Organisms display similarities of sequence, form, or life history that cannot be accounted for by their family tree.
Computational implementations of the Darwinian mechanism only work in a very limited sense.
Doug Axe writes about luciferase, an evocatively named enzyme that makes fireflies glow while also pointing to one test, among others, that Darwinism fails.
For years, Internet Darwin activists have cited the TalkOrigins Speciation FAQ. People who believe this FAQ demonstrates that Darwinian processes can produce large-scale biological change have been badly misled.
Wallace would break from Darwin in 1869 and develop a theory of intelligent evolution that in many ways presaged modern intelligent design theory.