8 ms·

I am a molecular biologist but not a virologist. This article is stupid. The furin cleavage site, with almost identical sequences is present in several ancestra

I am a molecular biologist but not a virologist. This article is stupid. The furin cleavage site, with almost identical sequences is present in several ancestral coronaviruses to Sars cov II. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ Serious virologists went over the furin cleavage site in close detail already and none of them seemed very convinced it was anything but natural in 2020. Also, stick any 13 bp dna sequence into BLAST and you will find some strange matches if you include the right databases. That this particular 13 base pairs matches some bit of the human genome (inverted, mind you) is not really that surprising.

loceng 5y ago
So this is the very beginning of an argument. "Serious virologists" isn't proof. Which virologists think it's natural, and which think it's unnatural? Now lets see the data and thorough reasoning by each, and see the rebuttals of each for their opposition's reasoning, etc. Until this is laid out clearly it's all shallow discussion - that no one should blindly trust or believe. The above is the scientific process, method. There clearly isn't consensus yet.
- ajross 5y ago
  > Which virologists think it's natural, and which think it's unnatural? Literally no one, including the authors of this paper, contends the sequence is "unatural".
  - loceng 5y ago
    Are you meaning to say natural or unnatural?
    - dapids 5y ago
      What do you think? Kinda a pedantic response for a spelling mistake.
      - peteradio 5y ago
        Both are 1 letter off from the presumed correct word: unatural + n == correctly spelled unnatural unatural - u == correctly spelled natural How the hell are you supposed to guess as if the context of viral sequencing is somehow easy to parse correctly?
      - loceng 5y ago
        Seriously? Is this the quality of discussion HN is regularly becoming? You want me to make an assumption? Is that how you operate in conversation - assumptions to fill in the gaps when something isn't clear? You realize that their saying "natural" or "unnatural" completely changes what they're saying to the polar opposite, right? So now clarity is pedantic? Seriously? If HN had subreddits there'd be one similar to /r/WatchRedditDie
        IncRnd 5y ago
        It's not an assumption for people who read the article. You'd know what the authors were claiming - natural, unatural, or unnatural.
- yxwvut 5y ago
  There are arguments from improbability in the article that rely on implicit assumptions that are obviously wrong once made explicit, akin to a creationist arguing for the improbability of the human genome's complexity as though it arose like a shuffled deck of cards.
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 ago
  This comment would be better without the first sentence.
  - PragmaticPulp 5y ago
    At 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
      - 5y ago
johndcook 5y ago
Are you suggesting the editors of Frontiers in Virology are not serious virologists?
- Frost1x 5y ago
  Not my domain but I had to search the publisher and journal. Frontiers Media has several editorial related controversies. https://en.m.wikipedia.org/wiki/Frontiers_Media https://en.m.wikipedia.org/wiki/Frontiers_Media The fact is that the state of research, peer review, and publication in academia is in complete shambles, in my professional opinion. The amount of system gaming in research has lead me to question most publications and claims I see anymore, unfortunately. I know the system, many of pressures / incentives, and I know a lot of the games played to optimize around these. It's impossible to be any bit lazy and give into any semblance of authoritative findings anymore unless you too just want to play the publication ranking game to stay afloat or get ahead in your career. We need a massive overhaul of research culture in the US, IMHO.
  - paulnpace 5y ago
    Wikipedia has never been a source. It is demeaning to pretend it is one, and naive to believe it is a neutral aggregator.
    - IncRnd 5y ago
      Don't throw the baby out with the bathwater. While Wikipedia has never been a source, the particular linked wiki page clearly links to multiple controversies in the footnotes. Take a look starting at [37] https://en.m.wikipedia.org/wiki/Frontiers_Media#cite_note-37 https://en.m.wikipedia.org/wiki/Frontiers_Media#cite_note-37
      - paulnpace 5y ago
