Upsetting Pet Theories:
Surprising New Evidence that Molecular Clocks Can Run Very Fast

Author: John Woodmorappe
Subject: Biology
Date: 01/01/1998

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Molecular clocks don’t always tick at the steady, slow rate many evolutionists predicted. This article reports on new evidence that the divergence of molecular structure in mitochondrial DNA can occur many orders of magnitude more rapidly than was earlier supposed. This can bring the time for speciation down from millions of years to only several thousand years, which, of course, is consistent with the biblical time framework.

Evolutionists have long attempted to date the origin of taxonomic groups through the use of molecular clocks. Using two (or more) species, they determine the differences in a given stretch of their DNA molecules, and then see how long ago, according to the fossil record, those taxonomic groups diverged. The rate of divergence over time gives one a “clock” of molecular change. The problem with this approach is that the clocks are often very contradictory.

However, there was thought to have been one ideal molecular “clock” that was largely exempt from these problems. This “clock” is mitochondrial DNA (hereafter abbreviated mtDNA). Most of the cell’s DNA resides in the nucleus, and serves as the cell’s “government”. However, the mitochondria, the organelle in the cell which serves as the cell’s power station, also has some DNA (see Figure 1). Evolutionists have long believed that this mtDNA is a relic from the cell’s evolutionary past, ostensibly billions of years ago. They imagine that the mitochondria was once a separate living entity, and its DNA served a governing function analogous to the cell’s nuclear DNA.

There are a number of reasons why mtDNA was thought to be an ideal molecular “clock.” First of all, unlike nuclear DNA, mtDNA is not divided during cell division. It simply gets duplicated through a carbon-copy like duplication when cells divide, with the duplicate going to the daughter cell. During sexual reproduction, mtDNA passes down through the mother’s lineage, so there is no complicating addition of paternal mtDNA.

Finally, mtDNA was thought to receive mutations that were predominantly neutral. That is, most mutations in mtDNA would be exempt from natural selection, because those mutations would neither help the organisms out-compete other similar organisms, nor create a disadvantage for organisms in competition with others. Therefore, so it was reasoned, one only had to count the number of mutants in the mtDNA between any taxonomic groups, and one could approximate how long ago they diverged.

Not surprisingly, given standard geological dating, the figures were on the order of millions of years. A sequence- divergence rate of only 2% per million years has been quoted (MacRae and Anderson 1988, p. 485).

Now comes new evidence, however, that mtDNA is subject to natural selection. Moreover, not only does this occur within a species, but also within a relatively small, well-defined population. To top it all off, the variation also occurs in a short period of time.

Contrary to conventional evolutionary wisdom, some earlier evidence indicated that mtDNA is not subject only to neutral mutations (Fos et. al. 1990, MacRae and Anderson 1988). However, much of this evidence was ignored because it did not fit the reigning evolutionary belief in the primacy of neutral mutations (Malhotra and Thorpe 1994, p. 37).

The new field evidence indicates, however, that mtDNA is subject to natural selection. Malhotra and Thorpe (1994) studied the sequence of mtDNA among certain lizards in islands of the Caribbean Sea. They found morphological (i.e., anatomical) variation in these lizards, following moisture gradients on the islands: the animals’ coloration, number of scales, and body proportions varied with local ecological conditions.

What is really surprising, however, is the fact that the mtDNA of the lizards also follows these ecological gradients! This strikes at the very heart of the prevalent belief that mtDNA is very stable, and only changes slowly through the accumulation of neutral mutations over many millions of years.

The implications of this finding are significant. Instead of accumulating mutation-by-mutation over millions of years, mutations in mtDNA can become rapidly fixed in a population. Major divergences in the mtDNA could have occurred in thousands, instead of millions of years. This is in line with the biblical time frame.


Fos, M., Dominguez, M. A., Latorre, A., and A. Moya. 1990. “Mitochondrial DNA evolution in experimental populations of Drosophila subobscura.” Proceedings of the National Academy of Sciences 87: 4198-4201.

MacRae, A. F., and W. W. Anderson. 1988. “Evidence for non- neutrality of mitochondrial DNA haplotypes in Drosophila pseudoobscura.” Genetics 120: 485-494.

Malhotra, A., and R. S. Thorpe. 1994. “Parallels between island lizards suggests selection on mitochondrial DNA and morphology.” Proceedings of the Royal Society of London (Series B) 257: 37-42.

Topics: baraminology, molecular biology, Created kinds, unorthodox science, weird but true, YEC, anti-Darwinism, little- known information, eye-opening data, cognitive dissonance, phylogenetic reconstruction, baramins, molecular phylogenies