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After government officers detained Columbia University student Mahmoud Khalil in his university residence, Jameel Jaffer knew a major battle was coming.

The director heads a Columbia-affiliated institute focused on protecting free speech protections. The student, a green card holder, had been involved in Palestinian solidarity encampments on campus. Months earlier, Jaffer's organization had hosted a conference about constitutional protections for noncitizens.

"We felt a direct link to the case, because we're part of the university," Jaffer stated. "And we saw this detention as a major violation of constitutional freedoms."

Major Legal Win Challenging Administration

Last week, Jaffer's team at the Knight First Amendment Institute, along with the law firm their co-counsel, secured a landmark victory when a federal judge in Massachusetts ruled that the arrest and planned removal of Khalil and additional activists was unconstitutional and purposely created to suppress protest.

Government officials announced they'll challenge the verdict, with White House spokesperson a spokeswoman describing the judgment an "outrageous ruling that undermines the safety and security of our nation".

Growing Divide Between Institute and University

This decision raised the profile of the Knight Institute, propelling it to the forefront of the conflict with Trump over fundamental American values. Yet the victory also underscored the growing divide between the institute and the institution that houses it.

This legal challenge – described by the presiding official as "perhaps the most important to ever fall within the authority of this district court" – was the first of multiple challenging Trump's unusual attack on higher education to reach court proceedings.

Court Testimony

Throughout the two-week trial, academic experts testified about the atmosphere of fear and self-censorship ushered in by the arrests, while immigration officials disclosed information about their dependence on dossiers by rightwing, pro-Israel groups to pick their targets.

Veena Dubal, chief lawyer of the academic organization, which filed the lawsuit along with some of its chapters and the academic group, called it "the primary constitutional lawsuit of the Trump administration this time around".

'University and Organization Are On Different Sides'

While the legal success was praised by supporters and academics across the country, Jaffer received no communication from university leadership after the decision – a reflection of the disagreements in the positions taken by the organization and the institution.

Even before the administration began, Columbia had represented the declining tolerance for Palestinian advocacy on American universities after it called police to clear its campus protest, disciplined multiple activists for their activism and dramatically restricted demonstrations on campus.

Institutional Agreement

Recently, the university reached a deal with the federal government to provide substantial funds to resolve discrimination allegations and submit to significant limitations on its independence in a move broadly criticized as "surrender" to the administration's bullying tactics.

Columbia's compliant stance was sharply contrasted with the Knight Institute's defiant one.

"We're at a time in which the university and the organization are on different sides of these critical questions," observed a former fellow at the Knight Institute.

Institute's Mission

The Knight Institute was established in 2016 and is located on the university grounds. It has obtained significant funding from the university as part of an arrangement that had both providing millions in operating funds and endowment funds to launch it.

"Our vision for the organization in the years ahead is that when there is that moment when the administration has gone in the wrong direction and fundamental rights are threatened and no one else is prepared to step forward and to say, this must stop, that's when the this organization that will stepped forward," said the former president, a constitutional expert who established the institute.

Public Criticism

Shortly after campus developments, Columbia and the Knight Institute were positioned on opposing sides, with the institute regularly criticizing the university's handling of pro-Palestinian protests both in private communications and in increasingly unforgiving official comments.

In one letter to university leadership, the director condemned the decision to suspend campus organizations, which the institution said had broken rules related to holding campus events.

Growing Conflict

Later, the director again condemned the university's decision to call law enforcement onto campus to remove a non-violent, student protest – leading to the detention of numerous activists.

"The university's decisions are separated from the values that are central to the university's life and mission – including free speech, scholarly independence, and equality," he wrote this time.

Activist Viewpoint

Khalil, in particular, had pleaded with university administrators for protection, and in a published article written from detention he stated that "the reasoning used by the federal government to single out myself and fellow students is a direct extension of the university's suppression approach regarding Palestine".

Columbia reached agreement with the federal government just days after the case wrapped in court.

Institute's Response

Shortly after the agreement was revealed, the Knight Institute published a strong criticism, stating that the agreement sanctions "a remarkable shift of independence and control to the administration".

"University administration ought not agreed to this," the statement said.

Wider Impact

The institute doesn't stand alone – groups such as the ACLU, the free speech organization and additional civil liberties groups have opposed the government over constitutional matters, as have unions and Harvard University.

Nor is it exclusively focusing on campus issues – in additional lawsuits to the government, the organization has sued on behalf of agricultural workers and environmental advocates challenging federal departments over environmental datasets and fought the suppression of government documents.

Special Situation

However its protection of campus expression at a university now synonymous with compromising on it puts it in a uniquely uneasy situation.

The director expressed sympathy for the lack of "good options" for Columbia's leaders even as he described their agreement as a "major error". But he emphasized that despite the organization positioned at the opposite end of its host when it comes to addressing the administration, the institution has permitted it to operate free of pressure.

"Especially right now, I don't take this independence as automatic," he stated. "If Columbia tried to limit our activities, I wouldn't be at the university any more."