tag:blogger.com,1999:blog-37148773.post4788252474414490400..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: How do you explain the differences between chimpanzees. humans, and macaques?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger83125tag:blogger.com,1999:blog-37148773.post-23755650887589782942015-03-01T17:09:43.353-05:002015-03-01T17:09:43.353-05:00Ok, Ok. I continue...
On the first and second para...Ok, Ok. I continue...<br />On the first and second paragraph of your response, I do not dispute the clock function , I want to highlight is the problem of assuming ( hypothesis ) that the differences between genomes of closely related species as indicators of evolutionary changes . Is absent evidence to say that only that percentage is responsible for the difference between one and the other species.<br />This hypothesis should be rejected when the results of applying this method of dating do not match those of the fossil record (assuming it is more accurate) .<br />I have clear that the method is not circular , but you claim that if their results offset by a "few" million years would make one calibration (this is a lifesaver to molecular method , when it should be re-evaluated the hypothesis that already mentioned) .<br />I believe that restricting the application of molecular method to modern species does not remove the problem I mentioned ; only minimizes the error becomes more evident when going backwards in the clade .<br />Regarding the third paragraph , I understand that the fossil with which the comparison is made must be a common ancestor before the node divergence ( hopefully it was the fossil node, but that does not happen ) .<br />However , this uncertainty increases the probability of failure in comparison dating. It is a problem that adds to those already mentioned.<br /><br /><br /> socolhttps://www.blogger.com/profile/16698091294650506037noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17770500050365782612015-03-01T03:35:46.545-05:002015-03-01T03:35:46.545-05:00There it is again - dot-dot-dot...There it is again - dot-dot-dot...AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46561200289246311922015-02-28T20:30:22.267-05:002015-02-28T20:30:22.267-05:00Thanks for your interest in answering my questions...Thanks for your interest in answering my questions. There are points given for more discussion ... but thanks .socolhttps://www.blogger.com/profile/16698091294650506037noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-91962996141492634792015-02-28T07:22:28.061-05:002015-02-28T07:22:28.061-05:00I notice that "Terborg" has not answered...I notice that "Terborg" has not answered. Apparently Terborg was aware of what would happen if he tried to answer.<br /><br />The whole "front loading" hypothesis doesn't make sense for two reasons:<br /><br />(1) It is incoherent, as Diogenes implied. Where is the "front"? 500 million years ago? Was the genetic program to make, say, whales already built into Cambrian chordates? Along with the program to make puffer fish?<br /><br />(2) It could not be maintained in the face of mutation. If the whale program was sitting there in the genome 500 million years ago, what prevented it from being eroded by mutation before it was time to come up with whales?<br /><br />A front-loading designer not only has to build in the structures of all possible descendants, but He has to make sure that the programs are maintained with no disruptive mutations occurring before the program is needed. And each time there is a speciation the programs somehow have to know that in one lineage the whale program won't be needed but in the other it will.<br /><br />The Designer is awfully busy in that "scientific" view: not only is it true that "His eye is on the sparrow" but He's busy preventing the wrong kinds of mutations in all species, throughout the whole process of front-loaded evolution.<br /><br />In which case it is not clear why He needed to front-load in the first place, if He could just order up the right mutations when needed.<br />Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21074231031526945072015-02-28T06:31:24.098-05:002015-02-28T06:31:24.098-05:00Correction - intervening fossils do have a use, si...Correction - intervening fossils do have a use, since the divergence clock cannot be younger than them. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57247942943225885652015-02-28T06:18:41.694-05:002015-02-28T06:18:41.694-05:00In the case of a simple bifurcation to 2 modern sp...In the case of a simple bifurcation to 2 modern species, there is no issue. You count the sequence differences between them, and you measure the rate at which the modern clock ticks. In a simplistic model, basic arithmetic gives you a rough time in years since divergence. No fossils are involved. Say you get 10 million years by this method. <br /><br />Then say you find a fossil which is close to the main branch of both your modern species. You date it, get 7 million years, and consider that date to be more reliable. So the molecular clock is out. But it's still clearly functioned as a clock, it wasn't defined circularly or by fossil calibration, and it wasn't a million miles out. You take the recalibration into account when you go further back, using your clade to count differences with a sister group.