tag:blogger.com,1999:blog-8434207374852632666.comments2020-11-25T01:16:55.922-08:00The Golden Gnomon 黄金识子 Huang-jin Shi-zignomonhttp://www.blogger.com/profile/03362808932731126552noreply@blogger.comBlogger71125tag:blogger.com,1999:blog-8434207374852632666.post-82299961509560194812020-11-25T01:16:55.922-08:002020-11-25T01:16:55.922-08:00Right here is the perfect site for anybody who wan...Right here is the perfect site for anybody who wants to understand this topic. You understand so much its almost tough to argue with you (not that I really will need to…HaHa). You certainly put a fresh spin on a topic that has been discussed for a long time. Wonderful stuff, just excellent!buy erection pillshttps://erectiledysfunctionpillscvs.com/noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-41285541287376263422020-11-25T00:41:15.171-08:002020-11-25T00:41:15.171-08:00My brother recommended I may like this website. He...My brother recommended I may like this website. He was totally right. This publish truly made my day. You cann't consider simply how much time I had spent for this information! Thank you!erectile dysfunctionhttps://besterectiledysfunctionpills.com/noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-35760924166060979162017-11-23T20:07:46.009-08:002017-11-23T20:07:46.009-08:00Dear German,
Your expertise on this subject has be...Dear German,<br />Your expertise on this subject has been very impressive, deeper than even most in the field who seem to be mostly content with running software.Can you imagine that not a single person among the 13 billion Chinese appears to be aware of the 34 year old out of Asia model? Of course it did not help that Nature 1987 Cann et al paper had this to say on the Johnson et al 1983 paper that first proposed the Asia model :"Two previous studies of human mtDNA have included African individuals (21, 28), both support an African origin..." (ref 21 is the Johnson et al 1983 paper). Clearly, the Africa Eve model was from its birth based on uncertain assumptions (molecular clock and infinite site model), misrepresentation of facts, and ignoring equally if not more valid alternative models. Why an esteemed English journal would in this case reduce their standards to psudoscience levels should be an interesting topic for future historians. Was it because the Africa model was originally an English invention (Stringer. also Darwin regarding homo in general)? One could not help but to wonder and there has to be some good reasons for such bizarre behavior. The common sense rationale for the Asia model was way stronger than anything used to justify the Africa model. And yet it was annihilated by Nature without offering even a single reason. Absolutely absurd. Well, now the pay back time has arrived. <br /><br />Your comment on the progressive reduction of pan-human alleles in Africa is right on target. It is a common sense rationale which explains why Johnson et al 1983 and Yuan et al 2017 could have independently used the same logic to derive the out of Asia mtDNA model. <br /><br />I understand that the click sound or its like is also present in some tribes in Australia. <br /><br />Again, thank you for the very helpful comments.<br /><br />Best regards,<br />Shignomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-14215247278186959962017-11-21T05:52:42.767-08:002017-11-21T05:52:42.767-08:00Dear Shi, this is a great exchange and I'm hap...Dear Shi, this is a great exchange and I'm happy to have been on-point with Johnson et al. 1983. I think one other way in which an out-of-Africa interpretation of mtDNA evidence has been flawed is its famous claim that extra-African diversity is a subset of African diversity. In reality, African diversity is a subset of pan-human mtDNA diversity. We have a set of alleles shared by all of humans, then we have a set of alleles shared by all of non-Africans and by many Africans (L3) and then we have a cascading reduction in those shared alleles as we go into L3'4, L3'4'6, L2'3'4'6, L2'3'4'5'6, L1'2'3'4'5'6 and L0'1'2'3'4'5'6. By logic, since humans constitute a clade to the exclusion of Neandertals, Denisovans, etc. and there's no clade uniting San and Pygmies with Neandertals, Densovans, etc., this pattern of progressive reduction in pan-human alleles in Africa means that some Sub-Saharan Africans have a subset of pan-human alleles and are therefore derived from non-Africans.