Many people, including many important and well-respected scientists, just don't want there to be anything beyond nature. They don't want a supernatural being to affect nature.

It was a shock to people of the nineteenth century when they discovered, from observations science had made, that many features of the biological world could be ascribed to the elegant principle of natural selection.

If you take away a rock from a pile of rocks you haven't changed much. It's still a heap of rocks - just a rock or two smaller. Take away a component from the mousetrap and it isn't a mousetrap any more.

I find the idea of common descent (that all organisms share a common ancestor) fairly convincing, and have no particular reason to doubt it.

For example, both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C. ... It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans. ... Despite some remaining puzzles, there's no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.

In order to say that some function is understood, every relevant step in the process must be elucidated.

Although Darwin was able to persuade much of the world that a modern eye could be produced gradually from a much simpler structure, he did not even attempt to explain how the simple light sensitive spot that was his starting point actually worked.