This is a tense moment for science in America, now that a president who is skeptical of proven ideas like climate change and vaccine safety is in office. Donald Trump once called the National Institutes of Health — a research facility that has saved millions of lives — “terrible.”

When Trump assumed command of the federal government on Friday, he inherited thousands of civil servants who produce critically important research on disease threats, natural disasters, climate change, and so much more. This week, there are already several reports out that suggest major changes could be afoot.

These developments could be early-stage transition pains that will get worked out over time. We don’t know. But when considered alongside Trump’s Cabinet appointments and loose relationship with the truth, it seems like science in the age of Trump is on track for massive upheaval.

What we know about what’s happening at scientific agencies

At the Environmental Protection Agency

Just this week: The Trump administration froze new scientific grants at the Environmental Protection Agency. The EPA gives out billions of dollars every year to fund research and projects throughout the country. “These grants help states pay to track air pollution, say, or restore watersheds, or support researchers studying various environmental problems,” Vox’s Brad Plumer explains.

It’s unclear how long the freeze will last, and if it pertains only to new grants or to existing grants as well. As ProPublica reports:

One EPA employee aware of the freeze said he had never seen anything like it in nearly a decade with the agency. Hiring freezes happened, he said, but freezes on grants and contracts seemed extraordinary. The employee said the freeze appeared to be nationwide, and as of Monday night it was not clear for how long it would be in place.

But either way, the agency seems to be a target of a Trump administration hammer. Axios found there may be $815 million in budget cuts coming for the EPA, for various “environment programs and management.” The Huffington Post also reported the EPA is banned from communicating via press releases or social media communications during this time, in another blow.

On Tuesday, Reuters reported that the Trump Administration has ordered the EPA take down its climate change webpage. The EPA climate change page contains links to emissions data and explainers on the current consensus in the field. (And note: the EPA scientific integrity policy states “To operate an effective science and regulatory agency like the EPA, it is also essential that political or other officials not suppress or alter scientific findings.”

It’s currently unclear if the climate change page removal will happen. On Wednesday, Inside EPA reported that Trump’s EPA team have agreed to “stand down” on the order to remove the webpage.

BREAKING: Trump bans EPA employees from providing updates on social media or to reporters, bars awarding new contracts or grants. — The Associated Press (@AP) January 24, 2017

At the Centers for Disease Control and Prevention

Other government agencies are experiencing disruptions to their science communications too. Over at the CDC, officials abruptly canceled a long-scheduled major meeting Monday on the health risks climate change poses to humans with no explanation, according to the Washington Post.

Georges Benjamin, executive director at the American Public Health Association, was booked to be one of the keynote speakers at the event. “This was a preemptive decision on the part of CDC in light of the perspective of the new administration toward climate change,” he told Vox. “It is unusual to do this, but the incoming administration has been so openly opposed to climate change work that it seemed prudent.”

At Health and Human Services

Employees at the Department of Health and Human Services, which the CDC is a part of, were ordered this week to avoid “any correspondence to public officials,” like, say, members of Congress, the Huffington Post reports. “Instead, they have been asked to refer questions to agency leadership until the leadership has had time to meet with incoming White House staff about the new administration’s policies and objectives, according to a congressional official who was also informed of the communications freeze.”

That means staffers throughout the HHS won’t be able to communicate with congressional members on issues pertaining to regulations or legislation. The Huffington Post notes that the freeze may make it hard for congressional offices to relay the latest information about Medicare or the Affordable Care Act to constituents who call in for help.

At the United States Department of Agriculture

BuzzFeed first reported that a research division of the USDA was on a communications lockdown.

“Starting immediately and until further notice, [the Agricultural Research Service] will not release any public-facing documents,” ARS chief of staff Sharon Drumm wrote in January 23 email to employees that was leaked to BuzzFeed. “This includes, but is not limited to, news releases, photos, fact sheets, news feeds, and social media content.”

“Lockdown” may be overstating what's going on here. ARS spokesperson Christopher Bentley told us that the change in policy will not stop researchers from publishing their work in academic journals. “There has been absolutely no change in that practice. ... the science goes out as the peer review process validates it.”

