4 ms·
Omg you fell for that article. Look at those dendrograms carefully. They bias to load up the dendrograms with "degenerate sequences" with very close/obscure a
by dnautics 5y ago
Omg you fell for that article. Look at those dendrograms carefully. They bias to load up the dendrograms with "degenerate sequences" with very close/obscure accession numbers, and basically hide the diversity of viral sequences between the furin-bearing coronaviruses and SARS-CoV-2 (fig 5, which completely omits betacoronaviruses, a clade that contains SARS-CoV-2).
Furin cleavage sites are rare in coronaviruses, and even rarer in the closest ones to SARS-CoV-2. It's the case that there was a research proposal to put a furin cleavage site into bat coronaviruses to fuck around and find out precisely because they are rare in most classes but conspicuous (and possibly related to pathogenicity) in others (https://www.documentcloud.org/documents/21066966-defuse-proposal https://www.documentcloud.org/documents/21066966-defuse-prop...).
(Ps i am also a former molecular biologist that worked in gain of function for non pathogenic bioengineering and I used to look at dendrograms to steal ideas from nature to improve enzyme function -- and I was successful: https://jbioleng.biomedcentral.com/articles/10.1186/1754-1611-7-17 https://jbioleng.biomedcentral.com/articles/10.1186/1754-161...)
Edit: clarified that betacoronaviruses contains SARS-CoV-2, because some armchair analysts don't stop to understand figures
- kevinmchugh 5y agoThis comment would be better without the first sentence.
- PragmaticPulp 5y agoAt minimum, an explanation of how the linked research (which shows that the cleavage sites are indeed common, as the parent comment explained) is somehow wrong. It doesn’t make any sense to insist they aren’t common in response to a paper showing specific examples of them occurring in nearby SARS-CoV-2 ancestors.
- dnautics 5y ago
- PragmaticPulp 5y agoThe point was that the furin cleavage site does appear in other Coronaviruses, and therefore it’s not a random appearance in this one. The specific details of the paper you’re nit-picking aren’t relevant. The sequence either appears elsewhere or it doesn’t, but it clearly appears elsewhere in Coronaviruses. Therefore, comparing the appearance of the sequence in another Coronavirus to random chance is a flawed comparison.
- dnautics 5y agodo you understand that there is no one "the sequence"? At best you could be referring to it as "a furin cleavage site"/"a sequence". Moreover, we know that the specific furin cleavage sequence in the SARS-Cov-2 occurs nowhere else among coronaviruses.
- PragmaticPulp 5y ago> do you understand that there is no one "the sequence"? The linked paper is, literally, about a specific sequence. That’s the paper we’re discussing in this comment section.
- dnautics 5y agoI'm sorry, that is simply not the case, neither at the protein level nor at the DNA level. Furin cleavage sites have diversity. The canonical minimal furin cleavage site sequence is RX(R/K)R, which had a highly variable amino acid and a choice between the two basic amino acids in another position. This variability is sampled across the coronavirus furin cleavage site sequences.
- shadowgovt 5y agoThe next question, to my mind, is "How common is that cleavage site in other viruses, especially other viruses endemic to the origin location of SARS-Cov-2?" With a follow-up of "How possible would it be for multi-virus splicing to generate that sequence from two otherwise-unrelated, possibly damaged sequences ending up head-to-tail in the DNA of a host cell?" We know of other novel viruses that have resulted from sequences of multiple viruses being spliced together in a living host naturally. I don't know how we'd disambiguate that possibility from human synthesis.
- PragmaticPulp 5y ago
- dnautics 5y ago
- dapids 5y ago
- dang 5y agoPlease do not respond to a bad comment by breaking the site guidelines yourself. That only makes everything worse. https://news.ycombinator.com/newsguidelines.html https://news.ycombinator.com/newsguidelines.html
- celticninja 5y agoThat's a lot of pent up anger being thrown around there.
- dang 5y agoPlease do not respond to a bad comment by breaking the site guidelines yourself. That only makes everything worse. Also, we've had to ask you about this kind of thing frequently in the past, and you said you wouldn't do it any more. https://news.ycombinator.com/newsguidelines.html https://news.ycombinator.com/newsguidelines.html
- celticninja 5y agoI felt it was an observation not an attack.
- dang 5y agoI hear you. Personal observations using negative psychological language are likely to come across as attacks no matter what you do, and they're also not particularly substantive, as well as nearly always off topic. Best to avoid. https://hn.algolia.com/?dateRange=all&page=0&prefix=false&sort=byDate&type=comment&query=disambiguate%20burden%20by:dang https://hn.algolia.com/?dateRange=all&page=0&prefix=false&so... https://hn.algolia.com/?sort=byDate&type=comment&dateRange=all&page=0&prefix=false&query=%22internet%20psychiatric%20diagnosis%22 https://hn.algolia.com/?sort=byDate&type=comment&dateRange=a...