<br /><br />Of course, you can get a lot more sophisticated and account for substitution biases, concentrate on definitively silent sites, and so on, to improve the accuracy of the clock. But I don't see the issue. When you date that oldest fossil, you have an individual prior to the emergence of the phenotypic differences that seem to concern you. Fossils on either branch, harbouring some of the incipient differences between the modern species, are no use for calibrating the molecular clock, which starts with molecular data from 2 extant leaves and attempts to date the node connecting them.AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5520581336756876822015-02-27T23:41:07.187-05:002015-02-27T23:41:07.187-05:00Alan
I think we agree is that the molecular clock ...Alan<br />I think we agree is that the molecular clock itself is not reliable, and reading depends heavily on what was found with the dating by radioisotope.<br /><br />Then returning to the post of MORAN, says:<br /><br />"The Differences between each pair of species is consistent With<br />an approximate molecular clock Corresponding to a constant mutation<br />rate over million of years.The absolute levels of sequence identity<br />(Ie 98-99% for chimp / human) is consistent With The time of<br />divergence from a common ancestor based on the fossil record and<br />other criteria. "<br /><br />But if the molecular clock is calibrated dating<br />fossils.<br />Then implicitly when measured with the clock differences between species; the results will HAVE to be consistent with what is known about divergence times (Fossil) between humans and chimpanzees or humans and macaques.<br />Thus, the supposed consistency really is unclear or may not exist.<br /><br />The molecular clock just tells me there is a mutation from time to time.<br />But these substitutions do not imply that evolutionary change is occurring (selectively positive mutation or negative) is like we have a burning car but neutral; the motor (clock) is revolutionizing but the car does not move (evolutionary change) and we can not determine at what point does it but only with reference to an external agent (fossil).<br />So if we take the differences between pairs of species genomes and measure with a molecular clock have to do some delicate assumptions:<br /><br />For example; 1% of Sequence identy differentiates human chimp genome is unique for the first (but gorilla genome have identical regions corresponding to the 1% that man would suppose exclusive ) .<br /><br />Also assume that the differentiating sequence was given at that precise combination within a universe of probabilities.<br />Considering the above , I consider that there is no theoretical basis for comparative claims between the results obtained with a molecular clock and dated with the fossil record , because in its definition are engaged.socolhttps://www.blogger.com/profile/16698091294650506037noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32873334951305363702015-02-27T16:06:10.696-05:002015-02-27T16:06:10.696-05:00Yahoo posted an article today about humans/chimps:...Yahoo posted an article today about humans/chimps:<br /><br />http://news.yahoo.com/big-brain-gene-found-humans-not-chimps-192932726.htmlThe whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49501186750396281482015-02-27T10:59:54.332-05:002015-02-27T10:59:54.332-05:00If your claims were true for biology, everybody wo...<i>If your claims were true for biology, everybody would know about it. And there would be not be a scientific ID community.</i><br /><br />Just quoting for posterity. You have to almost stand in awe at the stupidity of this argument.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-91029192060576624082015-02-27T10:41:53.415-05:002015-02-27T10:41:53.415-05:00They also donate coding sequence, and serve to dis...<i>They also donate coding sequence, and serve to disrupt equal crossover, and intron excision, and cause fatal mutation. None of these can be seen as, especially, a role.</i><br /><br />Of course they can! TEs are in fact nothing but jum[p]ing mutators, mental disease producers, retropseudogene insertors, copy-number-variation enhancers, etc, etc, etc. They are all of that and more...frontloading!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48819716101249565662015-02-27T10:31:02.994-05:002015-02-27T10:31:02.994-05:00PT,
