One must question the theology underlying the concept of God’s 'benevolence', as
defined by the primitive mind. That is, we ought not suppose that God is
not at work if we find proof of 'abandoned' lines in species development, nor
yet if there exists competition in Nature- rather, we ought to
remember that 'all things work together for good for those who love
God'. That is, if we cannot understand the grand design, and if it
does not conform to our anthropocentric desire for a tidy, painless
existence, we ought to remember that whatever chastening exists,
exists for our own good. Thus we may collapse the argument not to
whether God exists or not in the face of evidence for a mechanism of selection, but to the problem of evil (theodicy) which leads us to reexamine how we are defining our
basis for accepting or rejecting God's existence.
It seems the question also relates to whether God is necessary as a prime cause for the universe, and whether natural selection is sufficient for the same.
As a scientist, I cannot refute the direction in which geological evidence points - that of a long, slow process of transmutation. But as one who also believes in, and has personally been the recipient of divine revelation (http://www.answering-islam.org/Testimonies/paulm.html), I would say it is not permissible to reject God as the one who, as with other laws of the universe, is the motive agent behind the mechanism. To those who question the value of testimony, I say, life is the lab, if you are in doubt, seek God with all your heart, and you will receive irrefutable (for you, in any case) proofs, empirical evidence to put a monkey wrench into all your philosophical musings.
I would even, if I doubted my own senses which may indeed drink in God’s glory, take Descartes' cogito and say, with all sincerity, "I think (or more aptly, I contemplate), therefore God is". That is, while some may believe in the mechanism of emergent properties, I propose that this does not entail atheism, for no proof of such can ever exist, being something so completely exhaustive that no one could ever begin to approach it.
As for Darwin, I cannot understand how atheism can be seen as the logical consequence of it, especially as an examination of the concept of 'random' mutations will reveal. I believe that there is much ambiguity in this facet of selection- it requires faith, in essence, in a mechanism which cannot be completely validated save by attendant phenomena which might be adequately explained by alternative theories. For one thing, quantum physics suggests a 'stochastic' distribution of electrons about a nucleus, but in fact, when one 'steps outside time', to see the cloud in its various logical permutations, there is structure, on the whole. This structure, being that it exists outside of time, suggests it lies entirely in that domain where God resides- eternity. Or, our inability to see patterns does not imply the absence of a pattern, only a pattern of such a type which we do not yet recognize, either for its simplicity or for its complexity.
It is folly for us to presume to tell God just how to establish the reality of a theistic universe. The desire for uniformity in nature is read into the scripture, which seems inappropriate given that Jesus established that God speaks in parables