In a 52-46 party-line vote Tuesday afternoon, the Senate confirmed Anthony Tata to become the under secretary of defense for personnel and readiness, the top official overseeing the health and well-being of the more than 3 million uniformed and civilian personnel working for the Defense Department.

Tata is a retired Army brigadier general whose post-military career includes serving as a school district administrator in Washington, D.C., and North Carolina and as North Carolina's secretary of transportation, a job he abruptly resigned from.

Read Next: Here Are the 596 Books Being Banned by Defense Department Schools^[2]

More recently, he has been a steady presence on Fox News as a political and military commentator.

Toward the end of the first Trump administration, in 2020, Tata was nominated to be under secretary of defense for policy, essentially the No. 3 position in the Pentagon. But his nomination was withdrawn after Republicans who led the Senate Armed Services Committee canceled his confirmation hearing amid mounting controversy over incendiary statements, including calling former President Barack Obama a "terrorist leader."

At his confirmation hearing in May^[3] to become Pentagon personnel chief, Tata expressed regret for the comments that doomed his previous nomination and said they were "out of character."

But he also defended more recent comments that Democrats grilled him about. Those more recent statements include social media posts in which he said that all four-star officers appointed by former President Joe Biden should be fired and that the Posse Comitatus Act, the law that prohibits the military from conducting domestic law enforcement in most cases, should be "suspended."

Democrats argued that those statements, coupled with his past comments, are disqualifying.

"I respect and I appreciate his military service, but his record of public statements and behavior toward individuals with whom he disagrees politically is disqualifying for a position of this significance," Sen. Jack Reed, D-R.I., the ranking member of the Senate Armed Services Committee, said on the Senate floor Tuesday. "I am concerned Mr. Tata has a misguided and discriminatory view of the military and civilian workforces he would oversee."

At the hearing, Tata claimed that his reference to Posse Comitatus was meant to be a call for better border security and that he did "not know" whether the law should be suspended. Tata also maintained that his call to fire officers was about reinforcing the need to follow lawful orders regardless of politics and that he would not support a "blatant purge" of military officers.

While Republicans recoiled at Tata's comments the first time he was nominated, they dismissed his comments this time around.

"The thing I've learned about Tony is that he takes responsibility for his words and actions," Sen. Thom Tillis, R-N.C., said in May while introducing Tata at his confirmation hearing. "He learns from his past mistakes, which is a testament of a good leader."

Related: Nominee for Pentagon Personnel Chief Grilled Over Comments Calling for Purge of Generals^[4]