Posted by Reed A. Cartwright on December 17, 2006 01:12 AM

Over at Dembski & Co., there are some recent posts (here, here, and here) complaining about molecular clocks and arguing that well known and long established limitations of molecular clocks invalidate evolutionary biology.

I find it sad that a week after scientists used molecular clocks to show that the Tripoli Six did not cause an HIV outbreak, the anti-evolutionists at UD throw up some posts ignorantly questioning the well established and understood procedure. I feel like arguing that anti-evolutionists want these six innocent health workers to be executed, but I’m sure that is not the case. They just don’t get the science or even care to. But the science is important, and the ignorance engendered by anti-evolution can have life-and-death consequences.

I don’t know what the people of UD learned in their evolutionary biology graduate programs, but in my program we were taught that the molecular clock is a methodological assumption and that if we use it long enough, we will work with datasets that violate it.

Now the molecular clock is a rather simple thing. It involves one major assumption: that the rate of substitutions per million years is constant among the molecules (DNA or proteins) that you are comparing. Yes, that is an assumption, and science typically makes assumptions when it tries to estimate or calculate some measurement of interest. For example, chemistry students work with ideal gases, and physics students work with ideal springs. Likewise, biology students work with ideal organisms.

The simple procedure looks like this. First you need some DNA or protein sequences. If you know the time of separation between at least two of your sequences, then you can calculate a rate of substitutions per million years from the pair. Using this rate and the above assumption, the time of separation between any two of your other sequences can be estimated. This can allow one to estimate when speciation occurred or a taxon was formed. Of course, this procedure can be made more complex as needed. There are models that use relaxed molecular clocks, multiple calibration points, etc., and many evolutionary biologists don’t even work with molecular clocks. Thus, strict molecular clocks are not as pervasive as some would think.

Clearly from what we know about organismal evolution, datasets with organisms that are closely related or distantly related can and probably will violate the assumptions of the molecular clock: the former because not enough generations have elapsed for the weak law of strong numbers to average out evolutionary variation and the later because evolution can and will make rates in distantly related species uncorrelated.

Now in my grad program, we were also taught that you must calibrate every molecular clock that you do. You can’t take a molecular clock estimate from plants and apply it to mammals and expect to get reasonable estimates of divergence time. You can’t take an estimate based on mutations in a pedigree and apply it to substitutions between species and get reasonable estimates of divergence time. This is known and not a surprise, yet anti-evolutionists have acted like this is some new nail in the coffin of evolution. (I will point out that I’ve taught such limitations to undergraduate evolutionary biology students. Too bad more people haven’t had me for a TA.)

We know these limitations of molecular clocks. We knew them decades before ID was a twinkle in creationists’s eyes. Does that mean that scientists don’t make mistakes when it comes to applying molecular clocks to real data? Of course not. We can expect that scientists, especially ones lacking a thorough training in molecular evolution, will make mistakes when applying this procedure. We can also expect mistakes to occur if the procedure is applied when there is limited data, as can often be the case when someone is trying to build a dataset on some obscure taxa combining results from different fields like biochemistry, genetics, paleontology, and paleogeology. We can also expect that estimates, derived from the molecular clock assumption, can be very wrong and contradictory. But that can happen when you are estimating something.

The bottom of the story is that the anti-evolutionists are not telling us anything that we don’t already know and don’t already work around. (In fact, they often lift such cautions from papers of evolutionary biologists without mentioning to their congregations that evolutionists are pointing these things out, not creationists.)

Ideally, I’d include several references in this post, but I’m nine hours from campus and when I get back I’ll be continuing my work on analyzing human, chimp, rat, and mouse genomes using non-molecular clock models. (I guess that the Dogmatic Darwinists haven’t gotten to me yet.) Hopefully, one of the other pandits that works with molecular data will fill in the blanks this week for our readers.