Talk:Molecular clock

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Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 04:23, 17 January 2022 (UTC)

Use of non-coding DNA

The article has information on the problem of non-equal clock rates due to differences in the selection pressure. There is the alternative approach of getting over the problem of selection pressure by choosing sequences which are presumably non-coding and therefore untouched by selection. Randall L. Small, Julie A. Ryburn, Richard C. Cronn, Tosak Seelanan and Jonathan F. Wendel 1998. The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany. 1998;85:1301-1315. [1]. Why is this not more popular ? (My own guess is that this is perhaps because it is easy to fish functionally equivalent sequences across two species, but not so easy to find two "equivalent" non-coding regions). Perhaps this can be covered in the article. Shyamal 03:07, 13 May 2007 (UTC)

Schwartz's fringeness and confusion

I find the Schwartz's references and links rather... bad. Whereas there well may be some challenges to molecular clock, he, Uatu only knows why, equates that with a challenge to "darwinism" (!), and based on that makes a whole illogical opposition while proposing his neo-saltationism. Even if we maintain that the molecular clocks are steady, it does not mean that the adaptive evolution (which is only a minor part, that presumably does not affect the clock meaningfully) would be steady, or that phenotypic change would also need be steady, with all the mutations causing only similar degrees of phenotypic change. I'm not quite sure of what I'm going to say, but I think I've read that he proposes that only a single mutation could have originated the eyes without natural selection, based on the fact that, in a few eyeless fish species, a single mutation can make they develop eyes - which is only possible because the genetic recipe for the eyes was there first, only was "deactivated" when they adapted to dark waters, so it's still there to eventually be brought back. Besides that, he proposes that orangutans are our closest relatives, not chimps. The close kinship with chimps is "only" based on genetic evidence. (The morphological similarities between orangutans and humans can also be accounted with more conventional explanations, such as the idea that humans left from an arboreal lifestyle and retained/refined the bipedalism of an orangutan/gibbon-like ancestor, while chimps and gorillas independently evolved the knuckle gait.)

Now, I'm not quite sure if this sort of peculiar circumstances would mean anything for wikipedia standards, I'm not just asking to remove because I don't like all that fringeness... if there's nothing "official" against that, ok, I'll just shut up, it remains there... but that's a shame... --Extremophile 06:51, 29 September 2007 (UTC)

I removed the sciencenews external link, which at the least is sensationalist and fairly unhelpful. As to the Schwartz reference within the text, I don't know, but it doesn't seem unreasonable to me as it is used. Of course, the primate phylogeny issue is something that has been extremely contentious since molecular evolution first came on the scene and people started claiming that chimps were our closest relatives. In the article, Schwartz is described as being on the same side as Ayala on this issue, which certainly doesn't lend any support to the idea that challenging the molecular clock challenges Darwinian evolution generally (at least in this context).--ragesoss 13:23, 29 September 2007 (UTC)

Wikipedia:Articles for deletion/Genetic equidistance

Expert opinions on the notability of this topic would be appreciated. Tim Vickers (talk) 16:59, 15 February 2009 (UTC)

I'm almost an expert on this, I'm a phd entomologist with a strong interest in phylogenetic methods. I'm working on a small article on why molecular clocks don't work and I came here to check out what the plebs thought about them. I'd like to rework this article when I get a chance but as I mentioned I really don't think they work (I'm not alone on that). I'll try to be balanced but maybe we should get someone else who knows a bit about it to go over the article after I rework it to provide a case for molecular clocks. —Preceding unsigned comment added by Thebike (talk • contribs) 05:07, 25 June 2010 (UTC)

You "small article" might have been pre-empted already... in any case, this needs to go in there. It is, in hindsight, more surprising that the stuff works as well as it does. Neither did Pauling have much experience in biology (genius though he was, most of his contributions to the field turned out to be wildly wrong), nor did Zuckerkandl have any experience in the modern synthesis of evolution. In short, their underlying assumption is so outrageous given the known influences on mutation rates in the real world that it should have been tested more thoroughly, rather than assuming that the clocklike behaviour of cyt b was representative.

