God, or any sufficiently powerful supernatural entity (if such a being exists), could have designed us to operate miraculously. We could see through pores in our skin, hear via golden halos, and float from place to place--all without any mechanism for how our bodies function. Instead we have a naturally comprehensible biology of which we have a deep understanding. Why would God make us, and all organisms, in such a way when he could have just as easily made magic-powered life?
I wonder why God, if he exists, would make the workings of anything subject to human discovery. I say anything, but really it could be everything. We have yet to find something that science is fundamentally incapable of explaining. Before the apologists chime in, yes, I realize there are aspects of nature we have yet to understand, but that doesn’t show that they are fundamentally beyond natural understanding. Take something like human consciousness. We knew next to nothing about it in the recent past, but now we know of neurons and synapses. We know roughly where in the brain is most important for memory and cognition. We know how chemicals affect thoughts, perception and personality. It seems everything is within our ability to grasp.
I know that these questions I pose may be unanswerable. I don’t expect the believer to know God’s motivation for making things how they are, even if God exists. Mysterious ways and all that. But consider this, believers: since everything that God created, if he did, seemingly operates by an intelligible natural process, why reject evolution by natural selection as the process responsible for the diversity and apparent design of life? If the evidence supports it, and it does, denying it outright because it isn't miraculous is a bizarre exception considering all the things you accept that are not magical. Evolution happens and the process is unguided by any external agency--embrace this knowledge or ask yourself why God would make this one aspect of reality supernatural. Or ask God. If he answers, let me know.