In his annual letter, Flagship Pioneering’s Noubar Afeyan lays out a choice between near-term “human-made miracles” and a reversion to the pain and suffering of past diseases due to “growing contempt” in the U.S. for the scientific method.
2025 was a time of science generating “human-made miracles,” Flagship Pioneering CEO Noubar Afeyan wrote in his annual letter Monday. However, he added that he also believes the U.S. is “at risk of taking a sledgehammer to our miracle machine.”
Attributing the term “man-made miracle” to a former head of state he met at UN General Assembly Week last fall, Afeyan said in his letter that the phrase stuck with him because “it is an apt description of what biotechnology, at its best, can do: miraculously consign to history some of the worst fates that befall humans – debilitating illnesses, devastating diseases.”
The dignitary referenced Gilead Sciences’ twice-yearly HIV injection lenacapavir, according to Afeyan, who added a couple of his own human-made miracles to the list: the first-ever personalized CRISPR treatment, created for a nine-month-old boy named KJ with an ultrarare genetic condition, and clinical trials of organ xenotransplants engineered across species lines.
As the J.P. Morgan Healthcare Conference gets underway in San Francisco, Afeyan issued a stark warning about the environment in which these “miracles” were made. “This past year, those conditions were under threat in the United States in ways I have never seen in my nearly 40 years in biotech, nor ever imagined I’d witness,” he wrote.
Afeyan went on to cite proposed U.S. government budget cuts to the National Institutes of Health and National Science Foundation, “slashed funding” for basic research, fewer grants in every area of science and medicine and the cancelation of thousands of existing projects. Indeed, in August 2025, the Department of Health and Human Services began a “coordinated wind-down” of nearly two dozen mRNA vaccine research projects under the Biomedical Advanced Research and Development Authority.
“Even more disastrous,” Afeyan wrote, “is the rejection of the academic scientific enterprise, the severing of its 70-year partnership with the U.S. government, and the growing contempt for the scientific method.”
“Skepticism is an important part of the scientific method,” he continued. “Debate about approaches and outcomes is central to how science works. But what we are seeing is skepticism that has curdled into an across-the-board, corrosive doubt in the scientific method itself.”
“If we lose our ability to collectively resolve our skepticism through the scientific method,” Afeyan concluded, “we won’t just slow the miracle machine, we’ll throw it into reverse.”
Real-World Effects
Afeyan pointed to the reappearance of measles as one example of this phenomenon. A deadly disease declared eliminated 25 years ago, measles could soon lose that status, he wrote, if the case numbers continue to climb.
“The resurgence of measles is not the result of, say, a random genetic mutation,” Afeyan wrote in his letter. “It is the result of choices, policy decisions, to turn our backs on decades of science.”
Afeyan is not the only scientific leader who has recently expressed concern about the potential for a reversal of scientific progress.
After the U.S. federal government reduced the number of childhood vaccinations it recommends from 17 diseases to 11—leaving out shots for flu, rotavirus and more—medical experts eviscerated the decision.
“If there’s a fairly rapid erosion in vaccine rates, I think you would immediately see children suffering preventable illness,” Paul Offit, director of the Vaccine Education Center at Children’s Hospital of Philadelphia, told The Atlantic, recalling the devastation rotavirus used to cause during his pediatric residency. Offit was part of the team that created a vaccine for the disease, RotaTeq, which was licensed in 2006.
Afeyan concluded his letter by raising a parallel threat facing the U.S. biopharma sector: China.
“At the same time that some in the U.S. are undermining the scientific method, the Chinese government has been investing heavily in it,” he wrote.
In the past nine years, the number of novel medicines in China has increased eightfold, nearly equaling U.S. input, according to Afeyan. Between 2015 and 2018, the workforce at China’s drug regulator—the National Medical Products Administration (NMPA)—quadrupled, Afeyan added, allowing it to clear a backlog of 20,000 new drug applications in two years. He noted that the FDA reviews “only a few hundred new drug applications each year.”
In contrast to China’s buildup, Health Secretary Robert F. Kennedy slashed some 3,500 positions at the FDA in a mass workforce overhaul soon after taking office, though this did not appear to have an impact on the rate of novel approvals granted by the agency in 2025.
“If we continue to discredit and defund the scientific method,” Afeyan wrote, “the U.S. risks becoming an innovation desert, reliant on China for new medicines and technologies and helpless to protect our own people in times of crisis, ranging from biological warfare to the next pandemic.”
