Talk:Molecular equidistance

Suspicious Article
I was poking around on Michael Denton's cytochrome c argument and ran across this entry in Wikipedia. Although it is muddy reading and equivocates a good deal, it seems to be making the dubious case, originally put forward by Michael Denton, that molecular equidistance is some sort of astounding revelation that turns contemporary biology on its head.

Actually -- and the article seems to tapdance on this issue -- all it says is that modern species that stem from a common ancestor demonstrate a roughly similar divergence in the structures of molecules such as cytochrome c from the time of their divergence. This is not just unsurprising, it's what would be expected.

Denton did make an issue of the implicit assumption in this argument that there are uniform rates of divergence of cytochrome c along different lineages, claiming that there was no way such a "molecular clock" could be so constant. That was what I was scouting out when I found this article -- as best I can tell, the answer to that is that there is a debate over the issue.

What made me suspicious about his article was the closing comments about most biologists not realizing that monkeys are equally related to chimps and humans. Uh ... did somebody conduct a poll on the matter? I'm not a biologist, I'm not even a scientist, but anybody who bothered to read a bit on evolutionary biology even at a popular level would know that apes and humans are on one branch of the primate family tree, monkeys are on another, and like on any good tree the members of one branch have the same general relationship to members on another. Few would have any trouble with the idea that lions and tigers are equally related to wolves, even if they'd never heard of molecular equidistance. I would be astounded to find that most biologists are not as well versed on the subject as I am.

That statement sounds only too much like saying: "People who haven't investigated the matter at all might have some mistaken ideas about it." Yep, that's what usually happens when people express opinions on matters that they haven't done any homework on. "So what's your point?"

I can't figure out if this article is an oblique exercise in Darwin-bashing, or if it's just so badly written and ambiguous that it can be interpreted as one. Either way, it needs to be rewritten into a form where it is possible to figure out what it is really trying to say. MrG 4.225.210.108 (talk) 15:57, 12 January 2008 (UTC)


 * Agreed. This is so POV it's embarrassing; it reads like a promotional tract. I'll see what I can do... &mdash; Scientizzle 00:06, 15 January 2008 (UTC)

Thanks. I expanded your edit a bit, Denton's position was a little more elaborate than that. He is generally regarded as something of a cut above most Darwin-bashers, with a good professional background and the ability to sometimes ask penetrating questions. This doesn't mean he's not wrong, of course, it's just that he deserves a more respectful rebuttal than, say, Casey Luskin. Larry Moran and Gert Korthof have some interesting stuff on their sites on Denton (and if you read Korthof's site don't miss his dismemberment of Lee Spetner). MrG 03:19, 15 January 2008 (UTC)

Molecular equidistance and Evolution: A Theory in Crisis
Does this topic get any significant coverage that isn't connected with this book? If not, then it should probably be merged into the book's article. HrafnTalkStalk 09:44, 15 January 2008 (UTC)

It is most strongly associated with Denton but is part of the standard Darwin-basher kit. It has been recycled by Christian Schwabe and Philip Johnson in their writings. This is not to make a case one way or another as to the disposition of this article, just providing some data. MrG 4.225.214.233 (talk) 12:49, 15 January 2008 (UTC)


 * Johnson is most likely simply repeating Denton without much in the way of elaboration (e.g. see discussion here), particularly as Johnson has no background in science to allow independent analysis and both Johnson & Denton were both active in the early days of ID. I'm not familiar with Christian Schwabe, let alone with his usage of the term. HrafnTalkStalk 14:57, 15 January 2008 (UTC)

See Korthof's site for his review of Schwabe's work, which is unconventional to the point of totally mind-boggling. Johnson's technical analysis was not "likely" to be repeating Denton; Johson's entire technical argument in DARWIN ON TRIAL was judged by Korthof as a copy of Denton's. Again, just providing data, the disposition of this article is a matter of indifference to me. MrG 15:03, 15 January 2008 (UTC)

Merger proposal
The result was merge into Evolution: A Theory in Crisis. -- HrafnTalkStalk 14:59, 19 January 2008 (UTC) Given that there doesn't appear to be much notability for this topic that isn't associated/derivative of this book, and as they're both short articles, I've gone ahead and nominated it for merging into Evolution: A Theory in Crisis. Nominated HrafnTalkStalk 16:09, 15 January 2008 (UTC)


