Michael Ruse, author of Defining Darwin, Essays of the History and Philosophy of Evolutionary Biology concluded that “Indeed, the truth is that there is virtually nothing today in evolutionary studies that correspond exactly to the facts of the Origin.”

For Charles Darwin, molecular clocks were the farthest his mind, not to mention cellular biology or DNA. In 1859, inheritance was thought to occur by blending the characteristics with the new information learned by the “gemmules” in the parents. Gregor Mendel, the Austrian monk, in 1865 eventually decimated blending inheritance, but the foundation of modern genetics went unrecognized until rediscovered by Hugo de Vries and Carl Correns in 1900.

To estimate the pace of evolution, in 1962 molecular biologist Emile Zuckerkandl and Nobel Prize winner Linus Pauling were working at California Institite of Technology on hemoglobin evolution and expressed the idea of “molecular anthropology” as a new discipline. The idea was later termed the molecular clock theory. The purpose of the molecular clock is to estimate the rate of evolution for individual molecules. In 1962, molecular sequence problems were just emerging.

Zuckerkandl and Pauling postulated that in a protein, each amino acid randomly changes at a constant rate. If the estimated time for divergence between species and the number of amino acid changes since that time can be determined from the fossil record, the rate of change can be calculated. This rate of molecular change (time per amino acid change) has been called the molecular clock.

As the molecular data began to accumulate during the early 1990s, it became increasingly apparent that the theory was intrinsically even more problematic when examining evolution from the context of the entire organism and the fossil record. At the core of Darwinian evolution are the successive, slight changes in molecules. However, how different molecules can evolve at different rates in the same organism emerged as an enigma.

Information from the molecular clock was once thought to be one of the most useful tools in establishing evolutionary biology. How the evolution of each molecule can run by a different molecular clock in the same organism continues to undermine a cohesive theory of molecular evolution.

The pursuit to resolve the clock issue has reemerged onto center stage because the rate of molecular change is foundational to evolution. If the molecular mechanisms of evolution cannot be traced, the only logical conclusion is that molecular biology has played no role in evolution.

In 2007, Naoyuki Takahata, of The Graduate University for Advanced Studies in Japan, wrote in the journal Genetics, “It is now clear that any kind of molecular clock ticks erratically, but it is nevertheless widely used [unfortunately] for estimating species divergence times.”

How Zuckerkandl and Pauling’s simple postulate has become so complicated begs the question, are molecular clocks real? Professor of evolutionary biology Thomas Cavalier-Smith of the University of Oxford in England wrote in Philosophical Transactions of the Royal Society B in a paper entitled Cell Evolution and Earth History: Stasis and Revolution that the answer is no: “Evolution is not evenly paced and there are no real molecular clocks.”

Available evidence bodes negatively for the usefulness of molecular clocks in establishing any shape for the Tree of Life. What was originally thought to become a cornerstone for molecular evolution is now irreconcilable with evolution and created chaos in evolutionary thought. Difficulties associated with attempting to explain how a family of homologous proteins could have evolved at constant rates have created chaos in evolutionary thought.

Rather than supporting the theory of evolution, the molecular clock evidence and the sequence data actually undermine the theory of evolution through “successive, slight” variations in molecular biology. Just as hope in the fossil record, the origin of life, and the sequence of amino acids dissipated, the hope that molecular clocks will become an evidential, evolutionary cornerstone is vaporizing. In 2005, geneticist Giuseppe Sermonti wrote: “Once the universal ‘molecular clock’ was shelved, biochemists ceased to question (in any case dubious) datings proposed by paleontologists.”

Molecular biologists beginning in the early twentieth century had expected to trace the organization of inorganic to organic molecules as well as the successive molecular changes as the species evolved. Clearly, however, the convergence of molecular evidence does not support the theory. Darwin concluded in The Origin of Species if the evidence does not support “numerous, successive, slight modifications, my theory would absolutely break down.”

Molecular clocks, as evidence for evolution, continue to be unsuccessful in delivering on earlier expectations.