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

The director leads a university-connected center focused on defending free speech protections. Khalil, a permanent resident, had been active in pro-Palestinian encampments on campus. Months earlier, Jaffer's organization had organized a conference about free speech rights for noncitizens.

"We felt a direct link with this situation, since we're at Columbia," Jaffer explained. "And we saw this arrest as a serious infringement of First Amendment rights."

Major Legal Win Against Administration

Recently, the institute's lawyers at the free speech organization, together with the law firm Sher Tremonte, achieved a landmark victory when a federal judge in Massachusetts ruled that the detention and planned removal of Khalil and additional activists was unconstitutional and intentionally designed to suppress protest.

The Trump administration has said it will appeal the verdict, with White House spokesperson a spokeswoman describing the ruling an "unacceptable decision that undermines the protection of the country".

Growing Divide Separating Organization and Institution

This decision elevated the visibility of the Knight Institute, propelling it to the frontlines of the conflict against Trump over fundamental American values. However the victory also underscored the widening chasm between the institute and the university that houses it.

The case – described by the judge as "possibly the most important to ever fall within the jurisdiction of this district court" – was the initial of several opposing Trump's unprecedented assault on higher education to reach court proceedings.

Court Testimony

Throughout the court proceedings, academic experts gave evidence about the climate of terror and self-censorship caused by the detentions, while immigration officials revealed details about their dependence on reports by conservative, pro-Israel organizations to pick their targets.

Veena Dubal, general counsel of the academic organization, which brought the case together with some of its chapters and the Middle East Studies Association, described it "the primary constitutional case of the Trump administration this time around".

'University and Institute Occupy Opposing Positions'

Although the court victory was hailed by advocates and scholars across the country, Jaffer received no communication from university leadership after the ruling – a reflection of the disagreements in the positions taken by the institute and the university.

Prior to the administration began, the university had come to symbolize the shrinking space for pro-Palestinian speech on American universities after it called police to clear its campus protest, disciplined multiple activists for their protests and severely limited protests on campus.

Institutional Agreement

Recently, the institution reached a deal with the Trump administration to pay millions to resolve antisemitism claims and submit to major restrictions on its autonomy in a action widely condemned as "capitulation" to the administration's bullying tactics.

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

"This is a moment in which the institution and the institute hold opposing views of these fundamental issues," observed a former fellow at the Knight Institute.

Organization's Purpose

The Knight Institute was established in 2016 and is housed on the Columbia campus. It has received significant funding from the university as part of an arrangement that had each contributing millions in operating funds and long-term financing to launch it.

"Our vision for the institute in the long-term future is that when there is that moment when the administration has overstepped boundaries and fundamental rights are threatened and no one else is prepared to take action and to say, enough is enough, it will be the Knight Institute that will taken action," stated the former president, a First Amendment scholar who established the institute.

Public Criticism

Following recent events, the university and the the organization found themselves on different sides, with the institute frequently objecting to the institution's management of campus demonstrations both privately and in progressively critical public statements.

In correspondence to university leadership, Jaffer criticized the action to suspend campus organizations, which the institution said had violated policies related to holding campus events.

Escalating Tensions

Later, Jaffer further criticized the university's decision to summon police onto campus to remove a non-violent, student protest – resulting in the arrest of more than 100 students.

"Institutional policies are separated from the principles that are essential for the university's life and purpose – including free speech, scholarly independence, and fair treatment," he wrote this time.

Activist Viewpoint

The detained student, in particular, had pleaded with university administrators for support, and in an op-ed composed while jailed he wrote that "the logic employed by the administration to target myself and fellow students is an outgrowth of Columbia's repression playbook concerning Palestinian issues".

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

Institute's Response

Shortly after the agreement was announced, the organization published a scathing rebuke, stating that the settlement sanctions "an astonishing transfer of independence and control to the government".

"University administration should not have agreed to this," the statement said.

Wider Impact

The institute has allies – groups such as the ACLU, the Foundation for Individual Rights and other civil liberties groups have challenged the government over free speech issues, as have unions and Harvard University.

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

Special Situation

But its protection of campus expression at a university now associated with making concessions on it places it in a uniquely uneasy situation.

Jaffer expressed sympathy for the absence of "good options" for Columbia's leaders while he characterized their decision to settle as a "serious mistake". But he emphasized that despite the organization positioned at the opposite end of its parent institution when it comes to dealing with the president, the institution has allowed it to function free of pressure.

"Especially right now, I appreciate this independence for granted," he stated. "Should the university attempt to restrict our work, I wouldn't remain at the university any longer."