So, no alleles...but regulatory changes. TEs,...PT,<br /><br /><i>So, no alleles...but regulatory changes. TEs, suffling of preexisting genetic info...No addition of new genes required....frontloading.</i><br /><br />Alleles are different versions of a locus in a population. So a few regulatory differences would still be differences in a few alleles. Even if it wasn't, even if the definitions didn't match, the important point Allan was making is that few changes have phenotypic effects, with "few" being relative to the rest of changes, which would be mostly neutral or nearly neutral. You missed the point in exchange for a meaningless diatribe, attempting to make your case on definitions, rather than on understanding the point: that among many changes, just a relatively few might account for phenotypic/visible differences.<br /><br />Try some better understanding next time.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-26810609313881968832015-02-27T08:06:57.647-05:002015-02-27T08:06:57.647-05:00"Neodarwinian bias is now slowly being remove...<i>"Neodarwinian bias is now slowly being removed by many of my friends of ENCODE."</i><br /><br />Holy fucking shit, did he actually write this? Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42231683131632174732015-02-27T07:39:58.343-05:002015-02-27T07:39:58.343-05:00Neodarwinian bias is now slowly being removed by m...<i> Neodarwinian bias is now slowly being removed by many of my friends of ENCODE. And that is the way to go.</i><br /><br />ROTFLMFHO!!!!!!Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35671462634417857212015-02-27T06:21:25.819-05:002015-02-27T06:21:25.819-05:00Peer, have the "front loading hypothesis"...Peer, have the "front loading hypothesis" or "front loading theories" that you are promoting been checked and reproduced in the lab? <br /><br />What are the details of the "front loading hypothesis" or "front loading theories" that you accept as being accurate?<br /><br />Has "A special theory of evolution (limited common descent, more than one LUCA)" been checked and reproduced in the lab? <br /><br />Do you believe in 'special creation' of humans from dust and a rib? If so, has 'special creation' of humans from dust and a rib been checked and reproduced in the lab? <br /><br />Do you believe and claim that yhwh-jesus-holy-ghost exist and that they are 'God'? If so, has the existence of yhwh-jesus-holy-ghost been checked and reproduced in the lab, and has the veracity of your claim that yhwh-jesus-holy-ghost are 'God' been checked and reproduced in the lab? The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-73422476547349564742015-02-27T06:17:42.696-05:002015-02-27T06:17:42.696-05:00pretending there is nothing but protein/coding exo...<i>pretending there is nothing but protein/coding exones</i><br /><br />I think your implication that 'neo-Darwinians' argue or believe that there is nothing to evolution (descent with heritable modification) beyond changes to coding regions is something of a strawman.AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69408354411772184342015-02-27T05:54:44.231-05:002015-02-27T05:54:44.231-05:00PT: So, no alleles...but regulatory changes. TEs, ...PT: <i>So, no alleles...but regulatory changes. TEs, suffling of preexisting genetic info...No addition of new genes required....frontloading. </i><br /><br />That's something of a rabbit out a hat, there. "stuff ... more stuff ... hey presto! frontloading!". You think that there are no genetic changes beyond 'shuffling'? And what is it with you people and ellipses?AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72977704346393667992015-02-27T04:52:13.857-05:002015-02-27T04:52:13.857-05:00I was involved in a project to determine TEs (tran...<i>I was involved in a project to determine TEs (transposable and transposed elements, which are in fact nothing but jum[p]ing promoters and enhancers) [...] </i><br /><br />Although some TEs can end up serving such a functional role, it's a bit of a stretch to say that's what they <i>are</i>. They also donate coding sequence, and serve to disrupt equal crossover, and intron excision, and cause fatal mutation. None of these can be seen as, especially, a role. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13558248244808326132015-02-27T04:50:18.978-05:002015-02-27T04:50:18.978-05:00The whole NGS tecnology to analyse and compare gen...The whole NGS tecnology to analyse and compare genomes is so immensely NeoDarwinian biased, pretending there is nothing but protein/coding exones, we missed a lot! <br /><br />A few years ago I received a grant to study and compare the TE compartments of the genome. To mzysurprise not a single NGS platform had factored in that the difference between species and health and disease could be in the dark regions of the genome! Incredible isnt it? They were unable to handle it and my colleagues and I had to invent our own methods. Neodarwinian bias is now slowly being removed by many of my friends of ENCODE. And that is the way to go. <br />peerhttps://www.blogger.com/profile/13511262660273927645noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67556650274528957052015-02-27T04:41:49.240-05:002015-02-27T04:41:49.240-05:00Not really. An allele is a variant of a particular...Not really. An allele is a variant of a particular genetic sequence of interest. If you have a region ->xxxyyy<-, where the arrows represent positionally