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After federal agents arrested Columbia University student a student activist in his campus housing, the institute director knew a major battle lay ahead.

The director leads a university-connected center focused on protecting free speech rights. The student, a permanent resident, had been involved in Palestinian solidarity encampments on campus. Months earlier, the institute had organized a symposium about free speech rights for immigrants.

"We felt this connection to the case, because we're at Columbia," Jaffer explained. "And we saw this detention as a serious infringement of constitutional freedoms."

Major Legal Win Challenging Government

Last week, Jaffer's team at the free speech organization, along with legal partners their co-counsel, secured a landmark victory when a district court judge in Boston ruled that the detention and planned removal of Khalil and other pro-Palestinian students was illegal and intentionally designed to suppress protest.

Government officials announced they'll challenge the decision, with administration representative a spokeswoman calling the judgment an "unacceptable decision that undermines the protection of our nation".

Growing Divide Between Organization and Institution

This decision elevated the profile of the free speech center, catapulting it to the frontlines of the conflict with the administration over fundamental American values. However the victory also highlighted the growing divide between the organization and the institution that hosts it.

This legal challenge – described by the presiding official as "possibly the significant to ever come under the authority of this district court" – was the initial of multiple opposing Trump's unprecedented assault on higher education to reach court proceedings.

Court Testimony

During the two-week trial, academic experts gave evidence about the atmosphere of fear and self-censorship ushered in by the detentions, while immigration officials revealed information about their dependence on dossiers by conservative, Israel-supporting organizations to pick their targets.

A legal expert, chief lawyer of the academic organization, which filed the lawsuit together with local branches and the Middle East Studies Association, described it "the central constitutional case of the current government this time around".

'Institution and Organization Occupy Opposing Positions'

While the court victory was hailed by advocates and scholars across the country, the director heard nothing from Columbia after the ruling – an indication of the disagreements in the positions taken by the organization and the institution.

Even before Trump took office, the university had represented the declining tolerance for Palestinian advocacy on US campuses after it summoned officers to remove its student encampment, disciplined dozens of students for their activism and dramatically restricted protests on campus.

Institutional Agreement

This summer, the institution reached a deal with the Trump administration to pay millions to resolve discrimination allegations and submit to significant limitations on its autonomy in a move broadly criticized as "capitulation" to the president's bullying tactics.

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

"We're at a time in which the university and the institute are on different sides of some of these critical questions," noted Joel Simon at the free speech center.

Institute's Mission

The Knight Institute was established in 2016 and is located on the university grounds. It has received substantial support from the university as part of an arrangement that had both providing substantial amounts in program support 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 government has gone in the wrong direction and constitutional protections are at stake and few others is prepared to take action and to say, enough is enough, it will be the this organization that will stepped forward," stated Lee Bollinger, a constitutional expert who established the center.

Open Disagreement

Shortly after recent events, the university and the the organization found themselves on different sides, with Knight regularly criticizing the university's handling of pro-Palestinian protests both in private communications and in progressively critical public statements.

In correspondence to campus administration, Jaffer condemned the action to suspend two student groups, which the university said had broken rules concerning holding campus events.

Growing Conflict

Later, Jaffer again condemned the institution's choice to call police onto campus to remove a non-violent, pro-Palestinian encampment – leading to the detention of more than 100 students.

"Institutional policies have become disconnected from the principles that are central to the academic community and mission – such as expression, academic freedom, and fair treatment," he stated in that instance.

Student Perspective

Khalil, in particular, had appealed to university administrators for protection, and in an op-ed written from detention he stated that "the logic used by the federal government to target me and my peers is a direct extension of Columbia's repression approach concerning Palestine".

Columbia reached agreement with the federal government just days after the case wrapped in court.

Institute's Response

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

"Columbia's leaders should not have accepted this," the declaration stated.

Wider Impact

Knight doesn't stand alone – organizations such as the ACLU, the Foundation for Individual Rights and other rights organizations have challenged the government over constitutional matters, 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 sued on behalf of farmers and climate activists opposing government agencies over climate-related information and challenged the withholding of official reports.

Special Situation

However its defense of student speech at a university now synonymous with compromising on it puts it in a particularly difficult position.

The director expressed sympathy for the lack of "favorable choices" for university administration even as he characterized their agreement as a "major error". But he emphasized that despite the organization standing at the opposite end of its parent institution when it comes to dealing with the president, the institution has permitted it to function free of pressure.

"Especially right now, I appreciate this independence for granted," he said. "Should the university attempt to limit our activities, I wouldn't remain at the university any longer."