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After government officers arrested Columbia University student a student activist in his university residence, Jameel Jaffer understood a significant fight was coming.

The director leads a university-connected institute dedicated to protecting free speech protections. Khalil, a permanent resident, had been involved in pro-Palestinian protests on campus. Months earlier, the institute had hosted a symposium about free speech rights for immigrants.

"We felt a direct link with this situation, because we're at Columbia," Jaffer stated. "We viewed this detention as a serious infringement of constitutional freedoms."

Major Legal Win Against Government

Recently, the institute's lawyers at the Knight First Amendment Institute, together with legal partners Sher Tremonte, achieved a significant legal win when a district court judge in Massachusetts ruled that the detention and attempted deportation of the student and additional activists was illegal and intentionally designed to suppress protest.

The Trump administration has said it will appeal the decision, with White House spokesperson a spokeswoman calling the judgment an "outrageous ruling that hampers the safety and security of our nation".

Growing Divide Between Organization and University

This decision elevated the visibility of the free speech center, propelling it to the forefront of the conflict with Trump over fundamental American values. Yet the victory also underscored the widening chasm between the institute and the university that houses it.

This legal challenge – described by the judge as "possibly the most important ever fall within the authority of this district court" – was the first of several opposing Trump's unusual attack on universities to reach court proceedings.

Trial Revelations

Throughout the court proceedings, citizen and noncitizen scholars testified about the climate of terror and self-censorship ushered in by the arrests, while immigration officials disclosed details about their dependence on reports by conservative, pro-Israel organizations to pick their targets.

Veena Dubal, chief lawyer of the American Association of University Professors, which filed the lawsuit along with some of its chapters and the Middle East Studies Association, described it "the central constitutional case of the current government currently".

'Institution and Organization Occupy Different Sides'

While the court victory was praised by supporters and scholars across the country, the director received no communication from Columbia following the decision – an indication of the tensions in the positions taken by the institute and the institution.

Prior to the administration began, Columbia had come to symbolize the shrinking space for pro-Palestinian speech on US campuses after it summoned officers to clear its student encampment, disciplined multiple activists for their activism and severely limited demonstrations on campus.

Institutional Agreement

This summer, the university reached a deal with the federal government to pay millions to resolve antisemitism claims and accept significant limitations on its independence in a action broadly criticized as "capitulation" to the president's bullying tactics.

Columbia's compliant stance was sharply contrasted with the Knight Institute's principled position.

"This is a moment in which the institution and the organization are on different sides of some of these fundamental issues," observed a former fellow at the Knight Institute.

Institute's Mission

This organization was launched in 2016 and is housed on the Columbia campus. It has received significant funding from the institution as part of an agreement that had both providing substantial amounts in operating funds 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 administration has overstepped boundaries and fundamental rights are at stake and few others are willing to take action and to declare, this must stop, that's when the Knight Institute that will taken action," said Lee Bollinger, a First Amendment scholar who established the center.

Open Disagreement

Shortly after recent events, Columbia and the the organization were positioned on opposing sides, with the institute frequently objecting to the institution's management of pro-Palestinian protests both privately and in progressively critical public statements.

In correspondence to university leadership, Jaffer criticized the decision to penalize campus organizations, which the university said had broken rules related to holding campus events.

Escalating Tensions

Later, the director further criticized the institution's choice to summon law enforcement onto campus to remove a peaceful, student protest – leading to the detention of numerous activists.

"The university's decisions have become separated from the values that are central to the university's life and purpose – such as free speech, academic freedom, and fair treatment," he wrote this time.

Student Perspective

The detained student, in particular, had appealed to campus officials for protection, and in an op-ed written from detention he wrote that "the logic used by the federal government to target myself and my peers is a direct extension of Columbia's repression approach regarding Palestinian issues".

The university reached agreement with the Trump administration shortly after the trial concluded in court.

Institute's Response

Following the agreement was revealed, the organization published a scathing rebuke, concluding that the agreement sanctions "an astonishing transfer of autonomy and authority to the government".

"Columbia's leaders ought not agreed to these terms," the statement said.

Broader Context

The institute has allies – organizations such as the ACLU, the free speech organization and additional civil liberties groups have opposed the government over free speech issues, as have labor organizations and Harvard University.

Nor is it concentrating solely on university matters – in additional lawsuits to the government, the institute has filed cases on behalf of agricultural workers and climate activists challenging government agencies over climate-related datasets and fought the withholding of official reports.

Unique Position

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

The director expressed sympathy for the lack of "good options" for university administration even as he described their agreement as a "serious mistake". But he stressed that although the institute positioned at the opposite end of its parent institution when it comes to dealing with the administration, the university has permitted it to operate free of pressure.

"Especially right now, I appreciate that freedom for granted," he stated. "If Columbia tried to limit our activities, I wouldn't remain at Columbia any longer."