Scientists are likely to face a hard time when Donald Trump becomes president, and they need to "speak up" if they see their integrity or their work undermined, a top official in the Obama Administration has said.

Sally Jewell, the outgoing secretary of the interior, said at a meeting of the American Geophysical Union in San Francisco that science had been "foundational" to all parts of public policy under the Obama Administration. Many of these policies "are not going to be easy to undo", she said in a speech during the 20,000-strong gathering of Earth and space scientists.

Jewell said that she could not see why an incoming administration would want to unravel evidence-based policies, "because they are so important to the decisions that we make every single day".

Scientists on the streets

She noted a sense of "uncertainty" among scientists at what will be involved in the transition of administrations. Some scientists seemed more certain than others, and took to the streets of San Francisco to call for Trump to acknowledge that climate change is real.

"If you told me I would be here five years ago, I wouldn't believe you," Kim Cobb of Georgia Tech's School of Earth and Atmospheric Sciences told the San Francisco Chronicle.

"We have for too long as scientists rested on the assumption that, by providing indisputable facts and great data, that we are providing enough of an attack against the forces against science. Obviously that strategy has failed miserably."

One protester's placard read: "Ice has no agenda, it just melts."

Scientists at the meeting are also petitioning for Trump to "make appointing a Science Adviser an immediate priority".

The American Geophysical Union @theAGU started this petition to Trump to appoint a Science Advisor: https://t.co/BBjNObU3WZ Please sign. November 23, 2016

The petition calls for "an individual with a strong scientific background who understands the rigorous scientific method" to inform Trump's public policies.

The road ahead

In recent days a close adviser to Trump has hinted that Nasa's Earth science programmes will be scrapped. Nasa has been highlighting the value that these programmes bring to fields such as conservation, climate change and agriculture.

On the campaign trail Trump also previously argued for sizeable cuts to the Environmental Protection Agency, which is expected to hit its scientific research side the hardest. He has also threatened to withdraw from the global Paris Agreement to cut carbon emissions to cap climate change at less dangerous levels.

Trump's environment roll call so far

Trump's picks for his transition team included Myron Ebell to lead the EPA and Christopher Shank to lead Nasa – two more who deny that human activity is driving climate change.

Trump has also appointed climate denier Scott Pruitt to lead the Environmental Protection Agency after the transition period, and is reported to have nominated pro-fossil-fuel Ryan Zinke to replace Jewell as secretary of the interior.

These add to the growing number of high-profile figures the coming Trump Administration who are set to be heavily pro-fossil fuels and at best noncommittal about the reality and dangers of anthropogenic climate change.