They are still programmed machines built by machines.
If you can place any credibility in Skinner and his ilk, so are we. Many human biological functions (such as blood sugar/insulin curves) are classic problems in feedback control systems text books.
Certain parts of that are debatable. Recalling that the story is Science fiction, remember that Sharon rebelled against programming when she took Helo in different directions than she was instructed to do on Caprica.