Yet it must be said that for the last 10 Ma or so, the rate fluctuations do not differ wildly for most taxa. So molecular clocks do work well, but not as generally as assumed. It is in fact quite serendipitious that they do work at all (even though only in a more limited scope than initially postulated), because the fossil record over the last 10 Ma is not very informative; there is more material, but differences between (then-)sister taxa of course become less and less pronounced the closer we get to the present... tracing back evolutionary lineages of horses for example has allowed quite a good estimation of divergence times in the Neogene based on fossils alone, but the more recent diversificaiton is problematic because the lineages have not yet had time to evolve a sufficient "chain" of morphological differences.

In conclusion, I have yet to see more than a handful (at best) mol-clock studied going back into deep evolutionary time that evwen reasonably tie in with the fossil record. Even those that are calibrated by fossils are usually off quite a bit, and those that make little use of calibration are laughably wrong (some mol-clock based hypotheses leave no other conclusions that the ancestors of modern birds diverged right at the base of Theropoda). Overestimation for times of about 100 Ma may be 100%. The paper I linked above seems to be the second major effort to clarify why this is so (the first is the mammal paper the work is founded upon). Dysmorodrepanis (talk) 02:20, 3 October 2010 (UTC)

Do Molecular Clocks Run at All? A Critique of Molecular Systematics

From 2006

"....Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”

http://www.pitt.edu/~jhs/articles/Schwartz&Maresca_Mol_clocks.pdf

Turning Back the Clock: Slowing the Pace of Prehistory - AAAS Science 2012 "Researchers have used the number of mutations in DNA like a molecular clock to date key events in human evolution. Now it seems that the molecular clock ticks more slowly than anyone had thought, and many dates may need to be adjusted."

http://www.sciencemag.org/content/338/6104/189.summary

Somewhere in this article needs to make it clear that the molecular clock is based on several assumptions, that have been known to be very inaccurate. That is important enough to add to the introduction.184.153.187.119 (talk) 18:18, 19 February 2013 (UTC)

Well, the article does make it clear that the clock concept is based on several assumptions, but it does not deal specifically enough with the problem of varying mutation rates. I agree with you that the issues are important enough to mention in the lead. Looie496 (talk) 17:11, 24 February 2013 (UTC)

Over the last few weeks, I've been spending a lot of time on Google Scholar trying to learn about the earliest primates, mainly for the purpose of improving the article Evolution of color vision in primates. Since the article only focuses on simians, I wanted to learn what I could about prosimians (a paraphyletic group that includes lemurs, lorises, and tarsirs) as well as the very first primates. Along the way I ran into the molecular clock issue. There seemed to be absurdly old dates, putting the first primates at 85 mya instead of the 66 mya indicated by the fossil record (or less than 66 mya, depending on how you define "primate"). To make a long story short, I have found plenty of articles acknowledging the problem, identifying the assumptions that need fixing, and revised dates that are a far better match to the fossil record. For example, they now acknowledge something called the primate slowdown. The newer estimates for primate divergence are about 68-70 mya. It's beginning to look as if any molecular-clock date obtained more than five years ago is now considered obsolete and unreliable. They call those the "old dates," often prefaced with "laughably." Unfortunately, we seem to have lots of articles with those old dates. Zyxwv99 (talk) 01:39, 25 January 2015 (UTC)

Molecular clock in cheetahs

The article currently says "cheetahs for example, having gone through at least two population bottlenecks, could not be adequately studied based on a molecular clock model alone". A reference for this assertion was not supplied since requested in 2008. Recently this paper analyzed mitochondrial DNA and microsatellites in cheetahs. In section "Divergence time estimations" they write "We tested whether the assumption of a molecular clock was valid by performing a likelihood ratio test between the simpler clock model vs. the more complex model without clock. The log-likelihood of the more complex model was not significantly increased with respect to the simpler model (P > 0.05), supporting the assumption of a molecular clock". I'll delete the sentence about cheetahs from the article, unless someone objects or has another suggestion. H. sapiens (talk) 12:09, 21 January 2015 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Molecular clock/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

rated top as high school/SAT biology content - tameeria 14:51, 17 February 2007 (UTC) This article could use figures and references. Also, it should include several sections: The evolutionary molecular clock and molecular clocks for circadian rhythms and other temporal cycles in cells and organisms (e.g. hormone cycles in mammals, seasonal flowering time control in plants). - tameeria 19:04, 18 February 2007 (UTC) What you seek is a different article. Something that should link out of Chronobiology. Shyamal 10:27, 19 May 2007 (UTC)

Last edited at 10:27, 19 May 2007 (UTC). Substituted at 00:19, 30 April 2016 (UTC)