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Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

biorxiv.org

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Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#131

Post by lamontcg »

mikeyouse wrote: post #130
lamontcg wrote: post #128

Earlier quoted context omitted.

Here's another blue check immunologist on twitter with a substantially different take: https://twitter.com/K_G_Andersen/status/1583252866394771456

The authors of this paper are confused about the technology they're using... it's not a good sign about their conclusions.. https://twitter.com/matias_kaplan/status/1583235087067336704 https://twitter.com/NoahOlsman/status/1583275862442807299

Oh dear... Yeah, the author affiliations on the title paper made me wonder if they knew what they were doing at all.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#132

Post by VagueMag »

Fomite wrote: post #104
guelo wrote: post #66

I've seen several papers with the opposite conclusion. Why do we only see the lab leak hypothesis front paged on HN?

To my mind, there are a few reasons: 1) It makes the pandemic deterministic (bad lab security means an outbreak) instead of stochastic (wildlife spillover). That is, to be frank, even as an epidemiologist who is very skeptical of the lab leak hypothesis, a comforting thought. 2) It's a popular topic in the Substack/Medium set, because it moves the pandemic back into their wheelhouse of expertise, international relati…

> That is, to be frank, even as an epidemiologist who is very skeptical of the lab leak hypothesis, a comforting thought.

Yes, much more comforting to believe that the virus originated in a lab, that a successful (so far) conspiracy has been carried out to conceal its origins, and that there will be no transparency or accountability for any of the people involved, who are likely continuing similar research today.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#133

Post by jhanschoo »

tiagod wrote: post #112
timr wrote: post #81

Earlier quoted context omitted.

> First and foremost the central claim is that 5 potential restriction binding sites versus 2 means that SARS-CoV2 is non natural. That does not necessarily follow. Just as SARS-CoV2 is unusually infectious and damaging to humans it could just happen to have an additional 3 restriction binding sites. So there is nothing inconsistent with natural selection of viral characteristics, only a comparison between wild and l…

We've seen horizontal gene transfer in fish, was it aliens or natural selection? Extremely unlikely events happen when an extreme amount of attempts are made, and natural selection amplifies them if they increase fitness

Your reply after reading the explanation is like you seeing a farm of branded cows and wondering if it was due to extreme natural selection that caused that.

From the layperson article:

> In wild viruses, these cutting/pasting sites are randomly distributed because there's no evolutionary pressure for the virus to be thusly cut and pasted in nature. In infectious clones, however, the humans behind the screen tend to modify restriction sites in a regular way. For any given restriction enzyme or set of enzymes, the set of all cutting sites is called the “restriction map”, and looking at these restriction maps helps us see the fingerprint of infectious clones.

> It turns out, the sticky ends produced by BsaI/BsmBI digestion of SARS-CoV-2 are all unique, non-palindromic, and all contain at least one A or T - all criteria either required or recommended for in vitro genome assembly.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#134

Post by Fomite »

layer8 wrote: post #110
Fomite wrote: post #104

Earlier quoted context omitted.

To my mind, there are a few reasons: 1) It makes the pandemic deterministic (bad lab security means an outbreak) instead of stochastic (wildlife spillover). That is, to be frank, even as an epidemiologist who is very skeptical of the lab leak hypothesis, a comforting thought. 2) It's a popular topic in the Substack/Medium set, because it moves the pandemic back into their wheelhouse of expertise, international relati…

> It makes the pandemic deterministic (bad lab security means an outbreak) instead of stochastic "Bad lab security means an outbreak" is also stochastic though?

Not in the same way - it is admittedly still stochastic, but the product of conscious though, decisions, etc. that have very obvious bad actors and process improvements. So semi-deterministic might be a fairer way to put it. But at the very least, "Stochastic with a much, much smaller threat surface".

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#135

Post by Fomite »

VagueMag wrote: post #132
Fomite wrote: post #104

Earlier quoted context omitted.

