The published letters of Charles Darwin reveal a man who debated about design in a manner that seems "more tolerant and humble" than one encounters in the current debate, says Anthony Barnes in a book review in The Independent (U.K.). It could also be noted that Darwin was treated better by his critics 150 years ago than his followers--the dominant neo-Darwinists--treat their critics today.
Darwin himself obviously thought a lot about religion, but, like his successors, he had what seems like a rather puerile understanding of theology and philosophy. He told the American botanist Asa Gray that Darwin's own nose, which he considered large and unattractive, was evidence against design. "Will you honestly tell me that the shape of my nose was ordained and guided by an intelligent cause?" he chided Gray.
The existence of what appears to be sub-optimal design is a sad argument that cannot be evaluated scientifically. There is nothing in the scientific question of design to suggest that the source of design had to have our particular understanding of optimal design in mind. What appears sub-optimal at one time (the appendix, for example) turns out later to have had serious functionality. Furthermore, considerations of beauty (noses, female girth, etc.) are often products of culture, not science. Flaws in nature, likewise, do not disprove design.
What a shame that Darwin's faith and his knowledge of philosophy was not up to the quality of his scientific inquiry.
(Cross-posted at Discovery Blog)