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

The director heads a Columbia-affiliated center dedicated to defending free speech rights. The student, a permanent resident, had been active in Palestinian solidarity encampments on campus. Months earlier, the institute had hosted a conference about free speech rights for immigrants.

"We felt this connection to the case, since we're part of the university," Jaffer explained. "We viewed this arrest as a major violation of constitutional freedoms."

Landmark Victory Challenging Administration

Recently, the institute's lawyers at the Knight First Amendment Institute, together with legal partners Sher Tremonte, achieved a significant legal win when a federal judge in Boston ruled that the detention and planned removal of Khalil and other pro-Palestinian students was illegal and purposely created to suppress protest.

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

Increasing Separation Separating Institute and University

This decision elevated the profile of the free speech center, propelling it to the forefront of the battle with Trump over core constitutional principles. However the victory also highlighted the widening chasm between the organization and the institution that houses it.

This legal challenge – characterized by the judge as "perhaps the most important to ever fall within the authority of this district court" – was the first of multiple opposing Trump's unusual attack on universities to go to trial.

Trial Revelations

Throughout the two-week trial, academic experts testified about the climate of terror and self-censorship ushered in by the arrests, while immigration officials revealed information about their dependence on reports by rightwing, Israel-supporting groups to select individuals.

Veena Dubal, chief lawyer of the academic organization, which brought the case together with some of its chapters and the Middle East Studies Association, described it "the primary constitutional lawsuit of the Trump administration this time around".

'Institution and Organization Occupy Different Sides'

While the legal success was praised by advocates and scholars across the country, the director heard nothing from Columbia after the decision – an indication of the disagreements in the stances taken by the organization and the institution.

Even before the administration began, Columbia had come to symbolize the declining tolerance for pro-Palestinian speech on American universities after it summoned officers to remove its student encampment, suspended multiple activists for their activism and dramatically restricted protests on campus.

Institutional Agreement

This summer, the institution reached a deal with the Trump administration to pay millions to settle antisemitism claims and submit to significant limitations on its independence in a action broadly criticized as "capitulation" to the president's pressure strategies.

The university's compliant stance was starkly at odds with the Knight Institute's principled position.

"We're at a time in which the institution and the institute hold opposing views of some of these critical questions," observed Joel Simon at the Knight Institute.

Organization's Purpose

This organization was established in recent years and is located on the university grounds. 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 launch it.

"Our vision for the institute in the long-term future is that when there is a time when the government has gone in the wrong direction and fundamental rights are at stake and few others is prepared to step forward and to say, enough is enough, it will be the this organization that will stepped forward," said Lee Bollinger, a constitutional expert who helped create the institute.

Open Disagreement

Shortly after campus developments, the university and the the organization found themselves on opposing sides, with Knight frequently objecting to the institution's management of campus demonstrations both in private communications and in increasingly unforgiving official comments.

In one letter to campus administration, the director condemned the decision to penalize two student groups, which the institution said had violated policies related to holding campus events.

Escalating Tensions

Subsequently, the director further criticized the university's decision to summon law enforcement onto campus to remove a non-violent, pro-Palestinian encampment – leading to the arrest of more than 100 students.

"Institutional policies are disconnected from the values that are essential for the university's life and mission – including expression, scholarly independence, and fair treatment," he wrote this time.

Student Perspective

Khalil, in particular, had pleaded with campus officials for support, and in an op-ed composed while jailed he wrote that "the logic used by the federal government to target myself and my peers is a direct extension of the university's suppression playbook concerning Palestine".

Columbia reached agreement with the federal government shortly after the trial concluded in court.

Organization's Reaction

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

"University administration ought not accepted this," the statement said.

Wider Impact

The institute doesn't stand alone – organizations such as the ACLU, the free speech organization and other rights organizations have challenged the government over constitutional matters, as have unions and other institutions.

Nor is it concentrating solely on university matters – in other challenges to the government, the institute has filed cases on behalf of agricultural workers and environmental advocates challenging government agencies over environmental datasets and challenged the withholding of official reports.

Unique Position

But its defense of student speech at a institution now associated with making concessions on it places it in a uniquely uneasy position.

Jaffer expressed sympathy for the absence of "favorable choices" for Columbia's leaders even as he described their decision to settle as a "serious mistake". But he stressed that despite the organization standing at the opposite end of its host when it comes to dealing with the administration, the university has permitted it to operate free of pressure.

"Particularly currently, I don't take this independence as automatic," he stated. "If Columbia tried to limit our activities, I wouldn't remain at the university any longer."