Naturalism is the denial of anything supernatural. Modern science is naturalism at its most...well...natural. ;-) Modern science vigorously denies the supernatural. Science, if I may be allowed to personify it for ease of discussion, is very good at what it does. Science investigates and explains the natural world. By definition it is not supernatural, nor can it be so. Science is limited to looking at only the physical, or the effects of the physical (as in the case of theoretical math and physics, and evolution which can't always be observed directly).
But science isn't all-knowing. Scientist say they have refuted miracles, but that's impossible. Science can't deal in miracles at all. Since science can only measure the physical, they can only decern "miracles" once the miracles, or other supernatural event, has entered the natural realm where it is observable. Someone may be suddenly and inexplicably cured from cancer. Science can decern the effects..see that the person is now cancer-free...and perhaps form a hypothesis for why, but the act of healing isn't itself measurable. And since it isn't measurable, the cause may remain unknowable to science.
Science is invaluable for explaining the natural world. It isn't always "right," as history has proven, but it's moving forward, gaining more information and improving our understanding of our world and ourselves. Where "science" falls short is when it tries to go beyond its own limitations and promise more than it can deliver. Science could use a little humility. Scientists too often try to take the information gleaned and attempt to answer questions the information was never meant to answer. Proof of relationships between organisms says nothing about whether or not God created the universe. It only explains the relationship between the organisms. Evolution is an explanation for what we see. It can say nothing about what we can't see. We can't see God, and so science has nothing to say about God. Science shouldn't try.
On the other hand, I think religion shouldn't try to answer the questions of science. Perhaps "faith" needs a little more humility as well. As a believer, I firmly believe God created the universe. As a scientist I'm willing to look at the evidence left in the natural world about how the universe came into being. Somehow, somewhere, those two things (imo) don't contradict.
In a similar manner as the Theological Twister post, this is an area of continuing fence-straddling and mental conundrums for me. Only in this case I'm not assured of ever living without the conundrum. As long as we are bound to the natural, even as we house souls bound to the supernatural, we will feel the pull and strain. But I'd rather feel the strain than to try to live without either in my own life. I chose to believe two competing ideas at the same time, and will to live with the consequences.