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After government officers arrested the university student Mahmoud Khalil in his campus housing, the institute director knew a major battle lay ahead.

The director heads a Columbia-affiliated institute focused on protecting free speech rights. Khalil, a permanent resident, had been involved in pro-Palestinian protests on campus. Previously, Jaffer's organization had organized a conference about constitutional protections for noncitizens.

"We felt this connection with this situation, because we're part of the university," Jaffer stated. "We viewed this detention as a serious infringement of First Amendment rights."

Landmark Victory Against Government

Recently, the institute's lawyers at the Knight First Amendment Institute, along with the law firm Sher Tremonte, secured a significant legal win when a federal judge in Boston determined that the detention and attempted deportation of the student and additional activists was unconstitutional and purposely created to chill free speech.

The Trump administration announced it will appeal the verdict, with White House spokesperson a spokeswoman describing the judgment an "unacceptable decision that undermines the protection of our nation".

Growing Divide Separating Organization and Institution

This decision raised the profile of the Knight Institute, propelling it to the forefront of the conflict against the administration over fundamental American values. However the win also underscored the widening chasm between the institute and the university that hosts it.

The case – characterized by the judge as "possibly the most important ever come under the authority of this district court" – was the initial of several opposing Trump's unusual attack on universities to reach court proceedings.

Court Testimony

Throughout the two-week trial, academic experts gave evidence about the climate of terror and silencing caused by the arrests, while immigration officials disclosed details about their reliance on dossiers by rightwing, Israel-supporting organizations to pick their targets.

Veena Dubal, chief lawyer of the American Association of University Professors, which brought the case together with local branches and the Middle East Studies Association, called it "the primary civil rights case of the Trump administration this time around".

'University and Organization Occupy Opposing Positions'

Although the court victory was praised by supporters and scholars across the country, the director heard nothing from Columbia after the decision – a reflection of the tensions in the positions taken by the organization and the university.

Prior to Trump took office, Columbia had come to symbolize the shrinking space for pro-Palestinian speech on American universities after it called police to remove its student encampment, disciplined dozens of students for their activism and severely limited demonstrations on campus.

Institutional Agreement

This summer, the institution negotiated an agreement with the federal government to provide substantial funds to settle discrimination allegations and accept significant limitations on its independence in a move widely condemned as "capitulation" to the administration's bullying tactics.

Columbia's submissive approach was starkly at odds with the organization's defiant one.

"This is a moment in which the institution and the institute are on different sides of some of these critical questions," noted a former fellow at the Knight Institute.

Organization's Purpose

This organization was launched in 2016 and is housed on the Columbia campus. It has obtained substantial support from the university as part of an arrangement that had each contributing millions in program support and long-term financing to establish the center.

"Our vision for the institute in the years ahead is that when there is a time when the government has gone in the wrong direction and constitutional protections are threatened and few others is prepared to step forward and to say, this must stop, that's when the Knight Institute that will taken action," said Lee Bollinger, a First Amendment scholar who established the center.

Public Criticism

Following recent events, Columbia and the the organization found themselves on different sides, with Knight regularly criticizing the institution's management of campus demonstrations both in private communications and in progressively critical official comments.

In correspondence to university leadership, Jaffer criticized the action to suspend campus organizations, which the university said had violated policies related to organizing protests.

Growing Conflict

Later, the director further criticized the institution's choice to call police onto campus to clear a peaceful, student protest – leading to the arrest of numerous activists.

"The university's decisions are separated from the principles that are essential for the university's life and mission – such as expression, academic freedom, and fair treatment," he wrote in that instance.

Student Perspective

The detained student, specifically, had appealed to campus officials for protection, and in an op-ed written from detention he wrote that "the logic used by the administration to target myself and fellow students is an outgrowth of Columbia's repression playbook regarding Palestine".

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

Organization's Reaction

Following the agreement was revealed, the Knight Institute published a scathing rebuke, stating that the settlement approves "a remarkable shift of autonomy and control to the administration".

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

Wider Impact

The institute has allies – organizations such as the civil liberties union, the Foundation for Individual Rights and additional rights organizations have opposed the Trump administration over constitutional matters, as have unions and other institutions.

The institute isn't concentrating solely on campus issues – in other challenges to the government, the organization has filed cases on behalf of agricultural workers and environmental advocates challenging federal departments over environmental information and fought the withholding of government documents.

Unique Position

But its protection of campus expression at a institution now associated with compromising on it places it in a uniquely uneasy position.

Jaffer showed understanding for the lack of "good options" for university administration even as he described their decision to settle as a "serious mistake". But he emphasized that despite the institute standing at the opposite end of its host when it comes to addressing the president, the university has permitted it to function without interference.

"Particularly currently, I appreciate that freedom as automatic," he said. "If Columbia tried to restrict our work, I wouldn't remain at Columbia any longer."