One of the reasons many scientists acknowledge the insufficiency of Darwinism is because they know the accounting won't work. The mutation rate, the generation times, the strength of selection versus genetic drift, the population sizes, and the time available don't match up.The point here is not that it didn't happen, but that there's no plausible naturalistic explanation for its having happened. Scientists will continue to hold onto the standard model until something better comes along, of course, but they're growing increasingly uneasy with it which is why books like philosopher Thomas Nagel's Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False have created so much controversy and why they're being written at all. Nagel believes that the process of evolution is guided by some telic principle in the universe, that the process just couldn't, by chance, have led to conscious creatures who can think and and recognize moral value.
For example, supposedly humans last shared common ancestry with chimps about six million years ago. Since that time, we have accumulated significant differences with chimps -- genetic, anatomical, physiological, behavioral, and intellectual differences, among others. The genetic differences between humans and chimps are much more than the (shrinking) 1.2 percent difference in base pairs that is so often quoted in the media....we have more than 11.7 percent of our genome with unique features not present in chimps.
There is only so much time for these differences to have accumulated. Mutations arise and are propagated from generation to generation, so the number of generations limits how many mutations can accumulate. The estimated mutation rate is about 10-8 per base pairs per generation, and we have an average generation time of somewhere between 10 and 25 years. Our estimated breeding population size six million years ago is thought to have been about 10,000.... Based on these numbers, one can estimate how many years it would take to acquire all those mutations, assuming every mutation that occurred was saved, and stored up.
But there's a difficulty -- it's called genetic drift. In small populations, like the 10,000 estimate above, mutations are likely to be lost and have to reoccur many times before they actually stick. Just because of random effects (failure to reproduce due to accidental death, infertility, not finding a mate, or the death of all one's progeny), a particular neutral mutation may have to arise many times before it becomes established in the population, and then many more years before it finally becomes fixed (that is, before it takes over the population and replaces all other versions).
How long before a single, new mutation appears and becomes fixed? An estimate from a recent paper using numerical simulations is 1.5 million years. That is within the range of possibility. But what if two specific mutations are needed to effect a beneficial change? Their estimate is 84 million years. Other scientists have done this calculation using analytical methods, but their numbers are even worse. One report calculates 6 million years for one specific base change in an eight base target typical of the size of a DNA binding site to fix, and 100 million years to get two specific mutations. (That work was later amended to 216 million years.) Extrapolating from other published data merely confirms the problem....
Yet in all likelihood many more than two binding sites would be required to change anything significant, and those binding sites must be appropriate in location and in sequence to accomplish the necessary changes. They must work together in order for a specific adaptive change to happen.
Genes operate in networks, and to shift a gene regulatory network would require many mutations, and not just random ones. Remember there are anatomical physiological, behavioral, and intellectual differences to explain, multiple traits each requiring multiple coordinated mutations. Unless one invokes luck on a large scale, those traits would not have come to be.
Nagel is not a theist, nor an advocate of intelligent design, but an increasing number of thinkers like him, scientists and philosophers alike, are beginning to believe that naturalistic explanations are simply inadequate to account for the world we see around us. Gauger's essay gives us a glimpse of the kinds of reasons driving them to this conclusion.