I tend to think our mind consists of at least two levels of 'self'. The conscious and subconscious, which I tend to think are the 'animal mind' and 'soul mind' respectively. I say "at least" two levels of self because I'm not totally convinced the subconscious is the soul mind. The subconscious itself may be part of the physical/animal mind, but the point is, I believe our highest 'self' transcends the physical body and brain.
I think the brain is more of a control panel for our higher self. This is, of course, not the scientific view, which suggests that everything occurs in the brain itself. But I think the observed neural activity in the brain is not merely the result of the brain's physical functioning, but the result of that 'neural activity' interfacing with the brain.
Scientists have taught us many things about our limitations. They've taught us that our eyes can only see an itty bitty little bit of the light spectrum. There are certain things we can't hear. They've even taught us that this varies animal to animal. Dogs don't see as many colors as we do, but they can hear and smell things better than we do. But despite the limitations we have, scientists seem to ignore these limitations in their experiments. They only care to study what they can observe. If they can't observe it, then it must not be. How ironic?
To get to the point I want to make in this post though, when it comes to the brain, I think scientists may be limiting their answer to "why" the brain works with "how" it works because they cannot observe "why" it works. To use an analogy, if Person 1 is using a touchscreen cell phone and started moving an object around on the screen with his finger and then asked Person 2 why they object was moving, Person 2 would probably look at Person 1 stupid and answer, "Because your're moving it around." And yes, that is WHY the object is moving around...because someone is moving it.
But let's say Person 1 who is moving the object around on the screen is invisible. A Person 3 comes along and asks Person 2 how the object is able to move. To investigate, Person 2 may get a screwdriver and take the back off of the phone. After some investigation, Person 2 concludes that the circuit board is what enables the object to move on the screen. Not only that, it appears that the circuit board is what makes the whole phone function! But that is HOW it works. That doesn't answer WHY it's doing what it's doing.
The answer to WHY the circuit board is doing what it is doing is because the invisible Person 1 is instructing it on what to do. But because Person 2 and Person 3 don't see Person 1, they assume that the circuit board must hold all the answers, including the answer to why. As a result, the answer to 'why' gets lumped together with the answer to 'how', or they just continue to look at circuit board for many years trying to find an anomaly that may explain - or can be interpreted to explain - 'why'.
If Person 2 and Person 3 limit themselves to only considering what they can observe, then they may never understand that the intelligence - the why - behind the circuit board's operation is the invisible Person 1.
"We have to remember that what we observe is not nature in itself but nature exposed to our method of questioning." -Werner Heisenberg, theoretical physicist
P.S. Just to add another point to my post, lumping "how" and "why" together seems to be common in science. For instance, I googled the question of why the sun is hot. Here is the first answer to come up:
The sun is hot because the atoms deep inside the sun are undergoing nuclear fusion. Nuclear fusion releases a lot of energy. This energy excites all the other atoms in the sun, and causes them to move about. This is what heat is. So the nuclear reactions inside the sun cause the sun to be hot.That answer came from the University of Illinois Urbana-Champaign Physics Department.
But why are the atoms deep inside the sun undergoing nuclear fusion? Why does nuclear fusion release a lot of energy? Why does nuclear fusion even occur? What is it that makes the laws of physics what they are? Why is that the way it 'is'?
I think the answer given to why the sun is hot would be like someone asking a hunter why he shot a deer, and then the hunter answering because he "pulled a trigger on the gun, which ignited a reaction in the chamber, which propelled a bullet toward the deer, which blasted through the deer's heart, cutting off its blood circulation, which caused it to fall over dead." Imagine getting that answer instead of just getting an answer like, "To eat it." So in this case we have 'what' happened; the hunter pulled the trigger igniting a reaction that propelled the bullet towards the deer. As to 'how' the deer died, it was the bullet going through its heart and cutting off its circulation. But as to 'why' it all happened, it was because the hunter wanted to eat it.
Maybe this is the key difference in religious studies and scientific studies. Religion wants to know why, but science wants to know how. Perhaps we could have an even greater understanding of things if we recognize that each question needs to be answered separately.