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When federal agents detained Columbia University student Mahmoud Khalil in his university residence, the institute director understood a significant fight was coming.

The director leads a university-connected center dedicated to defending free speech rights. The student, a permanent resident, had been involved in Palestinian solidarity encampments on campus. Months earlier, the institute had organized a conference about constitutional protections for immigrants.

"We recognized a direct link with this situation, because we're part of the university," Jaffer stated. "We viewed this detention as a serious infringement of constitutional freedoms."

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 federal judge in Massachusetts ruled that the detention and planned removal of the student and additional activists was illegal and intentionally designed to chill free speech.

The Trump administration announced they'll challenge the verdict, with administration representative Liz Huston describing the ruling an "outrageous ruling that undermines the safety and security of the country".

Increasing Separation Separating Institute and University

The ruling raised the profile of the free speech center, propelling it to the frontlines of the conflict with Trump over core constitutional principles. Yet the win also highlighted the growing divide between the institute and the university that hosts it.

This legal challenge – characterized by the presiding official as "possibly the significant to ever come under the jurisdiction of this district court" – was the initial of multiple challenging the administration's unusual attack on universities to go to trial.

Trial Revelations

Throughout the two-week trial, citizen and noncitizen scholars testified about the atmosphere of fear and self-censorship caused by the arrests, while government agents revealed information about their reliance on dossiers by conservative, pro-Israel organizations to pick their targets.

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, described it "the primary constitutional lawsuit of the current government this time around".

'Institution and Institute Occupy Different Sides'

Although the legal success was praised by supporters and academics nationwide, the director heard nothing from Columbia after the ruling – an indication of the tensions in the stances staked out by the institute and the institution.

Prior to the administration began, Columbia had represented the shrinking space for pro-Palestinian speech on American universities after it called police to remove its campus protest, suspended multiple activists for their activism and severely limited protests on campus.

Institutional Agreement

Recently, the university reached a deal with the federal government to pay millions to resolve discrimination allegations and submit to significant limitations on its independence in a move widely condemned as "capitulation" to the administration's pressure strategies.

The university's submissive approach was starkly at odds with the Knight Institute's defiant one.

"This is a moment in which the institution and the institute are on different sides of some of these fundamental issues," noted a former fellow at the free speech center.

Institute's Mission

This organization was established in recent years and is located on the Columbia campus. It has received significant funding from the institution as part of an agreement that had both providing millions in program support and endowment funds to establish the center.

"Our vision for the institute in the long-term future is that when there is a time when the administration has overstepped boundaries and constitutional protections are threatened and few others is prepared to take action and to declare, this must stop, that's when the Knight Institute who will have stepped forward," said Lee Bollinger, a constitutional expert who helped create the center.

Open Disagreement

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

In correspondence to university leadership, the director criticized the action to suspend campus organizations, which the university said had broken rules concerning holding campus events.

Escalating Tensions

Later, the director again condemned the university's decision to summon police onto campus to remove a peaceful, pro-Palestinian encampment – resulting in the arrest of numerous activists.

"The university's decisions are separated from the principles that are central to the university's life and purpose – such as expression, academic freedom, and fair treatment," he stated this time.

Student Perspective

Khalil, specifically, had appealed to campus officials for protection, and in a published article written from detention he wrote that "the reasoning used by the administration to target myself and fellow students is an outgrowth of Columbia's repression playbook regarding Palestine".

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

Institute's Response

Shortly after the agreement was announced, the Knight Institute published a strong criticism, stating that the agreement sanctions "an astonishing transfer of independence and authority to the administration".

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

Wider Impact

Knight has allies – organizations such as the ACLU, the free speech organization and additional civil liberties groups have challenged the government over constitutional matters, as have unions and Harvard University.

Nor is it concentrating solely on campus issues – in additional lawsuits to the government, the institute has filed cases on behalf of agricultural workers and climate activists challenging government agencies over climate-related information and fought the suppression of official reports.

Special Situation

However its protection of campus expression at a institution now synonymous with making concessions on it places it in a uniquely uneasy situation.

The director expressed sympathy for the absence of "good options" for Columbia's leaders while he described their decision to settle as a "serious mistake". But he stressed that although the organization positioned at the other side of its host when it comes to dealing with the president, the university has allowed it to operate free of pressure.

"Particularly currently, I appreciate this independence for granted," he stated. "If Columbia tried to limit our activities, I wouldn't remain at Columbia any longer."