There are things which are common to all of us, such as the instinctive reaction to pulling your hand away from a naked flame.
The line between genetic "programming" and "learned behaviour", however, is not necessarily easy to spot.
There are some behaviours that are common to all of us born and raised in this country (ie, the West), that might not be found in a feral child raised by monkeys in the jungle (extreme example).
Given that the brain is experiencing stimuli in the womb, and therefore learning, and the brain is constantly being altered (physically) by stimuli, it might be very easy to assume that babies are born with "pre-programmed instincts"... when these might actually be learned behaviours that just happen to be common to all of us, as we all spent 9 months (give or take) in the womb.
But let's get back to AI, here. You said that we're "pre-programmed" to breathe, and to react to pain, etc. And we'd all agree, I hope, that those are very basic (tho vital) responses/behaviours.
Our more complex, sophisticated behaviours, are learned. You do not acquire the ability to drive through any instinct. Or to play guitar. Or to solve equations. All this is learned, studied, and perfected.
A piece of software can be programmed to perform a task that its human designer knew how to define in precise terms.
A computer can never learn to do anything if there is no human around to precisely define the problem and the method of its solution.
A computer cannot gaze at the stars, observe a falling apple, and make theories about the world it exists in.
This conversation to me only highlights the gulf between man and machine.