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After federal agents arrested the university student Mahmoud Khalil in his campus housing, the institute director knew a significant fight was coming.

Jaffer leads a Columbia-affiliated center dedicated to defending First Amendment rights. Khalil, a green card holder, had been active in Palestinian solidarity protests on campus. Months earlier, Jaffer's organization had organized a conference about free speech rights for noncitizens.

"We recognized a direct link to the case, since we're at Columbia," Jaffer explained. "We viewed this detention as a major violation of First Amendment rights."

Major Legal Win Against Administration

Recently, the institute's lawyers at the Knight First Amendment Institute, together with legal partners their co-counsel, secured a significant legal win when a federal judge in Boston ruled that the detention and planned removal of Khalil and other pro-Palestinian students was unconstitutional and intentionally designed to chill free speech.

Government officials announced it will appeal the decision, with White House spokesperson a spokeswoman describing the ruling an "unacceptable decision that undermines the safety and security of our nation".

Growing Divide Between Institute and Institution

This decision raised the profile of the free speech center, propelling it to the forefront of the battle with the administration over fundamental American values. However the win also highlighted the growing divide between the organization and the university that houses it.

This legal challenge – characterized by the judge as "perhaps the significant ever come under the jurisdiction of this district court" – was the first of several challenging Trump's unusual attack on higher education to go to trial.

Trial Revelations

Throughout the court proceedings, citizen and noncitizen scholars testified about the atmosphere of fear and self-censorship ushered in by the arrests, while immigration officials revealed details about their dependence on dossiers by rightwing, pro-Israel groups to select individuals.

Veena Dubal, chief lawyer of the academic organization, which filed the lawsuit along with local branches and the academic group, described it "the central constitutional lawsuit of the Trump administration this time around".

'University and Institute Are On Opposing Positions'

While the legal success was hailed by supporters and academics nationwide, the director heard nothing from university leadership following the ruling – an indication of the tensions in the stances taken by the institute and the institution.

Even before Trump took office, the university had come to symbolize the declining tolerance for Palestinian advocacy on American universities after it called police to clear its student encampment, suspended multiple activists for their activism and severely limited protests on campus.

Institutional Agreement

This summer, the university negotiated an agreement with the Trump administration to provide substantial funds to settle discrimination allegations and submit to major restrictions on its autonomy in a move widely condemned as "capitulation" to the administration's pressure strategies.

The university's submissive approach 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 these fundamental issues," noted a former fellow at the Knight Institute.

Organization's Purpose

This organization was established in 2016 and is located on the Columbia campus. It has obtained significant funding from the university as part of an agreement that had both providing substantial amounts 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 that moment when the administration has gone in the wrong direction and constitutional protections are threatened and no one else is prepared to take action and to say, this must stop, that's when the Knight Institute that will taken action," stated the former president, a constitutional expert who helped create the center.

Public Criticism

Shortly after campus developments, the university and the Knight Institute found themselves on different sides, with Knight frequently objecting to the institution's management of campus demonstrations both privately and in increasingly unforgiving public statements.

In correspondence to campus administration, Jaffer criticized the action to suspend two student groups, which the university said had broken rules related to organizing protests.

Escalating Tensions

Subsequently, the director again condemned the university's decision to summon police onto campus to remove a peaceful, student protest – leading to the detention of more than 100 students.

"Institutional policies are separated from the values that are central to the academic community and mission – including free speech, academic freedom, and equality," he wrote this time.

Activist Viewpoint

The detained student, in particular, had appealed to campus officials for support, and in a published article composed while jailed he stated that "the logic employed by the administration to target myself and my peers is an outgrowth of Columbia's repression approach regarding Palestine".

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

Organization's Reaction

Shortly after the deal was revealed, the organization published a strong criticism, concluding that the settlement approves "an astonishing transfer of autonomy and authority to the administration".

"University administration ought not agreed to this," the declaration stated.

Broader Context

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

The institute isn't exclusively focusing on university matters – in other challenges to the government, the institute has filed cases on behalf of agricultural workers and environmental advocates opposing government agencies over climate-related datasets and challenged the suppression of official reports.

Special Situation

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

Jaffer showed understanding for the absence of "favorable choices" for university administration while he described 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 dealing with the president, the university has allowed it to function without interference.

"Especially right now, I appreciate that freedom for granted," he said. "Should the university attempt to restrict our work, I wouldn't be at the university any more."