tag:blogger.com,1999:blog-37148773.post2631192169468881404..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Human Y Chromosome Mutation RatesLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger18125tag:blogger.com,1999:blog-37148773.post-17629383264176275252009-09-19T21:43:01.539-04:002009-09-19T21:43:01.539-04:00Dimwits. Start by reading A. Garciadiego, BERTRAN...Dimwits. Start by reading A. Garciadiego, BERTRAND RUSSELL AND THE ORIGINS OF THE SET-THEORETICAL 'PARADOXES.'<br /><br />Unfortunately, the confused ideas and faulty understanding of Borel and a huge and pernicious influence on Malecot, and through him, on Kimura.<br /><br />You don't understand Kimura as a constructivist--in fact, you don't know anything about his mathematical orientation, do you?<br /><br />Just try to identify where Kimura makes his constructivist intervention in his argument.<br /><br />Your own presumptuous constructivism is on the way out.John Ryskamphttps://www.blogger.com/profile/06154989992538796409noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8623226472559349532009-09-12T09:41:13.316-04:002009-09-12T09:41:13.316-04:00Larry Moran said...
"John Ryskamp says,
&quo...Larry Moran said...<br />"John Ryskamp says,<br /><br />" 'You are very, very out of touch with what is going on in theoretical biology. Hurry up and put yourself in touch with it.'<br /><br />Who are you referring to? Your comment doesn't make any sense."<br /><br />The things John Ryskamp says tend not to make very much sense, and he has an obsession with Motoo Kimura. It is quite revealing to read his "review" of Kimura's classic book at Amazon.athelnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62248801296390726812009-09-11T16:02:09.025-04:002009-09-11T16:02:09.025-04:00John Ryskamp says,
You are very, very out of touc...John Ryskamp says,<br /><br /><i>You are very, very out of touch with what is going on in theoretical biology. Hurry up and put yourself in touch with it.</i><br><br>Who are you referring to? Your comment doesn't make any sense.<br><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-39732735910772630272009-09-11T13:31:59.374-04:002009-09-11T13:31:59.374-04:00I think you should find out more about Kimura as a...I think you should find out more about Kimura as a constructivist mathematician. The question of the moment is:<br /><br />where is the constructivist intervention in Kimura's argument?<br /><br />As you will see from the paper below, historians are now approaching this question with respect to Darwin.<br /><br />They will certainly start approaching it with regard to Kimura.<br /><br />You definitely owe it to yourself to read A. Garciadiego, BERTRAND RUSSELL AND THE ORIGINS OF THE SET-THEORETIC 'PARADOXES.'<br /><br />Kimura's mathematical orientation--indeed his whole rhetorical orientation--comes from Malecot, who got his approach from Borel.<br /><br />Borel, along with Russell and Poincare, was one of the now-discredited purveyors of the "paradoxes" and they renewed the constructivist insistence that argumentation avoid "paradox" by containing an arbitrary insertion in the logic.<br /><br />Hence the quesion posed about Kimura.<br /><br />You are very, very out of touch with what is going on in theoretical biology. Hurry up and put yourself in touch with it.<br /><br /><br />Ryskamp, John Henry,Paradox, Natural Mathematics, Relativity and Twentieth-Century Ideas(June 17, 2008). Available at SSRN: http://ssrn.com/abstract=897085John Ryskamphttps://www.blogger.com/profile/06154989992538796409noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53420357352684335302009-09-10T12:46:20.159-04:002009-09-10T12:46:20.159-04:00Hi Larry,
Very provocative post.