But it does seem like there will be tighter control on science communications from the agency. Bentley said the Drumm email was "inaccurate" because the department will still be issuing press releases and other documents. The change, however, is that the whole "communications chain of command" will now have to be alerted in advance of a publication.

Later in the day Tuesday there was more walkback of the email. By Wednesday morning, USDA was telling reporters the memo should not have been sent, and has rescinded the order, according to a report in Buzzfeed.

UPDATE: USDA's Acting Secy on a call w/reporters said ARS memo should not have happened. USDA does have interim guidance for transition 1/2 — Chris Clayton (@ChrisClaytonDTN) January 24, 2017

Science advocacy groups are worried

For now, these moves seem mainly to be about the new administration asserting control over agencies and hitting pause on some of their current activities. Still, the changes have some scientists and transparency advocates worried.

“We are concerned about reports that federal agencies — including the Department of Agriculture and the Environmental Protection Agency — have issued directives to staff that may silence the voices of scientific researchers and others working for the federal government,” Rush Holt, the CEO of the American Association for the Advancement of Science, said in a statement Tuesday. “Our hope is that this is a temporary measure put into place until the new government agency heads are confirmed by the Senate.”

The Sunlight Foundation also issued a statement “adamantly” opposing government measures that limit transparency and the ability of publicly funded researchers to share their work.

Andrew Rosenberg, director of the Center for Science and Democracy at the Union of Concerned Scientists, expressed similar concerns in statement, saying, “These actions don’t just threaten scientists — they threaten everyone in the country who breathes air, drinks water and eats food.”

It’s worth noting that all these agencies have “scientific integrity policies” put in place by the Obama administration. The USDA’s policy, for instance, states, “Scientific and technical findings should not be suppressed or altered for political purposes.” The FDA’s state staff is allowed to “communicate their personal scientific or policy views to the public, even when those views differ from official Agency opinions.”

In addition to the communication freezes, Trump signed an executive order on Monday to institute a hiring freeze throughout the federal government. That will limit the ability of the government to hire new federal research scientists. An executive order freezing new governmental regulations puts science-based agencies’ regulatory powers on pause. (A regulations freeze is pretty typical for a new president, Plumer explains.)

Presidents have gagged or dismissed government scientists before

During the George W. Bush era, government scientists came forward about the White House meddling in their ability to do their work and speak openly about politically contentious findings or give interviews with the press. “Since taking office, the George W. Bush administration has consistently sought to undermine the view held by the vast majority of climate scientists that human-caused emissions of carbon dioxide and other heat-trapping gases are making a discernible contribution to global warming,” the Union of Concerned Scientists wrote in 2004.

Scientists in Canada also experienced a similar gag under the Conservative government of Stephen Harper. During his leadership from 2006 to 2015, the country made headlines for restricting communications by federal scientists, shutting down important research stations, phasing out the role of federal science adviser, and generally ignoring evidence in policymaking. As a New York Times editorial about Harper's Canada put it: "[This] war against science has been even more damaging to the capacity of Canadians to know what their government is doing."

It’s only week one of the Trump administration. But gagging government researchers is one of the worst-case scenarios scientists can imagine if this administration wages a war on research.

Trump’s Cabinet picks have some pretty weird views about science — though it’s not yet clear how they’ll manifest in policy

Trump’s pick for head of the Environmental Protection Agency, Oklahoma Attorney General Scott Pruitt, is pro-industry and anti-regulation. He refers to himself as the “leading advocate against the EPA’s activist agenda” and has long favored a state-led approach to environmental regulation. He joins Rex Tillerson, the nominee for secretary of state, and Ryan Zinke, Trump’s pick for Interior, as “lukewarmers” — or someone “who won’t be so crass as to claim that climate change is a hoax, and doesn’t really want to fight over whether climate change is happening, but has no intention of doing much about it,” as Vox’s Brad Plumer explained.

Trump chose Rep. Mick Mulvaney of South Carolina to head the White House's Office of Management and Budget. Mulvaney’s low opinion of science was expressed in a stunning September 9 Facebook post (that’s since been deleted but is still cached), where he asked, “... what might be the best question: do we really need government funded research at all.”

