Most difficult of all has been the question of the origin of life. The gap between the most complex system that might arise by chance alone and the simplest system capable of reproducing itself in the oceans of a proto-Earth only gets wider the more ingeniously we try to bridge it.
And the very process of evolution didn't come for free. Most genotype-phenotype maps are not capable of evolving at a decent rate. How did evolution evolve?
Questioning the plausibility of the simplest neo-Darwiniian models became scientifically respectable, and now it is almost mainstream. Evolution's capacity for creating diversity and complexity is far more efficient than we can yet explain. Evolution creates a powerful illusion of foresight and planning. The Great Chain of Being holds its mystique.
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