Now let me step back from the problem and very generally discuss natural selection and what we know about it. I think it is safe to say that we know for sure that natural selection, as a process, does work. There is a mountain of experimental and observational evidence, much of it predating genetics, which shows that natural selection as a biological process works.
David M. RaupA large number of well-trained scientists outside of evolutionary biology and paleontology have unfortunately gotten the idea that the fossil record is far more Darwinian than it is. This probably comes from the oversimplification inevitable in secondary sources: low-level textbooks semipopular articles, and so on. Also, there is probably some wishful thinking involved. In the years after Darwin, his advocates hoped to find predictable progressions. In general. these have not been found-yet the optimism has died hard and some pure fantasy has crept into textbooks.
David M. RaupThere are about 250,000 different species of fossil plants and animals known . . In spite of this large quantity of information, it is but a tiny fraction of the diversity that [according to the theory] actually lived in the past. There are well over a million species living today and . . [it is] possible to predict how many species ought to be in our fossil record. That number is at least 100 times the number we have found.
David M. RaupPerhaps the only thing that saves science from invalid conventional wisdom that becomes effectively permanent is the presence of mavericks in every generation - people who keep challenging convention and thinking up new ideas for the sheer hell of it or from an innate contrariness.
David M. RaupIn the beginning, there were bacteria.... [A] nearly universal assumption is that all subsequent life descended from the original life form through a continuous chain of ancestor-descendant pairs. This assumption looks good because all living organisms share biochemical traits. It is conceivable, of course, that life originated more than once on the early earth but that all except one life form died out early, leaving a single lineage as the ancestor of life as we know it. If this did happen, it was the first important species extinction.
David M. Raup