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It is not the case that all, or even nearly all, scientists are atheists. I happen to be an agnostic scientist; several of my most able colleagues are devout Christians and others belong to other denominations.

However, none of my religious colleagues ever invoke their deity of choice as a cause for any scientific phenomenon. The principle reason for this is Occam's Razor, which can be paraphrased as "If you have two explanations for the same thing, and only one of them requires something supernatural, the other one is better." That is to say, "A gust of wind knocked my CD tower over" is a better explanation than "My house must be haunted," and "A combination of genetic mutations and natural selection which has been observed and explains how modern life came to evolve" is a better explanation than "God... sorry, an Intelligent Designer did it."

Science requires finding as simple an explanation as possible for natural phenomena, testing to see if it hold true, and testing predictions made by the explanation against observations in the future. Biologists predicted that intermediate steps would shorten the so-called 'gaps in the fossil record'* - and they saw that the theory was good. Einstein predicted light would change path close to a massive object. The experiment was done, and they saw that it was good. Chemists, geologists, psychologists, even economists all do the same thing - hypothesise, predict, test. Some theories are very difficult to test - what happens in a black hole, for instance. However, the theories are there to be tested, and build on previous theories that have been shown to work.

Science frequently makes mistakes - we need only look at aether and geocentrism to see a couple of badly flawed theories. These were abandoned, not because someone said "Wait! No, we need some supernatural character to make this work!" but because someone said "There's a better, simpler way." Aether wasn't necessary to allow waves to travel; placing the Sun as the centre of astronomical calculations made everything much clearer - and made sense of subsequent observations that would have been impossible to reconcile otherwise. This is how science evolves: people have better ideas, that can be tested.

None ever needs to posit such ideas as "maybe the speed of light was different in the olden days" without at least suggesting a mechanism by which the change could have occurred. Oh, and look back to the second paragraph: God did it doesn't count.

In short, it is possible

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