tag:blogger.com,1999:blog-37148773.post7349351388706830639..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The 10th anniversary of the ENCODE publicity campaign fiascoLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger12125tag:blogger.com,1999:blog-37148773.post-60302109774214722842022-10-03T13:11:31.445-04:002022-10-03T13:11:31.445-04:00@Larry
I wouldn't appeal in general to whole ...@Larry<br /><br />I wouldn't appeal in general to whole genome duplication to account for large genomes in plants - while it accounts to the large genomes of neopolyploids such as Paris japonica relative to their diploid congeners plants have gone through repeated cycles of polyploidisation and diploidisation, and any correlation with the number of rounds of ancient polyploidisation is weak: Arabidospsis thaliana was the first plant genome sequenced partly due to its small genome (it was also a model organism for the study of plant development) but still shows evidence of 2 or 3 rounds of whole genome duplication.<br /><br />Gossypium (cotton) is a relatively young genus, but the random walk in genome sizes has been such that some diploid Australian cotton species have larger genomes than the tetraploid New World/Pacific species; this is not so much because the tetraploids (subgenus Karpas) have lost duplicated genes as that the Australian species (subgenus Sturtia) had acquited genomes twice the size of those of the the Afro-Asian (subgenus Gossypium) and American (subgenus Houzingenia) lineages.<br /><br />My layman's explanation for why plants in general have more genes than vertebrates (which have also gone through 3 rounds of whole genome duplication) is that plants have to synthesise all their own biomolecules - both in the essential bits of the metabolism, and in the secondary metabolites they produce to deter herbivores.Stewartnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87181692090251023372022-09-16T10:50:04.804-04:002022-09-16T10:50:04.804-04:00@John Harshman
The significance of a model can ju...@John Harshman<br /><br />The significance of a model can judged by its explanatory power, which is another way of saying that a good model explains observations and data much better than bad models. The junk DNA view of genomes explains the range of genome sizes much better than any model suggesting that most of the human genome is functional. <br /><br />This is why the Onion Test is so important in these discussions. <br /><br />The bigger problem is that a large number of junk DNA skeptics are really bad at seeing the "big picture" and putting their speculations into the broader context of all of life and all of the data. I think this is a failure of critical thinking. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28457343958300341892022-09-15T12:45:19.325-04:002022-09-15T12:45:19.325-04:00It's as if nobody has ever heard of the c-valu...It's as if nobody has ever heard of the c-value problem and need to discover it anew, without knowledge of the literature about it. Or without knowledge of onions, fugu, genome size databases, etc.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44808317061777513392022-09-14T17:20:17.654-04:002022-09-14T17:20:17.654-04:00I think Paris japonica, an alpine flower in Japan,...I think Paris japonica, an alpine flower in Japan, beats them all.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81209725841889297482022-09-14T16:33:43.240-04:002022-09-14T16:33:43.240-04:00I think ferns can beat lungfish.
"Estimates ...I think ferns can beat lungfish.<br /><br />"Estimates of fern genome sizes range from 0.77 pg for Azolla microphylla (heterosporous <br />leptosporangiate) to 65.55 pg for Ophioglossum reticulatum and 72.68 pg for Psilotum nudum (two <br />eusporangiate ferns; Bennett and Leitch 2001; Obermayer et al. 2002)."<br />https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4607520/<br /><br />Ophioglossum reticulatum has very high ploidy with 1440 chromosomes.<br /><br />Possibly the really important question in fern genomics is "How can we get a grant to sequence the really big ones?"Graham Joneshttps://www.blogger.com/profile/09212540504498321504noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5292184455649417542022-09-14T14:20:22.852-04:002022-09-14T14:20:22.852-04:00Just wait till they discover lungfish genomes ...Just wait till they discover lungfish genomes ...Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6177788519058370802022-09-14T13:19:07.041-04:002022-09-14T13:19:07.041-04:00@Joe
The sequences of two other fern genomes were...@Joe<br /><br />The sequences of two other fern genomes were published last week. The Ceratopteris richardii genome is also quite large (9.6 Gb, 7.5 Gb was sequenced) and 85% of it consists of repetitive DNA. Transposon-related sequences account for 75% of the genome. A total of 37,000 protein-coding genes were identified.<br /><br />There's evidence of two polyploidy events (whole genome duplications, WGD). One was only 60 My ago and the other was 300 My ago. There's no mystery about the large genome. It's due to the whole genome duplications and expansion of repetitive DNA. I assume that a very large percentage of the genome is junk DNA but the authors don't mention junk DNA for some strange reason.<br /><br />https://doi.org/10.1038/s41477-022-01226-7<br /><br />The other paper reports the sequence of the maidenhair fern genome sequence. The complete genome is 5.0 Gb of which 4.8 Gb was sequenced. 