tag:blogger.com,1999:blog-37148773.post1538901905143710472..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The 20th anniversary of the human genome sequence: 6. Nature doubles down on ENCODE resultsLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-37148773.post-42342649559178996262021-02-23T11:29:16.320-05:002021-02-23T11:29:16.320-05:00For a different perspective there's this:
The...For a different perspective there's this: <br />The ambivalent role of water at the origins of life<br />https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.13815<br />Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88080709232647416622021-02-22T11:04:18.948-05:002021-02-22T11:04:18.948-05:00Hello Larry, thanks for the neat post. Nice call. ...Hello Larry, thanks for the neat post. Nice call. <br /><br />I was wondering if you have also seen this?<br /><br />"The water paradox and the origins of life"<br />https://media.nature.com/original/magazine-assets/d41586-020-03461-4/d41586-020-03461-4.pdf<br /><br />It seems to argue in favour of a land-based "warm little pond" as the likely origin of life since water has a tendency to break the bonds in nucleotide- and amino acid polymers. So life must have started where water was limited. There is a need for "wet-dry cycles". Thus life did nnot in the ocean, but on land were water was only present intermittently. <br /><br />I don't particularly buy such "soup" hypotheses for the origin of life. I lean more towards of deep sea alkaline hydrothermal vents, as this seems way more thermodynamically plausible. From reading some of your old posts, I know you have a similar position. Do you have anything to say about this article? I think porous hydrothermal vents could potentially allow for the same conditions that allow polymers to persist and not breakdown, so water doesn't need to be absent (intermittently) all together. But I am not sure. What are your thoughts on this?Nesslig20https://www.blogger.com/profile/00209192071601766693noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61806738694026319912021-02-17T10:49:24.135-05:002021-02-17T10:49:24.135-05:00Oh, I have no clue where the figure of 130,629 com...Oh, I have no clue where the figure of 130,629 comes from. I was just pointing out that RNA genes, spurious or not, are not the only possible "elements".John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42206420074938941572021-02-17T07:59:13.834-05:002021-02-17T07:59:13.834-05:00Yes, but they claim in their supplements that they...Yes, but they claim in their supplements that they have identified >800k enhancers and >58k promoters. Apparently, (according to their supplemental data) not a single enhancer had been discovered before 2001. <br /><br />After this, I thought maybe they exclude enhancers but do count ncRNAs? But they never really list how many lncRNAs they think there are. (Apparently, they list 9.6k lncRNAs that have SNPs that associate with disease.)<br /><br />These non-nonsensical statements do not inspire much confidence.<br /><br />You can go see for yourself: https://media.nature.com/original/magazine-assets/d41586-021-00314-6/18835258apalazzohttps://www.blogger.com/profile/06077383161556651420noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64442438399639069182021-02-16T22:56:41.742-05:002021-02-16T22:56:41.742-05:00I think you may be missing some of those "ele...I think you may be missing some of those "elements" when you equate them with transcribed RNAs. That leaves out a large class of non-transcribed regulatory sequences (bonus! they actually do exist and are functional!), i.e. non-spurious transcription factor binding sites. Of course they are all very short and so comprise a negligible fraction of the genome. But they do add up if you're just counting "elements".John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1858845955359639452021-02-16T16:23:22.439-05:002021-02-16T16:23:22.439-05:00I sent an email message to all four authors asking...I sent an email message to all four authors asking them to explain what they mean by "not junk" and what they mean by 130,629 genomic elements. <br /><br />Note that one of the authors (Kellis) was the lead author on the 2014 "retraction" paper and he argued at that time that the original ENCODE paper was misunderstood.<br /><br />"Kellis says that ENCODE isn't backing away from anything. The 80% claim, he says, was misunderstood and misreported. Roughly that proportion of the genome might be biochemically active, he explains, but some of that activity is undoubtedly meaningless, leaving unanswered the question of how much of it is really 'functional'."<br /><br />https://sandwalk.blogspot.com/2014/05/how-does-nature-deal-with-encode.html Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80596262215823011742021-02-16T14:35:22.705-05:002021-02-16T14:35:22.705-05:00I tried to figure out what exactly they mean by &q...I tried to figure out what exactly they mean by "130,629 non-coding elements" and digging into the supplemental data, it all looks like random numbers to me. Such a lack of rigor is sad.apalazzohttps://www.blogger.com/profile/06077383161556651420noreply@blogger.com