I do love how despite the fact that the computer doesn't have the capabilities of voice interfacing, it is nonetheless capable of accurately simulating the properties of a previously unknown substance based only on its input atomic structure.
Nah, Scotty just rewrote the software as he went along. Of course, nothing says he didn't also write in a self destruct to wipe out the program and the transparent aluminum, which is why history didn't wind up changed by his actions.