“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
epicyclesmolecular clocks and arguing that well known and long established limitations ofepicyclesmolecular clocks invalidatePtolemaic astronomyevolutionary biology.I find it sad that a week after scientists used
epicyclesmolecular clocks to show that themoonTripoli Six did not causetidesan HIV outbreak, theCopernicansanti-evolutionists at UD throw up some posts ignorantly questioning the well established and understood procedure. I feel like arguing thatCopernicansanti-evolutionists want these six innocentastronomershealth workers to becast to the lionsexecuted, 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 byCopernican Theoryanti-evolution can haveastrologicallife-and-death consequences.I don’t know what the people of UD learned in their
Ptolemaic astronomyevolutionary biology graduate programs, but in my program we were taught that theepicyclemolecular clock is a methodological assumption and that if we use it long enough, we will work withstars, comets, and planetsdatasets that violate it.Now the
epicyclemolecular clock is a rather simple thing. It involves one major assumption: that the rate ofretrograde motionsubstitutions per million years is constant among thestars, comets, and planetsmolecules (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,alchemychemistry students work withtransmutation of the elementsideal gases, and physics students work withphlogistonideal springs. Likewise,astronomybiology students work withepicylesideal organisms.The simple procedure looks like this. First you need some
stars, comets, or planetsDNA or protein sequences. If you know the time oforbitseparation between at least two of yourastronomical objectssequences, then you can calculate a rate ofretrograde motionsubstitutions per million years from the pair. Using this rate and the above assumption, theorbital relationshiptime of separation between any two of your otherstars, comets, or planetssequences can be estimated. This can allow one to estimate whena deferantspeciation occurred oran equanta taxon was formed. Of course, this procedure can be made more complex as needed. There are models that use relaxedepicyclesmolecular clocks, multipleepicylescalibration points, etc., and manyPtolemaic astronomersevolutionary biologists don’t even work withepicyclesmolecular clocks. Thus, strictepicyclesmolecular clocks are not as pervasive as some would think.Clearly from what we know about
the earth-centered universeorganismal evolution, datasets withstars, comets, and planetsorganisms that are closely related or distantly related can and probably will violate the assumptions of theepicyclemolecular clock: the former because not enoughorbitsgenerations have elapsed for the weak law of strong numbers to average outtelescopic observationsevolutionary variation and the later becauseretrograde motionevolution can and will make rates in distantly relatedstars, comets, and planetsspecies uncorrelated.Now in my grad program, we were also taught that you must calibrate every
orbitmolecular clock that you do. You can’t takean epicyclea molecular clock estimate fromplanetsplants and apply it tocometsmammals and expect to get reasonable estimates oforbitsdivergence time. You can’t take an estimate based onepicyclesmutations in a pedigree and apply it toretrograde motionsubstitutions betweenstarsspecies and get reasonable estimates oforbitsdivergence time. This is known and not a surprise, yetCopernican theoristsanti-evolutionists have acted like this is some new nail in the coffin ofPtolemaic astronomyevolution. (I will point out that I’ve taught such limitations to undergraduateastronomyevolutionary biology students. Too bad more people haven’t had me for a TA.)We know these limitations of
epicyclesmolecular clocks. We knew themcenturiesdecades beforeCopernicusID was a twinkle inenlightenmentcreationists’s eyes. Does that mean that scientists don’t make mistakes when it comes to applyingepicyclesmolecular clocks to real data? Of course not. We can expect that scientists, especially ones lacking a thorough training inPtolemaic astronomymolecular 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 obscurecomettaxa combining results from different fields likealchemy, astrology, and phlogistonicsbiochemistry, genetics, paleontology, and paleogeology. We can also expect that estimates, derived from theepicyclemolecular 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
Copernicansanti-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 ofPtolemaic astronomersevolutionary biologists without mentioning topeople with common sensetheir congregations thatdogmatic Ptolemaistsevolutionists are pointing these things out, notreasonable people who know a design when they see onecreationists.)Ideally, I’d include several references in this post, but I’m
many furlongsnine hours from campus and when I get back I’ll be continuing my work on analyzingstellar, cometary, and planetary motionshuman, chimp, rat, and mouse genomes usingdifferent models that actually worknon-molecular clock models. (I guess that the DogmaticPtolemaistsDarwinists haven’t gotten to me yet.) Hopefully, one of the other pandits that works withepicyclemolecular 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.