tag:blogger.com,1999:blog-37148773.post2700810902994228419..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: John Parrington discusses pseudogenes and broken genesLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger11125tag:blogger.com,1999:blog-37148773.post-43317566614724922572015-07-27T15:24:46.577-04:002015-07-27T15:24:46.577-04:00Aceofspades, I think SM possibly is not distinguis...Aceofspades, I think SM possibly is not distinguishing between mere inheritance and conservation.Nullifidianhttps://www.blogger.com/profile/15207390447020990907noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13242137606362520432015-07-26T17:13:43.349-04:002015-07-26T17:13:43.349-04:00For fucks sake, put some numbers on those fucking ...For fucks sake, put some numbers on those fucking discoveries. What fraction of transposable elements have been discovered to have regulatory roles? I'm going to guess less that 1%. <br /><br />You don't get anywhere by just bringing references that say some transposable element somewhere possibly has a regulatory function. You need to look at how many there are and how many have been shown to have a function. Why doesn't this sink in with you people? It's the same stupid shit every time. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76325793534484136912015-07-26T13:04:32.089-04:002015-07-26T13:04:32.089-04:00This is true for each of the arguments for junk, n...This is true for each of the arguments for junk, none of which has anything to do with "DNA of unknown function".John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7066390835290462742015-07-26T11:58:32.303-04:002015-07-26T11:58:32.303-04:00Merely pointing out that the mutational load argum...Merely pointing out that the mutational load argument definitely requires the presence of a lot of "true junk" as different from "DNA of unknown function" in a genome as big as ours, so conflating the two is indeed a caricature.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-73594827956664631712015-07-26T10:25:14.230-04:002015-07-26T10:25:14.230-04:00??John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36084913119346130452015-07-26T05:52:18.849-04:002015-07-26T05:52:18.849-04:00What are you taking about? Which species have cons...What are you taking about? Which species have conserved junk DNA?<br /><br /> That sentence is contradictory since if a sequence is conserved then it is functional and it is not junkAceofspadeshttps://www.blogger.com/profile/09534611408824723712noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55372701396743943592015-07-26T03:19:46.742-04:002015-07-26T03:19:46.742-04:00"almost all of the transposon-related sequenc..."almost all of the transposon-related sequences are bits and pieces of transposons that haven't been active for millions of years"<br /><br />If "haven't been active" means not jumping around in the germline, then that is defensible. <br /><br />But if "haven't been active" means having no regulatory role or not jumping around in somatic cells, that may not be as defensible.<br /><br /><br />Inactivity in the germline does not preclude activity in somatic cells which is still mostly unexplored. There is evidence in neuron cells of such activity and there likely will be more discovered in the future. Evidence suggests transposition in somatic cells may be important in differentiating somatic cells.<br /><br />This paper touches on the TEs in somatic cells, including the neuron cells:<br /><br />"The necessary junk: new functions for transposable elements" by<br />Alysson R. Muotri, Maria C.N. Marchetto, in Human Molecular Genetics<br /><br />Furthermore, regulatory roles for transposon continue to be proposed such as having specific nucleosome binding properties, phasing of nucleosomes, serving as enhancers, epigenetic boundaries. <br /><br />2007 paper in Nature by R. Keith Slotkin and Robert Martienssen describe the regulatory roles of Transposable elements.<br /><br /> <br /><br />So what fraction of the genome? Maybe we'll find out by actually looking and that means supporting the work of ENCODE and ROADMAP rather than relying on evolutionary theory to dictate what can and cannot be functional in the cell.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-781977137917365002015-07-24T21:15:39.479-04:002015-07-24T21:15:39.479-04:00Septic Mind,
I think that if you actually tried t...Septic Mind,<br /><br />I think that if you actually tried to put together random words you wouldn't manage to be as incoherent as you are when you're serious.<br /><br />But you're no layman, right you little idiot?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25020745669461998262015-07-24T17:08:11.207-04:002015-07-24T17:08:11.207-04:00To quote Joe Felsenstein's PG handbook (Chapte...To quote Joe Felsenstein's PG handbook (Chapter III.6: Mutational load; emphasis added):<br /><br /><i>If much of the DNA is simply “spacer” DNA whose sequence is irrelevant, then there will be a far smaller mutational load. But notice that <b>the sequence must be truly irrelevant, not just of unknown function</b>. If the “extra” DNA has regulatory or chromosome-pairing function requiring it to have a specific base sequence, then mutations in that sequence will still cause a mutational load, even if these loci are not producing polypeptide chains.</i>Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9586711591916573522015-07-24T16:55:29.174-04:002015-07-24T16:55:29.174-04:00"We don't know why some "related&quo..."We don't know why some "related" species have preserved junk DNA while others didn't. We can't figure it out. We will trust that random and unintelligent processes must have known what they were doing. What choice do we have? We have to follow the argument that suits us and not where it leads. We are not creationists". - Expert Scientists in the Field<br /><br />Applause Jmachttps://www.blogger.com/profile/04392421995310271733noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9528364855784130252015-07-24T15:18:24.459-04:002015-07-24T15:18:24.459-04:00He also seems to be displaying the most common car...He also seems to be displaying the most common caricature of arguments for junk DNA: "We don't know what it's function is, therefore it's junk". Bet he can't find anyone actually making that claim, as opposed to using it as a strawman.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.com