Unusual Features of SARS-CoV-2 Genome Suggests Sophisticated Lab Modifications(zenodo.org)
zenodo.org
Unusual Features of SARS-CoV-2 Genome Suggests Sophisticated Lab Modifications
https://zenodo.org/record/4028830#.X195knUzZhG
26 comments
> ...this is candid scientific study and discussion of upmost importance.
Maybe it is not. Lots of discussions & discourses are going on in another thread actually: https://news.ycombinator.com/item?id=24476300
As a Chinese myself I appreciate this paper and the bravery of Yan putting herself in the spotlight in the name of science for this somewhat controversial claim with geopolitical implications. I'm no virologist so I can't comment on the claims that the sequence blast indicates the Orf8 protein of ZC45/ZXC21 share 94.2% identity with SARS-CoV-2 Orf8, and that no coronaviruses (discovered so far) share more than 58% identity with SARS-CoV-2 on this protein, etc, as well as the significant of these claims in supporting their thesis.
But after reading myriads of comments on HN and skimming through the paper a few more times, I have to admit the paper itself is not particularly interesting. It may even appear to some as a poorly written scientific paper, or in the words of djaque's, "a political hit piece cosplaying as a scientific article".
And now I find this whole thing much more intriguing from a meta perspective i.e. reading and making sense of people's reactions to the paper, their comments, perspectives, etc.
Maybe it is not. Lots of discussions & discourses are going on in another thread actually: https://news.ycombinator.com/item?id=24476300
As a Chinese myself I appreciate this paper and the bravery of Yan putting herself in the spotlight in the name of science for this somewhat controversial claim with geopolitical implications. I'm no virologist so I can't comment on the claims that the sequence blast indicates the Orf8 protein of ZC45/ZXC21 share 94.2% identity with SARS-CoV-2 Orf8, and that no coronaviruses (discovered so far) share more than 58% identity with SARS-CoV-2 on this protein, etc, as well as the significant of these claims in supporting their thesis.
But after reading myriads of comments on HN and skimming through the paper a few more times, I have to admit the paper itself is not particularly interesting. It may even appear to some as a poorly written scientific paper, or in the words of djaque's, "a political hit piece cosplaying as a scientific article".
And now I find this whole thing much more intriguing from a meta perspective i.e. reading and making sense of people's reactions to the paper, their comments, perspectives, etc.
oh, thanks. That post is also flagged.
HN community are extremely liberal. When they see Steve Bannon name, they automatically reject the paper. I wouldn't trust the comments, even if they claim they are subject experts here.
HN community are extremely liberal. When they see Steve Bannon name, they automatically reject the paper. I wouldn't trust the comments, even if they claim they are subject experts here.
I think what's interesting is the tone of the paper, and how people react to it differently.
It has occured to me in written Chinese, sentiments often get easily "embedded" in words v.s. in English. (i.e. perhaps a feature of logographic languages?) English expressions on the other hand are easier to stay "neutral".
When I first read the paper I actually found the articulation to have a "neutral" tone to it. But after knowing that it is afflicted with Bannon and realising that the paper implies of all scientists & researchers in the world, only those backed by an anti-CCP advocacy organization, are willing to do serious research to expose the cover-up (assuming there is one!), the words in the article now gives off an odd vibe. It is now a partisan piece.
It has occured to me in written Chinese, sentiments often get easily "embedded" in words v.s. in English. (i.e. perhaps a feature of logographic languages?) English expressions on the other hand are easier to stay "neutral".
When I first read the paper I actually found the articulation to have a "neutral" tone to it. But after knowing that it is afflicted with Bannon and realising that the paper implies of all scientists & researchers in the world, only those backed by an anti-CCP advocacy organization, are willing to do serious research to expose the cover-up (assuming there is one!), the words in the article now gives off an odd vibe. It is now a partisan piece.
