The American Geophysical Union is meeting in the city this week.
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"Our communities are under attack. What do we do? Stand up and fight back!" went the chants.
About 400 scientists and environmental activists gathered at Jessie Square Outside Moscone Center to stand up to Trump's position on climate change.
"Science and evidence is at risk of being ignored, disparaged and disregarded," said Peter Frumhoff, with the Union of Concerned Scientists.
Since winning the election, Mr. Trump has said he'll keep an open mind about the global climate deal struck in Paris, but during the campaign he tweeted that "the concept of global warming was created by and for the Chinese in order to make U.S. manufacturing non-competitive."
Those here also spoke out against his proposed appointments, including Oklahoma Attorney General Scott Pruitt as EPA chief and Exxon CEO Rex Tillerson as secretary of state.
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"I'm here because I'm terribly concerned about the incoming administration who are science deniers," said Richard Gray.
The American Geophysical Union bills itself as the world's largest association of earth scientists. This is its first major convention since the election. Among the hundreds of booths in the exhibit hall is one called Science is Never Settled.
A lone voice, Peter Ward found himself constantly defending his position on global warming
"We have never actually demonstrated in an experiment in the laboratory or in the field that when you increase greenhouse gases, you cause the air to get much warmer," he said.
Over 26,000 scientist and others are attending the convention that ends Friday.