This week's Time magazine has an interesting little debate between atheist/scientist Richard Dawkins and Christian/scientist Francis Collins.
The one thing that struck me about the whole debate was was how Dawkins was willing to assume that there may be millions of parallel universes (the multiverse) that we know nothing about and have no evidence for, yet entertaining the mere possibility that there is a God who created all of this was out of the question.
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In Dawkins's defense, there is empirical evidence that *something* screwy is going on with quantum mechanics, and the "multiverse" explains some of the screwiness. (Short version of an example of screwiness: a single photon going through a series of slits exhibits wave-like behavior--constructive and destructive interference--even without any other photons to interact with)
That being said, I do agree with you that scientists are often willing to resort to "and then a secular miracle occurs" to explain something. Of course, at the same time, we have to acknowledge that the "and then a miracle occurs" point keeps getting pushed back. Still, the leap of faith to deny God is at least as large as the one to acknowledge the possibility that He exists.
Dawkins was referring to String Theory and some of its conjectures. String Theory is yet short on proof, and may ever be, but it _is_ an attempt to account for the oddities observed in in the real world. He still has the advantage over believers, who have not been able to point at divine phenomena, or even define what they could be---what is the Lord made of, if not quarks and leptons like the rest of us? Are there special particles for miracles?
For deficiencies in String Theory, Smolin's The Problem With Physics is highly recommended.
For deficiencies in Richard Dawkins, the last two weeks' South Park are recommended. To be an atheist, you shouldn't have to be a jerk like Dawkins is in his new book.