tag:blogger.com,1999:blog-37148773.post571439582359149016..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: John Mattick presents his view of genomesLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger14125tag:blogger.com,1999:blog-37148773.post-27370984050035562872022-04-03T18:06:03.540-04:002022-04-03T18:06:03.540-04:00Mattick and several of the ENCODE researchers are ...Mattick and several of the ENCODE researchers are convinced that the superiority of humans is due to their increased intelligence. They seem to believe that the evolution of brain complexity is somehow related to huge increases in the number of noncoding genes. They don't explain this connection very well but they are sure to mention that brain tissue has a lot of transcripts.<br /><br />So do spermatocytes but that doesn't get the same attention. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20922138243916200782022-04-03T17:58:39.150-04:002022-04-03T17:58:39.150-04:00Mattick surely knows about Ryan's database. He...Mattick surely knows about Ryan's database. He knows that most frogs and all salamanders have genomes larger than ours. He knows that there are several mammals with larger genomes. He knows that there are crustaceans and insects that have larger genomes than humans.<br /><br />It's hard to understand why he doesn't recognize these facts when he presents his data. Is it ignorance, or is he deliberately trying to deceive?<br /><br />I struggled with the question of motive when I was writing my book. It doesn't make sense to assume that all those supposedly successful scientists are stupid and it doesn't make sense to assume that they are deliberately lying. <br /><br />Is it some form of mass delusion?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82583744220895243192022-04-02T19:20:41.847-04:002022-04-02T19:20:41.847-04:00The slide is probably considerably older than the ...The slide is probably considerably older than the talk, and the talk is three years old.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17528602227112538392022-04-02T15:41:03.462-04:002022-04-02T15:41:03.462-04:00"I do believe the bar graph is assembled base..."I do believe the bar graph is assembled based on sequenced genomes, which of course are biased toward small ones."<br /><br />If that's the case, it's quite out of date. There are plenty of assembled genomes that are larger than the human genome.Dave Carlsonhttps://www.blogger.com/profile/18110718908216269032noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64536296156871194982022-04-02T09:46:54.846-04:002022-04-02T09:46:54.846-04:00It's not genome size, but the fraction of the ...<i>It's not genome size, but the fraction of the genome that is noncoding.</i><br /><br />That amounts to the same thing, given that the coding part doesn't vary by that much. Huge genomes are mostly non-coding, small genomes mostly coding. And we also need to worship the ferns, which are evidently much more complex than mammals.<br /><br />Developmental complexity is defined by the number of cell types, and that depends on how closely you look and how finely you choose to divide them. Largely subjective.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58103307239302281512022-04-02T03:37:05.294-04:002022-04-02T03:37:05.294-04:00It's not genome size, but the fraction of the ...It's not genome size, but the fraction of the genome that is noncoding. You need to look at the colours (three orange vertebrates, three red invertebrates, etc) to see the 'developmental complexity'.<br /><br />It looks like we still have to worship lungfush and salamanders, but we get to look down on pufferfish.<br /><br /><br /><br />Graham Joneshttps://www.blogger.com/profile/09212540504498321504noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5708628159045746402022-04-02T03:13:27.582-04:002022-04-02T03:13:27.582-04:00Yes, but is that statistically significant?Yes, but is that statistically significant?Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-341456293573718872022-04-01T17:52:55.776-04:002022-04-01T17:52:55.776-04:00"(6:00) The view that evolution of regulatory...<em>"(6:00) The view that evolution of regulatory sequences is mostly responsible for developmental complexity (Evo-Devo) has never been justified."</em><br /><br />I didn't watch the video but if he really made a point of that then it is just weird. I think it's well known that most animals share the vast majority of their protein coding genes, so since cells by dry mass are mostly protein, the differences in complexity and anatomical characteristics more broadly must lie predominantly in the regulation of expression of those proteins.<br /><br />Organisms aren't made of up of bulk lncRNA, so whatever functional roles the different types of RNAs might have, that Mattick refers to to argue the genome is mostly functional, is almost exclusively regulatory. Those RNAs that really are functional do not form the bulk of muscle or brain tissue(and most of it is fleeting in nature and quickly broken down again), so excluding ribosomal and tRNA, the remaining functional RNA have functions in gene-regulation. <br /><br />Does Mattick even know what his own position is?Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29297023675666218342022-04-01T12:19:41.082-04:002022-04-01T12:19:41.082-04:00I do believe the bar graph is assembled based on s...I do believe the bar graph is assembled based on sequenced genomes, which of course are biased toward small ones. Hence the predominance of prokaryotes and the absence of genomes larger than the human one. Now why didn't he use T. Ryan Gregory's genome size database? <br /><br />Given all that, what correlation does it show. The vertical axis is genome size. The horizontal axis is also just an ordering of taxa by genome size. So we see that genome size is strongly correlated with genome size.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34522569294950189692022-04-01T10:02:27.091-04:002022-04-01T10:02:27.091-04:00Two more words: dog's ass.Two more words: dog's ass.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65020377112224472982022-03-31T14:44:22.975-04:002022-03-31T14:44:22.975-04:00That bar graph does remind me of .. what was it ca...That bar graph does remind me of .. what was it called? The infamous "dogleg graph" on the amount of DNA versus complexity? I thought even that was more than passe' by now. I did a bit of searching and found you had posted about this many years ago ( https://sandwalk.blogspot.com/2007/09/genome-size-complexity-and-c-value.html ). And guess who it came from? Mark Sturtevanthttps://www.blogger.com/profile/05846892642161763103noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66454812595616186722022-03-30T18:40:58.286-04:002022-03-30T18:40:58.286-04:00two more words: Polychaos dubium two more words: Polychaos dubium Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86718876551025820632022-03-30T17:18:28.742-04:002022-03-30T17:18:28.742-04:00(13:40) The proportion of noncoding DNA increases ...<em>(13:40) The proportion of noncoding DNA increases with developmental complexity, topping out at humans.</em><br /><br />Wow! Somebody inform our lord and master, the lungfish!Joe Felsensteinhttps://www.blogger.com/profile/00430555755335300584noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31449780541752516292022-03-30T14:59:35.381-04:002022-03-30T14:59:35.381-04:00Won't ever pass our mutual friend T. Ryan Greg...Won't ever pass our mutual friend T. Ryan Gregory's onion testpaulbratermanhttp://paulbrterman.wordpress.comnoreply@blogger.com