Science can only use natural rules and laws as causations for explanations.
At root, you're approaching the problem from the materialistic standpoint, which a priori assumes that God plays no active role in the universe.
But suppose, for the sake of argument, that God exists, and that He was/is involved in the creation of life. In that case, your version of science would appear to be futile. But that's not a failure of science, per se, so much as it is a failure of your assumptions to account for all possible explanations. Your definition of "natural" would obviously be inadequate.
God is outside of those rules, he can break any rule he wants at any time, therefore any explanation using God as a causation will only be true when and if God decides to intervene.
This is a strawman argument, whereby you assume what God will or will not do, and then use it as a "proof" that God can play no role in scientific studies. However, we can just as easily assume that God is consistent, meaning that even if He chooses to break a rule in a particular case (i.e., perform a miracle), he does not therefore change the rules, which remain in force.
This is a very old idea. In Romans, for example, St. Paul says:
For what can be known about God is plain to them, because God has shown it to them. For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made. So they are without excuse. (Rom. 1:19-20)
At any rate, if God exists, then any science that excludes God among a list of possible causes would obviously be flawed.
In a sense, though, God really is "outside" of science, in the sense that He would necessarily be outside the universe in some manner. Science, being limited to what it could measure within the universe, would be unable conclusively to prove or disprove His existence.
That is not the same as saying we can't know He exists -- the idea of revelation offers a non-scientific means to understanding it.
Finally, if we assume (again for the sake of argument) the idea of a living and aware God, then we'd have to take into consideration the idea that He has reasons (whatever they may be) for not simply revealing Himself unambiguously to us