Thousands of scientists and their supporters flooded into Boston's Copley Square on Sunday in a show of defiance against a President they fear will exclude science from federal policy making and hobble U.S. research with funding cuts.

At an event organizers described as a momentum builder for a planned national "march for science" in Washington in April, the participants, some in lab coats, waved placards and listened as speakers encouraged them to mobilize to protect science in government and society at large. "We'd rather not be here. We'd rather be in our labs," Harvard professor and author Naomi Oreskes told the crowd.

Many of those who demonstrated were in Boston to attend the annual meeting of the American Association for the Advancement of Science, one of the world's largest gatherings of researchers and educators from across all branches of science. Some expressed concern over the negative impact of Donald Trump's court-suspended immigration ban and potential future measures to block visa holders and visitors from certain countries, including scientists, from entering the United States.

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Many of the conversations during the weekend meeting mirrored those of Canadian scientists, who in 2012 marched against lab closures and the silencing of federal researchers during the Stephen Harper era. But Rush Holt, a physicist and a former Democratic congressman who is the association's chief executive officer, said that in the current political climate, many U.S. scientists see "a challenge like they've never seen before."

He added: "There has been a growing erosion of the appreciation of science – a situation where ideological assertions are crowding out evidence in public and private debates."

The rally was the most visible sign this weekend of the collective alarm scientists say they feel as they watch Mr. Trump sow confusion and doubt on issues such as climate change and vaccination.

"It's pretty clear now that we have a President who resists facts when they don't comport with his predetermined views," said John Holdren, who was science adviser to U.S. president Barack Obama. Speaking on Saturday at a packed session organized by the Union of Concerned Scientists, Dr. Holdren laid out in stark terms the threat that the Trump White House, together with an enabling Congress, poses to science.

Scientists in the Environmental Protection Agency, the Food and Drug Administration and the Department of Energy are among the most likely targets as Mr. Trump and his appointees move to sweep aside regulations and suspend efforts to develop renewable energy.

More broadly, Dr. Holdren said, it will be impossible for Mr. Trump to make good on his election promises to cut taxes, protect entitlements and beef up the military without deep cuts in other areas, including the roughly $68-billion (U.S.) that Washington spends annually on civilian research and development.

Dr. Holdren said he was especially concerned for the National Science Foundation, which is a primary funder of non-medical basic research at U.S. universities and a partner in several international science projects. Equally at risk are Obama-era programs to improve STEM (science, technology, engineering and mathematics) education within the United States and build science partnerships abroad.

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"I fear we are in for a very rough ride," he said.

Others echoed the appeal to scientists to build public support by engaging with their communities and demonstrating the importance of their work to human health and well-being.

"Now is the time for a quantum leap into relevance," said Jane Lubchenco, the former head of the National Oceanic and Atmospheric Administration, which also participated in the session.

Dr. Lubchenco, a marine scientist at Oregon State University, cautioned researchers that they should be smart in their efforts to counteract a President known for labelling and attacking those who challenge him.

"Don't make science partisan. Don't buy into that framing," she said.

During her tenure in government, Dr. Lubchenco's agency was one of the first to adopt a scientific integrity policy that protects federal researchers who speak publicly about their research findings. Similar policies were put in place across the federal government while Mr. Obama was president, in response to allegations of political interference and muzzling during the previous Bush administration.

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Gretchen Goldman, a research director with the UCS, said the organization was in contact with integrity officers within in the federal government and on the lookout for any signs that protections on researchers are being dismantled.

"The bigger problem could be self censorship," she said.

She noted that the government had ample avenues for intimidation, including the so-called "Holman rule," a 19th-century procedural rule newly reinstated by the Republican-led House, that allows lawmakers to reduce the pay of an individual federal employee to $1.

During a public talk on Friday, Dr. Oreskes said that scientists are understandably uncomfortable with being perceived as activists rather than as neutral purveyors of factual information. Nevertheless, she said, citing the example of physicists who alerted the public to the danger of nuclear weapons during the Cold War, scientists today cannot afford to stay silent in hope that the validity of their research will stand on its own merits.

"The facts don't speak for themselves," Dr. Oreskes said.

Elsewhere at the meeting, attendees flitted around poster sessions and booths, including a table piled with T-shirts sporting equations, chemical formulas and other "nerdwear" classics.

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Asked about the demand for a much simpler shirt design bearing only the words "Make America Smart Again," Karen Walsh of Fit to a Tee Shirt Co. of Annapolis, Md., sighed and said, "I didn't bring enough."