 * I support the idea of a merger. If you compare the current version versus the prior incarnation, this one at least makes clear(er) what the subject is and why it may matter. There's almost nothing from Google that expands on the topic that I didn't include as a reference, and I've never read the book. (I'd never heard of the topic before it was brought up by our IP friend.) The topic, I think, is of minor note--co-opted by some creationists and largely ignored by biologists. This entire article could be added to the book's page, which would alleviate any concerns about topic notability without losing any information. &mdash; Scientizzle 17:41, 15 January 2008 (UTC)
 * Ok, now I get it. Yes, lets definitely merge it.--Filll (talk) 18:15, 15 January 2008 (UTC)

Discussion
Actually I think there is real science here, which might not have made its way into the article yet. For example, there are several different methods for determining genetic distances (why is it called molecular equidistance?) and there is a history of these methods and statistics etc. I do not think we have included this material yet, which might make this a far more reasonable article.--Filll (talk) 16:43, 15 January 2008 (UTC)

This from the NCSE may throw some light on the topic:

While "genetics distances" may be "real science", it would appear that "molecular equidistance" isn't -- in the same way that Kolmogorov complexity is meaningful while Specified complexity isn't. HrafnTalkStalk 17:30, 15 January 2008 (UTC) Also applicable is Sequences and Common Descent by Wesley R. Elsberry. HrafnTalkStalk 17:36, 15 January 2008 (UTC)


 * Ok, now I get it. Yes, lets definitely merge it.--Filll (talk) 18:15, 15 January 2008 (UTC)

It is incorrect to imply that the moleuclar equidistance phenomenon was first noted by Mike Denton. It was in fact first found by evolution biologist E. Margoliash in 1963 and published in PNAS, 50: 672-679. Margoliash wrote: "It appears that the number of residue differences between cytochrome C of any two species is mostly conditioned by the time elapsed since the lines of evolution leading to these two species originally diverged. If this is correct, the cytochromes c of all mammals should be equally different from the cytochromes c of all birds.  Since fish diverges from the main stem of vertebrate evolution earlier than ether birds or mammals, the cytochromes c of both mammals and birds should be equally different from the cytochromes c of fish.  Similarly, all vertebrate cytochrome c should be equally different from the yeast protein." The equidistance phenomenon is the most remarkable result of molecular evolution. It is a scientific fact that is independent of Denton and his book. Thus, it should not be merged or linked to the page on Denton.

The molecular clock explains the equidistance phenomenon by assuming a constant mutation rate in different lineages. But the constant mutation rate assumption has been falsified by numerous independent experiments and few evolution biologists now believe a constant clock (see the Wiki page on molecular clock). So, there is at present no scientific explanation for the equidistance phenomenon. The constant clock interpretation of the equidistance phenomenon is merely a restatement of the fact of equidistance and is hence a tautology rather than a real explanation. The question remains unsolved: how can vastly different species with vastly different mutation rates and generation times all end up being equally different from an outgrop? How can yeast and human be equally different from bacteria when the lineages leading to yeast and human clearly do not have the same mutation rate and generation time? So, the equidistance phenomenon is a challenge to the present evolution theory because the theory cannot explain it. —Preceding unsigned comment added by 192.231.106.2 (talk) 00:00, 31 January 2008 (UTC)


 * The article states that the "term that was first used by Michael Denton" (my emphasis), not that he was the first to note the phenomenon. Your quotation does nothing to contradict this. In any case, the merger discussion was concluded some time ago with a consensus to merge. Your recent attempts to undo this merger is in violation of WP:CONS. HrafnTalkStalk 04:24, 2 February 2008 (UTC)

The important and meaningful thing for a Wikipedia article is to inform people about truthful facts. Who first used the term 'molecular equidistance' is really a trivial matter. What is important is who discovered the fact first and whether it is a scientific fact and how to explain it. I hope we can agree on the following scientific facts:

1) the equidistance phenomenon was first discovered in 1963 by Margoliash;

2) it is a solid scientific fact that has since been independently confirmed repeatedly.

