2025 saw significant advancements in biotechnology, but also growing concerns about the future of scientific progress in the United States, according to Flagship Pioneering CEO Noubar Afeyan. In his annual letter released Monday, Afeyan highlighted recent achievements such as Gilead Sciences’ twice-yearly HIV injection lenacapavir and the first personalized CRISPR treatment for a child with a rare genetic condition. He also mentioned clinical trials involving organ xenotransplants.
Afeyan warned that these breakthroughs are at risk due to changes in U.S. policy and funding. “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.
He cited proposed budget cuts to major research agencies like the National Institutes of Health and National Science Foundation, reduced funding for basic research, fewer grants across science and medicine, and canceled projects. In August 2025, the Department of Health and Human Services began winding down nearly two dozen mRNA vaccine research projects through 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.”
As evidence of real-world effects from declining trust in science, Afeyan pointed to rising measles cases—a disease declared eliminated 25 years ago—which could lose its elimination status if trends continue. “The resurgence of measles is not the result of, say, a random genetic mutation,” he wrote. “It is the result of choices, policy decisions, to turn our backs on decades of science.”
Recent federal decisions have also reduced recommended childhood vaccinations from coverage against 17 diseases to 11—removing shots for flu and rotavirus among others—which has drawn criticism from medical experts such as Paul Offit at Children’s Hospital of Philadelphia.
Afeyan closed his letter by highlighting another concern: China’s increasing investment in biotechnology innovation while U.S. support wanes. Over nine years China has increased its number of novel medicines eightfold; between 2015-2018 its drug regulator quadrupled staff size to clear a backlog of new drug applications—while FDA reviews only several hundred annually.
In contrast with China’s expansion efforts detailed by BioSpace (https://www.biospace.com/article/deep-dive-chinese-biotech-innovation-can-t-be-stopped/), Health Secretary Robert F. Kennedy cut approximately 3,500 positions at FDA soon after taking office; however this did not affect approval rates for new drugs during 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.”
