Bradley Manning, soon to begin a 35-year sentence in the U.S. Disciplinary Barracks at Fort Leavenworth, Kansas, said on Thursday that he intended to transition to a female named Chelsea. Several hours later, The Daily Beast published an op-ed from contributor Mansfield Frazier, a former convict.

“We asked Mansfield, who has written for us often in the past, to write about his personal experience with transgender individuals in federal prison,” explained The Daily Beast’s editor, Deidre Depke (Editor-in-Chief Tina Brown was traveling on business when the piece was assigned and posted). “It was not meant to be a reported piece. We wanted an opinion column.”

After insufficient editorial review, Frazier’s piece was posted. And his opinions turned out to be controversial. He alleged that “true rape” is actually uncommon in the prison system, and that high recidivism rates are due in part to closeted homosexuals who return to prison so they can continue having sex with men — both dubious contentions that fly in the face of established facts.

The backlash was immediate. Media organizations and advocacy groups joined readers on Twitter to register their indignation. Nick Confessore, a reporter for The New York Times tweeted, “Uh, so @TheDailybeast just pubbed oped on how prison rape actually kind of awesome for gays.”

The comments section filled with many angry, often insightful responses, some of which Frazier responded to personally.

“We try to produce a site that has room for controversial or unpopular points of view,” Depke said. “When we began to get reaction, mostly via Twitter, we recognized that the piece was over the line–challenging the notion that rape is a problem in U.S. prisons. Of course that’s not true, in point of fact, it’s ridiculous.”

Editors removed the most offensive sections and inserted a note with figures on sexual abuse from Just Detention International (a group that itself denounced the piece as “deeply offensive and totally out of touch with reality,” in a statement posted to its website.)

Groups including Media Matters posted statements questioning the move.

“It’s unclear how The Daily Beast’s editor’s note does anything but make the publication of Frazier’s op-ed even more problematic. The Daily Beast recognizes that prison rape occurs, but still chose to publish a piece suggesting thattransgender people specifically don’t struggle with sexual assault and abuse. By agreeing to publish Frazier’s horrific op-ed, The Daily Beast helped whitewash the brutality experienced by one of the most vulnerable populations in the American criminal justice system.”

The column’s author said he was surprised by the intense reaction his column elicited.

“I didn’t expect that people were in such denial,” Frazier said in an interview. “There are some people who think that if you don’t sing their song the way they want you to, then you’re against them. But I’m the furthest thing from against homosexuals.” As an African-American with a criminal record, he said “I have to be for the underdog.”

Frazier denies condoning rape in his piece, (“Rape is a horrible crime.”) But he continues to insist that the statistics of prison sexual abuse are exaggerated. “I know the statistics are skewed. I’ve been in prison and I’ve seen it,” Frazier said. “I’m an expert from a real life experience.”

Government figures show that sexual abuse in prisons is a serious problem, with consequences for vulnerable populations. Some 200,000 men and juveniles in prison have been, or will be, victims of sexual assault and abuse, according to the Department of Justice. And more than one million inmates have likely been sexually assaulted in the last 20 years.

Moreover, the most vulnerable prisoners are often specifically and disproportionally targeted. Inmates with the highest rates of sexual victimization are those who report their sexual orientation as gay, lesbian, bisexual, or other, according to the Bureau of Justice Statistics. LGBT inmates are ten times more likely to be sexually abused than heterosexual counterparts: over 12 percent of LGBT prisoners reported sexual abuse last year.

The report also found inmates with mental health issues — which Manning has been diagnosed as having — are more likely to become sexual victims.

While the piece itself got almost everything wrong, according to experts and advocates, The Daily Beast’s handling of the blowback was also ripe for judgment.

Just Detention International called the Daily Beast’s removal of several paragraphs in the column “encouraging,” but others found the deletion unethical.

By Friday, a petition had been started on the blog, Prison Culture noting the column’s “victim-blaming and rape apologia,” and calling out the editorial decision to “surreptitiously” remove some of the article’s most offensive paragraphs. The petition urges people to demand an apology from The Daily Beast — to Manning and survivors of prison rape.

“I saw the original column and I have to say I was stunned. I couldn’t believe how despicable it was,” Mariame Kaba, the author of the petition and director of Project NIA, a community organizing group in Chicago, said in a phone interview.

“As somebody who works with young people who are incarcerated, I couldn’t understand any part of the piece. Additionally, I found it so homophobic, transphobic, and misogynistic,” she said.

Frazier’s column, Kaba said, isn’t just offensive, it’s harmful.

“By the comments, people believe that there is no rape. And people are dealing with this in real life,” she said. “This piece sets us back, those of us who are advocates on these issues, and it harms real people whose real bodies are behind bars. Taking one person’s supposed story and then magnifying that and generalizing that to a whole population, of 200,000 people who are being raped, it’s unconscionable.”

Does The Daily Beast regret publishing the piece? “Yes.” Depke said. “It was an error, plain and simple, and I’m personally sorry about it.”

The column that sparked all the outrage will remain online, although in its edited form.

“There’s no such thing as ‘removing’ anything from the Internet. Anyone who wants to find the story can find it, whether we remove it or not,” Depke said. “And I also don’t want readers to think that we are trying to cover something up.  We made a mistake, and we’re acknowledging it in the most transparent way we can.”