3) it is the most remarkable result of molecular evolution and the chief result that provoked the molecular clock or constant mutation rate idea and the underlying neutral theory of Kimura. This was admitted by Kimura himself: "Probably the strongest evidence for the theory is the remarkable uniformity for each protein molecule in the rate of mutant substitutions in the course of evolution” (Kimura and Ohta, 1971a, p.467, Nature 229: 467-479).  The statement by Kimura "the remarkable uniformity for each protein molecule in the rate of mutant substitutions in the course of evolution" is of course merely a restatement of the equidistance fact or a tautology.  It has no independent factual support other than the equidistance phenomenon itself and has in fact been falsified repeatedly.  It has as much support as the theory that God created the equidistance phenomenon or the theory that Darwin created the equidistance phenomenon. The equidistance phenomenon is not evidence of a uniform mutation rate nor is it evidence of any theory that is a merely a restatement of the fact. The uniform mutation rate theory or the God theory are merely two theories among many that could all be equally provoked by the equidistance phenomenon. To tell which theory is correct scientifically requires independent experiments and evidence. Of course, there is no independent data to support the God theory but neither there is for the uniform mutation rate theory. Not only there is no evidence for it, there are plenty against it. It even violates common sense and the main theme of Darwinism of natural selection of fitter mutations. As admitted by evolution biologists Nei and Kumar (2000, Molecular evolution and phylogenetics, page 188): "The constant rate of evolution was unthinkable for classical evolutionists."

4) Even the only accepted theory for the equidistance fact, the neutral theory, is not a satisfactory explanation. The evolution biologists M.J.F. Pulquerio and R.A. Nichols wrote in 2006 (Trends in Ecology and Evol. 22: 180-184): "The ‘Neutral Theory’ is not a complete explanation, however. For example, it predicts a constant substitution rate per generation, whereas empirical evidence suggests something closer to a constant rate per year."

5) the molecular equidistance and the constant mutation rate are two different expressions of the same fact but the fact remains unexplained by either expressions.  Instead of informing people the bare fact of equidistance, the evolution community has sold us their interpretation of the fact: the constant mutation rate.  The bare fact of the equidistance says nothing about the process of mutation during evolution, it merely shows the outcome of evolution.  But the constant rate theory talks about the process in addition to the outcome.  Rather than simply presenting facts and have people make up their own minds, the evolution community has replaced the facts with their interpretation of the facts.  This undermines the effort of humanity's search for the correct interpretation of the facts.  Go ask any high school student or college student or even biology professors the question: Are fishes more related to frogs or to human or equally related? Or are bacteria more related to yeast or to humans? You will find that the vast majority of them will answer that fishes are more related to frogs, just like they will correctly answer that humans are more related to frogs than to fishes. Believe me, I have personally asked ~50 biology professors including some young generation evolution specialists, no one had answered correctly. Talk about teaching evolution. If you are going to teach, then teach the whole story including the most remarkable result of molecular evolution. Why the most remarkable fact (the equidistance) is not taught in any textbooks? The closest thing to it is the molecular clock. But the clock is well known to be controversial. The clock is merely a hypothesis and could be wrong. Teaching the hypothesis rather than the bare fact that provoked the hypothesis easily misleads people to have doubts about the underlying fact. Why not teach the bare and incontroversial fact of equidistance? Why not teach how the most remarkable fact of molecular evolution supports the Darwinian theory of natural selection? The theory of natural selection is what is being taught to every high school students, which has led them to infer correctly that humans are more related to frogs than to fishes but which has also led them to infer incorrectly that fishes are more related to frogs than to humans. Why not teach them also that the equidistance fact supports this theory? (of course it does not, which is why it is never taught and why there comes the flawed neutral theory or the molecular clock)

6) Hence, the equidistance phenomenon is presently without a scientific explanation. The claim that all observations can be explained within the modern framework of evolutionary theory is factually untrue and should be deleted from any article on equidistance.

