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

The director leads a Columbia-affiliated institute focused on protecting First Amendment protections. Khalil, a green card holder, had been involved in Palestinian solidarity protests on campus. Previously, the institute had hosted a symposium about constitutional protections for immigrants.

"We recognized this connection with this situation, since we're part of the university," Jaffer explained. "We viewed this detention as a major violation of constitutional freedoms."

Landmark Victory Against Government

Last week, the institute's lawyers at the free speech organization, along with the law firm Sher Tremonte, achieved a significant legal win when a district court judge in Massachusetts determined that the arrest and attempted deportation of the student and additional activists was unconstitutional and purposely created to suppress protest.

The Trump administration announced it will appeal the verdict, with administration representative Liz Huston describing the judgment an "unacceptable decision that undermines the safety and security of the country".

Growing Divide Between Institute and Institution

This decision elevated the visibility of the Knight Institute, propelling it to the frontlines of the battle against Trump over fundamental American values. Yet the victory also highlighted the growing divide between the institute and the university that hosts it.

The case – characterized by the presiding official as "perhaps the significant to ever come under the authority of this court" – was the initial of multiple opposing Trump's unprecedented assault on universities to reach court proceedings.

Trial Revelations

Throughout the two-week trial, citizen and noncitizen scholars gave evidence about the climate of terror and silencing caused by the detentions, while government agents disclosed details about their reliance on dossiers by conservative, Israel-supporting organizations to pick their targets.

Veena Dubal, chief lawyer of the academic organization, which brought the case along with local branches and the Middle East Studies Association, called it "the central civil rights case of the current government currently".

'Institution and Organization Occupy Opposing Positions'

Although the court victory was hailed by supporters and scholars nationwide, Jaffer heard nothing from Columbia following the decision – a reflection of the disagreements in the positions taken by the institute and the university.

Prior to Trump took office, the university had represented the declining tolerance for pro-Palestinian speech on US campuses after it summoned officers to remove its student encampment, suspended multiple activists for their protests and severely limited protests on campus.

University Settlement

Recently, the institution reached a deal with the federal government to pay millions to resolve discrimination allegations and accept major restrictions on its independence in a move widely condemned as "surrender" to the administration's pressure strategies.

The university's submissive approach was starkly at odds with the Knight Institute's principled position.

"We're at a moment in which the university and the organization are on different sides of these critical questions," observed a former fellow at the free speech center.

Organization's Purpose

This organization was established in recent years and is located on the Columbia campus. It has obtained substantial support from the institution as part of an agreement that had each contributing substantial amounts in program support and long-term financing to establish the center.

"Our vision for the institute in the long-term future is that when there is that moment when the administration has gone in the wrong direction and constitutional protections are at stake and no one else is prepared to step forward and to say, this must stop, that's when the Knight Institute who will have stepped forward," stated the former president, a constitutional expert who helped create the center.

Open Disagreement

Following recent events, Columbia and the the organization were positioned on opposing sides, with Knight frequently objecting to the university's handling of pro-Palestinian protests both in private communications and in increasingly unforgiving official comments.

In correspondence to campus administration, the director condemned the decision to penalize campus organizations, which the institution said had violated policies concerning organizing protests.

Escalating Tensions

Subsequently, the director further criticized the university's decision to call police onto campus to remove a peaceful, pro-Palestinian encampment – leading to the detention of numerous activists.

"Institutional policies have become disconnected from the principles that are essential for the academic community and purpose – such as expression, academic freedom, and equality," he wrote in that instance.

Student Perspective

Khalil, in particular, had appealed to campus officials for protection, and in a published article written from detention he wrote that "the logic used by the federal government to target me and fellow students 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 agreement was announced, the organization published a scathing rebuke, stating that the settlement approves "a remarkable shift of independence and authority to the government".

"University administration should not have agreed to these terms," the declaration said.

Wider Impact

The institute has allies – groups such as the civil liberties union, the free speech organization and additional civil liberties groups have opposed the Trump administration over free speech issues, as have unions and other institutions.

The institute isn't concentrating solely on university matters – in other challenges to the Trump administration, the institute has sued on behalf of farmers and environmental advocates opposing government agencies over climate-related information and fought the suppression of government documents.

Unique Position

However its defense of student speech at a university now associated with compromising on it puts it in a uniquely uneasy position.

The director expressed sympathy for the lack of "favorable choices" for university administration while he characterized their agreement as a "major error". But he stressed that despite the organization positioned at the opposite end of its parent institution when it comes to dealing with the administration, the university has allowed it to function free of pressure.

"Especially right now, I appreciate that freedom for granted," he said. "Should the university attempt to limit our activities, I wouldn't be at Columbia any more."