<br /><br />BTW, a reverse tree explains nicely a few puzzling facts about African language: under the current interpretation Pygmies carry languages that are 70K years old, but they speak Niger-Congo or Nilo-Saharan languages that are less than 10,000 years old. Khoisans that presumably carry lineages that are 200,000 years old have language properties (clicks) that are unique to them and are not shared by any other languages (unless through very recent borrowing). If Khoisans are as old as the mainstream mtDNA tree has suggested and clicks are primordial humans sounds (or phonetic diversity is a primordial property of the human language), then we would expect some retention of clicks outside of Africa or outside of Khoisans. But the latter is not the case, so they are Khoisan-specific, hence more parsimoniously derived and recent, rather than basal and ancient.<br /><br />As a primary student of non-genetic evolutionary systems (kinship, folklore, language, see my book https://www.amazon.com/Genius-Kinship-Phenomenon-Diversity-Terminologies-ebook/dp/B005U4C2T8/ref=sr_1_2?ie=UTF8&qid=1511272304&sr=8-2&keywords=dziebel&dpID=51CMegbU7FL&preST=_SY445_QL70_&dpSrc=srch) I find it's very easy to reconcile those "cultural" systems with inverse uniparental trees than with the current one. <br /><br />All the best with your ongoing work. <br /><br />GermanGerman Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-17094622448606332832016-05-15T19:03:40.871-07:002016-05-15T19:03:40.871-07:00Simply not true. People has long found things that...Simply not true. People has long found things that resist explanation by the prevailing framework. The most astonishing one is called genetic equidistance. If science is about cheery picking, any fool can do it. Unfortunately for the fools and fortunately for humanity, one can make a pathetic living by cheery pick for only so long but not forever (~50 years in the case of genetic equidistance).gnomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-52596696257030344842016-05-15T00:45:02.879-07:002016-05-15T00:45:02.879-07:00As far as we know, there is no God. No one has yet...As far as we know, there is no God. No one has yet found anything that requires a God, so Occam's Razor implies that the simplest argument (there is no God) should be accepted. Why expend the extra effort to promote God, if it isn't necessary??? It seems like a waste of energy.Mike Vandemanhttps://www.blogger.com/profile/06318503820963850581noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-46353716675780025862015-05-17T12:50:16.180-07:002015-05-17T12:50:16.180-07:00Darwinists love that question. :)Darwinists love that question. :)Stripehttps://www.blogger.com/profile/11177167535623025339noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-6364388323442545522015-05-17T08:59:51.128-07:002015-05-17T08:59:51.128-07:00What is a "Darwinist"?What is a "Darwinist"?nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-80368258269939465702015-04-23T06:10:53.783-07:002015-04-23T06:10:53.783-07:00First and only law:
Nothing in biology makes sens...First and only law:<br /><br />Nothing in biology makes sense except in the light of reproduction.<br /><br />peerhttps://www.blogger.com/profile/13511262660273927645noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-77080285676556924922012-12-04T18:13:38.574-08:002012-12-04T18:13:38.574-08:00"3) If population A has high genetic diversi..."3) If population A has high genetic diversity while B low in most genome sequences, the typical interpretation today is that A evolved longer than B and gave rise to B. But this topology could be completely reversed if most sequences are under purifying selection with A under more relaxed selection than B."<br /><br />What other implications would this have for the traditional Out-of-Africa hypothesis? I remember reading on Dienekes blog that, although he was sceptical in regard to strong interpretations of the 'multi-regional model', it seems that new data from introgression studies also cast doubt on the 'standard' model as well. Is there any other news about their current status in population genetics?<br /><br />Nice blog, by the way. I'm new to this stuff, so please forgive me for any stupid questions.SeriousCatnoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-68320688500059425112012-10-02T13:51:37.920-07:002012-10-02T13:51:37.920-07:00Thank you for nothing. Just wasted an hour of my l...Thank you for nothing. Just wasted an hour of my life reading your whimsical nonsense. Sven Svenssonnoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-22976289878300247012012-06-01T12:21:58.244-07:002012-06-01T12:21:58.244-07:00Thanks. :)Thanks. :)Stripehttps://www.blogger.com/profile/11177167535623025339noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-74426808015553934312012-05-30T13:11:45.254-07:002012-05-30T13:11:45.254-07:00MA: minor allele of a SNP. A SNP typically has ju...MA: minor allele of a SNP. A SNP typically has just two alleles and the allele with a population frequency of <0.5 is termed the minor allele.