I barely know how to begin.

I think part of what I see as the problem of your position is covered by Dr. Manhattan:
Thermodynamic miracles... events with odds against so astronomical they're effectively impossible, like oxygen spontaneously becoming gold. I long to observe such a thing. And yet, in each human coupling, a thousand million sperm vie for a single egg. Multiply those odds by countless generations, against the odds of your ancestors being alive; meeting; siring this precise son; that exact daughter... Until your mother loves a man she has every reason to hate, and of that union, of the thousand million children competing for fertilization, it was you, only you, that emerged. To distill so specific a form from that chaos of improbability, like turning air to gold... that is the crowning unlikelihood. The thermodynamic miracle.
How many rapes are in my genetic history? How many people had to sail from different parts of Europe in what seem to me to be not much more than canoes in order to meet way the heck over on this continent in order to have sex at the exact moment with the exact sperm and egg meeting so their child could travel a couple hundred miles on horse and run into this other person and... It's not possible for me to exist. Go back 10,000 years and we have no means to imagining who will exist today. But it happened exactly as it happened, against a googol-to-one odds.
It seems to me you are looking at this impossibly complex thing - the mind - from the end, and saying it could not have come about.
But maybe all of that is not what you think, and I wasted time writing it. Well, I
did write it, and it
is Dr. Manhattan, so I'll leave it there.

Still, I think it's more accurate to say you believe the mind cannot exist within, or maybe cannot have come from, the natural laws we know. So I'll try to address those ideas, using this as my starting off point...
Zarathustra wrote:Fist and Faith wrote: We can examine every atom in a computer, and have no idea of what it is about to do. The same is true of the brain. Not being able to predict what a brain will do by examining every atom in it is not evidence that the mind is anything other than the brain's activity.
I thought that by determinism you mean that if we understood a system down to its atomic level, we'd understand everything about it. If you know its current state, and the laws describing its change of state, then you ought to be able to predict its next state ... unless something more is going on that reductionism doesn't capture. For the brain, I believe this "something more" that you can't capture is the subjective content of experience (which influences one state to the next). It won't show up under any objective examination of the positions of atoms. The content of a computer program, however, would.
Therefore, since there would exist something that can't be described deterministically in terms of objective matter, then mind is indeed something more than the brain functioning.
Argh. Sorry. I didn't word it very well. I meant
we can't predict what a computer is about to do by examining every atom. We could be on the holodeck, surrounded by a holo-representation of every atom in a computer. (Whatever scale we want. Atoms appearing the size of grains of sand, or basketballs, or whatever.) I don't imagine anyone would even know it was a computer, much less understand it to the degree we're talking about.
But an intellect VAAAAAAAASTLY greater than ours would. A great enough intelligence could understand what this group of atoms over here is currently doing, and how that will affect these atoms, and how electrons will move over here, then these atoms will do this, etc. And this intelligence would understand how that translates to the computer's operations.
And yes, I think the same can be said of the brain. Any number of things that might seem to poke holes in my position can be brought up. The problem with all of them is that they all exist within this reality. Therefore, the properties/characteristics of this reality are the answer.
-The mind controls the body.
-It does not do so by means other than bio-electrical/chemical.
-It cannot use those means without being
of those means.
-If it is of those means, it is subject to the same properties/characteristics as everything else made of those means.
That's where we will find the answers to the tough questions. I can come up with a scenario for how anything came about, whether it's the mind or the rules of baseball. The degree to which my answers are not satisfactory are due to the fact that I am not the right person to be answering. I'm not an expert in one damned thing, and all of this stuff is way beyond me. But the answer
must be in this stuff. The alternative is supernatural, by the literal definition. Beyond the laws of nature. But we know all of this is part of nature, so it cannot be beyond nature's laws.
And why should we think this is all beyond the laws of nature? With all the we've seen happen so far, all built from particles? Quarks and gluons join together be make protons and neutrons. Groups of protons and neutrons circled by electrons somehow manage to join together in specific ways, until we have RNA. Non-living, self-replicating. Eventually forming DNA. Somewhere along the line becoming living. How much of that sounds possible? And yet, out of that, comes us, life with minds of great awareness. It's the latest stage in an amazing progression. All driven by the ways particles interact. Yes, "higher" systems arise from "lower" systems. But the higher are not independent of the lower; they are merely an easier way for us to understand, and operate in, the higher level. We know how the particles behave when they are in groups we call "flesh", and in groups we call "metal". A surgeon does not need to understand how the scalpel's atoms separate the molecules of the flesh. But that's exactly what is happening, and it's happening because of the way particles interact. The antibiotic works by killing the bacteria. But it does so via some bizarre crap like hydroxyl radicals destroying the lipids and proteins in the cell walls of the bacteria. You can kill someone by not letting them breath. But that means the red blood cells could not pick up oxygen molecules and take them to the brain where they do whatever the hell they do there.
Now you say: "Yes, but this other phenomenon - the mind - is not like every other phenomenon."
And I say: "Neither is life."
You: "But life can be explained by the laws you're talking about. The mind cannot."
Me: "The mind exists in, and continually interacts with, those laws. It
is part of those laws. It cannot
not be. The explanation cannot be elsewhere. We just haven't come to understand it yet."
Pugh again: "If the human brain were so simple that we could understand it, we would be so simple that we couldn't."
There is no freedom from the realm of particles. The mind is entirely dependent on them. We can easily demonstrate this by removing or adding particles (brain injury, hormones/chemicals), and watching the mind change. Or disappear.
So that's what I think. Now you ask this:
Zarathustra wrote:What's the difference between a) natural selection shaping our genes and b) humans shaping their own genes through genetic engineering--if everything reduces down to particles/forces/fields?
This conversation brings to mind an episode of
Colombo. He needed to prove this guy did not have ESP. But the guy pulled off an amazing trick. Colombo was being helped by this kid who was an aspiring magician. The kid said something like, "To figure it out, we have to remember it's not real. He doesn't have ESP. It's a trick."
I'm not saying we're dealing with an illusion. I'm saying we know what our starting point is. We have to build the answer from particles up, and never forget that it all comes down to particles. When we look for the answer outside of the ways nature works, we have gone off track. We know this, because the mind, controlling the physical body by physical means, reveals that it is of the same system.