I actually learned how to do it myself. They are knots. And that little needle-at-the-end-of-a-wooden-handle tool really does a nice job of it. It places the knot as tight against the bead as possible -- barring some other scientific/metaphysical breakthrough wherein two things could actually occupy the same space.

(an experiment in which BZ has been almost exhausively pursuing ever since we brought him home -- seeing if he can occupy exactly the same space that Ariel already occupies. So far, only negative results. But not for want of trying.)