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When federal agents arrested the university student a student activist in his university residence, Jameel Jaffer knew a major battle lay ahead.

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

"We felt this connection to the case, because we're part of the university," Jaffer explained. "We viewed this detention as a serious infringement of First Amendment rights."

Major Legal Win Against Government

Last week, Jaffer's team at the free speech organization, together with legal partners their co-counsel, secured a significant legal win when a district court judge in Boston determined that the detention and attempted deportation of the student and other pro-Palestinian students was unconstitutional and intentionally designed to suppress protest.

The Trump administration has said it will appeal the verdict, with White House spokesperson Liz Huston describing the ruling an "outrageous ruling that undermines the safety and security of our nation".

Growing Divide Between Institute and Institution

The ruling raised the profile of the free speech center, catapulting it to the frontlines of the battle with Trump over core constitutional principles. However the victory also highlighted the growing divide between the organization and the university that houses it.

This legal challenge – described by the judge as "possibly the most important ever fall within the jurisdiction of this district court" – was the first of several challenging the administration's unprecedented assault on universities to go to trial.

Trial Revelations

During the court proceedings, citizen and noncitizen scholars gave evidence about the atmosphere of fear and silencing ushered in by the arrests, while government agents revealed information about their reliance on dossiers by rightwing, Israel-supporting organizations to select individuals.

Veena Dubal, chief lawyer of the American Association of University Professors, which brought the case along with some of its chapters and the academic group, described it "the central civil rights case of the Trump administration currently".

'Institution and Institute Occupy Different Sides'

While the legal success was hailed by advocates and academics across the country, Jaffer received no communication from Columbia after the decision – a reflection of the disagreements in the stances taken by the institute and the institution.

Even before the administration began, the university had come to symbolize the shrinking space for Palestinian advocacy on American universities after it called police to clear its student encampment, disciplined dozens of students for their protests and severely limited demonstrations on campus.

Institutional Agreement

This summer, the university reached a deal with the Trump administration to provide substantial funds to settle discrimination allegations and accept major restrictions on its independence in a move widely condemned as "surrender" to the administration's bullying tactics.

The university's compliant stance was sharply contrasted with the organization's principled position.

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

Institute's Mission

The Knight Institute was established in recent years and is located on the university grounds. It has obtained significant funding from the university as part of an agreement that had both providing millions in program support and endowment funds to launch it.

"Our vision for the organization in the long-term future is that when there is a time when the administration has overstepped boundaries and constitutional protections are at stake and no one else are willing to take action and to declare, this must stop, it will be the this organization who will have taken action," said the former president, a First Amendment scholar who established the center.

Open Disagreement

Following campus developments, the university and the the organization found themselves on opposing sides, with Knight frequently objecting to the institution's management of pro-Palestinian protests both in private communications and in progressively critical official comments.

In one letter to university leadership, Jaffer criticized the action to suspend two student groups, which the university said had broken rules concerning organizing protests.

Growing Conflict

Later, Jaffer further criticized the university's decision to call police onto campus to remove a non-violent, student protest – resulting in the arrest of numerous activists.

"Institutional policies are disconnected from the values that are central to the academic community and mission – including expression, academic freedom, and fair treatment," he wrote this time.

Activist Viewpoint

Khalil, in particular, had appealed to university administrators for support, and in an op-ed written from detention he wrote that "the reasoning used by the administration to target me and my peers is a direct extension of Columbia's repression approach regarding Palestine".

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

Organization's Reaction

Shortly after the agreement was revealed, the Knight Institute published a strong criticism, stating that the settlement approves "an astonishing transfer of independence and control to the government".

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

Broader Context

Knight doesn't stand alone – organizations such as the civil liberties union, the Foundation for Individual Rights and other civil liberties groups have opposed the Trump administration over constitutional matters, as have unions and Harvard University.

The institute isn't concentrating solely on campus issues – in additional lawsuits to the Trump administration, the organization has sued on behalf of agricultural workers and climate activists challenging federal departments over climate-related datasets and fought the suppression of official reports.

Special Situation

But its defense of student speech at a university now synonymous with compromising on it places it in a particularly difficult situation.

The director showed understanding for the lack of "favorable choices" for Columbia's leaders even as he characterized their decision to settle as a "major error". But he stressed that although the organization standing at the opposite end of its parent institution when it comes to addressing the president, the institution has permitted it to operate without interference.

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