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The Claudius Ptolemaeus of Molecular Clocks responds…

December 17, 2006 Posted by Dave S. under Intelligent Design
20 Comments

Ptolemy

“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.

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20 Responses to The Claudius Ptolemaeus of Molecular Clocks responds…

  1. 1
    tribune7December 17, 2006 at 2:00 pm

    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
    Geocentrics made accurate observations and drew correct conclusions too. It didn’t mak them right about geocentricism.
    , the Copernicans anti-evolutionists at UD
    Exactly! We are the Copernicans. :-)

  2. 2
    tribune7December 17, 2006 at 2:02 pm

    N0w that was poorly formatted:

    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

    Geocentrics made accurate observations and drew correct conclusions too. It didn’t mak them right about geocentricism.

    the Copernicans anti-evolutionists at UD

    Exactly! We are the Copernicans. :-)

  3. 3
    DaveScotDecember 17, 2006 at 2:36 pm

    Does strike work in comments? They obviously don’t cut & paste with the text.

  4. 4
    tribune7December 17, 2006 at 3:06 pm

    I was being lazy

  5. 5
    DaveScotDecember 17, 2006 at 4:30 pm

    What’s interesting is that the molecular clock hypothesis can be “very wrong and contradictory” in reality but still be science while if there’s even a possibility that ID is wrong it’s not science. No double standard there.

  6. 6
    bFastDecember 17, 2006 at 4:54 pm

    My favorite molecular clock is the HAR1F (I think that’s the right name.) The dear think ticked by 3 base pairs between the chimp and the chicken. (It codes to RNA, not to protein, therefore is base pair centric.) Between the chimp and the human, however, it did a total of 18 ticks.

    Let’s calculate out the clock for a minute. The common ancestor of the chicken and the chimp is about 200 mil ago. Therefore there is about 400 mil total time between the chicken and the chimp. Tick rate for this clock — 133 million years per bp.

    As there is no mutation between the chimp and the common ancestor of the human, we only need to count the human side of this divergence. That would be about 133 million years * 18 = 2.39 billion years. Not bad!

    To add insult to this injury, the folding of this RNA produces a lock and key configuration that, as far as I can tell, is absolutely resistant to mutation by a single base-pair method. In fact, it appears to me that it would take multiple simultaneous base-pairs to mutate, base-pairs that are not side-by-side. Ie, this little mutation is irreduceably complex.

    But hey, the molecular clock analysis of the thing is a lot more fun. In this case the clock is out by about 800 times!

    Further, it is my understanding that this is a growing pattern amongst mutated genes. They maintain status for a long time, then they make an impossible jump. Hmmm, sounds just like the rock record.

  7. 7
    JehuDecember 18, 2006 at 2:51 am

    “The lady doth protest too much, methinks.” -William Shakespeare

    My thoughts exactly. That is also what I thought when Panda’s Thumb attacked Paul Nelson’s lecture concerning ORFans.

    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 anti-evolutionists at UD throw up some posts ignorantly questioning the well established and understood procedure.

    Don’t you just love the illogic there? The “breathtaking inaninity” of it is staggering. The Tripoli Six were acquited using a molecular clock argument therefore the molecular clock must be true? How bizarre it that logic? What about the claim that the procedure is well understood? Does this guy even understand the inconsistency this poses to evolution?

    We know these limitations of molecular clocks. We knew them decades before ID was a twinkle in enlightenment creationists’s eyes.

    Apparenlty not. It is an inconsistency but because they have known about the inconsitency for decades it is okay?

    According to the article, “Dates from the molecular clock: how wrong can we be?” the situation is not well in hand.

  8. 8
    Designed JacobDecember 18, 2006 at 4:10 am

    Did the article actually compare a hypothesis of mutational gradualism with an ideal gas and an ideal spring?

  9. 9
    DaveScotDecember 18, 2006 at 4:27 am

    Jehu

    Check this out

    organisms that are closely related can and probably will violate the assumptions of the molecular clock because not enough generations have elapsed for the weak law of strong numbers to average out evolutionary variation

    Yet they wave around closely related HIV strains as proof the Tripoli Six are innocent. I guess closely related organisms can and probably will violate those assumptions…except when they don’t.

    Basically what Reed did was use 1000 words to obfuscate his agreement with us that molecular clocks are grossly unpredictable.

  10. 10
    DaveScotDecember 18, 2006 at 4:44 am

    jacob

    Did the article actually compare a hypothesis of mutational gradualism with an ideal gas and an ideal spring?

    You bet. Remove the strikeouts and the original article is perfectly intact. Amazing, isn’t it? It’s almost like Reed has no understanding of hard science and engineering yet desperately wants the soft theoretical science of historical biology to be comparable in precision and predictability so it gets the same level of respect and trust. You can’t make chicken salad out of chicken shi droppings.

