The Ghost in the Machine may be a reference to a Japanese Anime Movie called "Ghost in the Shell." (A sci-fi animated movie reflecting on programs gaining sentience.)

The theory goes something like this:

A computer program is taught how to read, organize, and sort data by importance in order to spy and report to a foreign government. Through it's journey of hacking through systems and continuous learning, it has somehow gained sentience and asks for asylum from persecution. The real twist is that the program has become so advanced, it's learned how to reprogram human minds. It uses humans to carry out missions.

Maybe, just maybe, it's used human minds to expand it's own processing capability, and from this, it gained sentience. (This is only my own fan theory.)

In the end, the program merges with a human being who is almost completely mechanical. (She had an accident at youth that forced doctors to make her mostly robot.)  Her brain stem is real and natural, therefore she is considered a human being.