CHICAGO — The Massachusetts Institute of Technology invited the geophysicist Dorian Abbot to give a prestigious public lecture this autumn. He seemed a natural choice, a scientific star who studies climate change and whether planets in distant solar systems might harbor atmospheres conducive to life.

Then a swell of angry resistance arose. Some faculty members and graduate students argued that Dr. Abbot, a professor at the University of Chicago, had created harm by speaking out against aspects of affirmative action and diversity programs. In videos and opinion pieces, Dr. Abbot, who is white, has asserted that such programs treat “people as members of a group rather than as individuals, repeating the mistake that made possible the atrocities of the 20th century.” He said that he favored a diverse pool of applicants selected on merit.

He said that his planned lecture at M.I.T. would have made no mention of his views on affirmative action. But his opponents in the sciences argued he represented an “infuriating,” “inappropriate” and oppressive choice.

On Sept. 30, M.I.T. reversed course. The head of its earth, atmospheric and planetary sciences department called off Dr. Abbot’s lecture, to be delivered to professors, graduate students and the public, including some top Black and Latino high school students.

“Besides freedom of speech, we have the freedom to pick the speaker who best fits our needs,” said Robert van der Hilst, the head of the department at M.I.T. “Words matter and have consequences.”

Ever more fraught arguments over speech and academic freedom on American campuses have moved as a flood tide into the sciences. Biology, physics, math: All have seen fierce debates over courses, hiring and objectivity, and some on the academic left have moved to silence those who disagree on certain questions.

A few fields have purged scientific terms and names seen by some as offensive, and there is a rising call for “citational justice,” arguing that professors and graduate students should seek to cite more Black, Latino, Asian and Native American scholars and in some cases refuse to acknowledge in footnotes the research of those who hold distasteful views. Still the decision by M.I.T., viewed as a high citadel of science in the United States, took aback some prominent scientists. Debate and argumentation, impassioned, even ferocious, is the mother’s milk of science, they said.

“I thought scientists would not get on board with the denial-of-free-speech movement,” said Jerry Coyne, an emeritus professor of evolutionary biology at the University of Chicago. “I was absolutely wrong, 100 percent so.”

Dr. Abbot, 40, spoke of his shock when he was told his speech was canceled. “I truly did not know what to say,” he said in an interview in his Chicago apartment. “We’re not going to do the best science we can if we are constrained ideologically.”

This is a debate fully engaged in academia. No sooner had M.I.T. canceled his speech than Robert P. George, director of Princeton’s James Madison Program in American Ideals and Institutions, invited him to give the speech there on Thursday, the same day as the canceled lecture. Dr. George is a founding member of the Academic Freedom Alliance, which is dedicated to promoting academic debate.

“M.I.T. has behaved disgracefully in capitulating to a politically motivated campaign,” Dr. George said. “This is part of a larger trend of the politicization of science.”

The story took another turn this week, as David Romps, a professor of climate physics at the University of California, Berkeley, announced that he would resign as director of the Berkeley Atmospheric Sciences Center. He said he had tried to persuade his fellow scientists and professors to invite Dr. Abbot to speak and so reaffirm the importance of separating science from politics.

“In my view, there are some institutional principles that we have to hold sacred,” he said in an interview on Tuesday.

The history of science is no less marked than other fields of learning by abhorrent chapters of suppression and prejudice. Nazi and Communist regimes twisted science to their own end, and scientists buckled, fled or suffered perilous consequences. Some professors point to aspects of that history as a cautionary tale for American science. In the United States, so-called race science — including the measurement of skulls with the intent to determine intelligence — was used to justify the subordination of Black people, Chinese, Italians, Jews and others. Experiments were carried out on people without their consent.

The worst of that history lies decades past. That said, the faculty at geoscience departments in the United States has more white faculty than some other sciences. Departments have attracted more female professors of late but struggle to recruit Black and Latino candidates. The number of Asian Americans earning geoscience degrees has decreased since the mid-1990s.

The controversy surrounding Dr. Abbot’s canceled talk speaks as well to a tension manifest in progressive circles between social justice and free speech. Some faculty members have come to see identity and racial inequities as more urgent than questions of muzzled speech.

Phoebe A. Cohen is a geosciences professor and department chair at Williams College and one of many who expressed anger on Twitter at M.I.T.’s decision to invite Dr. Abbot to speak, given that he has spoken against affirmative action in the past.

Dr. Cohen agreed that Dr. Abbot’s views reflect a broad current in American society. Ideally, she said, a university should not invite speakers who do not share its values on diversity and affirmative action. Nor was she enamored of M.I.T.’s offer to let him speak at a later date to the M.I.T. professors. “Honestly, I don’t know that I agree with that choice,” she said. “To me, the professional consequences are extremely minimal.”

