“you must calibrate every molecular clock that you do”… Reed A. Cartwright on The Panda’s Thumb
“We can also expect that estimates, derived from the molecular clock assumption, can be very wrong and contradictory.” ibid
Over at Dembski & Co., there are some recent posts (here, here, and here) complaining about epicycles molecular clocks and arguing that well known and long established limitations of epicycles molecular clocks invalidate Ptolemaic astronomy evolutionary biology.
I find it sad that a week after scientists used epicycles molecular clocks to show that the moon Tripoli Six did not cause tides an HIV outbreak, the Copernicans anti-evolutionists at UD throw up some posts ignorantly questioning the well established and understood procedure. I feel like arguing that Copernicans anti-evolutionists want these six innocent astronomers health workers to be cast to the lions 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 Copernican Theory anti-evolution can have astrological life-and-death consequences.
I don’t know what the people of UD learned in their Ptolemaic astronomy evolutionary biology graduate programs, but in my program we were taught that the epicycle molecular clock is a methodological assumption and that if we use it long enough, we will work with stars, comets, and planets datasets that violate it.
Now the epicycle molecular clock is a rather simple thing. It involves one major assumption: that the rate of retrograde motion substitutions per million years is constant among the stars, comets, and planets 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, alchemy chemistry students work with transmutation of the elements ideal gases, and physics students work with phlogiston ideal springs. Likewise, astronomy biology students work with epicyles ideal organisms.
The simple procedure looks like this. First you need some stars, comets, or planets DNA or protein sequences. If you know the time of orbit separation between at least two of your astronomical objects sequences, then you can calculate a rate of retrograde motion substitutions per million years from the pair. Using this rate and the above assumption, the orbital relationship time of separation between any two of your other stars, comets, or planets sequences can be estimated. This can allow one to estimate when a deferant speciation occurred or an equant a taxon was formed. Of course, this procedure can be made more complex as needed. There are models that use relaxed epicycles molecular clocks, multiple epicyles calibration points, etc., and many Ptolemaic astronomers evolutionary biologists don’t even work with epicycles molecular clocks. Thus, strict epicycles molecular clocks are not as pervasive as some would think.
Clearly from what we know about the earth-centered universe organismal evolution, datasets with stars, comets, and planets organisms that are closely related or distantly related can and probably will violate the assumptions of the epicycle molecular clock: the former because not enough orbits generations have elapsed for the weak law of strong numbers to average out telescopic observations evolutionary variation and the later because retrograde motion evolution can and will make rates in distantly related stars, comets, and planets species uncorrelated.
Now in my grad program, we were also taught that you must calibrate every orbit molecular clock that you do. You can’t take an epicycle a molecular clock estimate from planets plants and apply it to comets mammals and expect to get reasonable estimates of orbits divergence time. You can’t take an estimate based on epicycles mutations in a pedigree and apply it to retrograde motion substitutions between stars species and get reasonable estimates of orbits divergence time. This is known and not a surprise, yet Copernican theorists anti-evolutionists have acted like this is some new nail in the coffin of Ptolemaic astronomy evolution. (I will point out that I’ve taught such limitations to undergraduate astronomy evolutionary biology students. Too bad more people haven’t had me for a TA.)
We know these limitations of epicycles molecular clocks. We knew them centuries decades before Copernicus ID was a twinkle in enlightenment creationists’s eyes. Does that mean that scientists don’t make mistakes when it comes to applying epicycles molecular clocks to real data? Of course not. We can expect that scientists, especially ones lacking a thorough training in Ptolemaic astronomy 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 comet taxa combining results from different fields like alchemy, astrology, and phlogistonics biochemistry, genetics, paleontology, and paleogeology. We can also expect that estimates, derived from the epicycle 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 Copernicans 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 Ptolemaic astronomers evolutionary biologists without mentioning to people with common sense their congregations that dogmatic Ptolemaists evolutionists are pointing these things out, not reasonable people who know a design when they see one creationists.)
Ideally, I’d include several references in this post, but I’m many furlongs nine hours from campus and when I get back I’ll be continuing my work on analyzing stellar, cometary, and planetary motions human, chimp, rat, and mouse genomes using different models that actually work non-molecular clock models. (I guess that the Dogmatic Ptolemaists Darwinists haven’t gotten to me yet.) Hopefully, one of the other pandits that works with epicycle molecular data will fill in the blanks this week for our readers.
“The lady doth protest too much, methinks.” -William Shakespeare
The bottom line: Every so-called molecular clock has to be pencil-whipped into congruency with the indisputable testimony of the fossil record. And it isn’t just a little pencil whipping, it’s 2 to 20 times. In all fairness to Ptolemaic astronomy it at least only needed tiny tweaks to make it keep lining up with growing size and precision in the raw data. And it isn’t just between species of organisms, its between species of sequence within the same organism – unconserved, a little conserved, conserved, highly conserved, ultraconserved. There’s so little correlation it ought to be an enigma like c-value. Of course random mutation and natural selection explains it all. As we all know, random mutation and natural selection explains everything.
Molecular clocks work great except when they disagree with better dating methods by 2 to 20 times.
Natural selection can work so well that ~120 million years of random mutation on two different species of worm, with genomes comparatively scrambled moreso than man and mouse (~90my), somehow retained virtually identical phenotypes.
Yet sometimes natural selection does next to nothing when you find you can delete 1000 highly conserved man/mouse sequences from hundreds of mice and it results in perfectly healthy, normal mice.
And I almost forgot… humans have retrotransposon insertions that more closely match coelacanths than to other animals (except chimps) including mice, dogs, opossums, chickens, and frogs.