Two scientists in 1964 proposed that one could compare the genomes of modern organisms by looking for differences in the DNA sequences of specific similar genes. Then, armed with assumptions concerning the length of time involved to produce these differences, they then calculated the rate of change in the DNA sequence from the time that these groups had been one population (with a common gene sequence). Then, if they knew the rate of change, they could calculate the length of time since the populations diverged. Or if they knew the length of time since divergence, then they could calculate the rate. Obviously, the big unknown is the length of time. This has to be assumed. The idea that minor changes in the DNA code were proportional to time elapsed over the eons, then suggested a molecular clock. Assuming a constant rate of change, the greater the differences between two populations, the longer the time interval involved.
More recently however, scientists have expressed concern that the time estimates based on molecular clocks from the beginnings of development into so many animal body plans (Cambrian explosion), do not agree with conclusions based on looking at the fossils. The two time estimates were far out of synchrony. Some specialists have thus proposed “relaxed molecular estimates” where different organisms exhibit different rates of change. They therefore found that with different assumptions concerning rates of change in organisms with different body plans, they obtained divergence times which were much closer to fossil estimated ages than those based on a global constant clock.
Another striking example of problems with the molecular clock comes from another example of sudden appearance in the fossil record, namely the fossil examples of flowering plants which are found only in Cretacous rocks and higher. If evolution were true, this record would mean that the flowering plants (by far the most diverse and most numerous land plants) appeared only towards the end of the time of the dinosaurs.
Anyway, attempts to date the appearance of flowering plants by means of a molecular clock have been fraught with hazards!! Thus Charles Bell et al. described the difficulties: “Many previous efforts to date evolutionary divergences within angiosperms and within land plants using a strict molecular clock (i. e. assuming rate constancy among lineages) have yielded age estimates that not only vary dramatically, but are also grossly inconsistent with the fossil record. For example, using molecular data, the age of the angiosperms has been estimated as 420-350 mya, between 354-300 mya, and 200 mya. These dates would suggest an origin of the angiosperms that predates not only the angiosperm fossil record (about 135-125 mya), but …. even all vascular plants.” [Charles D. Bell, Douglas E. Soltis and Pamela S. Soltis. 2005. The Age of the Angiosperms: a Molecular timescale without a clock. Evolution pp. 1245-1258. See p. 1248] [mya= millions of years ago] In view of these difficulties, several specialists have approached the issue using a relaxed molecular clock “given that genes may evolve at heterogeneous rates in different lineages.” [p. 1245]
The bottom line is that if the calculations for the molecular clock do not fit your expectations, then plug a different rate of change into your equation. Sooner or later, you will obtain an answer you like! The molecular clock is obviously a highly subjective and unreliable method for determining passage of time! It depends upon the dubious assumption of deep time. Why waste your time on such calculations?