BOULDER, Colo. — He was suspended for three semesters by the University of Colorado Boulder for “sexual misconduct,” even though police filed no charges against him and his accuser admitted she wanted to scare him when she made the complaint.

So John Doe, as he is known in court records, filed a lawsuit last week against the university saying his rights had been violated under Title IX, the 1972 law that forbids universities from discriminating on the basis of sex.

“CU Boulder has created an environment in which an accused male student is effectively denied fundamental due process by being prosecuted through the conduct process under the cloud of a presumption of guilt,” says the Nov. 21 lawsuit filed in U.S. District Court in Colorado. “Such a one-sided process deprived John Doe, as a male student, of education opportunities at CU Boulder on the basis of his sex.”

Women have for years invoked Title IX in fighting campus discrimination, most famously in matters related to women’s sports teams and their funding and facilities.

But now men are arguing that bias cuts both ways. In fact, the same Title IX law that federal officials and universities are citing in doubling down on what critics describe as a “rape culture” on campus is increasingly being cited by male students who contend they have been unjustly punished, even railroaded, based on their sex.

Andrew Miltenberg, a New York City lawyer who has filed eight such lawsuits, including the Colorado case, said the Obama administration has fueled an atmosphere on campus in which due process is taking a back seat to institutional self-preservation.

“I’m not an apologist for sexual misconduct,” Mr. Miltenberg said. “All I really want is for the process to be transparent and fair, and for the White House not to impose unrealistic standards on people, especially when it’s bowing to special-interest pressure.”

The federal crackdown can be traced to an April 2011 “Dear Colleague” letter from the Department of Education’s civil rights office, which put academic institutions on notice that sexual misconduct constitutes a violation of Title IX. The letter also lowered the standard of proof in handling such cases to a “preponderance of the evidence,” from the “clear and convincing evidence” standard some schools were using, much less the “beyond a reasonable doubt” rule of criminal rape cases.

In May, the agency released a list of 55 higher education institutions under investigation for possible Title IX violations “over the handling of sexual violence and harassment complaints.” The list has since grown to more than 80 universities and colleges.

Big risks

For academic institutions, the risks are huge. A finding against the school could result in a complete withdrawal of federal funding, which for large research universities could amount to as much as 20 percent of their budgets, said Joe Cohn, legislative and policy director of the Foundation for Individual Rights in Education.

“So whereas the incentives in the past may have been to sweep things under the rug, I think if advocates have accomplished anything on this, it’s changing the incentives structure so now it’s predominantly for schools to crack down on accused students to make sure that they get the feds off of their back,” Mr. Cohn said. “And stay out of the public relations disasters that other schools are experiencing.”

At the top of that list would be the University of Virginia, which was roiled by a Nov. 19 article in Rolling Stone in which a student identified only as “Jackie” says she was gang-raped in 2012 as part of a fraternity initiation. University President Teresa Sullivan reacted by suspending all fraternities until Jan. 9, apologizing to the student and calling for a police investigation of the charges.

Columbia University has taken an image hit with the highly publicized protest of senior Emma Sulkowicz, who began lugging a plastic mattress around campus in September after a student she accused of rape was not punished by the administration. Students elsewhere have emulated her with “Carry the Weight” protests at which they hold mattresses and pillows.

The result is that disciplining, suspending or even expelling male students accused of sexual assault is often the path of least resistance for universities, even if the facts of the case are ambiguous or police decline to pursue charges, said Sherry Warner Seefeld, president of Families Advocating Campus Equality.

“Once the federal government made the mandate of, ‘You must use preponderance of evidence and if you don’t, we’re going to cut your federal funding,’ it puts a tremendous amount of pressure on universities to show that they are in fact being responsive to accusations of sexual assault,” Ms. Warner said. “And so they have to have numbers.”

She founded the group in July after years spent defending her son Caleb Warner, who was suspended from the University of North Dakota in February 2010 after a classmate accused him of rape. He was never charged with a crime, and police ultimately issued a warrant for the accuser for filing a false complaint.

Even so, the university, which used the lower “preponderance of the evidence” standard to find Mr. Warner guilty, refused at first to grant him a rehearing. The provost vacated the ruling against him in October 2011, but by that time he had entered another field and was no longer interested in finishing college, Ms. Warner said.

Ms. Warner, a high school history teacher in Fargo, North Dakota, said she receives phone calls every week from students and college employees describing a situation that “looks exactly like McCarthyism.”

“I have had college personnel email me only using their first name and saying, ‘Thank you for forming your organization, it’s a much-needed organization, it’s a witch hunt here on campus and I don’t dare use my real name or tell you what campus I’m on because they will come after me,’” she said.

In the courts

Whether the male students’ Title IX claims will succeed is a matter of debate, given that the lawsuits are still making their way through the court system. Schools facing such claims include Vassar College, the University of Massachusetts-Amherst, Wesleyan University, Columbia University and Drew University.

Among those skeptical of the cases’ chances is Wendy Murphy, a victims’ rights lawyer in Boston, who told Insider Higher Ed, “It’s a little bit like saying whiteness is a problem under civil-rights laws.

“In terms of the scope of the rule, nobody will argue with you that it doesn’t cover maleness, or that men as a class can’t be harmed,” Ms. Murphy said in a 2013 article. “But the issue is, do they have the same moral claim to be able to use the law in a technical sense?”

In the Colorado case, the lawsuit says John Doe met a female student at a campus party and they went to his room to have what he described as consensual sex. She texted him the next night asking him to join her at another party, but he declined, saying he was out of town. She later described the encounter to her resident adviser, who called police.

University of Colorado attorney Patrick O’Rourke said in an email that officials would issue a response to the just-filed Title IX lawsuit after gathering more information but added, “We have great confidence in the campus investigators who handle these very difficult cases.”

Others argue that universities are far out of their depth in dealing with sexual assault cases. Accusations of rape should be referred immediately to law enforcement and medical personnel, instead of having “the dean of the physics department, a professor in the English department, and a sophomore studying anthropology try to figure out if a date rape occurred,” Mr. Cohn said.

Indeed, the most severe punishment a campus committee can mete out is expulsion — a solution that, in the worst-case scenario, would merely put a rapist back on the street anyway.

“The simple fact is that these internal boards were designed to adjudicate charges like plagiarism, not violent felonies,” said the Rape, Abuse and Incest National Network in a Feb. 28 letter to the White House. “The crime of rape just does not fit the capabilities of such boards. They often offer the worst of both worlds: they lack protections for the accused while often tormenting victims.”

While universities have a duty to address sexual-assault claims under Title IX, there are steps that can be taken short of leading the investigations, such as offering support and steering students to the proper authorities, Mr. Cohn said.

“As long as campuses continue to adjudicate these cases, we’re going to see tremendous injustices in both directions, places where it seems clearly someone was truly guilty and going unpunished, cases where people are being severely punished without reliable evidence,” Mr. Cohn said. “And we’re going to see a lot of those situations until we start rethinking how we’re going to address this issue.”

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