Molecular Clock

Different species of organisms have enormous regions of DNA that are the same or very similar. Humans and chimpanzees, for example, share about 98 percent of their DNA. We share much less of our DNA with rodents and amphibians and insects.

In a general way, the percentage of shared DNA might be a means to establish a molecular clock that is, the more DNA that is shared, the more recent was the separation of the family tree. And, if by accident, the changes in the DNA happened to proceed at a common rate, then one could set up a timeline also.

However, the genetic changes do not occur with any regularity. Why not?

Answer

The changes in the DNA during the evolution of organisms do not occur at a common rate because any change in a critical essential protein coding does not produce a viable organism even though a change in the nonessential DNA might—that is, changes in the DNA that do not affect the biochemistry critically will be tolerated. There are vast regions of DNA where such ineffective changes can occur, but any change in the other regions programmed for the production of essential biomolecules will be disastrous. If we assume the ideal case, that in principle the changes would be equally probable at any random location along any DNA chain, and we assume that the organism will grow and reproduce the next generation, then we could have a molecular clock. However, as we know, just as all genes are not equal in value at any given time, all DNA sequences are not equal in value. In particular, some DNA sequences code for proteins that control the expression of other DNA genes themselves, turning them on and off at appropriate times in the development of cells in the organism. The Hox protein in insects, for example, will determine the structure of several different body parts, and slight changes in its amino acid sequence are major contributors to insect evolution. Therefore, both complementary DNA strands at the critical location need not be affected for the appearance of obvious phenotype changes.

However, the whole DNA mechanism and its subsequent biochemistry in the cell are much more robust than originally realized. The fact that many of the amino acids have several DNA base code triplets of nucleic acids for their selection is a built-in resiliency that can produce a viable organism even when the DNA has an error of this kind. In addition, if the erroneous amino acid substitutes at a location that is not critical for the 3-D shape and the operation of the protein, once again there is a built-in resiliency. Let’s face the fact that Nature is much more clever than we can ever hope to be!