Natural selection is easily visualized when one considers one structure or process evolving to respond to conditions, but every organism involves biliions of structures, processes and relationships, all interlinked at the molecular level, evolving in parallel. How is this coordinated and managed?

Another clue that perhaps natural selection isn't the only process involved in evolution is those extremely small populations of certain animals, for example, some whales, who seem to be genetically quite robust and only contain several thousand individuals, sometimes further subdivided into distinct geographic populations. How can a random process operate here? Even humans appear to have evolved from a stock that at one time had been reduced to a few tens of thousands of individuals, geographically isolated in small bands. It's easy to visualize insects and bacteria evolving stochastically with populations in the billions, but pandas?

Speaking of insects, many creatures evolve parallel morphological forms.
Insects not only evolve a physical configuration, they simultaneously evolve several: larval, pupal, and adult stages and in social insects one genetic plan can be somatically modified into various castes by just altering the diet. Some species even have alternating body plans, such as ferns and some cnidarians (coelenterates). And what about the really weird reproductive cycles, like slime molds? It's hard to visualize how natural selection alone could pull this off.

Darwin got it right, but he didn't get the whole story. And I want to make clear I'm not groping for a supernatural explanation here. All our experience tells us that the complexity of nature operates on the basis of pre-existing and very simple rules that are comprehensible to the human mind. If we abandon that, we abandon our reason and we slide into superstition.