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After federal agents detained the university student Mahmoud Khalil in his campus housing, the institute director understood a major battle lay ahead.

The director heads a university-connected center focused on protecting free speech rights. The student, a permanent resident, had been involved in pro-Palestinian encampments on campus. Months earlier, Jaffer's organization had organized a symposium about constitutional protections for noncitizens.

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

Major Legal Win Challenging Government

Recently, Jaffer's team at the free speech organization, together with the law firm Sher Tremonte, secured a landmark victory when a federal judge in Massachusetts ruled that the detention and attempted deportation of Khalil and other pro-Palestinian students was unconstitutional and intentionally designed to chill free speech.

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

Increasing Separation Separating Institute and University

The ruling elevated the visibility of the free speech center, catapulting it to the frontlines of the battle against the administration over fundamental American values. However the win also underscored the widening chasm between the institute and the university that hosts it.

The case – described by the judge as "possibly the significant to ever fall within the authority of this district court" – was the first of several opposing Trump's unprecedented assault on universities to reach court proceedings.

Trial Revelations

Throughout the two-week trial, academic experts testified about the climate of terror and silencing ushered in by the detentions, while government agents disclosed information about their reliance on dossiers by rightwing, pro-Israel organizations to pick their targets.

A legal expert, general counsel of the academic organization, which filed the lawsuit along with some of its chapters and the Middle East Studies Association, described it "the central constitutional case of the current government currently".

'Institution and Organization Occupy Opposing Positions'

Although the legal success was praised by advocates and scholars nationwide, the director received no communication from university leadership after the decision – an indication of the tensions in the stances taken by the institute and the university.

Prior to Trump took office, the university had represented the declining tolerance for Palestinian advocacy on American universities after it summoned officers to remove its student encampment, disciplined multiple activists for their activism and severely limited demonstrations on campus.

University Settlement

Recently, the university negotiated an agreement with the Trump administration to pay millions to settle discrimination allegations and accept significant limitations on its autonomy in a action broadly criticized as "surrender" to the administration's pressure strategies.

The university's compliant stance was starkly at odds with the Knight Institute's principled position.

"This is a moment in which the university and the institute hold opposing views of these critical questions," observed a former fellow at the Knight Institute.

Organization's Purpose

The Knight Institute was established in 2016 and is located on the Columbia campus. It has received substantial support from the university as part of an arrangement that had both providing substantial amounts in operating funds and endowment funds to launch it.

"My hope for the institute in the years ahead is that when there is that moment when the administration has overstepped boundaries and fundamental rights are at stake and few others is prepared to take action and to declare, enough is enough, that's when the Knight Institute who will have stepped forward," stated the former president, a First Amendment scholar who helped create the center.

Open Disagreement

Following recent events, Columbia and the the organization found themselves on opposing sides, with Knight regularly criticizing the institution's management of campus demonstrations both in private communications and in increasingly unforgiving public statements.

In one letter to university leadership, the director condemned the decision to suspend campus organizations, which the university said had violated policies concerning organizing protests.

Escalating Tensions

Later, the director again condemned the university's decision to call law enforcement onto campus to remove a non-violent, student protest – resulting in the arrest of more than 100 students.

"Institutional policies are separated from the values that are essential for the university's life and purpose – including expression, academic freedom, and fair treatment," he wrote in that instance.

Student Perspective

Khalil, in particular, had appealed to campus officials for support, and in a published article composed while jailed he wrote that "the logic employed by the federal government to single out me and fellow students is a direct extension of the university's suppression approach regarding Palestinian issues".

Columbia settled with the Trump administration just days after the trial concluded in court.

Organization's Reaction

Shortly after the agreement was announced, the organization published a strong criticism, concluding that the settlement approves "a remarkable shift of independence and authority to the government".

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

Broader Context

The institute doesn't stand alone – groups such as the ACLU, the Foundation for Individual Rights and additional civil liberties groups have opposed the government over constitutional matters, as have unions and Harvard University.

The institute isn't exclusively focusing on campus issues – in additional lawsuits to the Trump administration, the organization has sued on behalf of agricultural workers and climate activists challenging government agencies over environmental information and challenged the withholding of official reports.

Unique Position

However its defense of student speech at a university now associated with making concessions on it puts it in a particularly difficult position.

The director showed understanding for the lack of "favorable choices" for Columbia's leaders even as he characterized their agreement as a "serious mistake". But he stressed that despite the institute positioned at the other side of its parent institution when it comes to addressing the president, the university has allowed it to operate without interference.

"Particularly currently, I appreciate this independence for granted," he said. "If Columbia tried to restrict our work, I wouldn't remain at the university any more."