InGodITrust writes:
Darwin would not have arrived at his theory by contemplating the crazy plumage of some birds; rather, he had to find a way to reconcile the plumage with his theory.
"Crazy plumage of some birds" is one of the pieces of evidence Darwin used to support his theory in
Origin of Species. This is from the section on sexual selection:
Darwin writes:
The rock-thrush of Guiana, birds of Paradise, and some others, congregate; and successive males display their gorgeous plumage...
So Darwin quite obviously contemplated crazy bird plumage while formulating the theory of evolution.
InGodITrust writes:
I wonder if, starting with natural selection as a given, there are cases in which scientists struggle for an explanation that fits in.
Natural selection is what produces adaptation, so you're seeking characteristics for which evolution has produced reduced overall adaptation. I can't think of any such characteristics off the top of my head, but there must be some, and scientists probably wouldn't try to explain them using natural selection. I think it was WK who already mentioned a couple other factors that contribute to the path of evolution, like genetic drift and pleiotropy.
--Percy