This question is better suited for a philosopher rather than a biologist: http://en.wikipedia.org/wiki/Philosophy_of_mind
Usually.
Biology can explain how neurons in the brain (computer) works. It can also potentially explain how thought and logic play out (program logic). But how do you explain consciousness in this metaphor? this.isRunning? Or does it make more sense to say that even if we understood all of biology, there are still things that we won't fully understand?