        When it comes to heavily manipulated "sources" like Wikipedia, I "throw the baby out with the bathwater" (yet another lazy attempt at reasoning is to use phrases like that as justification for, well, anything) is because you cannot see what is not presented in the article, usually in the form of others who will contradict the claims of whatever criticism the page is presenting with equal or stronger sources. Wikipedia guards such open discussion with a lot of dirty tactics which include collusion between article guardians and admins who will have your account locked and IP address blocked from editing in less than one hour of a "violation", and they do not notify you through email of their activities so you have to go discovering what they are doing through their Kafkaesque procedures of adjudication which are decided without any defense from the accused and evidence that doesn't truly qualify as evidence based on any reasonable standard for evidence. A relatively newer policy implemented through their MediaWiki project is a "feature" whereby an edit can be permanently hidden from view, so future editors cannot go back and see what edits were removed or reverted. This goes completely against the original concept of a wiki and bolsters my claims that Wikipedia should never be used as a source because in the most contentious articles they will hide removed edits containing information they don't like. The result of this is editors who have contradicting opinions from the Wikipedia-approved opinion will stop editing simply because it isn't worth the effort as Wikipedia always wins (because it is Wikipedia's website). Wikipedia is a dumpster fire full of bias, pettiness, and structured manipulation. Linking there or using those pages demonstrates laziness and a near complete lack of higher reasoning.
lettergram 5y ago
> Serious virologists went over the furin cleavage site in close detail already and none of them seemed very convinced it was anything but natural in 2020. https://www.projectveritas.com/news/military-documents-about-gain-of-function-contradict-fauci-testimony-under/ https://www.projectveritas.com/news/military-documents-about... DoD analysts letter: https://assets.ctfassets.net/syq3snmxclc9/2mVob3c1aDd8CNvVnyei6n/95af7dbfd2958d4c2b8494048b4889b5/JAG_Docs_pt1_Og_WATERMARK_OVER_Redacted.pdf https://assets.ctfassets.net/syq3snmxclc9/2mVob3c1aDd8CNvVny...
deleted 5y ago
[deleted]
moralestapia 5y ago
>This article is stupid. Whoa, that says a lot about what kind of scientist you are ... I have a published paper under the "Frontiers in" brand and can assure you that the people behind it (staff and editors) are among the most professional in what they do. "Frontiers in" does not publish fringe science, they are quite rigorous in their process. Also the paper is written by quite reputable people and backed by several institutions. If their claims were "stupid" (as you arrogantly put it) they would have spotted it before you, trust me.
- flobosg 5y ago
  There have been some controversies though: https://en.wikipedia.org/wiki/Frontiers_Media#Controversies https://en.wikipedia.org/wiki/Frontiers_Media#Controversies
  - moralestapia 5y ago
    They seem to have 123 retractions across their whole editorial offer. http://retractiondatabase.org/RetractionSearch.aspx#?jou%3dfrontiers%2bin http://retractiondatabase.org/RetractionSearch.aspx#?jou%3df... That's actually quite a good record for a publisher with 80 or so journals and ~270,000 published papers. Edit: you're right @flobosg, I was looking at another comment with a similar username and my mind just squashed them together :P.
    - flobosg 5y ago
      > I know you stated somewhere else that this is not your domain You are confusing me with someone else.
  - paulnpace 5y ago
    Anyone taking a discipline seriously would never link to Wikipedia, with the exception of when Wikipedia, itself, is topical. It is usually a sign of laziness and weak positions on the part of the person linking to the article.
    - deleted 5y ago
PragmaticPulp 5y ago
> I am a molecular biologist but not a virologist. This article is stupid. The furin cleavage site, with almost identical sequences is present in several ancestral coronaviruses to Sars cov II. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ It seems the presence of the furin cleavage site in any other Coronavirus would be enough to invalidate this paper’s comparison to pure random chance. Why would the authors misuse statistics comparing this to random chance when there are published examples of the furin cleavage site appearing elsewhere? It doesn’t make any sense.
- ImaCake 5y ago
  Yes, possible DNA sequences do not occur with equal frequencies. The whole point of selection pressure is that it selects for specific sequences. The same sequence occurring in a host species and a parasite is also not surprising. Rare events could result in horizontal transfer of genetics between host and parasite. Such things have been documented before.

