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Molecular Clocks: Michael Denton continues to be vindicated

Salvador Cordova
December 14, 2006
Intelligent Design
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Back in 1985 Denton wrote of the Molecular Clock Hypothesis which was concocted by Schlemiel Zuckerkandl:

…the idea of uniform rates of evolution [molecular clocks] is presented in the literature as if it were an empirical discovery. The hold of every evolutionary paradigm is so powerful that an idea [molecular clocks] which is more like a principle of medieval astrology than a serious twentieth-century scientific theory has become a reality for evolutionary biologists…the biological community seems content to offer explanations which are no more than apologetic tautologies.

Michael Denton, Evolution: A Theory in Crisis (1985)

Well this principle of “medieval astrology” used by evolutionary biologists continues to come apart.

See this article in a peer-reviewed scientific journal:
Dates from the molecular clock: how wrong can we be?

Large discrepancies have been found in dates of evolutionary events obtained using the molecular clock. Twofold differences have been reported between the dates estimated from molecular data and those from the fossil record; furthermore, different molecular methods can give dates that differ 20-fold. New software attempts to incorporate appropriate allowances for this uncertainty into the calculation of the accuracy of date estimates. Here, we propose that these innovations represent welcome progress towards obtaining reliable dates from the molecular clock, but warn that they are currently unproven, given that the causes and pattern of the discrepancies are the subject of ongoing research. This research implies that many previous studies, even some of those using recently developed methods, might have placed too much confidence in their date estimates, and their conclusions might need to be revised.

This article was motivated by the experience of a colleague who estimated the time since the separation of two taxa from the number of substitutions that had accumulated between their DNA sequences; in other words, he was using the molecular clock. On submitting the work for publication, he was startled to be advised by a referee that his estimate was wrong by a factor of ten. The argument concerned the tick rate of the molecular clock; that is, the rate of accumulation of substitutions per million years. How could the scientific community hold two such contradictory opinions simultaneously?

Our colleague’s original calculation was based on a rate estimated from inter-species comparisons, whereas the referee preferred a rate obtained from a pedigree study. Later, we address why such discrepancies exist between estimates of substitution rates. The central lesson for this article, however, is the realization that reasonable scientists working with the molecular clock can be using estimates that are so different. If neither the fast estimate nor the slow estimate were self-evidently wrong, it suggests that it is difficult to validate them using our knowledge of biogeography and the fossil record. Methods are currently being devised that deal with uncertainty about the variation in the rate and about the timing of the calibration points. Here, we consider the prospects of obtaining date estimates that take account of these issues when constructing their standard errors (or analogous measures of uncertainty): is there likely to be so much uncertainty about molecular dating that the estimates are no longer useful? We fear that, for many current studies, the answer is yes. However, it might be possible to gain extra precision using recently developed methods. The degree of improvement depends on the pattern of variation in the rate of molecular evolution and the availability of calibration points. We currently do not know enough to be confident in the prospects of these new methods, and some initial results are discouraging.
…..

And the bad news continues. Darwinism continues to self-destruct on its own demerits.

Finally, I should add, one of Behe’s first ID-friendly peer-reviewed articles extended Denton’s claims. See: Histone deletion mutants challenge the molecular clock hypothesis.

Behe is getting some vindication as well.

