On Monday evening, I asked, in a blog post, whether we are approaching The End of Stanford. The Wall Street Journal had just published a story about a new start-up called Clinkle, which has, as the paper mildly put it, “deep roots” in the university. More than a dozen students have left school to work at it. Professors have invested. An emeritus dean has advised it. The president of the university, John Hennessy, who had a career as a technology entrepreneur and who now sits on the boards of Google and Cisco—companies which could reasonably be expected to one day compete with or acquire the start-up—was the academic advisor of the C.E.O. The story made me wonder where Stanford ends and Silicon Valley begins. Or, put cheekily, is Stanford now just a tech incubator with a football team?

Many on campus liked neither my question, nor my joke. I also got a lot of personal feedback from students. I’m a Stanford graduate, so how could I fail to understand that it still produces Rhodes Scholars and has Rodin statues? Yes, many people say, influence on campus continues to shift from techies to fuzzies, as they're called. But the university has given the world H.P., Cisco, Google, Netflix, Instagram, and Snapchat. Put all the companies founded by alums on an island, and they’d make something like the tenth largest economy in the world. (I’ve co-founded a Valley-backed one, too.) All good, right? “Why so down now?” asked one commentator on the original blog post.

Here’s why. Start with the complicated power dynamics that arise when professors invest in student companies. Does the student who let the professor put money in expect a good grade? What if the company falters? What if the student doesn’t want the professor to invest? Does another student who wants to start a competitive company need to fear a bad grade? There are gradations, and it matters, of course, whether a professor invests when a student is currently enrolled in his class—or might enroll in a future one. But financial relationships are charged and emotional and universities need to be very careful. Stanford, a university spokesman told me, deals with these potential financial conflicts by requiring internal disclosure and departmental review. Is that enough?

What about students dropping out? Of course, it should happen—from time to time. No one begrudges Bill Gates leaving Harvard. There are moments to pursue entrepreneurial dreams; Stanford, to its credit, allows students to stop out and then return. But one student leaving is not the same as a dozen going off in a block. And a dozen students leaving for a company whose founder worked closely with the university’s president is even now extraordinary. Will the computer-science department become something like the Kentucky basketball team?

And here’s the biggest question. Stanford is in the middle of a massive experiment in online education. In 2011, a hundred and sixty thousand students around the world signed up to take a class that the university offered online. Following the success, the professor quit to work at an education start-up. Hennessy has talked eloquently and extensively about his desire to take much of what is analog about Stanford and make it digital. “There’s a tsunami coming,” he told Ken Auletta, in an interview for a feature in this magazine.

This is all very fine—exciting, even. But it’s also fraught. The university is likely to change more in the next ten years than in any previous decade. Other educational institutions will follow its lead. The choices it makes will also, quite possibly, enrich companies around Silicon Valley—and Stanford knows well by now that wealthy alumni write checks to their alma mater. The lines between Silicon Valley and Stanford are ever more steadily blurring. When the needs of education conflict with the prerogatives of headlong enrichment, which will Stanford choose?

Photograph, of students at Stanford University, by Susan Ragan/Bloomberg/Getty.