The Conscience Circuit is described to allow a robot to develop a sense of mortality to discern good from evil so to discern being manipulated by those like Professor Gill. However, Paul Walker's Conscience Circuit is left incomplete and thus enables Paul to possess free will to act beyond his programming (which differs in each series).
However, the Conscience Circuit doesn't appear to be everything for a robots sense of morality as there are times when Paul actually harmed people (including innocent ones) out of self defense or rage. This could be the result of Paul growing up and becoming more human.The downside to the incomplete Conscience Circuit is that Paul is susceptible to the ultrasonic frequencies that compromise the melody produced by Professor Gill's flute.