If you or anyone can reasonably challenge any of the above six facts as untrue, please do. If not, please join the effort to tell facts as they are. Facts can be misused. Just because the equidistance fact has been misused before (perhaps by Denton to some degree and also by the evolution community in claiming it as evidence of constant mutation rate) is no reason to deny the truthfullness of the fact and its honest implications for the present evolutiont theory. The more the peolpe who know about the fact, the higher the chance for the fact to be correctly and scientifically explained. —Preceding unsigned comment added by 192.231.106.2 (talk) 22:02, 4 February 2008 (UTC)


 * The phrase "Molecular equidistance" appears to be more heavily associated with Denton than with Margoliash. Can you present any evidence that it's use as a description of Margoliash's work has received widespread acceptance? Margoliash's work is already covered in articles such as Distance matrices in phylogeny & Computational phylogenetics. HrafnTalkStalk 15:56, 5 February 2008 (UTC)

You are right about the term being linked with Denton more than with Margoliash. But this is apparently due to the reluctance of the evolution community to publisize the equidistance phenomenon. Even Margoliash himself shyed away from using again his term "equally different" first used in his 1963 paper. Go read the article by Margoliash and Fitch in 1967 (Fitch WM, Margoliash E. (1967, Science 155: 279-84.). In the Table 3 of that article, the equidistance of cytochrome C is plain obvious.  But no where in the paper you will find the word "genetically equal".  Instead, you find the opposite "not equidistant genetically.".  They found some slight difference in genetic distance and concluded that they represent significant difference.  They say:'Indeed, from any phylogenetic ancestor, today's descendants are equidistant with respect to time but not, as computations show, equidistant genetically."  They give absurd examples of this:"For example, from the point at which the primates separate from the other mammals, there are, on the average, 7.5 mutations in the descent of the former and 5.8 in that of the latter, indicating that the chage in the cytochrome c gene has been much more rapid in the descent of the primates than in that of the other mammals." Of course, we now know that 7.5 and 5.8 are not significant differences and are merely sampling variations around a mean. The equidistance phenomenon does not mean exact identity and shows small variations around a mean. The likely reason for why Margoliash and Fitch avoided emphasizing the equidistance in their 1967 paper is because the implications of the equidistance is "unthinkable for classical evolution biologists" who still dominate in the 1960s. The theory of natural selection of fitter mutations predicts non-equidistance. The climate of 1960s and 70s favors non-equidistance, as indicated by this statement by Brian Clarke in his 1970 Science paper (22 May, 1970, 1009-1011): "Nevertheless, even if we make the unlikely supposition that the phenomenon is general (the constant rate), a rough constancy of rate is easily explained by a selective theory." So, Even after 7 years of discovering the constant rate or equidistance phenomenon, the mainstream evolution biologists still consider such phenomenon to be "unlikely". Of course, Clarke's claim that the constant rate can be easily explained by a selective theory is plain fantasy, which is why the accepted theory for the phenomenon today is the neutral theory of Kimura rather than that of selective theories by Clarke or a few others that poped up in the 60s and 70s.

From such beginings of Margoliash and Fitch paper in 1967 of interpreting small differences in distance as significant, we have now today evolution biologists who routinely interpret equidistance as being non-equidistant. They have developed a test called the relative rate test to see if there is non-equidistance. But such a test is flawed. It does not consider sampling variations. It presupposes the truth of gradual mutation when no one really knows whether punctuation also occurs. Furthermore they are either ignorant of the contradictions of their conclusion or chose to just ignore it. The following is an example of a contradiction.

In the example of albumin, bird is 47% identical to human and 44% to rat. Nei and Kumar in their book (Molecular evolution and phylogenetics) page 193 concluded after performing the relative rate test that rat has faster mutation rate than human in the albumin gene. But this creates a contradiction. To consider such small differences as being significant makes it impossible to reconcile it with other contradicting fact where a frog albumin gene is 38% identical to human and 40% to rat. It is self-contradicting for the rat lineage to have a faster mutation rate than humans when birds are the outgroup but a slower mutation rate than humans when frogs are the outgroup. If the faster mutation rate than humans with birds as the outgroup is real, the rate with frogs as the outgroup can only be faster and cannot possibly be slower or equal. Therefore, the facts can only be explained by considering such small differences as insignificant variations of the equidistance phenomenon. Rats and humans are equidistant to birds as well as to frogs.