85% of the genome is repetitive DNA and most of this is transposon-related.<br /><br />There's no evidence of a recent WGD (<300 My) in the maidenhair fern genome. The authors report 31,000 protein-coding genes and 9,000 noncoding genes.<br /><br />In my opinion, most of the genome is junk DNA due to expansion of repetitive sequences so there's no great mystery about why the genome is larger than the human genome. But if the numbers of protein-coding genes are accurate, then some of the increase in genome size among ferns compared to mammals is due to more genes with large introns. Thus, part of the expansion includes insertion of junk repetitive DNA elements into introns. For some strange reason, these authors also avoid using the term "junk DNA" and avoid any mention of the possibility that much of the genome could be nonfunctional. <br /><br />https://doi.org/10.1038/s41477-022-01222-x<br /><br />The bottom line is that there isn't anything to see in the three fern genome sequences to alter the view that genome expansion is due to polyploidy events and transposon-related sequences giving rise to lots of junk DNA. <br /><br />There have been a least a dozen popular science articles about this work but none of them have mentioned junk DNA. Almost all of them treat large genomes as an important mystery that's puzzling scientists.<br />Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51299304350241257212022-09-13T14:41:17.913-04:002022-09-13T14:41:17.913-04:00The state of acceptance of the very-little-junk-DN...The state of acceptance of the very-little-junk-DNA delusion is illustrated by an article in today's New York Times section ScienceTimes. A report by Oliver Whang is called Cracking the Case of the Gient Fern Genome and starts:<br />"Humans, like many complex organisms, have large genomes, which contain the codes for our lives. Want to explain your dark hair, thin bones, and existential dread? Look to your 46 chromosomes and three billion nucleotide base pairs. But those numbers are nothing compared with the genomes of another organism, which contains twice as many base pairs and three times as many chromosomes."<br />He goes on to reveal that this is a Flying Spider Monkey Tree Fern, found in Southeast Asia. (He ignores even more massive genomes in lungfish).<br />Then he continues:<br />"What accounts for, or requires, so much DNA is what Fay-Wei Li, a botanist at the Boyce Thompson Institute calls 'the biggest question in fern genomics'"<br />The rest of the article does not address the question but concerns other ferns that have been found to have similar sized genomes.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35387247315321089822022-09-05T13:31:42.468-04:002022-09-05T13:31:42.468-04:00@Georgi
Yes, but the Kellis et al paper was eight...@Georgi<br /><br />Yes, but the Kellis et al paper was eighteen months later and there had been plenty of time to recognize what had happened in September 2012. <br /><br />The ENCODE leaders could had said in that paper that they disowned the 80% function claim and did not dispute the existence of lots of junk DNA. They didn't say that and I think it's because most of them are very much opposed to junk DNA. <br /><br />Do you agree? Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76865492547937069872022-09-05T13:11:41.529-04:002022-09-05T13:11:41.529-04:00As I said, once something has been given a very pu...As I said, once something has been given a very public platform and lay people see it for the first time, no amount of damage control can help fix things in the short term.<br /><br />We had a lot of those discussions here at the time if you recall.<br /><br />The 80% claim was never discussed by anyone prior to it appearing on September 5th 2012, it just appeared in the 2012 paper, and even then nobody in the know would have paid much attention to it (because they know what stood behind that number) if it wasn't for the media publicity (which again is something that came out of the blue for most).<br /><br />I certainly didn't wake up on that day ten years ago with the expectation that what happened would happen.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48694132325754013172022-09-05T10:04:21.865-04:002022-09-05T10:04:21.865-04:00@Georgi
Many editors on Wikipedia see the Kellis ...@Georgi<br /><br />Many editors on Wikipedia see the Kellis et al. paper as a defense of the ENCODE position. Is that what you thought when you were writing your part of the paper?<br /><br />Did the people in your lab at the time think that they were disproving junk DNA? Did you ever talk about it in group meetings? <br /><br />Where are you now?<br />Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23989358503895224392022-09-05T08:46:18.343-04:002022-09-05T08:46:18.343-04:00Yeah, we knew it was going to happen like that 10 ...Yeah, we knew it was going to happen like that 10 years ago, and here we are.<br /><br />It's the usual pattern -- the first that people here is what most of them remember as ground immutable truth, especially if it is designed to pander to their biases, then the corrections after that nobody pays attention to, and thus the damage is done and becomes very hard to undo.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.com