Here's a specific example of your slime mold hypothesis [1] in which a slime mold grew a network just like Tokyo's rail system.

Slime mold doesn't have the same ring as "rail network planning AI", but it seems that's what it is.

1: https://outline.com/t8hxKh (original: https://www.wired.com/2010/01/slime-mold-grows-network-just-...)