loceng 5y ago

So this is the very beginning of an argument. "Serious virologists" isn't proof. Which virologists think it's natural, and which think it's unnatural? Now lets see the data and thorough reasoning by each, and see the rebuttals of each for their opposition's reasoning, etc. Until this is laid out clearly it's all shallow discussion - that no one should blindly trust or believe. The above is the scientific process, method. There clearly isn't consensus yet.

ajross 5y ago
> Which virologists think it's natural, and which think it's unnatural? Literally no one, including the authors of this paper, contends the sequence is "unatural".
- loceng 5y ago
  Are you meaning to say natural or unnatural?
  - dapids 5y ago
    What do you think? Kinda a pedantic response for a spelling mistake.
    - peteradio 5y ago
      Both are 1 letter off from the presumed correct word: unatural + n == correctly spelled unnatural unatural - u == correctly spelled natural How the hell are you supposed to guess as if the context of viral sequencing is somehow easy to parse correctly?
    - loceng 5y ago
      Seriously? Is this the quality of discussion HN is regularly becoming? You want me to make an assumption? Is that how you operate in conversation - assumptions to fill in the gaps when something isn't clear? You realize that their saying "natural" or "unnatural" completely changes what they're saying to the polar opposite, right? So now clarity is pedantic? Seriously? If HN had subreddits there'd be one similar to /r/WatchRedditDie
      - IncRnd 5y ago
        It's not an assumption for people who read the article. You'd know what the authors were claiming - natural, unatural, or unnatural.
yxwvut 5y ago
There are arguments from improbability in the article that rely on implicit assumptions that are obviously wrong once made explicit, akin to a creationist arguing for the improbability of the human genome's complexity as though it arose like a shuffled deck of cards.

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 ago
This comment would be better without the first sentence.
- PragmaticPulp 5y ago
  At 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
    - 5y ago

johndcook 5y ago

Are you suggesting the editors of Frontiers in Virology are not serious virologists?

Frost1x 5y ago
Not my domain but I had to search the publisher and journal. Frontiers Media has several editorial related controversies. https://en.m.wikipedia.org/wiki/Frontiers_Media https://en.m.wikipedia.org/wiki/Frontiers_Media The fact is that the state of research, peer review, and publication in academia is in complete shambles, in my professional opinion. The amount of system gaming in research has lead me to question most publications and claims I see anymore, unfortunately. I know the system, many of pressures / incentives, and I know a lot of the games played to optimize around these. It's impossible to be any bit lazy and give into any semblance of authoritative findings anymore unless you too just want to play the publication ranking game to stay afloat or get ahead in your career. We need a massive overhaul of research culture in the US, IMHO.
- paulnpace 5y ago
  Wikipedia has never been a source. It is demeaning to pretend it is one, and naive to believe it is a neutral aggregator.
  - IncRnd 5y ago
    Don't throw the baby out with the bathwater. While Wikipedia has never been a source, the particular linked wiki page clearly links to multiple controversies in the footnotes. Take a look starting at [37] https://en.m.wikipedia.org/wiki/Frontiers_Media#cite_note-37 https://en.m.wikipedia.org/wiki/Frontiers_Media#cite_note-37
    - paulnpace 5y ago
      When it comes to heavily manipulated "sources" like Wikipedia, I "throw the baby out with the bathwater" (yet another lazy attempt at reasoning is to use phrases like that as justification for, well, anything) is because you cannot see what is not presented in the article, usually in the form of others who will contradict the claims of whatever criticism the page is presenting with equal or stronger sources. Wikipedia guards such open discussion with a lot of dirty tactics which include collusion between article guardians and admins who will have your account locked and IP address blocked from editing in less than one hour of a "violation", and they do not notify you through email of their activities so you have to go discovering what they are doing through their Kafkaesque procedures of adjudication which are decided without any defense from the accused and evidence that doesn't truly qualify as evidence based on any reasonable standard for evidence. A relatively newer policy implemented through their MediaWiki project is a "feature" whereby an edit can be permanently hidden from view, so future editors cannot go back and see what edits were removed or reverted. This goes completely against the original concept of a wiki and bolsters my claims that Wikipedia should never be used as a source because in the most contentious articles they will hide removed edits containing information they don't like. The result of this is editors who have contradicting opinions from the Wikipedia-approved opinion will stop editing simply because it isn't worth the effort as Wikipedia always wins (because it is Wikipedia's website). Wikipedia is a dumpster fire full of bias, pettiness, and structured manipulation. Linking there or using those pages demonstrates laziness and a near complete lack of higher reasoning.

