One of the remarkable things about these trees is that the branches have similar lengths. Beginning at the base of the tree, the distance to plants, animals, fungi, and bacteria is about the same. It differs by a factor of two, at most, for any species. This is evidence of a molecular clock—a roughly constant rate of evolutionary change for every lineage over a period of hundreds of millions of years. (Cytochrome c is not the ideal sequence for showing this since it's pretty small as far as proteins go. Substitutions of only a few amino acids can make a big difference to branch lengths. Larger proteins show more regular molecular clocks.)
We know why there's a molecular clock. It's because the vast majority of changes in the amino acid sequences of proteins are due to fixation of neutral, or nearly neutral, mutations by random genetic drift. As with any stochastic process, the law of large numbers produces a predictable pattern. In this case, a relatively constant rate of change over hundreds of millions of years.
As it turns out, the overall rate of fixation of neutral alleles should be close to the mutation rate. This is a conclusion derived from population genetics models and those models are well supported by evidence. Since mutation rates are similar, if not identical, between species this rate becomes roughly constant in each lineage. The branch lengths in the cytochrome c tree reflect this indirectly since they result from a combination of fixation times and mutation rates. Furthermore, they are amino acid sequences so a lot of the underlying mutations at the nucleotide level are hidden.
Michael Denton knows of this population genetics explanation since he mentions it on page 289 of Nature's Destiny: How the Laws of Biology Reveal Purpose in the Universe.
Comparisons of these two rates, the rate of mutation and the evolutionary substitution rate, have revealed the very surprising fact that the two rates are the same. This remarkable finding that the difference between the DNA sequences of different species have been generated by mutation and that other factors such as natural selection could only have played a relatively minor role.Denton knows that the data supports such an idea because he brings up cytochrome c on the next page.
By comparing sequences a curious pattern was observed. For example, in the case of cytochromes, all the higher organism cytochromes (yeasts, plants, insects, mammals, birds, etc.) exhibit an almost equal degree of sequence divergence from the bacterial cytochrome in Rhodospirillum. This means that all their cytochrome genes have changed to about the same degree—in other words, have evolved at a uniform rate.The uniform rate of change is what impresses Michael Denton. As I mentioned above, Denton knows that adaptation (selection) is ruled out as an explanation. Unlike many other IDiots, Denton knows that pan-adaptationism (often called Darwinism) is not the prevailing view in evolutionary biology.
Random genetic drift is a perfectly reasonable explanation of the molecular clock but Denton rejects that explanation. He says that,
Explanations of uniform rates of evolution in protein genes in terms of genetic drift of neutral mutations fare no better. The rate of genetic drift in a population is determined by the mutation rate. This is not controversial. Although mutation rates for many organisms are somewhat similar per generation time—10^-6/gene/generation—the problem is that generation times are vastly different, so that the rate of mutation per year in, say, yeast, may be 100,000 times greater than a tree or a mammal such as man or elephant, organisms that have long generation times. (p. 291)The generation time argument is a bit bogus for several reasons. First, mutation rates are based on changes per cell division (replication) and not generation time. Thus, in mammals such a mouse, there are about 50 cell divisions between zygote and gamete and the organism reproduces in about 100 days. Thus, there is, on average, one mutation-causing replication event every two days. This is no more than the average "generation time" of single-celled organisms such as yeast or bacteria. (Bacteria divide once every few days, at most, contrary to what most people believe.)
The second reason for skepticism is that for most of the history of life the "generation time" of different organisms isn't that much different. Large terrestrial mammals, for example, have only been around for about 15% of the time since single-celled life began.
Molecular biologists and population geneticists have thought about these things. They conclude that the evidence favors the idea that phylogenetic trees are due to fixation of nearly neutral alleles by random genetic drift. This explains the molecular clock.
Denton doesn't buy it. He thinks the molecular clock proves Intelligent Design Creationism.
These twin discoveries—that the mutation rate equals the evolutionary substitution rate, and that the rate of change in many genes is regulated by a clock which seems to tick simultaneously in all branches of the tree of life—may represent the first evidence, albeit indirect, that the mutational processes that are changing the DNA sequences of living things over time are indeed directed by some as yet unknown mechanism, or more likely mechanisms. Of course, these discoveries do not prove directed evolution, but it is far easier to imagine them as the outcome of some sort of direction than the outcome of purely random processes. (p. 292)In other words, Michael Denton can't imagine how stochastic evolutionary processes might work, so God did it. Another argument from ignorance, albeit an ignorance that's on a much higher level than the ignorance usually on display on creationist websites and blogs. (Michael Denton is by far, the most knowledgeable IDiot when it comes to understanding evolution and molecular biology. Perhaps it's why he's out of favor with the true IDiots.)