This is part of a discussion I had with Jewish Philosopher regarding evolution (isn't it always, sigh...). I had to edit it here and there for it to make any sense in this kind of presentation, but if you want to see it in its original entirety, just click on the link above.
Now, this whole post does not have anything much to do with evolution specifically, but it is useful as a way for me to explain my view of how science operates and how it is a rather different kind of way of thinking.
"I still have no idea why "God did it" cannot be the truth, whether we want label that fact science, theology or whatever."
It can be truth, but unless you can demonstrate it with direct evidence and a definition of what God is and how he did that creating then all you have is speculation and it cannot be called scientific. You may come to your conclusions through extrapolations of known facts, but you are necessarily making assumptions (skeptics would call them unwarranted ones) that are not founded in scientific methodology when you approach metaphysical levels. It is unavoidable.
Science tells us what the conclusions can be based on the evidence at hand. The conclusions may not be what is actually true though. But most rationally-minded people have trouble dismissing the conclusions of science because the known objective evidence is always on their side.
At the end of the matter, what we can say of evolution is that it is true as far as we know (specific mechanisms notwithstanding), but that our knowledge could be flawed in some way. Scientists are not stupid people, they know that evolution is far from a complete theory and they have vigorous debates amongst themselves about how evolution may have happened. None seriously posit a divine director though because no evidence points to that above any possible natural causes. It's not that that is an impossible conclusion, but that it's not a reasonable conclusion before they consider more naturalistic explanations.
"As far as I can tell, and please correct me if I am wrong, you are basically saying that since evolution is atheist [does not involve a god] therefore it is inherently superior to intelligent design theory which is theistic."
No, that's incorrect. I didn't say anything about superiority, just about how science operates and thus how scientific an explanation can be. And the interpretation of evolution being atheistic or not is irrelevant. Theism is simply an added concept not needed to explain how evolution occurred, as far as we understand evolution at this time.
In the same way one might study a murder mystery there are certain ways of going about figuring the puzzle that make more sense than others. You find evidence, you talk to witnesses, you figure it out without supposing miraculous events, etc. Because if you suppose a miracle happened, then why would any piece of evidence ever indict any individual? It could have been a miracle that his evil twin popped into existence, did the deed and then popped out of existence. Absurd, to say the least, no?
Now science is like this kind of rational investigation - but, I said, it is conceivable that even rational investigations can be wrong. Maybe some evidence is missing, maybe someone didn't think something through enough, etc. So in reference to evolution, it is not a _necessary_ conclusion to discount supernatural intervention, but it is also not something that is rationally required.
Scientific investigations are only superior in the sense that they take into account all the available objective evidence and rational considerations. But in doing so they are inherently limited. For the world as it actually is may be more than what is known today or what the human mind can conjure up to explain the observations.
Science's power is in the fact that it sticks to the facts and doesn't extrapolate beyond them. In fact, evolution says nothing about God one way or the other. In the same way science doesn't posit God to be the force pulling us down to Earth or the force that makes water boil, science doesn't posit God to be the force that causes evolution to occur. Now, it could be that God is involved in all those things, but it is just not a required actor to explain the facts that we know about.
"To continue with your crime analogue, let’s take the still controversial President Kennedy assassination. The President is riding through Dallas. Suddenly, a piece of lead shaped like a bullet strikes his head and kills him. I would logically conclude that this act was committed by an intelligent being. In other words "Oswald did it." However let’s say that someone would claim that involving an intelligent being is entirely unnecessary. There is no reason why a meteorite shaped exactly like a bullet could not have caused the President’s death. Would this be accepted by the police? Is this somehow a more rational and scientific point of view?
This is exactly how I feel when debating evolution. An evolutionist will claim that involving an intelligent designer is entirely unnecessary to account for life; a natural process, however poorly understood or unlikely, could somehow have done it. Maybe. But why does he have to insist on that? Why not reach the apparently simple, obvious conclusion, accepted by everyone before Darwin, that there exists an intelligent designer who created life – in other words "God did it"? I cannot help but feel some sort of mental block is in involved here; a profound emotional denial."
You said: "Suddenly, a piece of lead shaped like a bullet strikes his head and kills him. I would logically conclude that this act was committed by an intelligent being."
Why? You're not making that conclusion based on that simple analyzation, there are numerous unstated pieces of information that are involved. One, bullets often come from guns fired by people. Two, people are generally intelligent beings. Three, the President of the United States is not an unusual target for assassins, etc.
If you knew nothing of bullets and you knew nothing of politics or people then that initial statement that a "piece of metal struck a guy in a car" could easily be explained by a meteorite. Only once you have all that additional information does it make sense to posit an intelligence out there with an intent to kill.
Before you can posit an intelligent creator you need to have at least some of those kinds of similar information. How did it do the creating? Why did it do the creating? Is there an intent with creation? What is this intelligence? How does it work?
You don't have any of that information and that is why science cannot seriously posit it. Science sticks to the facts. It is a deeply conservative methodology in that way.
"I cannot help but feel some sort of mental block is in involved here; a profound emotional denial."
I don't think you understand how science operates. Science is not in the business of telling you absolute Truth (with a capital T) or how to live your life or what politics to follow. It is a conservative methodology which follows the known facts and makes theories based on what is known. It may be wrong it may be right, but either way its methodology is certainly a rational one.
What a belief in God is is a step away from the conservative rational methodology to what one believes is correct anyway. It is an assumption found without conclusive evidence. People who follow strict scientism though cannot make that jump. They follow that conservative methodology even into their personal lives and beliefs. It is more often a love for science and rationalism than an attack on God which leads people to rational atheism. It is the outcome of purely rational conservative thought.