Comments
[...] is poised to provide data which will overturn the prevailing ideas about molecular clocks (See: Molecular Clocks: Michael Denton continues to be vindicated). I will elaborate in the comment section if anyone is interested. In brief, we do not have [...] Solexa: A development which may lead to measuring claims of ID proponents | Uncommon Descent
[...] In contrast, Michael Denton and Michael Behe successfully anticipated the scientific developments which we see today (much to the embarrassment of Darwinists). Behe in fact published a peer-reviewed article critical of the molecular clock hypothesis almost 17 years ago in Trends in Biochemical Science! [See: Histone deletion mutants challenge the molecular clock hypothesis.] Behe built on the work of Denton in 1985. [See Molecular Clocks: Michael Denton continues to be vindicated.] [...] Zuck is out of luck, marsupial findings vindicate Behe, Denton, Hoyle | Uncommon Descent
bFast: "To the best of my knowledge the molecular clock hypothesis is rarely used to calculate divergence. Rather, that is determined by what layer in the rocks the fossils are found, by isotopic dating methods, by presumed phylogenic tree constructions, etc." What I'm referring to are articles where, based on molecular divergences in certain pseudo-genes, or duplicated genes, they want to rearrange dates for divergences between certain higher order taxa. (It's a rather new phenomena) Indeed, the fossil record tells a certain story, and serves as a fairly good yarstick; but now it seems that some scientists are putting more faith in their molecular divergences than even in the fossil record, forgetting as they do, that the fossil record is basically used to calibrate the "tick" in the molecular clocks. Simply put, I bridle at their unjustified level of confidence in such measurements. PaV
Dizzy, when I first encountered Denton's cytochrome C case, around 2002, it piqued my curiosity, so I did some exploring. At that point, the molecular clock hypothesis was pretty active. They were beginning to use it to estimate diversion dates, that sort of thing. Now, a few years later, the molecular clock has fallen badly into disrepute. It seems that the clock can be used in a limited way if circomstances are "just so". However, these "just so" conditions do not allow it to explain the cytochrome C, not by any means. As I said in an earlier post, the molecular clock hypothesis was, I understand, developed specifically to address the perfection of the phenotype map in the cytochrome C molecule. This hypothesis falling into disrepute should be causing a stir in the scientific community in light of the cytochrome C. To my knowledge it is not -- however, I am an outsider. (I have often seen, however, that we tend to say "oh, that problem is solved", only to forget that the solution is no longer valid.) As far as the cytochrome C goes, I have noticed some changes to the analysis of that data. (There may be data on more species now.) The phylogenic tree remains to be recognized. However, there are a number of reported exceptions. Most noteable of these is that the cytochrome C in the rattlesnake is very like the human version. In general, I see no reason to believe that anything substantive has changed reguarding Denton's cytochrome C analysis, except that the molecular clock hypothesis has been weakened. bFast
Dizzy, what is the date of the article to which Sal linked? After you have answered that question, think about the implications of it in regards to the question you asked. Jehu
Seems nothing has happed in this field since Denton (1985) Looking at my clock, I notice I am living in a different century, 21 years later. I wouldn't be surprised if science had not made more noticeable progress in that time period than ID. Right or wrong? Dizzy
Sal, Thanks for the link. I always thought Denton was wrong in his cytochrome C argument. I thought this because although I had never read Denton's argument I had read some articles that rebutted it. Obviously the articles I read rebutted a strawman. I feel like I have been decieved. The Darwinist apologists have less credibility in my eyes than ever. They cannot be trusted. Denton spends pages rebutting the argument he supposedly didn't understand. Denton understands it alright, and then he trashes it. BTW this was an interesting comment by Denton.
In closely related species such as man and chimpanzee, where the generation rates are similar, one might therefore expect approximately similar rates of drift to have occurred in homologous loci over several generations.
As it turns out, the human and chimpanzee genome do not reflect a uniform rate of drift. Remember? After they sequenced the chimpanzee genome they noticed the lack of uniform drift so they decided that a lot of horizontal genetic transfer had occurred between man and chimpanzee through a hybrid race. Jehu