I selected it as...Hi Larry,<br /><br />Very provocative post.<br />I selected it as one of my MolBio picks of the week at ResearchBlogging in my blog.<br />You can check my picks here: http://bit.ly/2OLy0e<br /><br />Cheers,<br />-AAlejandro Montenegro-Monterohttps://www.blogger.com/profile/18078462764857337905noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-37297890654938924172009-09-10T12:45:03.940-04:002009-09-10T12:45:03.940-04:00This comment has been removed by the author.Alejandro Montenegro-Monterohttps://www.blogger.com/profile/18078462764857337905noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41701283602257504042009-09-07T06:45:10.429-04:002009-09-07T06:45:10.429-04:00Then what are all those broken transposons doing i...Then what are all those broken transposons doing in your genome?<br /><br />BTW, not only is the claim that there is no junk DNA in human genome bogus, but a number of features of the human and other eukaryotic genomes are only explainable in the light of understanding the quantitative balance between selection and mutational processes (and how the latter can end up dominating the process under certain conditions which happen to be met in most eukaryotes). <br /><br />Alternative splicing is a particularly bad example to use because while there might be advantage of having alternative isoforms of genes, this:<br /><br />A) does not explain how introns arose initially<br />B) does not explain why we have so many of them compared to the number of functional alternative splicing events<br />C) does not explain why introns are so long in humans and so short in other species<br />D) does not explain why there are no introns in prokaryotes<br />E) does not explain a number of other peculiar features of the system in mammals and other eukaryotes<br /><br />All of the above are only explainable by the neutral theory of molecular evolutionGeorgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54405845304944848632009-09-07T05:02:04.075-04:002009-09-07T05:02:04.075-04:00The meme, that most of our genome is junk, should ...The meme, that most of our genome is junk, should have died in the 1970s. It appears that the human ability, to recirculate bad copies of an opinion, is quite resilient. Alternative splicing discoveries continue to leave the classic gene expression model behind. Go in peace and marginalize my introns no more.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41560842603601734482009-09-04T16:49:12.013-04:002009-09-04T16:49:12.013-04:00To Dave, yes... but this assumes there is no extre...To Dave, yes... but this assumes there is no extreme codon bias in the organism in question. Strong codon bias may have an effect on translation of these "redundant" codons. Probably not an issue for mammalian Y chromosomes.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24482605617466885752009-09-02T16:41:39.894-04:002009-09-02T16:41:39.894-04:00Now somebody please correct me if I'm wrong, b...Now somebody please correct me if I'm wrong, but doesn't the fact that there is redundancy in the third position of many codons mean that even functional dna sites (ie. those that are expressed and result in protein formation) can experience neutral mutations?Dave Carlsonhttps://www.blogger.com/profile/18110718908216269032noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40696473082707114072009-09-02T14:27:01.859-04:002009-09-02T14:27:01.859-04:00So is that just "junk" ?
Obviously not....<i>So is that just "junk" ?</i><br /><br />Obviously not.<br /><br />More generally one could say that two alleles that code for different trait values may very well happen to result in equal fitness. Brown eyes vs. blue eyes in populations where there are plenty of both, for example.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-50640087114111550452009-09-02T14:15:16.415-04:002009-09-02T14:15:16.415-04:00To add to what Bjørn said, the mutations might als...To add to what Bjørn said, the mutations might also appear neutral because they make a functional difference but it is too small to observe easily or to cause a significant selection pressure.<br /><br />Suppose a human baby is born able to synthesise vitamin C. How would we know? Well, in theory it might go for a long time without eating any citrus fruits, and it wouldn't develop scurvy. OK, and how likely is that? Well, not likely. And would anyone report it? Probably not, they'd chalk it up to good luck.<br /><br />So is that just "junk" ?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55077889931765504412009-09-02T09:00:19.589-04:002009-09-02T09:00:19.589-04:00Should be
http://www.nature.com/news/2009/090827...Should be <br /><br />http://www.nature.com/news/2009/090827/full/news.2009.864.html?s=news_rss<br /><br />Their is some odd <br> text string in the middle of the link address that is disabling the link.The Other Jimhttps://www.blogger.com/profile/17570666738076378921noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15661669025695167572009-09-02T08:32:17.446-04:002009-09-02T08:32:17.446-04:00The "Human Mutation Rate Revealed" like ...The "Human Mutation Rate Revealed" like does not seem to be working.Bryanhttps://www.blogger.com/profile/16672407110077541595noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5044212601428677262009-09-01T23:06:41.507-04:002009-09-01T23:06:41.507-04:00I saw the paper a few days ago and earlier today I...I saw the paper a few days ago and earlier today I was thinking exactly about these issues.<br /><br />It has occurred many time to me that the whole "debate" about evolution is so tragically far removed from the actual science, that we often focus more on fighting with lunatics than on reflecting on the implications of the science. <br /><br />Because I highly doubt there are any people in the creationism/ID crowd that actually understand how much worse than what they are fighting against the neutral theory of molecular evolution really is (from their persepctive), and on how solid ground (both theoretically and in terms of support by the data) it is. <br /><br />Of course, this only shows how ignorant they are, but it also shifts the focus away from the more productive discussions we could be having.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48236231598669981032009-09-01T23:06:09.590-04:002009-09-01T23:06:09.590-04:00This comment has been removed by the author.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21871482507919364262009-09-01T21:03:54.087-04:002009-09-01T21:03:54.087-04:00For a different perspective on male mutation rates...For a different perspective on male mutation rates, I suggest this paper:<br /><br />Male mutation rates and the cost of sex for females. Nature 369:145-147 (1994)<br /><br />http://www.nature.com/nature/journal/v369/n6476/abs/369145a0.htmlRosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80460974565561613812009-09-01T17:13:41.102-04:002009-09-01T17:13:41.102-04:00most mutations are neutral (i.e. most of our genom...<i>most mutations are neutral (i.e. most of our genome is junk).</i><br /><br />That most mutations are neutral does not mean that most of the genome is junk. Neutrality at functional sites increases robustness through canalization.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.com