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When federal agents detained the university student a student activist in his campus housing, the institute director knew a major battle lay ahead.

Jaffer heads a Columbia-affiliated institute focused on defending free speech protections. Khalil, a permanent resident, had been active in Palestinian solidarity encampments on campus. Previously, the institute had hosted a symposium about free speech rights for noncitizens.

"We recognized a direct link with this situation, because we're part of the university," Jaffer explained. "And we saw this arrest as a serious infringement of constitutional freedoms."

Major Legal Win Against Administration

Last week, Jaffer's team at the Knight First Amendment Institute, along with the law firm Sher Tremonte, secured a landmark victory when a federal judge in Boston ruled that the detention and planned removal of Khalil and additional activists was unconstitutional and intentionally designed to chill free speech.

The Trump administration has said they'll challenge the verdict, with administration representative a spokeswoman describing the judgment an "outrageous ruling that undermines the protection of our nation".

Increasing Separation Separating Institute and University

This decision raised the visibility of the Knight Institute, catapulting it to the frontlines of the conflict with the administration over fundamental American values. However the win also highlighted the widening chasm between the organization and the institution that houses it.

This legal challenge – characterized by the presiding official as "perhaps the significant to ever come under the jurisdiction of this court" – was the initial of multiple challenging the administration's unprecedented assault on higher education to go to trial.

Trial Revelations

During the two-week trial, citizen and noncitizen scholars testified about the atmosphere of fear and self-censorship caused by the arrests, while government agents disclosed information about their dependence on reports by rightwing, pro-Israel organizations to pick their targets.

Veena Dubal, general counsel of the academic organization, which brought the case along with local branches and the Middle East Studies Association, described it "the primary civil rights lawsuit of the Trump administration currently".

'Institution and Organization Are On Different Sides'

Although the legal success was hailed by advocates and academics across the country, Jaffer received no communication from Columbia after the decision – an indication of the disagreements in the positions staked out by the institute and the university.

Prior to Trump took office, the university had represented the declining tolerance for Palestinian advocacy on US campuses after it called police to remove its campus protest, suspended dozens of students for their activism and severely limited demonstrations on campus.

University Settlement

Recently, the institution negotiated an agreement with the Trump administration to provide substantial funds to settle discrimination allegations and submit to significant limitations on its autonomy in a action broadly criticized as "surrender" to the administration's bullying tactics.

The university's compliant stance was sharply contrasted with the organization's defiant one.

"This is a moment in which the institution and the organization are on different sides of these critical questions," observed Joel Simon at the Knight Institute.

Organization's Purpose

This organization was launched in 2016 and is housed on the university grounds. It has obtained significant funding from the university as part of an arrangement that had each contributing millions in operating funds and endowment funds to launch it.

"Our vision for the organization in the years ahead is that when there is that moment when the government has overstepped boundaries and constitutional protections are threatened and no one else are willing to take action and to say, enough is enough, that's when the Knight Institute that will taken action," stated Lee Bollinger, a First Amendment scholar who established the center.

Public Criticism

Following campus developments, Columbia and the the organization found themselves on opposing sides, with the institute regularly criticizing the university's handling of pro-Palestinian protests both privately and in progressively critical public statements.

In one letter to university leadership, the director condemned the decision to suspend campus organizations, which the institution said had broken rules concerning holding campus events.

Growing Conflict

Subsequently, Jaffer again condemned the institution's choice to summon police onto campus to remove a non-violent, student protest – leading to the arrest of numerous activists.

"The university's decisions are disconnected from the principles that are essential for the academic community and mission – including free speech, scholarly independence, and fair treatment," he wrote in that instance.

Activist Viewpoint

Khalil, in particular, had pleaded with campus officials for support, and in a published article composed while jailed he wrote that "the logic employed by the administration to target myself and my peers is an outgrowth of the university's suppression playbook regarding Palestine".

The university reached agreement with the Trump administration shortly after the trial concluded in court.

Organization's Reaction

Shortly after the agreement was announced, the organization published a scathing rebuke, concluding that the settlement sanctions "a remarkable shift of autonomy and authority to the government".

"Columbia's leaders ought not agreed to these terms," the statement stated.

Broader Context

Knight has allies – groups such as the ACLU, the Foundation for Individual Rights and other rights organizations have opposed the government over constitutional matters, as have unions and other institutions.

Nor is it concentrating solely on campus issues – in additional lawsuits to the Trump administration, the organization has sued on behalf of farmers and environmental advocates opposing federal departments over climate-related datasets and fought the withholding of official reports.

Unique Position

But its protection of student speech at a university now synonymous with making concessions on it puts it in a particularly difficult situation.

The director showed understanding for the lack of "good options" for Columbia's leaders even as he described their agreement as a "major error". But he stressed that although the institute standing at the other side of its parent institution when it comes to addressing the president, the institution has allowed it to function free of pressure.

"Especially right now, I don't take this independence for granted," he said. "Should the university attempt to restrict our work, I wouldn't be at the university any more."