For the benefit of the UD readers, here is the oft celebrated and debated chapter in Denton's book. BioChemical Echo of Typology Many thanks to Mario Lopez for his sholarly work to make this PDF available to us. In the chapter it discusses the problem of species-specific tick rates. The much criticized "molecular transitionals" attributed to Denton is actually Denton presenting a formerly believed evolutionary viewpoint that became so untenable that no-one today on either side accepts. What has been established is that there are no living molecular transitionals (it has been beleived fish, amphibians, and reptiles are "living transitionals", hence we would expect the molecules to follow the pattern of "living transitionals). This of course has been shattered by the typological (hierarchical) view of biology. The Darwinists retreated and reformed their theory then to argue Darwinism creates a hierarchical view of reality. To make this possible, a molecular clock was needed. Well, Denton then demonstrates why the clock is broken. The answer for the pattern is ID. ID proponents may debate common ancestry versus special creation, but they both agree the hierarchical pattern is not achievable by a molecular clock, or at least anything resembling a universal clock. If there is a molecular clock at work, it would have to be finely tuned through mulitple clocking mechanisms for each protein in each species. Thus ironically, this clock would have to be designed as well, and a far more sophisticated clock than Paley's watch! scordova
Jehu, what can I say, except that DaveScot is right -- we're suffering from epicyclitis when it comes to the molecular clock. If an honest look at the cytochrome C molecule is taken, science blows itself apart in a confusion of "on the one hand ... and on the other hand..." just as Denton said. I contend that the phenotype map generated by the cytochrome C is either a primary control mechanism for the PEH, or is the copyrigth notice of the designer. Either way, its designed folks! bFast
Techniques used to calibrate molecular clocks were refined centuries ago: http://en.wikipedia.org/wiki/Epicycle History repeats itself. :lol: DaveScot
bFast,
Jehu, have you read what Denton says about the cytochrome C? If the clock does not tick PRECISELY by years, not generations, then the cytochrome C makes no sense whatsoever in a neo-Darwinian context. The options facing the scientific community are simple, either the molecular clock is precise or the cytochrome C stunningly doesn’t fit!
Correct me if I am wrong but my understanding is that the drift of cytochrome C appears to have no correlation to the generation time of the species. Other papers I have read have made the same observation about other genes; molecular drift rates do not correlate to the generation times of the species. Darwinism predicts that molecular drift will correlate to generation time. Therefore, a "special tick rate" must be inferred for each species to rationalize why they don't appear to correlate to generation time. Jehu
Scordova, for the cytochrome C to render as it does, it cannot have unique tick rates for each species,
Actually that was Denton's point regarding fruit flies vs. Cicadas. A fruit-fly reporduction cycle is 440 faster, so, for the molecular clock to give equidistance, the fruit-fly must mysteriously mutate it's DNA copyingt a rate 440 slower than the cicada, since the fruitfly reproduction cycle is 440 faster than the cicada. More nuances are being introduced, such as the need for "special relativity" in molecular clocks (no kidding). See coppedge's take : Molecular Clock Relativity scordova
An illuminating Denton interview is here: http://webcast.ucsd.edu:8080/ramgen/UCSD_TV/6467OnDarIntWit.rm GilDodgen
[...] Molecular Clocks I’ve always wondered how scientists are able to date things that have happened so far in the past. It turns out their ability to do so is not nearly as good as they thought. Uncommon Descent comments on an article from a peer reviewed scientific journal entitled “Dates from the molecular clock: how wrong can we be?” The article falls under the “Trends in Ecology & Evolution” category. I wonder if one of the trends is admitting that they have to completely overhaul their theory every ten minutes to fit some new scientific discovery that goes against everything they believe? In any case, here’s the abstract: Large discrepancies have been found in dates of evolutionary events obtained using the molecular clock. Twofold differences have been reported between the dates estimated from molecular data and those from the fossil record; furthermore, different molecular methods can give dates that differ 20-fold. New software attempts to incorporate appropriate allowances for this uncertainty into the calculation of the accuracy of date estimates. Here, we propose that these innovations represent welcome progress towards obtaining reliable dates from the molecular clock, but warn that they are currently unproven, given that the causes and pattern of the discrepancies are the subject of ongoing research. This research implies that many previous studies, even some of those using recently developed methods, might have placed too much confidence in their date estimates, and their conclusions might need to be revised. Bookmark to: [...] THE SEARCH FOR PURPOSE » Blog Archive » Molecular Clocks