identifiable flanking sequence, then ->xxxxyy<-, ->yyy<-, ->xxxxxxyyy<-, -><- etc are all alleles of that sequence. <br /><br />I think confusion often arises because people think in terms of functional regions - protein coding, for example, so a duplication of a protein coding gene might seem like '2 alleles'. But the 2-copy genomic region is an allele of the 1-copy genomic region, within the population. As far as a diploid is concerned, alleles are just regions that can be homozygous or heterozygous within it. The boundaries of the allelic region can be narrowed or widened. So ->GeneGENE<- can be seen as heterozygous with ->Gene<-, or as two separate allelic regions, the homozygous ->Gene<- and heterozygous ->GENE<- and -><-. A gap can be an allele of a non-gap.AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48785529633955824702015-02-27T04:36:20.146-05:002015-02-27T04:36:20.146-05:00@ Moran,
Moran: The differences between the nativ...@ Moran,<br /><br />Moran: The differences between the natives of Japan and the pygmies of central Africa are at least as great as the differences between most closely related species.<br /><br />After rereading this statement> what difference do zou refer to...SNPs:? <br /><br />As far as I know nobody ever compared whole genomes. I am pretty sure that if one perfoms that unfiltered we will see a lot of surprises, which will blow NeoDarwinism ideology further out of the water. peerhttps://www.blogger.com/profile/13511262660273927645noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56739333582946870322015-02-27T04:15:13.695-05:002015-02-27T04:15:13.695-05:00socol,
Do you really are getting some consistenc...socol, <br /><br /><i>Do you really are getting some consistency between what obtained with the molecular clock and fossils . ?</i><br /><br />Within the known limitations of the method, yes. You'll really have to be a bit more specific about the period you're concerned about. Fossils are used to calibrate molecular data, sure - there are numerous mechanisms that may cause the clock to drift from a steady tick. But tick it does. It records relative time well enough, but on absolute time it's not as steady as radio-isotopes, which is why fossils (where available) tend to be the overriding reference. But there is a lag here, between the point of divergence from a common ancestor and the appearance of forms in fossils, and so molecular clocks would tend to point deeper than fossils even in an ideal world. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54155008487542434252015-02-27T04:15:11.673-05:002015-02-27T04:15:11.673-05:00So, now you have to define what an allele is. Say,...So, now you have to define what an allele is. Say, the entire coding part of a gene duplicates and now it is twofold present in the genome...do we call the entire region an allele. If so, than you are right. But in science we should be more specific. Using the same term for duplication and insertion for allele makes it very confusing. That-s why we call them duplications and deletions. Allele is a very non=specific term.peerhttps://www.blogger.com/profile/13511262660273927645noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28517667527114437282015-02-27T04:08:16.993-05:002015-02-27T04:08:16.993-05:00@ Allan,
Most differences observed in fossils wil...@ Allan,<br /><br />Most differences observed in fossils will likely be due to regulatory changes in development, which represents rather a small subset of the functional genome, itself a small subset of the overall genome. Most differences between genomes will be in the other bit. Even if every functional part has changed, that's still much smaller than the rest. <br /><br />So, no alleles...but regulatory changes. TEs, suffling of preexisting genetic info...No addition of new genes required....frontloading. <br /><br />I already thought so, because the neodarwinian concept of biology is completely down and out. peerhttps://www.blogger.com/profile/13511262660273927645noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33173101065689020092015-02-27T03:58:37.332-05:002015-02-27T03:58:37.332-05:00Why can't duplications and insertions be allel...Why can't duplications and insertions be alleles?AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5889628920912395072015-02-27T03:57:42.779-05:002015-02-27T03:57:42.779-05:00@ Diogenes. Jibbers Crabst, we observed evolution ...@ Diogenes. Jibbers Crabst, we observed evolution producing increases in complexity, functional information, specified complexity, irreducible complexity! ID was falsified every way it could be falsified! You lose, that's all!<br /><br />It is not about winning or losing. It is about science. If your claims were true for biology, everybody would know about it. And there would be not be a scientific ID community.<br /><br />So, Diogenes, leave your tub, and please expand with a scientific observation or reference which can be checked ad reproduced in the lab. peerhttps://www.blogger.com/profile/13511262660273927645noreply@blogger.com