The molecular clock keeps evolutionary time

In the 1960s molecular biologists learned how to analyze protein molecules and determine the sequence of amino acids that comprise a protein. It was then discovered that a given protein molecule varies somewhat from species to species. For example, hemoglobin, a blood protein, has similar function, overall size and structure in different species. But its amino acid sequence varies from species to species. Emile Zuckerkandl and Linus Pauling reasoned that if such sequence differences were the result of evolutionary change occurring over the history of life, then they could be used to estimate past speciation events—a notion that became known as the molecular clock. (Zuckerkandl and Pauling)

In later decades this concept of a molecular clock, relying on the assumption of a roughly constant rate of molecular evolution, became fundamental in evolutionary biology. (Thomas, et. al.) As the National Academy of Sciences explained, the molecular clock “determines evolutionary relationships among organisms, and it indicates the time in the past when species started to diverge from one another.” (Science and Creationism, 3) Indeed the molecular clock has been extolled as strong evidence for evolution and, in fact, a common sentiment has been that evolution was required to explain these evidences. As a leading molecular evolutionist wrote, the molecular clock is “only comprehensible within an evolutionary framework.” (Jukes, 119, emphasis in original)

The claim that the molecular clock can only be explained by evolution is, however, now a moot point as the mounting evidence shows that molecular differences often do not fit the expected pattern. The molecular clock which evolutionists had envisioned does not exist. The literature is full of instances where the molecular clock concept fails. For example, it was found early on that different types of proteins must evolve at very different rates if there is a molecular clock. For example the fibrinopeptide proteins in various species must have evolved more than five hundred times faster than the histone IV protein. Furthermore, it was found that the evolutionary rate of certain proteins must vary significantly over time, between different species, and between different lineages. (Thomas, et. al.; Andrews, 28)

The proteins relaxin, superoxide dismutase (SOD) and the glycerol-3-phosphate dehydrogenase (GPDH), for example, all contradict the molecular clock prediction. On the one hand, SOD unexpectedly shows much greater variation between similar types of fruit flies than it does between very different organisms such as animals and plants. On the other hand GPDH shows roughly the reverse trend for the same species. As one scientist concluded, GPDH and SOD taken together leave us “with no predictive power and no clock proper.” (Ayala)

Evolutionists are finding growing evidence that the purported rates of molecular evolution must vary considerably between species for a wide range of taxa, including mammals, arthropods, vascular plants, and even between closely related lineages. As one study concluded, “The false assumption of a molecular clock when reconstructing molecular phylogenies can result in incorrect topology and biased date estimation. … This study shows that there is significant rate variation in all phyla and most genes examined …” (Thomas, et. al.)

Evolutionists continue to use the molecular clock concept, but the many correction factors highlight the fact that the sequence data are being fit to the theory rather than the other way around. As one evolutionist warned, “It seems disconcerting that many exceptions exist to the orderly progression of species as determined by molecular homologies; so many in fact that I think the exception, the quirks, may carry the more important message.” (Schwabe)


Andrews, Peter. 1987. “Aspects of hominoid phylogeny” in Molecules and Morphology in Evolution, ed. Colin Patterson. Cambridge: Cambridge University Press.

Ayala, F. 1999. “Molecular clock mirages.” BioEssays 21:71-75.

Jukes, Thomas. 1983. “Molecular evidence for evolution” in: Scientists Confront Creationism, ed. Laurie Godfrey. New York: W. W. Norton.

Schwabe, C. 1986. “On the validity of molecular evolution.” Trends in Biochemical Sciences 11:280-282.

Science and Creationism: A View from the National Academy of Sciences. 2d ed. 1999. Washington, D.C.: National Academy Press.

Thomas, J. A., J. J. Welch, M. Woolfit, L. Bromham. 2006. “There is no universal molecular clock for invertebrates, but rate variation does not scale with body size.” Proceedings of the National Academy of Sciences 103:7366-7371.

Zuckerkandl, E., L. Pauling. 1965. “Molecules as documents of evolutionary history.” J Theoretical Biology 8:357-366.