The definition of science: What should it be?

You're just making this up. Aren't you? I mean, you didn't actually look up "methodological naturalism" at all before you posted this, right? Here's the first paragrahp from the Wikipedia entry on "methodological naturalism":

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Naturalism is any of several philosophical stances, typically those descended from materialism and pragmatism, that do not distinguish the supernatural from nature. Naturalism does not necessarily claim that phenomena or hypotheses commonly labeled as supernatural do not exist or are wrong, but insists that all phenomena and hypotheses can be studied by the same methods and therefore anything considered supernatural is either nonexistent, unknowable, or not inherently different from natural phenomena or hypotheses.

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Now, how did you get what you posted from that? Why is it that your definition of "methodological naturalism" seems to have absolutely nothing to do with either "naturalism" or "methodology"? Not really. There's the real definition, as defined by people who are methodological naturalists; and then there's the definition you posted, which you just made up.That doesn't really "confuse the issue." The only thing confused seems to be your understanding of what words mean.Since you oppose methodological naturalism, could you post a coherent explanation of what "methodological supernaturalism" would be? For that matter, what is the supernatural? There's only one coherent definition that I'm aware of:

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Supernatural abilities are magical and go away in an antimagic field but are not subject to spell resistance. Supernatural abilities cannot be dispelled. Using a supernatural ability is a standard action unless noted otherwise. Supernatural abilities may have a use limit or be useable at will, just like spell-like abilities. However, supernatural abilities do not provoke attacks of opportunity and never require Concentration checks. Unless otherwise noted, a supernatural ability has an effective caster level equal to the creature's Hit Dice.
The saving throw (if any) against a supernatural ability is 10 + 1/2 the creature's HD + the creature's ability modifier (usually Charisma).

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Doesn't seem very relevant to science, though. (Courtesy of Bronze Dog.)

I dunno. What is it?

There's a 3rd option - ask us questions. Ask us to explain things you don't understand.I get that evolution doesn't make sense to you. But surely you recognize that it makes sense to us? Why don't you ask us the questions you need to ask to understand why?

So, your response to my suggestion that you ask questions to learn more is to insunuate that I want to herd you into a gas chamber and murder you?

This is what could be called "the fallacy of false parity." Other people have hit most of your errors but I thought I'd take this one: This is demonstratably false. All one needs to do is observe that atheism predates evolution to refute your assertion that evolution forms a basis for atheism.

Because a half truth is better than an all lie.

So you say, but here we are using computers to access the internet, you from California and me from Missouri, thanks to the study of physics, chemistry, and mathematics. I'm sure you're nowhere near as old as your avatar (I'm certainly not as green and leggy as mine) but you probably know people who are; they're still alive because of advances in medicine and biology.It certainly wasn't religion that brought us any of those things. The fact that science is the tool for approaching truths and developing models about the natural world is obvious to the most casual observer.

If you say so, but honestly I'm not aware of any area where the basic idea of consensus observation wouldn't work. Maybe you have something in mind? And I put my trust in those who get results. The results of science are manifest. The results of wooly, spiritual thinking? Bupkis.

Wrong theories don't get much work done.

No, they didn't. And to portray the Holocaust as some kind of atheistic, scientistic investigation carried out with no regard to human sensibilities is absurd, and displays an ignorance of history.The Holocaust was a sectarian conflict between German Christians and Jews, just about any way you look at it. Mengele wasn't a scientist; he was a sadist in a lab coat. A torturer, not an experimenter.And I don't find the testimony of two dead white guys that the culture they grew up in and lived all their lives in was better than everybody else's very compelling. Everybody says that about their own culture.Norman Borlaug used science to save 1.5 billion lives. That's "billion" with a "b." Your religion had absolutely no power to do the same. If not for science, they would have starved to death.

That you, apparently, have a really weird definition of "work." Apparently, you look back over the scientific, medical, and technological achievements of the last 600 years - extending life, conquering diseases and famines, exploring the world of the atom and the far reaches of the solar system - and don't see anything particularly interesting or significant.