  11. 11
    bFastDecember 18, 2006 at 9:44 am

    Let me defend the folks down at PT from the blanck and white thinking that sometimes goes on in this forum.

    Just because the molecular clock hypothesis is not adequate to explain precision such as is found in the cytochrome C, that doesn’t mean that all discussions of a molecular clock are invalid.

    From what I have seen, genes are subject to a true “genetic drift”. Which is to say, there is a period in the life-cycle of a gene where the gene is floating on a sea of random chance. As such, if we know where the gene is, and where the gene started from, and how resistant it is to mutation, we can gestimate about how long it took to get from hither to thither.

    Now, there is stuff going on in genes that just don’t fit no molecular clock — the HAR1F for example. But that doesn’t mean that every mention of the molecular clock is automatically invalid.

  12. 12
    scordovaDecember 18, 2006 at 1:11 pm

    At issue with molecular clocks is the issue of bad extrapolations that are common in the Darwinists community.

    In engineering, an example of a bad extrapolation is the following: “if I get a bigger engine for a car, I can get it to go faster, thus I can build a car that can travel faster than mach ten if I simply have a bigger engine” The problem of the molecular clock is the issue of bad extrapolations.

    At issue is not that some sequence divergences can not sometimes be explained by some sort of clock, nor that hierachical phylogentics are not observed in the breeding lab (we can often trace the ancestry of various lab cultures and the ancestry of mutations in the lab). At issue is the adequacy of extrapolating these changes to huge time scales and major changes in organisms.

    Denton’s argument is citing the adequacy of a random diffusion mechanism (neutralism ala kimura and friends) or selection.

    However, what has happened is that both the selectionists and the neutralists find fatal flaws in each other’s arguments.

  13. 13
    JehuDecember 18, 2006 at 1:18 pm

    As such, if we know where the gene is, and where the gene started from, and how resistant it is to mutation, we can gestimate about how long it took to get from hither to thither.

    Yes, but how do you know how resistant the gene is to mutation? By how much it has changed since the time of divergence? Do you see circular reasoning?

  14. 14
    scordovaDecember 18, 2006 at 1:57 pm

    Reed Cartwright wrote:

    The bottom of the story is that the Copernicans anti-evolutionists are not telling us anything that we don’t already know

    Here is something else I’ll tell you that you don’t already know, and it’s from Allen Orr:

    “Natural Selection does trade in the currency of deisgn”

    Got that Reed, Natural selection is not correlated to many of the designs found in nature.

  15. 15
    scordovaDecember 18, 2006 at 2:41 pm

    By the way Reed, the issue is not whether molecular clocking of mutations exists, the question is whether a clock was at work to create the various patterns we see in biology like equidistance. You, like others have misrepresented what the argument is about.

    It’s like the question of natural selection and ID. It’s not a question whether natural selection takes place, but whether natural selection is adequate to explain the patterns in nature, which Allen Orr affirms it is not.

    Likewise the problem of the molecular clock is not that there are no molecular clocks, but rather the adequacy of the clock to explain the astonishing equidistances and other patterns found in biology.

  16. 16
    DaveScotDecember 18, 2006 at 4:18 pm

    Actually an hypothesis that fits all the evidence of coding gene change over time is the selfish gene theory. Coding genes are all there are in prokaryotes. Ostensibly coding genes came first in a bare bones fashion. Regulatory regions and intron splicing came along billions of years later in eukaryotes. The interesting contrast between coding genes and everything else is that coding genes 1) use a redundant code where their sequence can be changed without changing the protein product and 2) have redundancy in their design where even most mutations that result in amino acid substitutions don’t change biologic activity of the protein.

    Thus your essential bare bones coding gene is highly resistant to mutations that alter the function of its protein product.

    The later additions to genomes that regulate coding gene expression do not use the redundant genetic code. For those regulators to identify any particular gene for up-regulation or down-regulation they have to be able to get a match on the gene’s sequence. Synonymous substitutions in the gene and also mutations that change amino acid sequence but not protein function would hobble or eliminate the regulator molecule’s ability to get a sequence match while retaining the biologic importance (selection value) of the protein product – the gene lives on unobstructed by external regulation.

    Now let’s say that Dawkins is right and genes are clever, selfish little structures interested in propagating themselves. As such, the gene wouldn’t want interference from other structures that can regulate their expression. So they respond by changing their sequence information in such a way that their biological importance remains intact but the attempts by non-gene structures to regulate them is thwarted.

