Richard Wells wrote:
I do chuckle a little when I see "facts" emergec from bases like the concept of "DNA molecular clocks" that are at best theoretical postulates.

Me:
Like you, I was skeptical when I was first introduced to the idea of the molecular clock. However, I was won over because, like evolution, the molecular clock is not "just a theory" (as opponents of evolution suggest) but the only reasonable explanation for the set of accumulated facts in support of it, for most people who are rational. S.J. Gould writes in the essay "Our Greatest Evolutionary Step" in The Panda's Thumb:

'During the past fifteen years, students of molecular evolution have accumulated a storehouse of data on the amino acid sequences of similar enzymes and proteins in a wide variety of organisms. This information has generated a surprising result. If we take pairs of species with securely dated times of divergence from a common ancestor in the fossil record, we find that the number of amino acid differences correlates remarkably well with time since the split—the longer that two lineages have been separate, the more the molecular difference. This regularity has led to the establishment of a molecular clock to predict times of divergence for pairs of species without good fossil evidence of ancestry. To be sure, the clock does not beat with the regularity of an expensive watch—it has been called a "sloppy clock" by one of its leading supporters—but it has rarely gone completely haywire.'

My initial skepticism is shared by many Darwinians because of the way we were taught about evolution in schools. S.J. Gould explains:

'Darwinians were generally surprised by the clock’s regularity because natural selection should work at markedly varying rates in different lineages at different times: very rapidly in complex forms adapting to rapidly changing environments, very slowly in stable, well-adapted populations. If natural selection is the primary cause of evolution in populations, then we should not expect a good correlation between genetic change and time unless rates of selection remain fairly constant—as they should not by the argument stated above. Darwinians have escaped this anomaly by arguing that irregularities in the rate of selection smooth out over long periods of time. Selection might be intense for a few generations and virtually absent for a time thereafter, but the net change averaged over long periods could still be regular. But Darwinians have also been forced to face the possibility that regularity of the molecular clock reflects an evolutionary process not mediated by natural selection, the random fixation of neutral mutations."

To summarize, there are some molecules (such as serum albumin) that have no known function, and are therefore selectively neutral. A mistake in the replication of the gene coding for neutral molecules like serum albumin therefore would not be detrimental to the survival of an organism and are therefore not weeded out. In time, these mistakes accumulate in separate lineages, allowing us to trace the common ancestry of two organisms back in time. It is therefore not surprising that the molecular clock was formulated by Allan Wilson and his colleagues using a selectively neutral molecule such as serum albumin.

Richard Wells:
I was under the impression that the rate of nucleotide substitution is presumed to be a constant across the entire genome of a species, and the degree of divergence in these nucleotide sequences between two different species enables an estimation of the time of separation (ie the point when they branch from their common ancestor).

Me:
This is emphatically not the case. Different molecules do have different rates of mutation. That is because some molecules are constrained by natural selection while others are not. Those molecules that are necessary for a vital function tend to evolve very slowly whereas those that are selectively neutral can evolve quite rapidly. The same is true of morphological features as well. For example, in the article “Magnolias from Moscow” in Gould’s book Dinosaurs in a Haystack, Gould reported that DNA was successfully extracted from chloroplasts of 20million year old fossil leaves. Comparing the DNA to a closely related living species, only 17 mutations were found in a comparison of 820 base pairs, and 13 of these were found in the third position of the nucleotide sequence, resulting in no changes in the amino acid sequence. There were only 4 nucleotide substitutions that resulted in amino acid changes. In comparison, it has been estimated that one amino acid substitution occurs in serum albumin approximately every one million years. Chloroplast protein therefore evolves at a rate (4 amino acid substitutions over 20 million years or 1 per 5 million years) that is 1/5 the rate of serum albumin evolution. This is not surprising because a mutation that changes the function of chloroplast will be detrimental to the plant’s survival and thus these mutations will be quickly weeded out by evolution.

Richard Wells:
I'm not bagging the molecular clock hypothesis as erroneous - I just see fertile ground for unwarranted extrapolation.

Me:
Yes indeed. DNA data can be misinterpreted; mistakes can be made in obtaining data also. However, techniques are improving all the time. I have also pointed out some silly mistakes made by molecular systematists, who sometimes choose a member of the ingroup as an outgroup. Also, in the essay “Magnolias from Moscow”, Gould did report anomalous results from another study which reported a different rate of mutation for the same molecule. As he pointed out, there may be other factors involved. It is a long story. DNA data is far from bullet proof reliable, but the mistakes are being discovered and dealt with. Better molecular characters, such as SIN, are being found. More and more systematists, including those who used to rely on morphology alone, are turning to molecular characters to study phylogeny. However, phylogeny alone is only part of the picture. The other part of the picture is evolutionary divergence. At present, as Mayr and Ashlock pointed out, there is no way to classify organisms using molecules that are responsible for evolutionary divergence. The molecular systematists who try to classify organisms on the basis of neutral genetic changes such as serum albumin and mtDNA are giving us an incomplete and often misleading picture of evolutionary change. Those who ignore or dogmatically oppose molecular data, however, run the risk of behaving in a way that is similar to the creationists, who continue to maintain that evolution is not fact, just theory. The molecular clock, like evolution, is not merely a theory, but the most reasonable interpretation of the available data, at least according to most rational people. The molecular clock, like evolution, is a fact, not a theory.

Regards

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