I didn't notice the tone, but there must be some of it. I think the author tried their best to sound neutral but if they strongly believe what they believed it, it's unavoidable for letting personal opinion slip in. I once asked one of the author - nerdhaspower, to remove such words as "中共" from his site because they show confirmation bias. He refused. But in this paper, they did a much better job.
I don't believe the paper implied what you said. The first reference for example, also a well-written paper, is from a Harvard researcher, who has nothing to do with the organization.
I don't believe the paper implied what you said. The first reference for example, also a well-written paper, is from a Harvard researcher, who has nothing to do with the organization.
In the beginning some said that there was a bioresearch facility in Wuhan. But there is always secrets around these things.
There's a bioresearch facility in almost every city with a population over a few million people; it would be quite a surprise if there weren't one in Wuhan.
Yes, but in my understanding, it's in the top 2 research facilities in the world in Coronaviruses. It's the only BSL-4 level lab in China. According to their publications from January, they discovered the two Coronaviruses that were the closest to SARS-CoV-2. WIV is not an average bioresearch laboratory from the standpoint of the pandemic.
there are several there, specifically there because they're used to study cornoavirus in bats because bats seem to have so many of them. you setup base where your source is, that's just logic.
None of that means it was ENGINEERED there.
None of that means it was ENGINEERED there.
Actually the bats they suspect of carrying this virus aren’t from nearby.
The paper was published by four authors at "Rule of Law Society & Rule of Law Foundation". So I looked it up and found this: https://www.rolsociety.org/
Is the paper true? I am not qualified to pass judgement, but I'm not naive enough to see Steve Bannon is behind it and suspect this might be motivated by politics more than science.
Is the paper true? I am not qualified to pass judgement, but I'm not naive enough to see Steve Bannon is behind it and suspect this might be motivated by politics more than science.
Some observations:
- This is a paper published by members of an anti-China advocacy organization.
- It advocates actions against China in its abstract ("Our work emphasizes the need for an independent investigation into the relevant research laboratories")
- It includes a number of conspiratorial-sounding speculations ("However, this template virus ideally should not be one from Dr. Zengli Shi’s collections, considering that she is widely known to have been engaged in gain-of-function studies on coronaviruses. Therefore, . . . novel bat coronaviruses discovered and owned by military laboratories, would be suitable . . .")
- Some of its citations appear suspect. For example, it cites a previous study for the idea that certain variants were "discovered and owned by military laboratories," but the cited study says nothing like that.
- It criticizes "peer-reviewed" journals for rejecting its theories
- It is in a highly-technical subject area that is difficult for lay people to understand
In short, to me this looks like a piece of advocacy, not science.
That's not to say that it might not also be right. But personally I would trust mainstream scientists publishing in established journals. Those scientists--as the paper itself notes--have so far not adopted this idea.
- This is a paper published by members of an anti-China advocacy organization.
- It advocates actions against China in its abstract ("Our work emphasizes the need for an independent investigation into the relevant research laboratories")
- It includes a number of conspiratorial-sounding speculations ("However, this template virus ideally should not be one from Dr. Zengli Shi’s collections, considering that she is widely known to have been engaged in gain-of-function studies on coronaviruses. Therefore, . . . novel bat coronaviruses discovered and owned by military laboratories, would be suitable . . .")
- Some of its citations appear suspect. For example, it cites a previous study for the idea that certain variants were "discovered and owned by military laboratories," but the cited study says nothing like that.
- It criticizes "peer-reviewed" journals for rejecting its theories
- It is in a highly-technical subject area that is difficult for lay people to understand
In short, to me this looks like a piece of advocacy, not science.
That's not to say that it might not also be right. But personally I would trust mainstream scientists publishing in established journals. Those scientists--as the paper itself notes--have so far not adopted this idea.
Trusting the "mainstream" and the "establishment" is historically a poor bet when it comes to science that is controversial by nature.
Consider what a humanist scientist would want to believe to be true:
- Nature bestowed yet another pathogen upon humanity
or
- Science caused an accident that killed a million people
Even if it was a lab accident, it would be difficult to blame the whole of China for it. More likely, scientific work itself would be blamed, which could eradicate entire lines of research, threatening the livelihood and reputation of many scientists and lab workers.
