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Failure of Molecular Clocks: Important Implications for the Christian Faith

According to the biological evolutionary paradigm, molecular evolution parallels organic evolution. In other words, as the evolutionary changes proceed at the anatomical level (via the process of descent with modification from a common ancestor), molecular changes occur in the amino acid and nucleotide sequences of proteins and genes, respectively.1 These changes result from mutational events, the model says. Groups of organisms that have recently diverged from a common ancestor will have greater similarity in protein and gene sequences than groups of organisms that have diverged from the common ancestor in the more distant past.

If the mutational rate can be estimated and is approximately constant over time, then the time of divergence from the common ancestor can be determined from sequence differences. The mutational rate, or molecular clock, is estimated by comparing sequence differences for organisms with well-known times of origination (based on the fossil record).2 Once calibrated, the molecular clock can then be applied to estimate the time of origination for organisms with a poorly understood fossil record.

While straightforward in principle, application of molecular clock analysis is fraught with complications.3-4 For example, nuclear and mitochondrial genes mutate at different rates as do different genes/proteins within an organism. Moreover, the same gene/protein in different taxa (or groups) mutates at different rates.

Evolutionary biologists commonly use molecular clock analysis to estimate the timing of evolutionary events. Molecular clock analysis frequently yields results that disagree with the fossil record. One recent example that has implications for the biblical Creation Model is the dating of the origin of metazoons (complex animals). Based on the fossil record, essentially all animal phyla ever to exist throughout the earth’s history appeared suddenly and simultaneously within a narrow window of time (quite likely less than 3 million years) approximately 540 million years ago.5 This event, known as the Cambrian Explosion, creates a serious challenge to the evolutionary paradigm. In an attempt to escape the problem of the Cambrian Explosion, evolutionists have suggested that the Cambrian event is an artifact of an incomplete fossil record. To buttress this claim, evolutionary biologists have employed molecular clock analysis to argue that the divergence of animal phyla occurred as far back as 1.2 billion years ago.6 This would diffuse the explosive nature of the Cambrian event, giving the origin of animal phyla time to occur gradually over the course of 600 million years.

However, these molecular clock analyses have not gone uncontested.7 Recent work designed to evaluate the accuracy of the molecular clock technique, work done by two workers from the University of Illinois at Chicago (UI at C), decisively refutes the reliability of molecular clocks.8

In this study, the two biologists examined the accuracy of four molecular clocks operating within the order Perrisodactyla. This order includes the families Equidae (horses and zebras), tapiradae (tapirs), and Rhinoceritidae (rhinoceros). The Perrisodactyla fossil record is abundant and has well-defined origin dates. Based on the fossil record, the two researchers from UI at C defined two calibration points, at 3 million years ago and 50 million years ago, for two different genes yielding four molecular clocks. Unfortunately, all four molecular clocks produced disparate results, none of which agreed with the fossil record.

The failure of molecular clock analysis for such a cleanly-defined experimental system has two important implications for Christian apologetics:

  1. The molecular clock technique is not valid. This means that the results challenging the completeness of the metazoon fossil record and the reality of the Cambrian Explosion are highly suspect. This helps preserve the Cambrian Explosion as a phenomenon that runs counter to naturalistic evolutionary models and is consistent with a Creation Model. 
  2. At least one of the assumptions undergirding molecular clock analysis must be faulty. The two assumptions are these: a) molecular clocks exist; and b) natural process evolution is a fact.  Evidence pointing to the latter continues to mount.



  1. Monroe W. Strickberger, Evolution, 3rd. ed. (Sundbury, MA: Jones and Bartlett, 2000): 256-95.
  2. Strickberger, 283-86.
  3. Evelyn Strauss, “Can Mitochondrial Clocks Keep Time?” Science 283 (1999): 1435-38.
  4. Jane E. Norman and Mary V. Ashley, “Phylogenetics of Perissodactyla and Tests of the Molecular Clock,” Journal of Molecular Evolution 50 (2000): 11-21.
  5. Fazale R. Rana, “Cambrian Flash,” Connections 2, no. 1 (2000): 3.
  6. M. de L. Brooke, “How Old Are Animals?” Trends in Ecology and Evolution 14 (1999): 211-12.
  7. Francisco Jose Ayala, Andrey Rzhetsky and Francisco J. Ayala, “Origin of the Metazoan Phyla: Molecular Clocks Confirm Paleontological Estimates,” Proceedings of the National Academy of Sciences USA 95 (1998): 606-11.
  8. Norman and Ashley, 11-21.