The equidistance phenomenon, as you can see, has been mistreated by people from all kinds of faith. It is wrong to single out Denton. Evolution biologists have presented us a distorted version of the equidistance: the constant mutation rate or the molecular clock or the neutral theory. They somehow prefer not to use equidistance and refers the thing as molecular clock. Obviously, calling it equidistance is much harder to sell than calling it clock. It would make the inadequacy of the present evolution theory so much more obvious to any person whose knowledge of Dawinism is limited to natural seleciton of fitter mutations, which of course include 100% of high school and college graduates and 99.9% of biology professors. So, we are told that clock sometimes work and sometimes not, which would lead us to think that the equidistance is not a general phenomenon or is frequently vialated. When the clock is not working, we use natural selection to explain it and so we have made a flawed theory relavent.

But it is clear even when clock fails, the equidistance still holds. For example, The sequencing of the medaka genome (Nature, 447:714-719, 2007, June 7) reveals an extremely high SNP rate of 3.42%, which is 3 fold higher than the distance between chimps and humans and 8 fold higher than the SNP rate among inbreed mouse strains and 34 fold higher than the SNP rate of humans. The SNP rate of medaka fish is the highest seen in any vertebrate species. In the same time span, two different subpopulations of medaka fish has accumulated more mutations than two different species such as human and chimpanzee. So the fish lineage has faster clock rate than human or mouse, a violation of the constant clock. Howeve if you pick any gene and compare the distance of sea urchin to medaka fish, human, and mouse, you will find that sea urchin as the outgroup is equidistant to medaka fish, human, and mouse. So, despite the non-equal mutations rates or clock in fish, mouse and human, they are all equidistant to an outgroup. There is no clock but there still is equidistance. The clock has been routinely falsified but not the equidistance. It is wrong for the evolution specialists to use the term clock to represent the equidistance. In a few years, the idea of constant mutation rate or clock will be a laughing-stock while the equidistance will remain true for eternity.

It is now time to restore the phenomenon its proper place in human knowledge. The bare truth is this: it is an yet unexplained scientific fact. To find an explaination for the fact is what we should all aim for. To do this, we do not need to know who Denton is or who first used the term molecular equidistance. All we need to do is to read the 1963 and 1967 papers by Margoliash and if we are still not convinced by the generality of the equidistance, we could just randomly pick a gene and do a BLAST homology analysis of, say, compare fish to frog and fish to human and easily verify the truth of equidistance for ourselves. I have randomly selected and tested ~100 genes and have not found a single exception of equidistance (P<0.0001). —Preceding unsigned comment added by 192.231.106.2 (talk) 21:35, 5 February 2008 (UTC)

Well you make a compelling case. I think I need to call in an expert or two to look at this. If this is as you present it and others agree, maybe we should have a single standalone article here. It looks like this was some regular concept of genetics that Denton and other creationists seized on, giving it a bad name. I would be in favor of including a lot more of this material in an expanded and mainstream article, if it pans out. Comments?--Filll (talk) 21:45, 5 February 2008 (UTC)


 * if you read the article it states on page 675 "Relatively closely related species show few differences: there are only three variant residues between the horse and pig proteins. Phylogenetically distant species exhibit wider dissimilarities. The largest differences are observed between the vertebrate and yeast cytochromes c." All mammals share a single common ancestor with yeast, and have been diverging from that ancestor for the same length of time. So as you would predict, they have roughly the same level of sequence divergence to such a far-removed group. As that 1963 paper notes "It should be noted that the present results are compatible only with the commonly accepted scheme of evolution represented by series of branching lines, and are not consistent with a simultaneous formation of all species, which then proceed to accumulate mutations independently. In the latter case all the cytochromes c should be equally different from all others." Tim Vickers (talk) 22:37, 5 February 2008 (UTC)


 * I am not objecting to an article on Margoliash and his work, I am merely suggesting that "Molecular equidistance", a phrase more tightly associated with Denton's misrepresentation of said work, would tend to blur the line between the work and the misrepresentation, so would probably be an inappropriate title for such an article. HrafnTalkStalk 03:55, 6 February 2008 (UTC)

How about the title of "Genetic Equidistance" for an article on the equidistance phenomenon, and treat the term "molecular equidistance" as alternative name for the same thing. Indeed, the term 'genetically equidistant' is a more precise and meaningfull term, and has been used in scientific papers. For example the 1967 Margoliash paper used the term 'genetically equidistant'. Althouth the data in table 3 of that paper clearly shows rough genetic equidistance, the authers chose to ignore it and instead focus on the minor differences in genetic distance and incorrectly concludes that the data showed 'not genetically equidistant'.