The post was written in the midst of a heated debate in Congress about how much more money to allocate to the fight against the Zika virus. It wasn’t clear whether Mulvaney, a budget hawk, was referring to all of the government’s scientific research or just to government-funded research on Zika. But Mulvaney exaggerated the uncertainty around the link between the birth defect microcephaly and Zika to cast doubt on the need for Zika research funding. His argument, in other words, was: Scientists aren’t sure what’s going on with Zika, so why do we need research?

The Health and Human Services nominee, Rep. Tom Price, has drawn a lot of attention for his plans to get rid of Obamacare: He’s committed to repealing the Affordable Care Act and replacing it with policies that would disadvantage the poor and the elderly by cutting Medicare and Medicaid.

He’s also a member of the Association of American Physicians and Surgeons, a fringe conservative group with extremely alarming views on scientific matters. Here’s a rundown from a Mother Jones profile of the AAPS:

Think Glenn Beck with an MD. ... The AAPS statement of principles declares that it is "evil" and "immoral" for physicians to participate in Medicare and Medicaid, and its journal is a repository for quackery. Its website features claims that tobacco taxes harm public health and electronic medical records are a form of "data control" like that employed by the East German secret police. An article on the AAPS website speculated that Barack Obama may have won the presidency by hypnotizing voters, especially cohorts known to be susceptible to "neurolinguistic programming"—that is, according to the writer, young people, educated people, and possibly Jews. ...

Of course, Price may not espouse this group’s every quack theory. But as oncologist and science blogger David Gorski pointed out, it’s hard to imagine how an orthopedic surgeon who believes in science could buy into a group that’s been at odds with many of the foundational views of science and evidence-based medicine.

Betsy DeVos, Trump’s pick for secretary of education, is an education activist and billionaire philanthropist who has been active in the Michigan Republic Party since 1982. She is also a fundamentalist Christian and a member of the Christian Reformed Church in North America, a Protestant group that believes “all scientific theories be subject to Scripture and the confessions” and that “Humanity is created in the image of God; all theorizing that minimizes this fact and all theories of evolution that deny the creative activity of God are rejected.”

It’s not just her church, though, that augurs poorly for science in schools: DeVos is married to a man who lobbied for teaching intelligent design in science classes.

When Dick DeVos ran for governor of Michigan in 2006 — a campaign Betsy supported — he pushed the view that schools should teach children intelligent design alongside evolutionary theory. (Intelligent design is a form of creationism that contradicts evolutionary theory — the bedrock of biology — by suggesting that God and not natural selection explain how humanity evolved.)

There are still a lot of vacancies for other top science jobs

For now, many of the key science jobs haven’t been filled.

Trump has asked Francis Collins, the current director of the National Institutes of Health, to stay on board temporarily.

Trump hasn’t appointed a new NASA administrator either, though his allies have hinted they’d prioritize NASA’s space exploration missions at the expense of the administration’s Earth science programs. “NASA should be focused primarily on deep space activities rather than Earth-centric work that is better handled by other agencies [like NOAA],” a pair of Trump advisers wrote at Space News in October.

Trump hasn’t named a science adviser, though David Gelernter is in the running. He’s a Yale computer scientist, “anti-intellectual,” and critic of academia is reportedly in the running. Gelernter believes more than “90 percent of U.S. colleges will be gone within the next generation, as the higher-education world inevitably flips over and sinks.”

A successor to Tom Frieden, head of the CDC, has also not been appointed yet, and that’ll likely happen after Price is in place as head of Health and Human Services. Meanwhile, the potential candidates for FDA commissioner to date, like many of Trump’s Cabinet appointees, are outspoken critics of the agency they’d lead, and have talked openly about watering down its regulatory authority.

In the coming weeks and months, we’ll get a much clearer picture of the Trump administration’s plans to shake up government science. All signs point to big changes in the works. For now, however, the story of science under Trump is just beginning.

Are you a scientist with a story about changes under Trump? Send us an email.