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After government officers arrested the university student Mahmoud Khalil in his campus housing, Jameel Jaffer knew a major battle lay ahead.

The director heads a Columbia-affiliated center focused on defending First Amendment protections. Khalil, a permanent resident, had been involved in Palestinian solidarity encampments on campus. Months earlier, the institute had organized a conference about free speech rights for immigrants.

"We recognized this connection with this situation, since we're at Columbia," Jaffer stated. "We viewed this arrest as a major violation of First Amendment rights."

Major Legal Win Against Government

Last week, the institute's lawyers at the free speech organization, together with legal partners their co-counsel, achieved a landmark victory when a district court judge in Boston ruled that the arrest and planned removal of the student and other pro-Palestinian students was illegal and purposely created to suppress protest.

Government officials has said it will appeal the decision, with White House spokesperson Liz Huston calling the ruling an "outrageous ruling that hampers the protection of the country".

Growing Divide Between Organization and University

The ruling elevated the visibility of the Knight Institute, propelling it to the frontlines of the battle with Trump over core constitutional principles. However the victory also highlighted the growing divide between the organization and the institution that hosts it.

The case – characterized by the judge as "possibly the most important ever come under the authority of this court" – was the first of multiple challenging the administration's unprecedented assault on higher education to reach court proceedings.

Court Testimony

Throughout the court proceedings, citizen and noncitizen scholars testified about the atmosphere of fear and self-censorship caused by the detentions, while immigration officials revealed information about their reliance on dossiers by rightwing, Israel-supporting groups to pick their targets.

A legal expert, general counsel of the American Association of University Professors, which brought the case along with some of its chapters and the Middle East Studies Association, described it "the primary constitutional lawsuit of the current government this time around".

'Institution and Institute Occupy Opposing Positions'

Although the legal success was praised by advocates and scholars across the country, the director received no communication from university leadership after the ruling – an indication of the disagreements in the stances staked out by the organization and the university.

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

University Settlement

This summer, the university negotiated an agreement with the Trump administration to pay millions to resolve discrimination allegations and accept major restrictions on its independence in a move widely condemned as "surrender" to the president's bullying tactics.

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

"We're at a time in which the institution and the institute hold opposing views of some of these fundamental issues," noted a former fellow at the Knight Institute.

Organization's Purpose

This organization was launched in 2016 and is housed on the Columbia campus. It has obtained significant funding from the institution as part of an arrangement that had each contributing substantial amounts in program support and long-term financing to launch it.

"Our vision for the institute in the long-term future is that when there is that moment when the government has gone in the wrong direction and fundamental rights are threatened and no one else are willing to step forward and to say, this must stop, it will be the Knight Institute who will have stepped forward," stated the former president, a constitutional expert who established the institute.

Public Criticism

Following recent events, Columbia and the the organization were positioned on opposing sides, with Knight regularly criticizing the institution's management of pro-Palestinian protests both privately and in progressively critical official comments.

In correspondence to campus administration, Jaffer condemned the action to penalize two student groups, which the institution said had broken rules related to organizing protests.

Growing Conflict

Subsequently, the director further criticized the university's decision to summon law enforcement onto campus to remove a non-violent, student protest – leading to the arrest of more than 100 students.

"Institutional policies have become disconnected from the principles that are central to the university's life and mission – including free speech, scholarly independence, and fair treatment," he wrote in that instance.

Student Perspective

The detained student, specifically, had appealed to campus officials for protection, and in an op-ed composed while jailed he stated that "the reasoning employed by the administration to single out myself and fellow students is a direct extension of Columbia's repression approach regarding Palestinian issues".

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

Organization's Reaction

Shortly after the deal was announced, the Knight Institute published a strong criticism, concluding that the agreement sanctions "an astonishing transfer of autonomy and authority to the government".

"Columbia's leaders should not have agreed to this," the declaration said.

Broader Context

Knight doesn't stand alone – organizations such as the ACLU, the Foundation for Individual Rights and other rights organizations have opposed the government over free speech issues, as have unions and Harvard University.

The institute isn't exclusively focusing on campus issues – in other challenges to the Trump administration, the institute has sued on behalf of agricultural workers and climate activists opposing government agencies over environmental datasets and challenged the withholding of official reports.

Special Situation

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

Jaffer expressed sympathy for the lack of "good options" for university administration even as he characterized their agreement as a "serious mistake". But he stressed that although the institute positioned at the other side of its host when it comes to addressing the administration, the institution has allowed it to function without interference.

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