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After government officers detained the university student Mahmoud Khalil in his university residence, Jameel Jaffer knew a significant fight lay ahead.

Jaffer leads a university-connected center focused on defending First Amendment protections. Khalil, a permanent resident, had been involved in Palestinian solidarity protests on campus. Months earlier, the institute had hosted a conference about free speech rights for immigrants.

"We recognized this connection with this situation, since we're at Columbia," Jaffer stated. "And we saw this arrest as a major violation of First Amendment rights."

Major Legal Win Challenging Administration

Last week, Jaffer's team at the Knight First Amendment Institute, together with the law firm their co-counsel, secured a landmark victory when a federal judge in Boston determined that the detention and planned removal of Khalil and additional activists was unconstitutional and intentionally designed to chill free speech.

The Trump administration announced they'll challenge the verdict, with White House spokesperson a spokeswoman describing the ruling an "unacceptable decision that undermines the protection of our nation".

Growing Divide Between Institute and University

This decision elevated the profile of the Knight Institute, catapulting it to the forefront of the conflict with the administration over core constitutional principles. However the win also highlighted the growing divide between the organization and the university that hosts it.

This legal challenge – characterized by the judge as "perhaps the most important ever come under the jurisdiction of this district court" – was the first of several opposing Trump's unusual attack on higher education to reach court proceedings.

Court Testimony

During the court proceedings, academic experts testified about the atmosphere of fear and silencing caused by the arrests, while government agents revealed information about their reliance on reports by rightwing, Israel-supporting groups to select individuals.

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 central constitutional lawsuit of the current government currently".

'University and Institute Occupy Opposing Positions'

While the court victory was hailed by supporters and academics across the country, Jaffer received no communication from Columbia following the ruling – an indication of the tensions in the stances taken by the institute and the university.

Prior to Trump took office, Columbia had come to symbolize the declining tolerance for Palestinian advocacy on US campuses after it called police to remove its campus protest, disciplined multiple activists for their protests and dramatically restricted protests on campus.

University Settlement

Recently, the university negotiated an agreement with the federal government to provide substantial funds to settle antisemitism claims and accept major restrictions on its autonomy in a move broadly criticized as "surrender" to the administration's bullying tactics.

Columbia's submissive approach was starkly at odds with the organization's principled position.

"We're at a moment in which the institution and the organization are on different sides of these critical questions," noted Joel Simon at the Knight Institute.

Organization's Purpose

The Knight Institute was launched in recent years and is located on the Columbia campus. It has obtained significant funding from the university as part of an arrangement that had both providing substantial amounts in program support and endowment funds to establish the center.

"Our vision for the organization in the long-term future is that when there is that moment when the administration has gone in the wrong direction and fundamental rights are at stake and no one else are willing to step forward and to declare, enough is enough, that's when the Knight Institute who will have taken action," stated Lee Bollinger, a constitutional expert who established the institute.

Public Criticism

Following recent events, the university and the Knight Institute found themselves on opposing sides, with the institute frequently objecting to the university's handling of pro-Palestinian protests both in private communications and in progressively critical official comments.

In one letter to university leadership, Jaffer condemned the decision to suspend two student groups, which the institution said had broken rules related to organizing protests.

Growing Conflict

Later, Jaffer further criticized the university's decision to call law enforcement onto campus to clear a peaceful, pro-Palestinian encampment – resulting in the detention of numerous activists.

"The university's decisions are disconnected from the values that are essential for the academic community and purpose – including free speech, scholarly independence, and fair treatment," he stated in that instance.

Student Perspective

Khalil, specifically, had appealed to campus officials for support, and in a published article composed while jailed he wrote that "the reasoning employed by the administration to single out myself and my peers is a direct extension of the university's suppression playbook concerning Palestinian issues".

Columbia reached agreement with the Trump administration just days after the case wrapped in court.

Institute's Response

Following the agreement was announced, the organization published a strong criticism, stating that the settlement sanctions "an astonishing transfer of autonomy and authority to the administration".

"Columbia's leaders ought not accepted these terms," the declaration said.

Broader Context

The institute has allies – groups such as the ACLU, the Foundation for Individual Rights and additional civil liberties groups have challenged the Trump administration over constitutional matters, as have unions and Harvard University.

Nor is it exclusively focusing on university matters – in other challenges to the government, the organization has sued on behalf of agricultural workers and environmental advocates challenging federal departments over environmental information and fought the suppression of government documents.

Unique Position

However its defense of campus expression at a university now synonymous with making concessions on it places it in a particularly difficult situation.

Jaffer expressed sympathy for the lack of "favorable choices" for university administration while he characterized their agreement as a "serious mistake". But he stressed that despite the institute positioned at the other side of its host when it comes to addressing the president, the university has allowed it to operate free of pressure.

"Especially right now, I appreciate this independence as automatic," he stated. "Should the university attempt to limit our activities, I wouldn't remain at Columbia any more."