Science is largely concerned about what is the case with the physical world. Morality can be defined as what should be the case.
Sam Harris has written a book called "The Moral Landscape" and it is well worth reading. I agree with most of what he says in the book. But I do not agree with his idea that free will is an illusion (Indeed he has written an entire other, short volume called "Free Will" defending this idea). I do think that most discussions on free will occur at cross purposes. But Sam believes that free will makes no sense. I understand entirely his position and can defend that view, without lying, myself. However I actually do choose to believe in free will because the string of characters "free will" really can be defined in two quite different ways. One way - the route Sam takes - results in a completely coherent argument where determinism rules out free choice. But the other way says that there is no reason to believe choice cannot be a top-down phenomena.
Morality is what we choose to do and choices are real. The correct explanation for why it is that the thief stole the car is because he chose to. This is just as deep, just as fundamental as the explanation that "the thief stole the car because certain neurons over which he had no control fired". Or as opponents of free will would have it: over causes and events occurring inside his brain, and beyond, and over which he had no control.
Now clearly there are antecedent events outside our brain, of which we are not aware, which can and do cause events in our brain over which we have no control and so no choice. But this does not change the fact we have free will in the sense we make our own choices and we are responsible for those choices and those choices are free. There are levels of explanation at work here and just because one chooses to explain certain phenomena at the level of the atom, or the level of the neuron does not mean one has chosen the best level. This is the sense in which I mean I choose to believe in free will because I choose a particular level of explanation. And it's not the "everything is just atoms moving in the void as described by the laws of physics" level. And, by the way, that is the proper place of the laws of physics: they are descriptive not prescriptive. That is to say - the laws of physics cannot tell you what to do. Because they have no agency (no will, no capacity to think, no "free will" of their own). So they cannot force you to do things. In fact they are just a description of what it is, and is not, physically possible.
An example might serve my purpose well here. And I take this from David Deutsch's "The Fabric of Reality". He was using it to illustrate something a little different - but it works just as well here.
Consider the statue, made of brass, that stands in Trafalgar Square in London of the great wartime Prime-Minister Winston Churchill. Let's ask: at the tip of Mr. Churchill's nose: why is that one copper atom there?
One way to respond to this is to appeal to physics. We might say: well that atom was bumped there by another copper atom, and that atom bumped into position by another copper atom and so forth back to when the copper atoms were generated inside the supernova explosion of whatever star they came from and before that the protons were generated at the big bang. And in principle - if not in practice - we could trace the cause and effect of particles moving through the void back to the beginning of time if only we had knowledge of the equations of motion and positions of all the particles. And so the answer is: that atom is there because of its motion and the laws of physics governing its motion and the motion of all other particles which ever interacted with it.
Now clearly that is one possible answer. And it's correct. So far as it goes. But is it sensible or silly? Because here is another explanation - equally correct and one that makes more sense.
That copper atom is there because the statue is made of brass. The statue is made of brass because brass does not corrode and the people who make statues like to choose materials that will weather well over time. That particular statue is there because Winston Churchill was a great leader of World War 2 Britain and it is customary to honor great leaders like that by building statues of them and putting them in public places like Trafalgar Square. And that is why the copper atom is there.
So we have two explanations. Two correct explanations. But one of them makes more sense. It explains why the copper atom is there and not somewhere else (like the other side of the planet in the ground somewhere). It uses concepts from history and politics - emergent simplicity rather than the laws of physics. If we tried to explain history, politics and culture in terms of the laws of physics things become ridiculous quickly.
So why do people do what they do? Is it because one charged potassium atom goes this way rather than that way down an ion channel to cross a synapse causing a neuron to fire that otherwise wouldn't and which all in obedience to the laws of physics over which the person has no control, and this causes ultimately, the decision of the thief to steal the car? Is that the best way to look at things?
Or is it that the choice originates with the person? And the person, making the choice then causes neurons to fire?
There is no reason to think that only lower level phenomena can have causal effects on higher level ones. Higher level, emergent systems can effect lower level ones too. Consider: when you turn the steering wheel of the car, the causal chain works in the following way: a signal from your brain goes to the muscles in your arm and causes the wheel to turn. The axle then turns the wheels which causes the tires to follow and because of friction they grip the tar on the road and the car moves. Back at the point on the road where the tire was in contact with the road, the tar rises in temperature (only a small amount - but it's enough) and this means the atoms in the road are vibrating more. A high level phenomena (your turning of the wheel) has caused atoms in the road to vibrate more. Not the other way around.
That's not difficult to appreciate is it?
So it can be with your own brain.
So we are free to make our own choices. We choose what we want to do. But what should we want? We should want to increase the well being of conscious creatures. And we don't need to deny free will in order to appreciate this.
But although "increasing the well being of conscious creatures" is something it's difficult to deny is better than not increasing the well being of conscious creatures how best to actually to do this is a moral question. What path towards better well being should we take? In short: what should we do to increase well being? This moral question can't be answered by simply saying "well do whatever it takes" because there might be infinitely many possible paths that will increase well being of all conscious creatures by the same amount and new knowledge (which we cannot predict) could be discovered and change the amount by which that well being changes. Morality is always about what to do next. And I try to explain that here http://www.bretthall.org/the-moral-landscape-challenge.html