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After federal agents detained the university student Mahmoud Khalil in his university residence, the institute director knew a major battle lay ahead.

The director leads a Columbia-affiliated center focused on defending First Amendment protections. Khalil, a permanent resident, had been involved in pro-Palestinian encampments on campus. Months earlier, Jaffer's organization had organized a symposium about free speech rights 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 constitutional freedoms."

Landmark Victory Challenging Administration

Last week, Jaffer's team at the Knight First Amendment Institute, along with legal partners their co-counsel, achieved a significant legal win when a federal judge in Massachusetts determined that the arrest and planned removal of Khalil and other pro-Palestinian students was illegal and purposely created to chill free speech.

Government officials has said it will appeal the decision, with White House spokesperson a spokeswoman describing the judgment an "outrageous ruling that hampers the protection of the country".

Growing Divide Separating Organization and Institution

The ruling elevated the profile of the Knight Institute, propelling it to the frontlines of the conflict against Trump over core constitutional principles. Yet the victory also highlighted the growing divide between the institute and the institution that hosts it.

This legal challenge – described by the judge as "perhaps the most important to ever fall within the jurisdiction of this court" – was the first of multiple challenging the administration's unprecedented assault on universities to reach court proceedings.

Court Testimony

Throughout the two-week trial, citizen and noncitizen scholars gave evidence about the climate of terror and silencing caused by the arrests, while immigration officials disclosed information about their reliance on reports by conservative, pro-Israel organizations to pick their targets.

Veena Dubal, chief lawyer of the academic organization, which filed the lawsuit along with local branches and the Middle East Studies Association, called it "the primary constitutional lawsuit of the current government this time around".

'Institution and Institute Are On Opposing Positions'

Although the court victory was hailed by supporters and academics across the country, Jaffer heard nothing from Columbia after the decision – a reflection of the disagreements in the positions taken by the organization and the institution.

Prior to the administration began, Columbia had come to symbolize the declining tolerance for pro-Palestinian speech on US campuses 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 university negotiated an agreement with the federal government to pay millions to settle antisemitism claims and submit to significant limitations on its independence in a move broadly criticized as "capitulation" to the administration's bullying tactics.

The university's submissive approach was sharply contrasted with the organization's defiant one.

"We're at a time in which the institution and the organization hold opposing views of these critical questions," noted a former fellow at the Knight Institute.

Organization's Purpose

This organization was launched in 2016 and is located on the university grounds. It has received substantial support from the university as part of an agreement that had both providing substantial amounts in program support and long-term financing to establish the center.

"My hope for the institute in the years ahead is that when there is that moment when the government has overstepped boundaries and constitutional protections are at stake and no one else are willing to take action and to say, this must stop, it will be the this organization that will stepped forward," said the former president, a First Amendment scholar who established the institute.

Public Criticism

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

In correspondence to university leadership, Jaffer condemned the decision to penalize two student groups, which the institution said had violated policies concerning holding campus events.

Escalating Tensions

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

"Institutional policies have become disconnected from the values that are essential for the university's life and mission – such as free speech, scholarly independence, and fair treatment," he wrote in that instance.

Activist Viewpoint

Khalil, in particular, had appealed to university administrators for protection, and in an op-ed written from detention he stated that "the reasoning employed by the administration to single out myself and fellow students is a direct extension of Columbia's repression playbook concerning Palestinian issues".

Columbia settled with the federal government just days after the trial concluded in court.

Organization's Reaction

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

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

Broader Context

The institute doesn't stand alone – groups such as the ACLU, the free speech organization and other rights organizations have opposed the government over free speech issues, as have labor organizations and other institutions.

The institute isn't concentrating solely on university matters – in other challenges to the government, the institute has sued on behalf of agricultural workers and environmental advocates opposing federal departments over environmental information and challenged the withholding of official reports.

Unique Position

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

The director expressed sympathy for the lack of "favorable choices" for university administration even as he characterized their decision to settle as a "major error". But he emphasized that although the organization positioned at the other side of its host when it comes to addressing the administration, the institution has allowed it to function without interference.

"Particularly currently, I don't take this independence as automatic," he said. "Should the university attempt to limit our activities, I wouldn't be at the university any longer."