<br /><br />RIL: Recombinant inbred lines. The RIL panels are derived from breeding of parental strains differing in phenotypes and genotypes. The F1 and F2 or up to F10 progenies are intercrossed to maximize random recombination and hence allelic diversity in the offspring, which were then randomly selected for inbreeding up to 20 generations to generate the final panel of RILs homozygous for almost all variants or SNPs. During the random mating and subsequent inbreeding process, there are ample opportunities for harmful variants to be negatively selected and for neutral variants to drift. Since natural selection already occurs at fertilization, many individuals may die or be aborted before birth due to abnormal development caused by harmful variants. So, while the population size of a RIL panel is small, which favors neutral drift, the actual size of the offspring population of the original parents is much greater and includes many that were never born due to negative selection of harmful variants. Therefore the frequencies of variants that exist in the established RIL panel are the result of natural selection and/or neutral drift.gnomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-43721854874960117872012-05-30T00:02:05.281-07:002012-05-30T00:02:05.281-07:00What is "MA" and "RIL"?What is "MA" and "RIL"?Stripehttps://www.blogger.com/profile/11177167535623025339noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-75527878863058759102011-09-22T07:02:22.650-07:002011-09-22T07:02:22.650-07:00Any replies?
I'd guess not.Any replies?<br /><br />I'd guess not.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-52559610353638500232011-09-22T06:52:21.893-07:002011-09-22T06:52:21.893-07:00Hi there,
You write:
"Thus, there is a stro...Hi there,<br /><br />You write:<br /><br /><i>"Thus, there is a strong consensus in the field that even if the molecular clock is implausible which nearly everyone admits,"</i><br /><br />This is inaccurate. What nearly everyone admits is that there is little evidence for a <b>universal</b>, aka global, molecular clock. So-called <a href="http://www.ncbi.nlm.nih.gov/pubmed/15008417" rel="nofollow"> local molecular clocks</a> have been and are being used for a variety of reasons. You should look into it.<br /><br /><i>" one can still use other methods to infer molecular phylogeny within the overall paradigm originally started by the molecular clock concept. </i><br /><br />This is just ludicrous. Molecular phylogenetic analyses were performed decades before the notion of a molecular clock was put on paper. If analyses can be performed without reference to molecular clocks, how on earth can such methods be part of some "overall paradigm originally started by the molecular clock concept"?<br /><br /><br /><i> It is a self-deceiving illusion in my opinion, </i><br /><br />I wouldn't put much stock in your opinion. You have claimed to have single-handedly overturned the Neutral Theory and the conclusions of all molecular phylogeny publications that did not produce arrangements that you think are correct. Yet here we are, 3-4 years later, and none of your amazing paradigm busting papers has made it into print. <br /><br />One cannot overturn the relevance of methods that have actually been tested - <br /><br /><a href="http://www.sciencemag.org/content/254/5031/554.short" rel="nofollow">Gene trees and the origins of inbred strains of mice</a><br /><br /><a href="http://www.sciencemag.org/content/255/5044/589.short" rel="nofollow">Experimental phylogenetics: generation of a known phylogeny</a><br /><br />- premised on their desires.<br /><br />sorry.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-56845378473877726402011-07-11T12:18:12.982-07:002011-07-11T12:18:12.982-07:00uh, just in case: my account is gimmy971@gmail.com...uh, just in case: my account is gimmy971@gmail.com<br /><br />thanks, ciaoLorenzonoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-51333840534879000242011-07-11T11:41:40.499-07:002011-07-11T11:41:40.499-07:00Hi, did you have a chance to take a look at "...Hi, did you have a chance to take a look at "The Codes of Life - The Rules of Macroevolution" (Springer, 2007) by Marcello Barbieri? The whole book is pretty big, but the 20-pages article of M. Barbieri himself (Chapter 2 - The Mechanisms of Evolution) is worth reading.<br />If you want, you can contact me on my google account for further details..