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When government officers arrested Columbia University student Mahmoud Khalil in his university residence, the institute director knew a significant fight was coming.

The director leads a university-connected center dedicated to defending First Amendment rights. Khalil, a permanent resident, had been involved in pro-Palestinian encampments on campus. Months earlier, the institute had organized a symposium about constitutional protections for immigrants.

"We recognized this connection to the case, since we're at Columbia," Jaffer explained. "We viewed this arrest as a serious infringement of constitutional freedoms."

Major Legal Win Against Government

Recently, Jaffer's team at the Knight First Amendment Institute, along with legal partners their co-counsel, secured a significant legal win when a federal judge in Massachusetts determined that the arrest and attempted deportation of Khalil and additional activists was illegal and purposely created to chill free speech.

The Trump administration announced they'll challenge the decision, with White House spokesperson Liz Huston describing the judgment an "outrageous ruling that undermines the protection of the country".

Increasing Separation Between Organization and University

This decision elevated the profile of the free speech center, catapulting it to the forefront of the battle with Trump over core constitutional principles. However the victory also underscored the growing divide between the organization and the university that hosts it.

The case – described by the judge as "perhaps the significant to ever come under the jurisdiction of this district court" – was the initial of several opposing the administration's unusual attack on universities to reach court proceedings.

Court Testimony

During the two-week trial, citizen and noncitizen scholars testified about the atmosphere of fear and silencing ushered in by the detentions, while immigration officials revealed information about their dependence on reports by rightwing, Israel-supporting organizations to select individuals.

A legal expert, chief lawyer of the American Association of University Professors, which filed the lawsuit together with some of its chapters and the academic group, called it "the central constitutional case of the current government currently".

'Institution and Institute Are On Opposing Positions'

Although the court victory was praised by advocates and academics nationwide, Jaffer received no communication from university leadership following the ruling – an indication of the tensions in the positions staked out by the institute and the university.

Prior to Trump took office, the university had come to symbolize the shrinking space for Palestinian advocacy on American universities after it summoned officers to clear its campus protest, suspended dozens of students for their activism and severely limited demonstrations on campus.

Institutional Agreement

This summer, the institution reached a deal with the Trump administration to pay millions to resolve discrimination allegations and submit to major restrictions on its autonomy in a action widely condemned as "surrender" to the administration's pressure strategies.

Columbia's submissive approach was sharply contrasted with the Knight Institute's principled position.

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

Organization's Purpose

The Knight Institute was established in 2016 and is located on the university grounds. It has received significant funding from the university as part of an agreement that had each contributing millions in program support and long-term financing to launch it.

"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 fundamental rights are threatened and few others is prepared to take action and to declare, this must stop, that's when the Knight Institute who will have stepped forward," said Lee Bollinger, a constitutional expert who helped create the center.

Open Disagreement

Shortly after campus developments, Columbia and the Knight Institute were positioned on different sides, with Knight regularly criticizing the institution's management of campus demonstrations both in private communications and in progressively critical public statements.

In one letter to university leadership, Jaffer criticized the action to penalize two student groups, which the university said had violated policies concerning holding campus events.

Escalating Tensions

Subsequently, the director again condemned the institution's choice to summon police onto campus to clear a non-violent, student protest – leading to the detention of more than 100 students.

"The university's decisions have become disconnected from the principles that are central to the academic community and purpose – including free speech, scholarly independence, and fair treatment," he wrote this time.

Student Perspective

The detained student, 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 fellow students is an outgrowth of the university's suppression playbook regarding Palestinian issues".

Columbia settled with the Trump administration just days after the trial concluded in court.

Organization's Reaction

Shortly after the agreement was announced, the Knight Institute published a scathing rebuke, stating that the settlement approves "an astonishing transfer of independence and authority to the administration".

"Columbia's leaders should not have accepted this," the declaration stated.

Broader Context

The institute doesn't stand alone – organizations such as the civil liberties union, the free speech organization and additional civil liberties groups have challenged the government over free speech issues, as have labor organizations and Harvard University.

Nor is it exclusively focusing on university matters – in additional lawsuits to the government, the organization has sued on behalf of agricultural workers and environmental advocates challenging government agencies over climate-related information and fought the withholding of official reports.

Special Situation

But its protection of campus expression at a institution now synonymous with making concessions on it places it in a uniquely uneasy position.

Jaffer showed understanding for the absence of "favorable choices" for university administration while he characterized their decision to settle as a "serious mistake". But he emphasized that despite the organization standing at the opposite end of its parent institution when it comes to dealing with the president, the university has permitted it to function without interference.

"Particularly currently, I don't take this independence as automatic," he said. "If Columbia tried to restrict our work, I wouldn't be at the university any longer."