Tobin makes references to David Lynch films a number of times on Permutation. The song "Like Regular Chickens" contains a line of dialogue spoken in Eraserhead, while the title of the song "People Like Frank" is a line of dialogue from Blue Velvet. The song also samples a part of Angelo Badalamenti's score to that film. "Fast Eddie" is probably a reference to Lynch's Lost Highway character Mr. Eddie.
On the LP edition of the album, "Melody Infringement" is added as a bonus track