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When federal agents arrested the university student Mahmoud Khalil in his university residence, the institute director understood a significant fight lay ahead.

Jaffer heads a Columbia-affiliated center dedicated to protecting free speech rights. The student, a green card holder, had been involved in pro-Palestinian protests on campus. Previously, Jaffer's organization had organized a conference about free speech rights for immigrants.

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

Major Legal Win Challenging Government

Recently, the institute's lawyers at the Knight First Amendment Institute, together with the law firm their co-counsel, secured a landmark victory when a federal judge in Boston ruled that the arrest and planned removal of Khalil and other pro-Palestinian students was illegal and intentionally designed to suppress protest.

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

Growing Divide Between Organization and Institution

This decision elevated the profile of the free speech center, propelling it to the forefront of the conflict against Trump over fundamental American values. However the victory also underscored the growing divide between the organization and the university that hosts it.

This legal challenge – described by the presiding official as "perhaps the significant to ever fall within the jurisdiction of this district court" – was the first of multiple opposing the administration's unprecedented assault on higher education to go to trial.

Trial Revelations

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 dependence on reports by conservative, Israel-supporting groups to select individuals.

A legal expert, chief lawyer of the American Association of University Professors, which filed the lawsuit along with local branches and the Middle East Studies Association, called it "the central civil rights case of the Trump administration currently".

'Institution and Organization Occupy Different Sides'

While the court victory was praised by supporters and academics across the country, Jaffer heard nothing from Columbia following the decision – an indication of the tensions in the stances taken by the organization and the institution.

Prior to the administration began, the university had represented the shrinking space for Palestinian advocacy on American universities after it summoned officers to remove its student encampment, disciplined dozens of students for their protests and dramatically restricted protests on campus.

University Settlement

Recently, the university reached a deal with the Trump administration to provide substantial funds to resolve antisemitism claims and accept major restrictions on its autonomy in a action broadly criticized as "surrender" to the administration's pressure strategies.

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

"We're at a moment in which the institution and the organization are on different sides of these fundamental issues," noted a former fellow at the Knight Institute.

Organization's Purpose

The Knight Institute was launched in 2016 and is located on the university grounds. It has obtained significant funding from the university as part of an arrangement 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 that moment when the administration has gone in the wrong direction and constitutional protections are threatened and few others are willing to take action and to declare, enough is enough, it will be the Knight Institute that will taken action," stated Lee Bollinger, a constitutional expert who established the center.

Open Disagreement

Following campus developments, Columbia and the Knight Institute were positioned on different sides, with the institute frequently objecting to the university's handling of campus demonstrations both in private communications and in increasingly unforgiving public statements.

In one letter to campus administration, Jaffer condemned the action to suspend campus organizations, which the university said had broken rules concerning organizing protests.

Escalating Tensions

Subsequently, Jaffer further criticized the university's decision to summon law enforcement onto campus to remove a non-violent, student protest – leading to the detention of more than 100 students.

"The university's decisions have become separated from the principles that are essential for the academic community and mission – including free speech, scholarly independence, and equality," he stated this time.

Student Perspective

The detained student, in particular, had pleaded with university administrators for support, and in an op-ed composed while jailed he wrote that "the reasoning used by the federal government to single out me and fellow students is a direct extension of Columbia's repression approach regarding Palestine".

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

Institute's Response

Shortly after the deal was announced, the Knight Institute published a strong criticism, concluding that the agreement approves "a remarkable shift of independence and control to the government".

"University administration should not have accepted these terms," the statement stated.

Wider Impact

The institute doesn't stand alone – groups such as the civil liberties union, the free speech organization and other rights organizations have opposed the Trump administration over constitutional matters, as have labor organizations and other institutions.

Nor is it exclusively focusing on university matters – in other challenges to the government, the organization has filed cases on behalf of farmers and climate activists challenging federal departments over climate-related datasets and challenged the withholding of official reports.

Special Situation

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

The director showed understanding for the lack of "favorable choices" for university administration even as he characterized their decision to settle as a "serious mistake". But he emphasized that although the institute standing at the opposite end of its parent institution when it comes to addressing the administration, the institution has permitted it to function without interference.

"Particularly currently, I don't take that freedom as automatic," he stated. "Should the university attempt to restrict our work, I wouldn't be at Columbia any longer."