    I think the selfish gene theory is all wet for a number of other reasons but it would explain why the lack of predictability in how they mutate over time. Some have needed to respond more than others to “power plays” by regulatory structures. Any attempt to assign background mutation rates for comparative purposes would therefore be futile.

    Sequence variation that doesn’t change function is how computer viruses “evolve” to avoid detection by anti-virus software. Anti-virus software in large part works by selecting a short “signature” from the virus’ code then scanning all the data on the computer looking for that signature. All anyone has to do to make the computer virus undetectable again is make a synonymous substitution in the signature sequence.

    No doubt random mutation and natural selection play some role in evolution but computational genomics has revealed unequivocal exceptions that make RM & NS a subset of mechanisms that are in play. Molecular clocks all have to be calibrated in small or large degree by other dating mechanisms, worms that diverged a hundred million years ago have scrambled genotypes but identical phenotypes, and a thousand highly conserved non-coding sequences can be deleted from a mouse genome without any observed effect on the mice. As the genome bank expands there will undoubtedly be many more of these oddities found that seemingly violate the predictions of RM & NS. IMO there’s an elephant in the room. Francis Crick saw it, I see it, and many others see it. Life didn’t originate on this planet. It was placed here on purpose by an intelligent agency. The most elegant explanation IMO is that the intelligent agency responsible was the terminal product of a similar phylogeny elsewhere in the universe. Life, if nothing else, strives to continue itself and since planets all eventually become inhospitable to life it would need a mechanism of moving from one solar system to another. I propose that mechanism is the terminal product of evolution: a species that can customize life for new planetary environments, build telescopes to locate new planets, and build spacecraft to transport life to them. How many times this cycle has been replayed is anyone’s guess and how it got started may remain an unsolved mystery for all time. But that’s no reason to throw out the baby with the bathwater. We don’t know where the entire universe came from that doesn’t stop us from understanding it after its arrival.

    Further, if one adopts as givens that life was placed on this planet and its purpose was to eventually produce intelligent life that could start the cycle over again on a younger planet, we can ask ourselves what would be required for the emergence of a technological species able to transport life to a younger planet. The first thing would be atmospheric oxygen so that land-based life with fast metabolisms could be supported. Atmospheric oxygen would also be required to support combustion of fuels to power an industrial civilization. That would take a very long time. After the land based life is all over the place you’d next want to lay down huge deposits of easily accessable fuel like coal, oil, and natural gas. This would also take a very long time. Finally, when all the ducks are in a row, the technological species emerges with all the resources it needs to accomplish the mission goal – moving life to another planet where it can begin anew. Nothing in evolutionary biology makes sense except in the light of a front loaded genome placed here with a purpose. Once front loading and purpose are allowed into consideration then it all makes perfect sense.

    Note there’s no call upon religion or the supernatural in any of the above. It’s all perfectly compatible with what science has revealed and relies on nothing but logical connecting of the dots between disparate empirical observations in a way that makes sense of all the observations.

  17. 17
    JehuDecember 18, 2006 at 5:11 pm

    As such, if we know where the gene is, and where the gene started from, and how resistant it is to mutation, we can gestimate about how long it took to get from hither to thither.

    What about the theory that they were never the same? In that case, all of the attempts to find a pattern that can be explained by RM+NS is just chasing after a phantom that doesn’t exist.

  18. 18
    bFastDecember 18, 2006 at 5:29 pm

    DaveScot, interesting hypothesis. It does beg one interesting question, however. Current scientific understanding is that the universe had a beginning about 16 billion years ago. One could conceive of your model being brought back to the earliest planets. That might have been as far back as, say 10 billion years ago. The question of course is, how did that first life come into existance?

  19. 19
    JehuDecember 19, 2006 at 8:32 pm

    Apparently the molecular clock argument did not work. The Tripoli Six have been sentenced to death.

    http://www.washingtonpost.com/.....00178.html

  20. 20
    DaveScotDecember 22, 2006 at 5:48 am

    bFast

    The question of course is, how did that first life come into existance?

    As soon as some evidence becomes available I’ll let you know. Absent that it’s just another mystery. Mysteries happen. I don’t how the universe came into existence either. That’s another mystery. But running up against a brick wall where there’s no more evidence to work with doesn’t prevent one from reaching conclusions about the side of the wall you can observe.

    Who designed the designer is a bogus attack on ID. It’s the same as attacking NeoDarwinian theory for not explaining the origin of matter. We can observe the effects of intelligence without knowing where it came from just as we can observe the effects of matter without knowing where it came from. I won’t indulge in attacking NDE for failing to explain where matter came from. I don’t need to as it’s got plenty of other flaws. It’s revealing of the strength of arguments against ID that the one most often cited is a lame infinite regression.

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