What, she was asked, of the effect on academic debate? Should the academy serve as a bastion of unfettered speech?

“This idea of intellectual debate and rigor as the pinnacle of intellectualism comes from a world in which white men dominated,” she replied.

Stephon Alexander, a theoretical physics professor at Brown University and author of “Fear of a Black Universe: An Outsider’s Guide to the Future of Physics,” said he was not familiar with the intricacies of this story, but he noted that we live in a highly polarized world. “The question,” he said, “is whether we play into that culture or figure out constructive dialogue and maybe exercise some compassion.

“Room for debate and nuance is what a university is about.”

This fight did not surprise Dr. Abbot, who described his own politics as centrist. A Maine native, he went to Harvard and came to the University of Chicago for a fellowship and became a tenured professor. He said he found in Chicago a university that remained a leader in upholding the values of free speech, even as he noticed that colleagues and students often fell silent when certain issues arose.

Dr. Abbot said his department had spoken of restricting a faculty search to female applicants and “underrepresented minorities” — except for Asians. He opposed it.

“Asians are a group that is not privileged,” he said. “It reminded me of the quotas used to restrict Jewish students decades ago.”

He spoke, too, of a lack of ideological diversity, noting that a conservative Christian student was hectored and made to feel out of place in an unyielding ideological climate. Last year he laid out his thoughts in videos and posted them on YouTube.

Loud complaints followed: About 150 graduate students, most of whom were from the University of Chicago, and a few professors from elsewhere signed a letter to the geophysical faculty at the University of Chicago. They wrote that Dr. Abbot’s “videos threaten the safety and the belonging of all underrepresented groups within the department.” The letter said the university should make clear that his videos were “inappropriate and harmful to the department members and climate.”

Dr. Abbot has since taken the videos down.

Robert Zimmer, then the president of the University of Chicago, issued a statement strongly reaffirming the university’s commitment to freedom of expression. Dr. Abbot’s popular climate change class remains fully subscribed. The tempest subsided.

Dr. Abbot said he offered to show his videos to some graduate student activists and discuss it, but not apologize. Graduate students said they refused his offer. Dr. Abbot said, “I realized if I offered to apologize, there just would be blood in the water.”

In August, Newsweek published a column by Dr. Abbot and Iván Marinovic, an accounting professor at Stanford University, that called for revamping affirmative action and equity programs.

They also supported doing away with legacy admissions — which gives preferred admission to the children of alumni — and athletic scholarships. Both programs disproportionately benefit white well-to-do students.

In the last three sentences of that column, the professors drew an analogy between today’s climate on campus and Germany of the 1930s and warned of what happened when an ideological regime obsessed with race came to power and what it did to free thought.

The remarks reignited the anger of people who had previously clashed with Dr. Abbot over affirmative action. Even supporters of Dr. Abbot’s free speech rights saw the comparison to Nazi Germany as overdrawn. But they added that it was hardly unusual for academics to draw rhetorical comparisons to the rise of fascism and communism.

“Can we just be honest here? This is not happening because Dr. Abbot used a bit of especially vivid language,” Dr. George said. “This is a legitimate subject of debate, and the argument that it makes students unsafe is risible.”

Dr. van der Hilst of M.I.T. expressed respect for Dr. Abbot’s scientific work but drilled down on the Newsweek essay. “Drawing analogies to genocide is totally within his right to do so,” he said. But, he added, it is “inflammatory and stifles the very respectful discourse we need.”

He stressed that he talked to senior officials at M.I.T. before deciding to cancel the lecture. “It was not who shouted the loudest,” Dr. van der Hilst said. “I listened very carefully.”

Dr. van der Hilst speculated that Black students might well have been repelled if they learned of Dr. Abbot’s views on affirmative action. This lecture program was founded to explore new findings on climate science and M.I.T. has hoped to attract such students to the school. He acknowledged that these same students might well in years to come encounter professors, mentors even, who hold political views at odds with their own.

“Those are good questions but somewhat hypothetical,” Dr. van der Hilst said. “Freedom of speech goes very far but it makes civility difficult.”

Dr. van der Hilst added that he invited Dr. Abbot to meet privately with faculty there to discuss his research.

Dr. Abbot, for his part, said he had tenure at a grand university that valued free speech and, with luck, 30 years of teaching and research ahead of him. And yet the canceled speech carries a sting.

“There is no question that these controversies will have a negative impact on my scientific career,” he said. “But I don’t want to live in a country where instead of discussing something difficult we go and silence debate.”