Ooh, my favorite debate topic merged with my favorite manga! Sorry, but I fear I'm about to overdo this.
First of all, I disagree with the conclusion you guys have reached that God is irrelevant in Edward's mind. Ed's flat out met the Guy! The shadow-being which is at the doors is God. He said so.
Online Manga Viewer 1.2 Alpha The powers that he plays around with in that chapter suggest to me that he wasn't bluffing.
This raises the question of what Ed was talking about in the first chapter, saying he was an atheist when he'd already talked face to face with God. I think he meant that he was an atheist not for the normal reason, lack of belief in a god, but because he did not worship a god. While we tend to divide people into theist, atheist and agnostic today, atheism and agnosticism are technically the same thing-- a lack of religion. Ed lacks a religion because he does not worship a god. Mostly. I'll come back to that.
The other confusing thing Edward said in that chapter was "Alchemists are scientists, so we can't believe in vague things like the "Creator" and "God." Ed sees laws as limits, and God in this story is what limits him from resurrecting his mother, and certainly makes fixing his brother very difficult. Ed is saying that alchemists must deny their limitations, especially when they are vague and uncertain. After all, you won't know where the limit is until you have passed it. Of course, Ed has passed his limit by attempting to resurrect his mother, but he does recognize this limit now. He makes the reference to Icarus' flight, which fortifies the idea of God (represented by the sun) being a limit on human potential.
You could also interpret that as Ed denying the existence of specifically the god which Rose was describing.
Now, as far as alchemy being a science, it is. In real life. A failed science, since to transform another element into gold would take more energy than its value in oil would provide. Of course, alchemy in the story is very different, but it's virtually chemistry. In chemical reactions, you put in a certain amount of matter, and get out the same amount. It's equivalent exchange. We don't fully understand where the energy to create the reaction comes from in alchemy, but that's the only part that can be construed as magic.
Lee's comment while he and Ed were inside Gluttony that Ed's transmutation looked like prayer suggests one source of the power-- that alchemists are actually demanding it from God. In that sense, since alchemists are always interacting with God, it could be called both a science and a religion. However, this doesn't explain why Father could stop it, but I expect that will be shown in time.
As far as science not having any more credibility than religion, I'm not quite sure how to debate that. In my mind, logic is simply a component of science, and to use science to prove science doesn't make any sense. Um, whatever, I'll give it a whirl.
When people learn, they are preforming a simplified version of the scientific process. Humans learn through experiment, through touching the stove, observing the pain, and concluding that it is detrimental to touch it. Every one of us performs experiments every day. It is how we instinctively find truth, it is how all life looks for truth.
Wolven, your description of scientific experiments implied that they are inherently tainted. They are not. If you count the number of deer in a field, you learn the number of deer in the field. If you return and count again the next year, and the next, you will learn if the deer population is increasing or decreasing. You must be careful not to disturb the deer or the environment, but researchers are trained in that. Give me a way that this experiment could be contaminated, and I believe I will be able to solve the problem.
Even if the scientist deliberately acts as "God" in an experiment, truth can be found in it. The scientist can gather a bunch of supplies, and try to use them to light a match. The fact that he is trying to light that match does not change the fact that, when it catches on fire, the scientist will know for certain that those materials can light that match.
One argument that I hate to hear is an appeal to the majority. "If all these people believe this, it must be true." But I've never argued this before, so I guess I will throw the argument out there anyways. There are no truths more universal and undeniable than those given by science. It is always easy to find someone who disagrees with any statement made through religion. I have never heard anyone deny that fire is relatively hot. Of course, some ideas given by science are more controversial, but the same is true for religion. If science can give truths which everyone agrees on, and religion cannot, then is science not more credible?