Though I am skeptical, I myself would like to believe the first scenario to be true. I might even be inclined to believe that misleading the public on it is the right thing to do, all potential consequences considered.
Consider what a humanist scientist would want to believe to be true:
- Nature bestowed yet another pathogen upon humanity
or
- Science caused an accident that killed a million people
Even if it was a lab accident, it would be difficult to blame the whole of China for it. More likely, scientific work itself would be blamed, which could eradicate entire lines of research, threatening the livelihood and reputation of many scientists and lab workers.
Though I am skeptical, I myself would like to believe the first scenario to be true. I might even be inclined to believe that misleading the public on it is the right thing to do, all potential consequences considered.
The lead author is a Chinese MD/PhD trained in China who worked in a public health lab at Hong Kong University and has verifiable publication history. Based on a cursory reading it seems that all of the claims in the paper are based upon publicly-available research (over 100 citations) so there is no reason these claims cannot be evaluated through peer review.
The "Rule of Law Foundation", who sponsored this paper, was established by Guo Wengui. https://en.wikipedia.org/wiki/Guo_Wengui
https://foreignpolicy.com/2020/08/26/guo-wengui-chinese-bill...
Personally, after reading a lot about the virus, I think there's a good chance that it has an artificial source. I'm very wary about this paper though, both because I can't fully understand all of the arguments, and because it comes from a political, rather than academic institution, and because it's being pushed by groups and people that obviously have no idea whether or not it's scientifically valid or not, but they like the conclusion.
(I put this comment on all duplicates of this post)
I posted what appears to be the top comment on the previous submission of a similar paper describing the probable laboratory origins of SARS-CoV-2 (https://news.ycombinator.com/item?id=23875758), so I'll try and do another quick summary here. (Caveat: I have no particular expertise in this area, I just read a lot of scientific research)
The lead author here is an immunologist who, unlike the authors of prior papers alleging laboratory origin, is Chinese and was trained in Chinese institutions. At the time of the outbreak Dr. Li-Meng Yan was working in a public health lab at Hong Kong University and was asked to investigate. She claims that she fled to the US after realizing that there was a cover-up going on and she knew too much already.
The most striking and novel claim made here is that the bat coronavirus RaTG13, which is a 96% genetic match to the novel coronarivus, is a total fabrication. This argument is based upon a few key observations:
1. RaTG13 was supposedly discovered in 2013 but not publicly reported until after the outbreak already started, in a paper (published by researchers closely affiliated with the WIV) that claimed it as evidence SARS-CoV-2 likely originated from bats.
2. A number of independent preprint papers raise significant concerns about the veracity of RaTG13, and one published paper indicates that the RaTG13 spike protein is actually ineffective at binding to ACE2 receptors in horseshoe bats (the supposed reservoir).
3. After excluding RaTG13, the next closest relatives are two bat coronaviruses (ZC45/ZXC21) that were discovered and characterized by Chinese military research labs. A Chinese lab published research near the start of the outbreak which identified these viruses as the closest relatives, and that same lab was apparently closed for "rectification" shortly thereafter.
The paper goes on under the assumption that ZC45 or ZXC21 was the backbone for engineering the SARS-CoV-2 virus, noting how the particular characteristics of the genomic match (100% E protein, 94% Orf8 protein) align with what one would expect after the gain-of-function modifications that produced the unusual RBM and furin cleavage site which were also identified in the Sørensen paper. This paper goes into much more detail on those two points, and provides counterfactuals to describe how unlikely these observations would be in a naturally-evolved virus.
In the second half of the paper the authors describe in detail how a lab with sufficient technical acumen could engineer a virus like SARS-CoV-2 through a sequence of well-defined steps, with references to published research demonstrating these capabilities. Then they postulate the exact components involved in engineering the actual SARS-CoV-2, along with a projected timeline of six months for the whole process.
