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When federal agents arrested Columbia University student a student activist in his university residence, Jameel Jaffer understood a major battle lay ahead.

The director heads a Columbia-affiliated center focused on protecting First Amendment protections. The student, a permanent resident, had been active in pro-Palestinian protests on campus. Months earlier, Jaffer's organization had hosted a symposium about constitutional protections for immigrants.

"We felt this connection with this situation, because we're part of the university," Jaffer stated. "We viewed this arrest as a major violation of constitutional freedoms."

Landmark Victory Challenging Government

Last week, Jaffer's team at the free speech organization, together with the law firm Sher Tremonte, secured a landmark victory when a district court judge in Boston determined that the arrest and attempted deportation of the student and additional activists was illegal and intentionally designed to chill free speech.

Government officials has said it will appeal the decision, with administration representative a spokeswoman calling the judgment an "unacceptable decision that hampers the protection of the country".

Growing Divide Separating Organization and Institution

This decision elevated the profile of the Knight Institute, catapulting it to the forefront of the battle against Trump over core constitutional principles. Yet the win also highlighted the growing divide between the organization and the institution that hosts it.

This legal challenge – characterized by the presiding official as "perhaps the most important ever fall within the authority of this district court" – was the initial of multiple opposing the administration's unusual attack on universities to go to trial.

Court Testimony

Throughout the court proceedings, citizen and noncitizen scholars gave evidence about the atmosphere of fear and silencing caused by the arrests, while immigration officials disclosed details about their dependence on reports by conservative, pro-Israel groups to pick their targets.

Veena Dubal, general counsel of the academic organization, which filed the lawsuit along with local branches and the Middle East Studies Association, called it "the central civil rights lawsuit of the current government currently".

'University and Institute Occupy Opposing Positions'

Although the court victory was praised by advocates and scholars nationwide, the director received no communication from university leadership following the decision – a reflection of the disagreements in the stances staked out by the organization and the institution.

Prior to the administration began, Columbia had represented the declining tolerance for Palestinian advocacy on US campuses after it summoned officers to remove its campus protest, disciplined multiple activists for their activism and severely limited protests on campus.

Institutional Agreement

Recently, the institution reached a deal with the federal government to provide substantial funds to settle antisemitism claims and accept major restrictions on its independence in a action widely condemned as "capitulation" to the president's bullying tactics.

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

"This is a time in which the university and the organization are on different sides of some of these critical questions," observed a former fellow at the Knight Institute.

Institute's Mission

This organization was established in recent years and is housed on the Columbia campus. It has received substantial support from the institution as part of an agreement that had each contributing substantial amounts in operating funds 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 government has overstepped boundaries and fundamental rights are at stake and no one else are willing to step forward and to declare, enough is enough, that's when the Knight Institute who will have stepped forward," stated the former president, a constitutional expert who helped create the institute.

Open Disagreement

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

In one letter to campus administration, Jaffer condemned the action to suspend two student groups, which the institution said had violated policies concerning holding campus events.

Growing Conflict

Subsequently, the director again condemned the institution's choice to call law enforcement onto campus to clear a peaceful, student protest – leading to the detention of more than 100 students.

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

Activist Viewpoint

Khalil, specifically, had appealed to university administrators for protection, and in an op-ed written from detention he wrote that "the reasoning employed by the federal government to single out myself and my peers is a direct extension of Columbia's repression playbook concerning Palestinian issues".

Columbia settled with the federal government just days after the trial concluded in court.

Institute's Response

Shortly after the deal was revealed, the Knight Institute published a scathing rebuke, stating that the agreement approves "an astonishing transfer of autonomy and authority to the government".

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

Wider Impact

The institute doesn't stand alone – groups such as the ACLU, the free speech organization and additional civil liberties groups have opposed the government over constitutional matters, as have unions and other institutions.

The institute isn't exclusively focusing on university matters – in additional lawsuits to the Trump administration, the institute has sued on behalf of farmers and climate activists opposing government agencies over climate-related information and challenged the withholding of official reports.

Unique Position

But its defense of student speech at a university now associated with making concessions on it places it in a particularly difficult situation.

The director showed understanding for the lack of "favorable choices" for university administration even as he characterized their agreement as a "major error". But he emphasized that although the institute standing at the other side of its host when it comes to addressing the administration, the university has permitted it to operate without interference.

"Particularly currently, I appreciate this independence as automatic," he said. "If Columbia tried to limit our activities, I wouldn't remain at the university any longer."