lettergram 5y ago

> Serious virologists went over the furin cleavage site in close detail already and none of them seemed very convinced it was anything but natural in 2020. https://www.projectveritas.com/news/military-documents-about-gain-of-function-contradict-fauci-testimony-under/ https://www.projectveritas.com/news/military-documents-about... DoD analysts letter: https://assets.ctfassets.net/syq3snmxclc9/2mVob3c1aDd8CNvVnyei6n/95af7dbfd2958d4c2b8494048b4889b5/JAG_Docs_pt1_Og_WATERMARK_OVER_Redacted.pdf https://assets.ctfassets.net/syq3snmxclc9/2mVob3c1aDd8CNvVny...

deleted 5y ago

[deleted]

moralestapia 5y ago

>This article is stupid. Whoa, that says a lot about what kind of scientist you are ... I have a published paper under the "Frontiers in" brand and can assure you that the people behind it (staff and editors) are among the most professional in what they do. "Frontiers in" does not publish fringe science, they are quite rigorous in their process. Also the paper is written by quite reputable people and backed by several institutions. If their claims were "stupid" (as you arrogantly put it) they would have spotted it before you, trust me.

flobosg 5y ago
There have been some controversies though: https://en.wikipedia.org/wiki/Frontiers_Media#Controversies https://en.wikipedia.org/wiki/Frontiers_Media#Controversies
- moralestapia 5y ago
  They seem to have 123 retractions across their whole editorial offer. http://retractiondatabase.org/RetractionSearch.aspx#?jou%3dfrontiers%2bin http://retractiondatabase.org/RetractionSearch.aspx#?jou%3df... That's actually quite a good record for a publisher with 80 or so journals and ~270,000 published papers. Edit: you're right @flobosg, I was looking at another comment with a similar username and my mind just squashed them together :P.
  - flobosg 5y ago
    > I know you stated somewhere else that this is not your domain You are confusing me with someone else.
- paulnpace 5y ago
  Anyone taking a discipline seriously would never link to Wikipedia, with the exception of when Wikipedia, itself, is topical. It is usually a sign of laziness and weak positions on the part of the person linking to the article.
  - deleted 5y ago

PragmaticPulp 5y ago

> I am a molecular biologist but not a virologist. This article is stupid. The furin cleavage site, with almost identical sequences is present in several ancestral coronaviruses to Sars cov II. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ It seems the presence of the furin cleavage site in any other Coronavirus would be enough to invalidate this paper’s comparison to pure random chance. Why would the authors misuse statistics comparing this to random chance when there are published examples of the furin cleavage site appearing elsewhere? It doesn’t make any sense.

ImaCake 5y ago
Yes, possible DNA sequences do not occur with equal frequencies. The whole point of selection pressure is that it selects for specific sequences. The same sequence occurring in a host species and a parasite is also not surprising. Rare events could result in horizontal transfer of genetics between host and parasite. Such things have been documented before.