I posted what appears to be the top comment on the previous submission of a similar paper describing the probable laboratory origins of SARS-CoV-2 (https://news.ycombinator.com/item?id=23875758), so I'll try and do another quick summary here. (Caveat: I have no particular expertise in this area, I just read a lot of scientific research)
The lead author here is an immunologist who, unlike the authors of prior papers alleging laboratory origin, is Chinese and was trained in Chinese institutions. At the time of the outbreak Dr. Li-Meng Yan was working in a public health lab at Hong Kong University and was asked to investigate. She claims that she fled to the US after realizing that there was a cover-up going on and she knew too much already.
The most striking and novel claim made here is that the bat coronavirus RaTG13, which is a 96% genetic match to the novel coronarivus, is a total fabrication. This argument is based upon a few key observations:
1. RaTG13 was supposedly discovered in 2013 but not publicly reported until after the outbreak already started, in a paper (published by researchers closely affiliated with the WIV) that claimed it as evidence SARS-CoV-2 likely originated from bats.
2. A number of independent preprint papers raise significant concerns about the veracity of RaTG13, and one published paper indicates that the RaTG13 spike protein is actually ineffective at binding to ACE2 receptors in horseshoe bats (the supposed reservoir).
3. After excluding RaTG13, the next closest relatives are two bat coronaviruses (ZC45/ZXC21) that were discovered and characterized by Chinese military research labs. A Chinese lab published research near the start of the outbreak which identified these viruses as the closest relatives, and that same lab was apparently closed for "rectification" shortly thereafter.
The paper goes on under the assumption that ZC45 or ZXC21 was the backbone for engineering the SARS-CoV-2 virus, noting how the particular characteristics of the genomic match (100% E protein, 94% Orf8 protein) align with what one would expect after the gain-of-function modifications that produced the unusual RBM and furin cleavage site which were also identified in the Sørensen paper. This paper goes into much more detail on those two points, and provides counterfactuals to describe how unlikely these observations would be in a naturally-evolved virus.
In the second half of the paper the authors describe in detail how a lab with sufficient technical acumen could engineer a virus like SARS-CoV-2 through a sequence of well-defined steps, with references to published research demonstrating these capabilities. Then they postulate the exact components involved in engineering the actual SARS-CoV-2, along with a projected timeline of six months for the whole process.
Let’s weigh the probabilities. Event A: no journal in the world (including the myriad of tiny ones all over the place) is willing to honestly peer review an article about artificial origins of the virus. Event B: the authors know the article to be incorrect and unlikely to pass a fair review. Event A assumes a vast conspiracy incolving effectively all virologists in the world. Event B assumes the authors simply being human.
It’s not exactly a conspiracy because it doesn’t require coordination.
The idea is that if Covid came from a lab, it will make the field of virology as a whole look bad, because it implies studying viruses actually makes us less safe.
It can also be explained by respect of your colleagues - to accuse them of lying may hurt your career even if tue.
I’m not defending this paper - it raises too many red flags - but it’s easy to see why such theories are likely to come from outside the field.
The idea is that if Covid came from a lab, it will make the field of virology as a whole look bad, because it implies studying viruses actually makes us less safe.
It can also be explained by respect of your colleagues - to accuse them of lying may hurt your career even if tue.
I’m not defending this paper - it raises too many red flags - but it’s easy to see why such theories are likely to come from outside the field.
As if journals weren't the most pretentious and most political thing ever.
All the authors of this paper are from the "rule of law society," which features Steve Bannon on their home page.
This is a scientific paper written by 4 Ph.D's. It uses "rule of law society" as affiliation because this is the organization that helped the main author Dr. Yan escape from Hongkong. Dr. Yan has published in Nature, Lancet, Virology as first authors. The 3 other authors don't want to list their real affiliations because they want to remain anonymous. One of them is a professor at a US University. The other two are accomplished scientist in their own fields.
This is not conspiracy theory, this is candid scientific study and discussion of upmost importance.
Why is this buried?