"The two books for Francis Bacon are the word of God and the works of God, the Bible and the works of God in nature.
It's very important to realize that in return for telling us how texts of the Bible should be interpreted, people who investigated nature, call them naturalists, were also expected to supply evidences of God's beneficence, power, and wisdom in the works of nature. So the marvelous way in which a bivalve shell is constructed or the wonderful joint in your elbow or the patterns of life, the beauty of butterflies, all of these things can be studied by naturalists and said to be evidence of the Creator's wisdom and beneficence.
Darwin's starting point were these wonderful adaptations of organisms to their environment. Things seem to be made perfectly to live where they are: fish to swim, ducks to paddle, and so forth. These traditionally were evidences of the Creator's wisdom and goodness. Darwin says, 'We can explain how nature produced these adaptations to environment. We can explain how the beauty of a butterfly is useful to that butterfly in pursuing its way of life. I can come up with causes for this and it's up to you to believe that God created these things through these causes or not.'
Darwin evokes the works of God, the works of natural theology, the greatness of nature at the beginning of The Origin of Species because he really does believe those works in nature are beautiful and astonishing, and the adaptations are there. He's at one with the spirit of natural theology. Just read his prose in The Origin of Species. It exudes wonder at nature, but he can explain how it happened…
…Darwin has a vision of nature and it takes quite a while studying Darwin from when he was in his twenties really until, at the end of his life, he's working on earthworms, of all things. I do have the most profound respect for the way he doggedly pursued his vision of the history of life on Earth and how great things are caused by little things. Mountains move up by small increments, the soil of the Earth is recycled through earthworms, coral reefs grow by tiny increments over tens of thousands of years. No one can see these things happening. One has to be able to imagine them happening. And Darwin had that wonderful imagination. He had the capacity to sit still or stand still in a field or in a wood, for an hour at a time, and just watch and listen. There are few of us who have that today, and we're the worse for it”
~ James Moore, from "Evolution and Wonder: Understanding Charles Darwin," Speaking of Faith, Feb. 5, 2009.