Some thought-provoking observations on whale evolution by biochemist Jonathan Wells (a Berkeley graduate and vocal skeptic of strict philosophical naturalism):
In the case of the Durrett and Schmidt (2008) paper, evolutionary biologist Richard von Sternberg has applied the equations employed in that paper to whale evolution. The evolution of Dorudon and Basilosaurus (38 mya) may be compressed into a period of less than 15 million years. Such a transition is a fete of genetic rewiring and it is astonishing that it is presumed to have occurred by Darwinian processes in such a short span of time. This problem is accentuated when one considers that the majority of anatomical novelties unique to aquatic cetaceans (Pelagiceti) appeared during just a few million years – probably within 1-3 million years. The equations of population genetics predict that – assuming an effective population size of 100,000 individuals per generation, and a generation turnover time of 5 years – according to Richard Sternberg’s calculations and based on equations of population genetics applied in the Durrett and Schmidt paper, that one may reasonably expect two specific co-ordinated mutations to achieve fixation in the timeframe of around 43.3 million years. When one considers the magnitude of the engineering fete, such a scenario is found to be devoid of credibility. Whales require an intra-abdominal counter current heat exchange system (the testis are inside the body right next to the muscles that generate heat during swimming), they need to possess a ball vertebra because the tale has to move up and down instead of side-to-side, they require a re-organisation of kidney tissue to facilitate the intake of salt water, they require a re-orientation of the fetus for giving birth under water, they require a modification of the mammary glands for the nursing of young under water, the forelimbs have to be transformed into flippers, the hindlimbs need to be substantially reduced, they require a special lung surfactant (the lung has to re-expand very rapidly upon coming up to the surface), etc etc.
The broad point of Wells’s paragraph is this: random genetic variation accompanied by natural selection has very little time to work with in turning a cow-like land mammal into a whale. It strikes me as a pretty solid argument that something other than (or more than) random variation and natural selection are at work in evolution.
What say you?
Prometheus Unbound 
Isn’t this a simple lottery fallacy?
Yes, that *specific* evolutionary path has low probability, but that’s just like any *specific* person having a low probability of winning the lottery.
The probability of *someone* winning the lottery though, is almost certain.
Searching for the least probable variants (which will always exist, regardless of the mechanism) is just cherry-picking the data.
Imagine for a moment that whales *did* evolve purely according to “Darwinian processes”; are we able to tell one way or another? If not, then both Wells and his opponents are squarely in the realm of speculation.
If whales didn’t evolve by Darwinian processes then what is the suggested mechanism for their evolution and what is the evidence in favour of this secondary hypothesis over the first?
I don’t think science really works with “Some Other Thing” hypotheses. You either have to address the hypotheses on the table or provide a different one, specify it clearly, and examine the ability of the new hypothesis in terms of its predictive power and explanatory scope.
Wells doesn’t agree. Like other Discovery Institute cronies he’s content to attack evolution theory without providing testable alternative hypotheses. Wells clearly states as much in the 2006 Michael Shermer Jonathan Wells Evolution Debate
What gave you the idea that Jonathan Wells spells his name with an “M”? Actually, I’m a graduate student in evolutionary biology.
J
I don’t quite understand this comment. Who are you replying to? Who said Jon Wells spells his name with an M?
Well, I stand corrected. I simply assumed that Jonathan Wells blogged at Uncommon Descent as “Jonathan M”—a kind of ironic moniker. The flipping of one letter turned you into Jonathan Wells for me. I’ve always assumed that’s who was speaking when I see a “Jonathan M” post.
Sorry about that.
You write well on the subject.
—Santi
I say show me a paper published in a proper peer-reviewed journal, not a blog post nor a video, and maybe you deserve my attention.
Cheers