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After federal agents arrested the university student a student activist in his university residence, Jameel Jaffer understood a major battle was coming.

The director heads a university-connected institute dedicated to defending free speech protections. The student, a green card holder, had been active in pro-Palestinian protests on campus. Months earlier, Jaffer's organization had organized a symposium about constitutional protections for immigrants.

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

Major Legal Win Challenging Administration

Recently, the institute's lawyers at the Knight First Amendment Institute, together with legal partners their co-counsel, achieved a landmark victory when a district court judge in Boston determined that the detention and attempted deportation of Khalil and additional activists was illegal and purposely created to suppress protest.

Government officials has said it will appeal the verdict, with administration representative Liz Huston calling the ruling an "unacceptable decision that undermines the safety and security of the country".

Increasing Separation Separating Organization and University

This decision raised the profile of the free speech center, catapulting it to the frontlines of the conflict with Trump over fundamental American values. However the victory also highlighted the widening chasm between the organization and the institution that houses it.

The case – described by the judge as "perhaps the most important to ever come under the authority of this court" – was the initial of multiple challenging Trump's unusual attack on higher education to go to trial.

Trial Revelations

During the court proceedings, academic experts testified about the climate of terror and self-censorship caused by the detentions, while immigration officials revealed details about their reliance on reports by conservative, Israel-supporting organizations to pick their targets.

A legal expert, chief lawyer 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 Trump administration currently".

'University and Institute Occupy Different Sides'

While the court victory was praised by advocates and academics across the country, the director heard nothing from university leadership following the ruling – an indication of the disagreements in the stances taken by the organization and the university.

Even before 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 student encampment, suspended dozens of students for their protests and dramatically restricted protests on campus.

Institutional Agreement

Recently, the university reached a deal with the federal government to provide substantial funds to settle antisemitism claims and accept significant limitations on its independence in a action broadly criticized as "capitulation" to the administration's bullying tactics.

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

"We're at a moment in which the institution and the organization hold opposing views of some of these critical questions," observed a former fellow at the Knight Institute.

Organization's Purpose

The Knight Institute was launched in recent years and is located on the Columbia campus. It has obtained significant funding from the institution as part of an arrangement that had both providing millions in operating funds and long-term financing to establish the center.

"Our vision for the institute in the long-term future is that when there is a time when the government has overstepped boundaries and constitutional protections are at stake and no one else are willing to take action and to declare, enough is enough, it will be the Knight Institute that will stepped forward," stated Lee Bollinger, a constitutional expert who helped create the institute.

Open Disagreement

Following campus developments, the university and the Knight Institute were positioned on different sides, with the institute regularly criticizing the university's handling of campus demonstrations both in private communications and in progressively critical official comments.

In correspondence to university leadership, Jaffer condemned the decision to penalize campus organizations, which the institution said had violated policies concerning organizing protests.

Growing Conflict

Later, the director further criticized the university's decision to call police onto campus to remove a peaceful, student protest – leading to the arrest of numerous activists.

"Institutional policies are disconnected from the values that are essential for the university's life and purpose – such as expression, academic freedom, and equality," he wrote in that instance.

Activist Viewpoint

Khalil, specifically, had pleaded with campus officials for support, and in a published article written from detention he stated that "the reasoning employed by the administration to single out me and fellow students is a direct extension of the university's suppression playbook concerning Palestine".

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

Institute's Response

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

"Columbia's leaders should not have accepted this," the statement stated.

Wider Impact

Knight has allies – organizations such as the civil liberties union, the Foundation for Individual Rights and additional civil liberties groups have challenged the government over free speech issues, as have labor organizations 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 farmers and climate activists challenging government agencies over climate-related information and fought the withholding of government documents.

Special Situation

But its defense of campus expression at a university now associated with compromising on it places it in a particularly difficult situation.

Jaffer expressed sympathy for the lack of "favorable choices" for Columbia's leaders while he characterized their agreement as a "major error". But he stressed that despite the institute positioned at the other side of its host when it comes to addressing the administration, the university has permitted it to function without interference.

"Particularly currently, I appreciate that freedom as automatic," he said. "If Columbia tried to limit our activities, I wouldn't be at the university any more."