Muir founded the Sierra Club 128 years ago.
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On Wednesday, the club issued a statement saying they are going to "re-examine our substantial role in perpetuating white supremacy."
They cited Muir's friendships with people who believed in eugenics and said he "made derogatory comments about Black people and Indigenous people that drew on deeply harmful racist stereotypes".
"His legacy is things like the National Park Service, it's setting aside national park sites like Yosemite and Sequoia but it's also what he was doing at the time in the society he was living in," said John Muir National Historic Site Superintendent Tom Leatherman.
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"There was still a degree of racism to Muir even though he was so enlightened in so many other ways," Rice University historian Douglas Brinkley.
Brinkley wrote a book about Muir's friendship with President Teddy Roosevelt whose statue is now coming down at New York City's Museum of Natural History.
So what impact could these revelations have on John Muir's legacy? Could his name possibly be removed from buildings and parks around the Bay Area?
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"John Muir is like George Washington and Abraham Lincoln. He's for the ages. Muir's name will stay. There may be though, if you visit Muir Woods, an explanation that he wasn't a perfect human being," said Brinkley. "In some ways he was hostage to his time and wasn't a true progressive in today's sense when it comes to issues of racial equality."
"This is not a movement to get rid of his name or his place in history. It's more coming to terms and recognizing that we are not an organization exempt from all the harms of systemic racism in our society," said Sierra Club Board President Ramon Cruz.