Explore Evolution's arguments against molecular clocks are a bungled mishmash of actual facts, misinterpretations and completely spurious claims. First, the authors raise the issue of calibration of the molecular clock. This is an acknowledged potential problem in using the clock to date certain evolutionary events, especially those in the very deep past. Nevertheless, when appropriate methodology and controls are used, molecular clock dating has been shown to be reliable and consistent.
Explore Evolution is wrong to present molecular clocks as "evidence for Common Descent" or to claim that such a link constitutes circular reasoning. The authors do not bring any specific example of this usage of the molecular clock by biologists, so it is hard to evaluate in what context it has been made, if at all. Again, however, allegations of this claim being made by unspecified "evolutionists" and its refutation are found in several Creationist sources.
Explore Evolution claims:
Critics also dispute both the accuracy and the importance of the "molecular clock." They dispute the accuracy because of many known problems with calibrating such clocks. To time something accurately, you must know that your watch runs at a constant rate—that it doesn't speed up or slow down. Unfortunately, say the critics, the rate of mutation varies in response to a number of environmental factors. As a result, even if we knew when species diverged, we couldn't be sure that the molecular clock was "ticking" at a constant rate.Explore Evolution, p. 59
There are several problems in this paragraph. First, it illustrates a rather grating habit found throughout Explore Evolution: the appropriation of arguments made by evolution scientists as if they were made by "critics," followed by the misrepresentation of such arguments. In this case, it is not anonymous "critics" who have pointed out that the molecular clock can perform unevenly, it is the very same scientists who then improve and continue to use the molecular clock approach.
More specifically, scientists have identified two main potential sources of error in molecular clock studies. The first is unevenness in the "ticking" rate. The finding that different proteins evolve (indeed, must evolve) at different rates was already known in the 1960s, and it was incorporated into the early theoretical formulations of molecular clocks by Jukes, Dickerson, Kimura and others. Differences in clock rates for the same protein between evolutionary lineages became clear with the advent of large-scale gene sequencing in the 1980s (Wu CI, Li WH. 1985 "Evidence for higher rates of nucleotide substitution in rodents than in man." Proc Natl Acad Sci U S A. 82:1741-5. Li WH, Tanimura M. 1987 "The molecular clock runs more slowly in man than in apes and monkeys." Nature. 326:93-6). Both these kinds of differences are generally measurable, and can be accounted for using appropriate calibration methods and adjustments.
The choice and statistical evaluation of calibration points has been more difficult. In order to accurately date events, scientists must set the clock based on events that are recognized as being accurately dated based on independent fossil or (for more recent events) archaeological evidence. Once one or more such events (for instance, the separation of the lineages giving rise to birds and mammals) are identified, genetic differences in a specific set of proteins between relevant species (in this case, birds and mammals such as humans and chickens) can be measured to "set" the clock, which can then be applied to the separation of other lineages in comparable time frames. Calibration points, especially for analyses in the deep past, have been a source of sometimes heated debate among scientists (Graur D, Martin W. 2004 "Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision." Trends Genet. 20:80-6.; Hedges SB, Kumar S. 2004 "Precision of molecular time estimates." Trends Genet. 20:242-7; Glazko GV, Koonin EV, Rogozin IB. 2005 "Molecular dating: ape bones agree with chicken entrails." Trends Genet. 21:89-92). Still, the consensus is that application of the molecular clock with the appropriate controls and cautions can be useful and reliable.