It’s getting warmer by the day here in Silicon Valley, and yet there’s a growing chill descending on its incubation chambers.

The Trump administration, under the guise of fighting antisemitism and DEI, is threatening the Bay Area’s world-renowned academic research centers and, in so doing, risks undermining the secret sauce of Silicon Valley.

Over the last 70 years, Bay Area universities used their freedom and funding to make America great. Stanford University and UC Berkeley, leveraging their educational autonomy and federal investments, have trained the brains directly responsible for the technology underlying U.S. military, economic and scientific dominance.

The internet, search algorithms that birthed Google, public key cryptography, Unix, CRISPR gene editing, machine learning, natural language processing, touchscreen tech and quantum computing were all developed, in part, at Stanford or UC Berkeley with federal funding, particularly from the National Science Foundation and the National Institutes of Health.

But today scholars who typically have a lot to talk about are in crisis comms mode, walking on eggshells and sticking to carefully crafted statements.

Their cautiousness masks their foreboding — and their fears are well placed.

Crazy cocktail

Faculty and administrators at Stanford, UC Berkeley and San Jose State know what can happen if they attract attention from President Trump’s apoplectic administration:

Their personal information will be subpoenaed, like the data already turned over for hundreds of professors at UC Berkeley; their students will lose their visas, like dozens currently in a state of confusion and legal limbo at Stanford, Berkeley and San Jose State; and they will lose millions in research funding, like professors across Bay Area universities already have.

Welcome to 2025.

A president, who ran a fake university, has put someone who ran a fake wrestling league (and recently confused AI with A1) in charge of the crown jewels of American technological supremacy — its education system.

Add to that crazy cocktail some decades-in-the-making Republican resentment towards science and college education; a Congress unwilling to enforce its own laws specifically subsidizing scientific research and universities; a chainsaw-wielding, drug-addled billionaire’s semi-official cost-cutting crew; and the disingenuous battle cry of fighting antisemitism and reverse racism.

Stir all that up. Shake it. Stir again. And voila!

The result is a chaotic yet concentrated, multi-front war on colleges and universities that has already expanded way beyond Columbia University and Harvard University. Though they’ve attracted less public attention, the Bay Area’s universities are squarely in the crosshairs of multiple federal agencies:

San Jose State is being investigated by the Department of Education, which is investigating UC Berkeley, which is being investigated by the Department of Justice, which is also investigating Stanford.

If that sounds sprawling, it’s because it is. And what’s at stake here is more than meets the eye.

Dramatic cuts to NSF and NIH research and training programs, led by Elon Musk’s Department of Government Efficiency, are hitting Bay Area universities hard.

Stanford and Berkeley have both frozen hiring. Fearing the loss of $160 million of NIH funding has already interrupted research labs on campus, according to The Stanford Daily.

At UCSF, ophthalmology research studying effects of the shingles vaccine was cut, two years into what was a five-year study. Why? Because the NIH’s new policy is, per its termination letter, “not to prioritize research activities that focuses gaining (sic) scientific knowledge on why individuals are hesitant to be vaccinated and/or explore ways to improve vaccine interest and commitment.”

So medical research remotely touching on vaccines — unless it’s to disprove their efficacy — appears dead.

“I don’t know that they understood what I was doing,” said Nisha Acharya, the UCSF doctor leading the study, which could have helped prevent Americans from going blind.

Local academic researchers, whose work merely mentions “diversity” or “equity” or “inclusion” or “underrepresented groups” or “disabilities,” have seen their projects killed by DOGE.

At Berkeley, more than $11 million of NSF-supported environmental, educational and legal research was killed off by DOGE just in the last two weeks of April.

STEM is KIA

But the most long-lasting side effects of the Trump administration’s aggressive assault on academic research will be on nurturing the careers of future scientists, mathematicians and engineers.

“The biggest cuts across the board have been to training programs,” said Noam Ross, executive director of analytics nonprofit rOpenSci.

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Ross would know. Along with a group of other computational scientists, he has created a widely cited public dashboard keeping track of which programs are getting cut by the Trump administration. So far, $322 million in grants specifically funding STEM education have been cut, more than any other category.

And that’s also true locally.

DOGE has gutted career development programs to train physicists and biomedical researchers at San Jose State; computational researchers and roboticists at Berkeley; medical school students at UCSF and geneticists at Stanford.

One Trump administration cut at a time, Bay Area universities are losing their autonomy; and Silicon Valley and America are losing a generation of innovation.

Max Taves is deputy opinion editor at The Mercury News. He can be reached at [email protected].