I have thought a little more on why people do not want to present the equidistance together with the clock. It is true that the clock idea was first informally proposed in 1962 by Pauling and Zuckerkandl. This was one year before the formal proposal of the clock and the finding of genetic equidistance by Margoliash in 1963. But the hemoglobin data used by Pauling and Zuckerkandl showing constant rate in different species is merely a different expression of the same fact of genetic equidistance. The same sequence data set can be used to express two phenomena. For example, given the hemoglobin sequence of fish, frog, and human, you could do two kinds of sequence alignments and both would indicate a seemingly constant rate but would show very different flavors. In one alignment, you use human sequence to align with frog and fish, and you would find that human is more related to frogs than to fish. This alignment alone is sufficient to provoke the idea of a constant rate, which was roughly equivalent to what Pauling and Zuckerkandl had done. They did not do the second alignment or did not present it, which is, in our example, to use fish sequence to aligh with frog and human. In this case, we would find the phenomenon of genetic equidistance. Margoliash in 1963 presented both kinds of alignments and was therefore the first to discover the genetic equidistance phenomenon.

The key point here is that both kinds of alignments are dealing with the same sequence data set and either alingment alone can provoke the idea of clock. So, the clock idea was first proposed in 1962 without relying on the alignment showing equidistance. From this begining, people now often use the first kind of alignment to express the idea of clock rather than using the second alignment showing equidistance. In textbooks talking abuout molecular clock, you often see data showing that human is more related to mouse, less so to birds, still less to frogs, and still less to fish, etc. Apparently, this way of presentation does not cause obvious contradiction with the theory of natural selection of fitter mutations. Every high school student learned this presentation and can state correctly that human is more related to frogs than to fish. However, learning this would not allow them to infer or know that fish is equally distant to frog and human. They would be shocked if they were told this since their knowledge of Darwinism would not predict this. So, given the same sequence data set, one kind of alignment seems to make sense with Darwinism while the other not. Guess what would happen. Of course one is promoted while the other suppressed. This may explain why evolution biologists do not want to talk about the second alignment showing equidistance. I dont know if they know or care that they are misleading millions of educated people by their selective presentation of facts. They also mislead by hiding the fact that their theory of clock is not a true theoretical work but is merely a restatement of an empirical fact. They give people the impression that they first formulated the clock idea which forcasted the constant rate and then found evidence for the clock idea, which are the results of the two kinds of sequence alignments. But the plain truth is that they first had result from one of the two alighments and then came up with the clock idea to interpet the result. This is a classic example of tautology. —Preceding unsigned comment added by 192.231.106.2 (talk) 18:08, 6 February 2008 (UTC)


 * I think a merge with the book that popularised the phrase makes good sense - this isn't something people are going to search for. Other discussions of the published data on sequence similarity between species would fit better at phylogenetics or molecular clock. As to the idea itself, looking at figure 3 of would be a good starting point. Tim Vickers (talk) 22:50, 6 February 2008 (UTC)

To Hrafn, if you prefer to spread proven lie, no one can stop you and good luck.

To TimVickers, thank you for referring this wonderful article. Figure 3 of this paper shows again that the clock theory is false. Bacteria, archaea, and eukaryotes are widely thought to share a most recent common universal ancestor. They are equidistant in time to the universal ancestor. But Figure 3a shows that genetic distance within bacteria or archaea is much greater than within eukaryotes. So within the same time frame, the domain of eukaryotes has accumulated far less mutations than the domain of bacteria or archaea. Figure 3b shows that genetic distance is related to genome size, which contradicts the clock notion that genetic distance is strictly a function of time. —Preceding unsigned comment added by 192.231.106.2 (talk) 21:12, 7 February 2008 (UTC)


 * Wikipedia reports what is WP:verfiiable, in this case the usage of the phrase by Denton. It is not a soapbox for those wishing to rehabilitate the phrase. HrafnTalkStalk 01:25, 8 February 2008 (UTC)