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After federal agents detained Columbia University student a student activist in his university residence, Jameel Jaffer understood a major battle was coming.

Jaffer leads a university-connected institute dedicated to defending free speech protections. Khalil, a permanent resident, had been active in Palestinian solidarity protests on campus. Previously, Jaffer's organization had hosted a conference about free speech rights for immigrants.

"We recognized a direct link to the case, because we're part of the university," Jaffer explained. "We viewed this arrest as a serious infringement of constitutional freedoms."

Landmark Victory Challenging Government

Recently, Jaffer's team at the free speech organization, along with legal partners Sher Tremonte, achieved a significant legal win when a district court judge in Boston determined that the arrest and planned removal of Khalil and additional activists was unconstitutional and purposely created to chill free speech.

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

Increasing Separation Between Institute and University

The ruling raised the profile of the free speech center, propelling it to the forefront of the battle against the administration over core constitutional principles. However the win also highlighted the growing divide between the organization and the institution that houses it.

The case – described by the presiding official as "perhaps the significant to ever come under the authority of this district court" – was the first of multiple opposing the administration's unprecedented assault on higher education to reach court proceedings.

Court Testimony

Throughout the two-week trial, academic experts testified about the atmosphere of fear and self-censorship caused by the detentions, while immigration officials disclosed details about their dependence on dossiers by rightwing, pro-Israel groups to pick their targets.

A legal expert, general counsel of the academic organization, which brought the case along with local branches and the academic group, described it "the central constitutional case of the Trump administration currently".

'Institution and Organization Are On Different Sides'

While the court victory was praised by advocates and scholars across the country, Jaffer heard nothing from university leadership after the ruling – an indication of the disagreements in the stances staked out by the organization and the university.

Even before Trump took office, the university had represented the shrinking space for Palestinian advocacy on US campuses after it summoned officers to remove its campus protest, disciplined multiple activists for their protests and severely limited demonstrations on campus.

Institutional Agreement

This summer, the university reached a deal with the federal government to provide substantial funds to resolve antisemitism claims and accept major restrictions on its independence in a action widely condemned as "surrender" to the administration's pressure strategies.

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

"We're at a time in which the institution and the organization are on different sides of some of these critical questions," noted Joel Simon at the Knight Institute.

Organization's Purpose

This organization was established in recent years and is located on the university grounds. 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 launch it.

"My hope for the organization in the long-term future is that when there is that moment when the administration has overstepped boundaries and fundamental rights are at stake and no one else are willing to step forward and to declare, enough is enough, it will be the this organization who will have stepped forward," said Lee Bollinger, a First Amendment scholar who established the center.

Public Criticism

Shortly after campus developments, Columbia and the the organization found themselves on different sides, with the institute regularly criticizing 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 condemned the action to suspend two student groups, which the university said had broken rules concerning holding campus events.

Escalating Tensions

Subsequently, the director further criticized the university's decision to summon police onto campus to clear a peaceful, student protest – 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 mission – including expression, scholarly independence, and fair treatment," he stated in that instance.

Activist Viewpoint

The detained student, in particular, had pleaded with campus officials for protection, and in an op-ed composed while jailed he stated that "the reasoning employed by the administration to target me and my peers is an outgrowth of the university's suppression approach regarding Palestine".

Columbia settled with the Trump administration shortly after the case wrapped in court.

Institute's Response

Following the agreement was revealed, the organization published a strong criticism, stating that the settlement approves "an astonishing transfer of autonomy and control to the government".

"University administration ought not accepted this," the declaration said.

Broader Context

The institute doesn't stand alone – organizations such as the civil liberties union, the free speech organization and additional rights organizations have opposed the government over free speech issues, as have unions and other institutions.

The institute isn't exclusively focusing on university matters – in other challenges to the Trump administration, the institute has filed cases on behalf of farmers and climate activists opposing federal departments over climate-related information and challenged the suppression of government documents.

Unique Position

However its protection of campus expression at a university now associated 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 while he described their agreement as a "serious mistake". But he stressed that despite the institute standing at the opposite end of its parent institution when it comes to dealing with the administration, the university has permitted it to function without interference.

"Particularly currently, I don't take this independence for granted," he stated. "Should the university attempt to restrict our work, I wouldn't be at the university any more."