The move turned many scientists, unexpectedly, into activists. The diplomatic Daley helped Harvard create an institute in 2004 to work around the federal funding restrictions; California bucked the Bush administration by devoting its own state funds to the research. President Barack Obama eventually reversed the executive order in 2009, allowing federal funds to be used; today, embryonic stem cell based therapies are being tested in clinical trials, and studying them has helped unleash a wave of new medical insights.

As of Jan. 1, Daley occupies one of the highest-profile jobs in American medicine, a de facto spokesman both for research and medical practice. And he arrives at a moment when the entire field is nervous about what the Trump administration has in store. The White House seems not only indifferent to research, but also actively hostile to some strains of science; the future of the Affordable Care Act is uncertain at best. Drug prices, immigration and the national research budget — all issues crucial to the medical field — are all up for debate. By nature a scientist, accustomed to gathering evidence before opining about solutions, Daley says he thinks his experiences working in a field that was marginalized by politicians may provide some useful lessons for navigating what he called a "cacophony of confusion and alternative facts."

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Daley spoke to The Washington Post about his hopes and concerns as he takes the helm at Harvard Medical School — around the same time as President Trump. This interview has been edited for clarity and length.

Right now, there’s uneasiness in the scientific and medical communities over how evidence and research will be treated, ranging from vaccines to climate change. Having lived through a time when your work was directly politicized and targeted, what are your thoughts about how to approach a situation like that?

I think that the lessons that I learned in the early challenges and policy debates around embryonic stem cells have a lot to teach us for how to advocate forcefully in today’s world. We have to, as scientists, stick to our message, which is that science and evidence is the way to make informed decisions — whether those decisions are about advancing human health and wellness, or about advancing the environment and maintaining not only healthy air quality, but reducing risks to catastrophic climate change. These are all fundamentally, at some level, challenges and risks to human health.

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If I had one worry, as we see the cacophony of confusion and alternative facts, it's that we’re reverting to a pre-Enlightenment form of thinking, which will take us back to the days of blood-letting and faith-healing. And this is wrong. This is not the way to advance health and wellness for the greatest number, not a way to face our challenges. We are facing some of the greatest global challenges today — not just with global warming, but with threats to emerging pathogens, whether it’s Ebola or Zika. And if we start to question the nature and value of things like vaccines in human health, how are we going to be able to confront the challenges of new pathogens?

Do you think that this is something that's already happening, or is it a future worry?

The storm clouds are on the horizon. If I just speak to one issue that has a very direct effect on our community: Our biomedical research enterprise, as well as our clinicians draw on the best and brightest, from not only the United States, but around the globe. We are a magnet, we’re seen as the beacon of the best, cutting-edge research and the most effective and impactful clinical training and health care delivery. I’ve met with students from Iran and Syria who are here studying and about to graduate. And they’re worried that their parents are not going to be able to come see them receive their PhD or their MD. We’re worried about the pipeline — not only of trainees who keep us at the cutting edge, but patients. Our health care centers are magnets for patients from all over the world, and in many cases from the Middle East, and it stands in the way of our mission.

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The immigration policy of the Trump administration is evolving as we speak, but it sounds like you're worried about the message that recent actions send.

Our concern is that there is a megaphone that screams across the globe. Over the couple-hundred-year history of our country, it has been emblazoned on the Statue of Liberty: Give us your tired, your poor. We are a welcome beacon to immigrants from all across the globe; that’s been the message that has built our country. And now the recent message that has been sent is giving pause to those folks in other parts of the world, making them think twice about whether this is a welcoming community for them. I’ve already heard that some of our applicants to post-doctoral positions or training programs in our graduate schools are starting to be diverted to programs in Europe that are saying, "Hey, what can we do to take advantage of the talent pool that might not be going to the United States." That is chilling to me.

What are your thoughts on the plans to repeal the Affordable Care Act and what should come next?

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We now have, in Massachusetts, 96 percent of people covered, and I do think that’s created a sense in our medical students and our residents and our trainees, and even up to our faculty, that universal access [to health care] is a human right. I remember in my times in the hospital, there was something absolutely wonderful about the fact the homeless person coming off the street with a heart attack got the same intense, compassionate care as the Berkeley professor who had a heart event at Logan Airport — and that’s an actual case that took place when I was in training. There’s probably no other experience in my time as at trainee at the Harvard hospitals that made me feel more proud about the mission of Harvard medicine. I think that’s an aspiration — there was an attempt by the Obama administration to capture that as an aspiration, as the noblest calling of medicine, and I think that anything that is put in it place has to attempt to meet those same aspirations.

Stem cell science has come under political attack in the past, and Vice President Pence has said he opposes embryonic stem cell research. Are you worried about the future of your field?