When Darwin is relaying the alien's information regarding stellar distances (in order to establish a mathematical basis for communication), Lucas erroneously says that the distance from our Sun to the center of the galaxy is an "astronomical unit" (an AU is, in fact, the mean distance from Earth to our Sun).
The crew ascertain that the embodiment of the alien is simply silicon manipulated by magnetic fields. This is why it can pass through solid objects, while leaving behind a silicon residue. However, if this is correct, then no silicon at all would be able to pass through objects, leaving far more residue, and the 'alien' would disappear completely afterwards, until it found another source of silicon to become visible again.