A federal judge in Boston who sided with Harvard University and ordered the Trump administration to unfreeze nearly $2.2 billion in federal grants delivered a "gutsy challenge" to the U.S. Supreme Court and Trump, calling on lower courts to "safeguard academic freedom."

In the 84-page order, Judge Allison Burroughs calls the government's use of "combatting antisemitism" as a "smokescreen" for an "ideological assault" on universities, criticizing SCOTUS for its recent emergency rulings.

The administration's move to freeze the funding violated U.S. law and the Constitution's free speech protections, she wrote.

"Judge Burroughs’ ruling for Harvard, vacating $2.2 B in grant terminations, is well-written & brave, but teeters on a knife’s edge, as she admits, in trying to distinguish the SCOTUS’s Dept of Education v Calif & NIH v APHA rulings," Roger Parloff, senior editor at Lawfare, posted via X Thursday.

Burroughs cited Justice Neil Gorsuch's decision to reprimand and criticize district court judges not to "defy" the Supreme Court, adding that it was "unhelpful and unnecessary." She wrote that lower courts are working to make sense of cryptic Supreme Court orders that are not "models of clarity," especially as "they are working to find the right answer in a rapidly evolving doctrinal landscape ... without much guidance or consensus."

She distinguishes how in recent rulings, including the Dept of Education v. California and National Institute of Health v. American Public Health Association, which sent all or portions of those cases to the Court of Federal Claims, that unlike those cases she is ruling on claims brought under the First Amendment and Title VI of the Civil Rights Act.

"Still, she recognizes that 'it may well be' SCOTUS won’t agree with her—though she needles SCOTUS for failing to explain how its recent stay rulings are consistent with earlier, fully argued, SCOTUS precedents," Parloff said.

Gorsuch, who is part of a conservative majority, has sided with Trump. Recent emergency orders have not included full briefs and have been sometimes just a few sentences long, Bloomberg reports.

"Her final words seem to be a gutsy challenge to SCOTUS itself..." Parloff added.

“Now it is the job of courts to similarly step up, to act to safeguard academic freedom and freedom of speech as required by the Constitution, and to ensure that important research is not improperly subjected to arbitrary and procedurally infirm grant terminations, even if doing so risks the wrath of a government committed to its agenda no matter the cost."

"There is, in reality, little connection between the research affected by the grant terminations and antisemitism," Burroughs said.

She wrote that the move to freeze federal funding could do more to hurt Jewish scientists.

"And the research was frozen without any sort of investigation into whether particular labs were engaging in antisemitic behavior, were employing Jews, were run by Jewish scientists, or were investigating issues or diseases particularly pertinent to Jews (such as, for example, Tay-Sachs disease), meaning that the funding freezes could and will likely harm the very people Defendants professed to be protecting. And it is unlikely that any Jew, even directly impacted by antisemitism would be in favor of stopping research on, for example, Alzheimer's disease, heart disease, or autism to name a few, as a means of redressing their unrelated harm."