To my mind, there are a few reasons: 1) It makes the pandemic deterministic (bad lab security means an outbreak) instead of stochastic (wildlife spillover). That is, to be frank, even as an epidemiologist who is very skeptical of the lab leak hypothesis, a comforting thought. 2) It's a popular topic in the Substack/Medium set, because it moves the pandemic back into their wheelhouse of expertise, international relati…

> That is, to be frank, even as an epidemiologist who is very skeptical of the lab leak hypothesis, a comforting thought. Yes, much more comforting to believe that the virus originated in a lab, that a successful (so far) conspiracy has been carried out to conceal its origins, and that there will be no transparency or accountability for any of the people involved, who are likely continuing similar research today.

There have been a huge number of knock on ramifications in the field to the idea that the lab leak hypothesis might be true already.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#136

Post by entwife »

jalino23 wrote: post #13

do I understand this correctly? that the paper is saying that covid 19 is highly likely a synthetic virus?

On October 18, these three scientists presented an argument with evidence that Covid-19 was created in a laboratory. Their paper has not been peer reviewed, and it is self-published. The discussion here has a couple of counter-arguments. Non-experts would do well to wait for peer review before accepting these arguments.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#137

Post by Fomite »

rossdavidh wrote: post #129

The opening line: "To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident." Is that true? I mean I understand why people would be curious, but does it really matter, in terms of what we need to do? We know that viruses _can_ spillover from animals to people, and we know that viruses in a laboratory setting…

I think you have a reasonable point here.

I saw Marc Lipsitch give a talk with a back-of-napkin "Expected mortality from gain of function research" estimate in...I want to say 2013.

We know there's zoonotic spillover events of a number of scary pathogens, including the last two epidemic coronaviruses.

In a global sense of preventing future pandemics, an either/or framing is immensely flawed.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#138

Post by VagueMag »

Fomite wrote: post #135
VagueMag wrote: post #132

Earlier quoted context omitted.

> That is, to be frank, even as an epidemiologist who is very skeptical of the lab leak hypothesis, a comforting thought. Yes, much more comforting to believe that the virus originated in a lab, that a successful (so far) conspiracy has been carried out to conceal its origins, and that there will be no transparency or accountability for any of the people involved, who are likely continuing similar research today.

There have been a huge number of knock on ramifications in the field to the idea that the lab leak hypothesis might be true already.

You're talking about the field of above-board academic research. Academics didn't create SARS-CoV-2 and cover up their own role in it.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#139

Post by mzs »

jpeloquin wrote: post #91

"To avoid losing power with multiple comparisons, we focus our analysis on the BsaI/BsmBI sites in SARS-CoV-2 and compare the BsaI/BsmBI map in SARS-CoV-2 to all other restriction maps of all other CoVs used in our analysis." It's important to know whether or not the authors picked BsaI & BmBI blind, before looking at the genome. If they picked BsaI & BmBI with knowledge of the SARS-CoV-2 genome, that doesn't dodge t…

They weren't picked blind, they were picked since they are commercially available and conveniently split the genome into 6 similarly sized segments with the spike protein entirely in one. It's precisely what a bioengineer would have elected to use and why the paper concentrates on it.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#140

Post by wk_end »

astrange wrote: post #86
someuser54541 wrote: post #22

Genuinely surprises me that there are people out there who think or have been persuaded the virus is of natural origin. The lab right next to the market was literally studying and experimenting with the exact same type of virus. How can a someone think that that's just a coincidence? Add that to the fact that the funding for that research lab was approved by the same guy who become the de facto thought leader on the…

> The lab right next to the market was literally studying and experimenting with the exact same type of virus. How can a someone think that that's just a coincidence? If they built the lab next to the viruses that were already there, then it would be reverse causation, which isn't a coincidence, but also kind of is one. That's the meaning of "correlation is not causation".

Except they didn't. The WIV was founded decades before coronaviruses were a subject of interest, and the bat coronaviruses they were researching that SARS-CoV-2 is related to all come from caves in Yunnan, which is about 1,500km away.
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