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The remarks came during a first of its kind reconciliation meeting between members of the San Francisco Police Department the LGBTQ community.
"We the members of the SFPD are here tonight to reflect and to apologize for our past actions against the LGBTQ community and acknowledge harm that has been done that still lingers to this day to many people in the room," Chief Scott said at the Glide Memorial United Methodist Church.
"We're sorry for what happened. We're sorry for our role in it and we're sorry for the harm that it caused," he added.
The meeting was symbolically held on the 53rd anniversary of the Compton Cafeteria riot, when a group of trans women stood up to police at a restaurant in the Tenderloin neighborhood.
Joanne Chadwick is an 82-year-old activist who lived through that era. She even photographed police harassment towards the gay community at a New Year's dance, and smuggled out film in her bra.
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"I don't need the apology, but a lot of people who are no longer with us need the apology," Chadwick said, "So I'm here to accept the apology on their behalf because they died of AIDs, lots of things have happened in this time."
Chief Scott got an applause for his comments, but the night progressed with candid moments from members of the community.
Anubis Daugherty, 25, is formerly homeless. He says LGBTQ youth like him are still unfairly targeted and told the police chief that his apology "somehow rings hollow."
"So, you're essentially doing the same thing," Daughery said, "And I said that if you want to truly apologize for something you have to stop doing it."
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Chief Scott said he hopes the apology will help the community move forward.
"Why now?" Chief Scott asked the crowd. "For those of you who might wonder, I say because we are listening, we hear you and because it's time. Now is the time."
"Unless the wrongs of the past are acknowledged and dealt with appropriately, our past will continue to put a stain on the present and on our future," he continued.
In June, during LGBTQ Pride month, the NYPD police chief offered a similar apology for the police actions that led to the Stonewall riots.
The hosts of Monday night's meeting is just the first of many conversations with SFPD.