Jehu, have you read what Denton says about the cytochrome C? If the clock does not tick PRECISELY by years, not generations, then the cytochrome C makes no sense whatsoever in a neo-Darwinian context. The options facing the scientific community are simple, either the molecular clock is precise or the cytochrome C stunningly doesn't fit! BTW, it appears from what I have read that generation time plays a role, but not a linear role as once assumed. Of course, as soon as generation time plays a role, the cytochrome C becomes a problem for science. (One note to this is that the cytochrome C has not modified its function over time, if a gene is involved in the change of the phenotype it may mutate faster than the molecular clock without destroying science's explanation for the cytochrome C.) bFast
Once they get the computer program running so that all the "known relationships and dates" about the phylogenic tree bring the molecular data into line, there will no longer be a threat to TOE. Another problem solved by intelligent designed computers and intelligent programmers. idnet.com.au
bFast,
Scordova, for the cytochrome C to render as it does, it cannot have unique tick rates for each species, in fact it must tick at exactly the same rate in the flea, the worm, the oak tree, and man
Doesn't that depend on how you define the tick rate? You can either define it as per generation or per million years. If you define it as per generation then I think each species requires a special rate. I think per generation is the only rational way to state it. Jehu
PaV, "When you read articles that talk about this species and that having diverged X number of years ago, there’s never a sense that this “fact” is, in actuality, tentative." To the best of my knowledge the molecular clock hypothesis is rarely used to calculate divergence. Rather, that is determined by what layer in the rocks the fossils are found, by isotopic dating methods, by presumed phylogenic tree constructions, etc. Scordova, for the cytochrome C to render as it does, it cannot have unique tick rates for each species, in fact it must tick at exactly the same rate in the flea, the worm, the oak tree, and man. Special tick rates per protein, however, does seem to be the expectation of the molecular clock hypothesis. bFast
The criticizm Denton received over that chapter in his book was on the idea of "transitional" cytochrome-c. 20 years ago, that's what the Darwinists were looking for!!!! That theory was so bad, it was subsequntly canned, but the Darwinists of today fault Denton for merely quoting the viewpoint of Darwinists of the time, the idea of molecular transitionals!!! Denton found fault in that idea. He then went on to describe the diffusion model that is the basis of the molecular clock which was the "solution" to molecular transitionals. Well, he made a devastating case against molecular clocks (as well as against molecular transitionals) and so did Hoyle. For the clock to work one needed : 1. special tick rates for each species! 2. special tick rates for each protein! The molecular transitional appeared in Kenyon and Davis's Of Pandas and People and the Darwinists find fault in that representation. Well, Kenyon, Davis, and Denton were merely quoting the Darwinists mindset of time and how quickly the Darwinists will attribute their falsified ideas to creationists and IDers! scordova
Sal, thanks for posting the article. It's good to see: 1.) Denton vindicated, and 2.) the molecular clock nonsense have the rug pulled out from underneath it. When you read articles that talk about this species and that having diverged X number of years ago, there's never a sense that this "fact" is, in actuality, tentative. Now it appears it's not only tentative but wrong. PaV
Denton's discussion about the molecular clock, if I recall correctly, was in the context of the Cytochrome C gene. This gene renders an accurate picture of the phylogenic tree -- shockingly accurate, in fact. For details, "Evolution, a theory in crisis" is a must read. My understanding is that when this perfect phylogenic tree was discovered in the cytochrome C gene, it created some amount of stir in the scientific community. The molecular clock hypothesis, I understand, was developed to rescue science from this evidence. For the cytochrome C gene to render as it does, its molecular clock must tick perfectly. Its clock cannot vary due to "primitiveness" of the organism, it cannot vary due to phylogenic change in the organism, it cannot vary due to generation span of the organism, or due to survival rates. Because of this evidence presented by Denton, I have kept an eye on the molecular clock hypothesis. Perfect molecular clocks don't exist. Mouse genes, for instance, mutate at about twice the pace of human genes. The generation time of a mouse is much less than that of humans, so there is not a direct relationship between generation time and pace of mutations, but there is relationship. However, the phylogenic tree rendered in the cytochrome C does not permit any of this. The only explanation that I have found for the poetic perfection of the phylogenic tree in the cytochrome C is that the cytochrome C represents the designer's "copyright notice". Its right there, the scientific community is just actively ignoring it. bFast

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