These mysteries about how we evolved should not distract us from the indisputable fact that we did evolve.
To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I confess, absurd in the highest degree...The difficulty of believing that a perfect and complex eye could be formed by natural selection , though insuperable by our imagination, should not be considered subversive of the theory.
Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest... The origin of species — Darwin’s problem — remains unsolved.
No fossil is buried with its birth certificate. That, and the scarcity of fossils, means that it is effectively impossible to link fossils into chains of cause and effect in any valid way... To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story—amusing, perhaps even instructive, but not scientific.
[...] if truth be told, evolution hasn’t yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably. But hasn’t evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of ‘like begets like’. Even now, as its practitioners admit, the field of quantitative genetics has been of little value in helping improve varieties. Future advances will almost certainly come from transgenics, which is not based on evolution at all. [review of The Evolving World: Evolution in Everyday Life, Nature 442, 983-984 (31 August 2006)]