<br /><br />kind regards,<br />LorenzoLorenzonoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-13208217465784664142011-07-08T11:58:10.524-07:002011-07-08T11:58:10.524-07:00Thank you for the note.Thank you for the note.gnomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-69321859051964918592011-07-08T08:04:24.310-07:002011-07-08T08:04:24.310-07:00Uh, the quote from Popper went lost! here it is ag...Uh, the quote from Popper went lost! here it is again:<br /><br />"My view may be expressed by saying that every discovery contains ‘an irrational element’, or ‘a creative intuition’, in Bergson’s sense. In a similar way Einstein speaks of the ‘search for those highly universal laws . . . from which a picture of the world can be obtained by pure deduction. There is no logical path’, he says, ‘leading to these . . . laws. They can only be reached by the logic of science intuition, based upon something like an intellectual love (‘Einfühlung’) of the objects of experience"Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-74346006960062714452011-07-08T08:03:17.211-07:002011-07-08T08:03:17.211-07:00Ciao, here I add something from K. Popper:
<>...Ciao, here I add something from K. Popper:<br /><> -- K. Popper, The Logic of Scientific Discovery, Routger classics 2002, Pgg 8-9<br /><br />Footnotes say that the Einstein's quote is from "A. Einstein, Mein Weltbild, 1934, p. 168"<br /><br />It looks like there is a striking inter-disciplinary agreement on the key role played by intuition on scientific progress.. And this is "against method" as Feyerabend would say :-)<br /><br />It's a pleasure to read you, kind regards<br /><br />LorenzoAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-85049697440488370342011-03-27T07:16:11.577-07:002011-03-27T07:16:11.577-07:00Thank you for the note. The modern evolution theo...Thank you for the note. The modern evolution theory is not only preventing progress in the field of evolution, as you correctly noticed, but also in my opinion in the field of molecular medicine such as cancer and common diseases. A correct and truly fundamental theory of evolution should not only tell us about the past, but also about the present and future of human lives. The most effective and practical way to replace the Darwinian dogma is for a new theory to explain much more than just our evolutionary past. It must solve some important human health problems relevant to every human being and biologist in general. Other than bacteria drug resistance and things of that nature, the Darwinian paradigm is mostly irrelevant to most molecular biologists studying common diseases.gnomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-12577042821828076032011-03-11T09:56:17.033-08:002011-03-11T09:56:17.033-08:00The article of Woese is great. It seems to follow ...The article of Woese is great. It seems to follow the non-reductionist theories of "emerging complexity" proposed by Kauffman (and blessed by Gould) against the Modern Synthesis.<br />The reductionist approach, in general, was already heavy challenged in physics by Nobel P.W.Anderson in his article "More is different", and I much like the idea to bring physics/mathematical laws into biological evolution theories.<br />Btw, your Blog is wonderful! Finally something which positively challenges the "sacred cow" of neo-darwinist approach which looks, more and more, inadequate to explain macro-evolutionary processes, thus preventing fruitful progresses of in this field of knowledge.<br /><br />Ciao! LorenzoLorenzonoreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-2207662863073246082010-12-17T06:34:03.573-08:002010-12-17T06:34:03.573-08:00Yes, yeast is equidistant to trout and humans. Th...Yes, yeast is equidistant to trout and humans. The complexity of both trout and humans is greater than yeast. The maximum distance between a complex species and a simple one is equivalent to the maximum genetic diversity of the simple species. So, the maximum distance between trout and yeast or between human and yeast is determined by the genetic diversity of yeast and has very little to do with that of trout or human. You may want to read my paper on the overlap feature of the equidistance result or the one on the mgd hypothesis available at Nature Precedings.gnomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-8434207374852632666.post-89811239545180806622010-12-16T23:30:23.507-08:002010-12-16T23:30:23.507-08:00Just a quick question about the MGD. It is my unde...Just a quick question about the MGD. It is my understanding that yeast is equidistant to trout and humans. Since humans are more complex than trout, shouldn't yeast be closer to trout than to human? Or am I missing something? Thanks.Livingstone Morfordhttps://www.blogger.com/profile/01492454376086041663noreply@blogger.com