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After federal agents arrested the university student Mahmoud Khalil in his university residence, the institute director knew a major battle was coming.

Jaffer leads a university-connected institute dedicated to defending First Amendment protections. The student, a permanent resident, had been active in pro-Palestinian encampments on campus. Previously, Jaffer's organization had organized a conference about free speech rights for noncitizens.

"We felt this connection with this situation, because we're part of the university," Jaffer explained. "We viewed this arrest as a major violation of First Amendment rights."

Landmark Victory Challenging Government

Last week, Jaffer's team at the Knight First Amendment Institute, together with the law firm their co-counsel, achieved a landmark victory when a district court judge in Boston ruled that the arrest and planned removal of the student and additional activists was unconstitutional and intentionally designed to chill free speech.

The Trump administration has said it will appeal the decision, with administration representative Liz Huston describing the judgment an "outrageous ruling that hampers the safety and security of the country".

Increasing Separation Between Organization and Institution

The ruling raised the visibility of the free speech center, propelling it to the frontlines of the conflict against Trump over core constitutional principles. Yet the victory also highlighted the growing divide between the organization and the university that hosts it.

This legal challenge – characterized by the judge as "perhaps the most important to ever come under the jurisdiction of this district court" – was the first of several challenging Trump's unprecedented assault on universities to reach court proceedings.

Court Testimony

Throughout the two-week trial, academic experts gave evidence about the climate of terror and self-censorship ushered in by the arrests, while immigration officials revealed information about their dependence on dossiers by conservative, Israel-supporting organizations to select individuals.

A legal expert, general counsel of the American Association of University Professors, which filed the lawsuit along with some of its chapters and the Middle East Studies Association, called it "the primary civil rights case of the current government currently".

'Institution and Organization Are On Opposing Positions'

Although the court victory was hailed by advocates and academics across the country, Jaffer heard nothing from university leadership after the ruling – an indication of the tensions in the positions staked out by the organization and the institution.

Even before Trump took office, Columbia had represented the shrinking space for Palestinian advocacy on American universities after it called police to clear its student encampment, suspended dozens of students for their activism and severely limited demonstrations on campus.

University Settlement

This summer, the university reached a deal with the Trump administration to pay millions to settle antisemitism claims and submit to major restrictions on its independence in a action widely condemned as "capitulation" to the administration's bullying tactics.

The university's compliant stance was starkly at odds with the Knight Institute's defiant one.

"We're at a time in which the institution and the institute are on different sides of these fundamental issues," noted Joel Simon at the free speech center.

Institute's Mission

The Knight Institute was launched in 2016 and is housed on the Columbia campus. It has received substantial support from the institution as part of an arrangement that had both providing millions in program support and long-term financing to launch it.

"Our vision for the organization in the long-term future is that when there is that moment when the government has overstepped boundaries and constitutional protections are threatened and few others is prepared to take action and to say, enough is enough, it will be the Knight Institute who will have taken action," said the former president, a First Amendment scholar who helped create the institute.

Public Criticism

Shortly after campus developments, the university and the Knight Institute were positioned on opposing sides, with the institute regularly criticizing the institution's management of pro-Palestinian protests both in private communications and in increasingly unforgiving public statements.

In correspondence to campus administration, the director criticized the action to penalize two student groups, which the institution said had broken rules concerning holding campus events.

Escalating Tensions

Subsequently, the director again condemned the institution's choice to call law enforcement onto campus to remove a peaceful, student protest – leading to the arrest of numerous activists.

"Institutional policies have become disconnected from the values that are essential for the academic community and purpose – including expression, scholarly independence, and equality," he wrote in that instance.

Student Perspective

The detained student, specifically, had pleaded with university administrators for support, and in a published article composed while jailed he stated that "the logic used by the federal government to single out me and fellow students is an outgrowth of the university's suppression approach regarding Palestinian issues".

The university reached agreement with the Trump administration just days after the case wrapped in court.

Organization's Reaction

Following the deal was revealed, the organization published a scathing rebuke, stating that the settlement approves "a remarkable shift of independence and control to the administration".

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

Wider Impact

Knight has allies – organizations such as the ACLU, the Foundation for Individual Rights and other rights organizations have challenged the government over free speech issues, as have unions and other institutions.

The institute isn't exclusively focusing on campus issues – in additional lawsuits to the government, the organization has filed cases on behalf of agricultural workers and climate activists opposing government agencies over climate-related datasets and fought the withholding of official reports.

Unique Position

But its protection of student speech at a institution now synonymous with making concessions on it puts it in a uniquely uneasy situation.

The director showed understanding for the lack of "good options" for university administration while he described their decision to settle as a "major error". But he stressed that despite the institute standing at the opposite end of its parent institution when it comes to dealing with the president, the institution has permitted it to operate 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 remain at Columbia any more."