Convicted sex offender Jeffrey Epstein hobnobbed with some of the world’s leading scientists and thinkers, flying them on his private jet to a TED conference, socializing at exclusive soirees and spawning a web of financial relationships that have roiled two of the world’s most elite universities. Harvard University and the Massachusetts Institute of Technology are still investigating the extent of their financial relationships with Epstein. MIT President L. Rafael Reif is expected to address the issue at a faculty meeting Wednesday, and students protested last week.

But the scandal has cast a light on a social milieu of academic superstars that burnished the reputation and ego of a criminal, forcing uncomfortable and divisive conversations about who should bear the blame, how philanthropy shapes universities and whether the male-dominated power structure in science and technology helped enable Epstein.

“Outside the university where a lot of big money resides, we have the Silicon Valley bro-culture, the venture capital culture, the Biotech start-up culture, the boy-genius culture — all of which exclude women. Women can’t be equal inside the university without equal access at this nexus of academia and philanthropy,” said Nancy Hopkins, an emerita MIT biology professor who documented inequities at MIT in the 1990s, which at the time had tenured 197 men, but only 15 women.

While huge progress has been made within universities, Hopkins said, “this new old-boy network is even more difficult to fight because it lies outside the university.”

Harvard has disclosed it received nearly $9 million from Epstein, but the university’s president, Lawrence S. Bacow, said the school is not aware of any gifts after Epstein’s 2008 guilty plea for soliciting prostitution of a minor. MIT has disclosed receiving $800,000. A New Yorker story reported that $7.5 million was given to MIT at the behest of Epstein. MIT has retained an outside law firm to investigate its connections to Epstein. Both reviews are ongoing.

The revelations around Epstein and his contributions to the schools precipitated the resignation of Joi Ito, the director of the MIT Media Lab who received funding from Epstein long after the financier’s conviction as a sex offender.

The fallout from the disclosure of Epstein’s relationships with leading intellectuals began piecemeal this summer. One by one, prominent scientists and thinkers more accustomed to being celebrated for their world-changing ideas and research answered awkward questions about their connections to Epstein.

George Church, a renowned geneticist, apologized for receiving about $500,000 from Epstein between 2005 and 2007.

“There is a feeling of revulsion that I think is shared by most people who were in direct contact,” Church said.

Steven Pinker, a linguist at Harvard and best-selling author, said he never received money from Epstein but met with him three times over a dozen years — including being flown on Epstein’s private jet to a TED conference along with other colleagues.

“I found him to be a kibitzer, who liked to joke around with the guys, but had no serious interest in pursuing ideas and arguments,” Pinker said. After a second meeting, Pinker said he was told by a colleague that “Epstein then ‘voted me off the island,’ banning me from future meetings of the group, because I was spoiling his fun by trying to keep the conversation on track and bringing up data from relevant fields that got in the way of his musings.”

The upheaval has intensified as scholars debate publicly and among themselves whether gender biases and inequities in power within the academic culture may have helped protect and enable Epstein. Pressure to raise money for research, the allure of unrestricted donations for novel ideas and the aura of star scholars may have contributed to decisions that in retrospect look tawdry. Faculty members described responses ranging from horrified reactions to arguments that tainted money could be used to promote social good through research.

For years, leaders have been working to make sure that technology and science become more inclusive. But the Epstein scandal is a reminder that despite progress, some circles may have been more accessible to a known criminal than to many women.

Technology scholar danah boyd chose to talk about Epstein last week when she was given an award from the Electronic Frontier Foundation.

“I am here today in-no-small-part because I benefited from the generosity of men who tolerated and, in effect, enabled unethical, immoral, and criminal men,” boyd said.

“Many of us are aghast to learn that a pedophile had this much influence in tech, science, and academia, but so many more people face the personal and professional harm of exclusion, the emotional burden of never-ending subtle misogyny, the exhaustion from dodging daggers, and the nagging feeling that you’re going crazy as you try to get through each day. Let’s change the norms. Please help me,” boyd said.

Pattie Maes, chair of the Media Lab executive committee, said in an email there could be a silver lining — a renewed focus on making progress in inclusion and equality.

“We have already started that process at the Media Lab and have decided to conduct a thorough review and a reinvention of our funding, culture, research values and governance structure,” she said.

The debate over Epstein and his connections with premier universities has had its own ripple effects, including the resignation of Ethan Zuckerman, director of the Center for Civic Media at MIT and an associate professor of the practice at the Media Lab, who announced in August he could not ethically square his own work with the institution’s connections to Epstein.

J. Nathan Matias, a visiting scholar at MIT who is on the faculty at Cornell University, also announced he would leave at the end of the academic year because he could not, with integrity, continue his research at a place so entangled with Epstein.

On Monday, prominent computer scientist Richard Stallman resigned from his Free Software Foundation and from MIT, citing “pressure on MIT and me over a series of misunderstandings and mischaracterizations.” Stallman, an outspoken advocate for online freedom, had weighed in on the Epstein imbroglio on a departmental email chain.

He ruminated on what constituted sexual assault and rape in a defense of Marvin Minsky, the late artificial intelligence pioneer, who had been implicated in the Epstein scandal.

Stallman responded to an announcement of an Epstein protest with a complaint that it was an injustice to Minsky. The protest announcement said Minsky was “accused of assaulting one of Epstein’s victims.”

Stallman wrote, “The injustice is in the word ‘assaulting’. The term ‘sexual assault’ is so vague and slippery that it facilitates accusation inflation: taking claims that someone did X and leading people to think of it as Y, which is much worse than X.” Stallman wrote that if Minsky and the girl did have sex, the word “assaulting” presumes force or violence was used to coerce it.

On Saturday, Stallman wrote, “I want to respond to the misleading media coverage of messages I posted about Marvin Minsky’s association with Jeffrey Epstein. The coverage totally mischaracterized my statements.

“Headlines say that I defended Epstein. Nothing could be further from the truth. I’ve called him a ‘serial rapist’, and said he deserved to be imprisoned. But many people now believe I defended him — and other inaccurate claims — and feel a real hurt because of what they believe I said.

“I’m sorry for that hurt,” he wrote. “I wish I could have prevented the misunderstanding.”

Stallman did not immediately respond to messages seeking comment.

An MIT graduate, Selam Jie Gano, who called for Stallman’s resignation, wrote in a post on Medium that this was a chance for institutions to act.

“This conversation about Epstein, Minsky, and Stallman should motivate other institutions too. Even if they are certain they took no money from Epstein or never hosted Minsky or Stallman, this is a broader conversation about politics and ethics,” Gano wrote. “Who else has gone unchecked? When else have staff or administration felt like what they were doing was morally wrong?”

More than 100 people gathered Friday for a protest at MIT organized by students calling on the university’s president and others who were aware of Epstein’s donations to resign.