Question

what does it mean for a section of DNA to be considered a molecular clock.

Answer 1

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Basically, the molecular clock is based on the observation that some genes and other regions of genomes appear to evolve at average constant rates. You would look at certain types of mutations (e.g. silent mutations or changes in amino acid sequences) to determine this.

For example, the amino acid sequence of hemoglobin can be compared in vertebrates ranging from sharks to humans. When you plot the number of amino acid differences between species against the approximate date that the species diverged (based on the fossil record), you could see that the evolution of hemoglobin seems to proceed at a constant rate through time. The more time between the species' divergence from their common ancestor, the greater the difference in genes (e.g. number of nucleotide substitutions). But keep in mind that it's the AVERAGE rate of change that is being recorded; the rate of the clock may vary greatly from one gene to another; some genes evolve a million times faster than others.
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