I think it's important to mention what the term "bone machine" refers to. I think the concept is present both in the Pixies song, and behind the songs on the Tom Waits album. (While the Tom Waits album is not the soundtrack to a story, it was recorded in-between two albums, Franks Wild Years and The Black Rider, which were - it is my belief that, though there may have been no story intended, there is possibly one present.) To put it bluntly, a bone machine is a human. The term refers to the similarities between a human being and a robot, the difference being that we are made out of flesh and bone. Treating humans this way reminds me of the myth of Golem.

Tom Waits took this concept one step further, enunciating the thought process behind his album in a sound clip and interview CD put out for Bone Machine, entitled Operator's Manual. If the human is the machine, then who is the operator?