How can a certain bunch of atoms be more self aware than another bunch?
Good question, but I hope you didn't intend it to be merely rhetorical.
Even at this early stage of our investigations, there's good evidence that the answer has to do with whether a given bunch of atoms composes a being that possesses a complex network of neurons. Some bunches of atoms, such as the bunch that composes me, do compose such a being. Other bunches, such as the bunch that composes my favorite pen, do not.
Notice that we're not tempted to regard any of these similar questions as rhetorical: How can a certain bunch of atoms be more red than another bunch? How can a certain bunch of atoms have better eyesight than another bunch? And so on. I regard the question you asked as in the same boat as those.