Bunjo was a Millenarian math built around an empty salt mine two miles underground. Its fraas and suurs worked in shifts, sitting in total darkness waiting to see flashes of light from a vast array of crystalline particle detectors. Every thousand years they published their results. During the First Millennium they were pretty sure they had seen flashes on three separate occasions, but since then they had come up empty.
Compare this to the following paragraph from Lee Smolin's book "The Trouble with Physics" that tells the story of failed attempt to detect proton decay - the effect that, if observed, would confirm a wonderful physical theory known as SU(5):
... all you had to do was surround the tank with detectors and wait. Funds were raised, and huge tanks were built in mines deep underground. The result were impatiently awaited.
Alter some twenty-five years, we are still waiting. No protons have decayed.
Add to it that Stephenson specifically lists Smolin's book among the sources for Anathem at his Acknowledgements page, while Stephenson's praise for the book is printed on its back cover, and it's easy to imagine that the former quote is a joke at the expense of the latter.