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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?

#211

Post by divided »

MockObject wrote: post #208
divided wrote: post #79

Earlier quoted context omitted.

I don’t believe anyone is saying it’s needlessly complex, but Occam’s Razor isn’t “the second simplest explanation is usually the correct one.” On one hand you have the market which housed animals that throughout its history some have had and spread different coronaviruses naturally. Every prior pandemic has been believed to have been from animal to human transmission, it’s seemingly the simplest explanation. The lab…

> It’s not that it’s needlessly complex. It’s that you have a market with animals who have coronaviruses and you have a lab that studies coronaviruses. Both are reasonable explanations, but a pandemic similar to all other prior pandemics and lots of humans being exposed to lots of potential virus carriers with no protection _is_ a simpler explanation. The likelihood a lab accident is independent of "all other prior p…

When you hear hooves, think horses not zebras.

All throughout history viruses have spread from close animal contact with humans. Including—and I cannot stress this enough—a novel coronavirus circa 2002 that spread from bat to intermediary host to humans in a wet market in the very same country.

In comparison, for the lab leak you’re assuming a lab accident (rare), that it wasn’t noticed and quarantined immediately (even rarer), and that the wet market still randomly became the epicenter of early cases despite at that point the transmission being human to human (rare, there’d be no reason for it to be any more significant than any other place people gather).

So when we’ve never seen a significant outbreak from a lab accident (zebras) and throughout all of human history we’ve seen viruses spread to humans from close contact with animals (horses)… yes when there is ambiguity to what the cause is, defaulting to what we’ve always seen before—including literally just 20 years ago—is simpler.

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

#212

Post by z7 »

graeme wrote: post #10
jgeada wrote: post #6

So a likely extremely controversial paper being shared publicly to a non-expert audience prior to any peer-review. Is this going to be yet one more of those “will be withdrawn after peer scrutiny but by then it is too late because the false meme has been injected into the public consciousness” things?

They did share it with scientists. Here’s Francois Balloux saying he replicated the results, tried to find holes, couldn’t https://mobile.twitter.com/BallouxFrancois/status/1583165259...

Looks like he deactivated his account. I would guess the response to these tweets might have something to do with it.

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

#213

Post by lamontcg »

mikeyouse wrote: post #171
tripletao wrote: post #142

Earlier quoted context omitted.

Their terminology would indeed seem wrong, but the WIV has apparently used a similar assembly strategy (leaving the sites in the final assembly) before: https://twitter.com/jbkinney/status/1583267221047869441 I'd worry about their false discovery rate, for the same reason I worry about the large number of parameters in Pekar's epi model. It's still an interesting result, though.

As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. And even more worrying than the false discovery rate are all of the missing genomes they should be comparing. I fear they've left them off because they punch big ole holes in the theory... e.g. https://twitter.com/zhihuachen/status/1583258714340892672

Another good twitter thread on it this morning:

https://twitter.com/acritschristoph/status/15834864034169692...

This is the real kicker to me:

> What about missing sites? The authors propose that someone made a bizarre combination of additions and deletions of cut sites. RecCA matches SARS-CoV-2 at all missing sites because other viruses do. E.g. this one: similar to RpYN06 not just at the mutation, but the entire region.

Clear evidence of recombination across the whole region and not just mutations to manipulate the cut site.

And Francois Balloux seems to have deleted his twitter account this morning.

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

#214

Post by arisAlexis »

divided wrote: post #200
arisAlexis wrote: post #183

Earlier quoted context omitted.

How many bat coronaviruses existed in the vicinity of the Wuhan market, including the specimens from the laboratory ? How many bats were freely roaming in the neighborhood? That's a much better probability analysis, not a flu virus in Antarctica

Right, what I’m saying is we know The bats don’t need to be at all near the market, the theory is an intermediate host was in the market. A bat could infect the host population days prior or years prior. A long potential span of time. It might be illustrative to look at MERS. They found camel populations >3,000 miles away from the outbreak with antibodies to MERS. One potential explanation is the virus doesn’t sicken…

Because the theory of intermediate host hasn't Led anywhere after 3 years but we know for sure and as a fact that experimentos with bat coronaviruses did happen 1km from epicentro, I don't get why people insist so much. I think it's more like "I hope it's not true" thing.

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

#215

Post by MockObject »

divided wrote: post #211
MockObject wrote: post #208

Earlier quoted context omitted.

> It’s not that it’s needlessly complex. It’s that you have a market with animals who have coronaviruses and you have a lab that studies coronaviruses. Both are reasonable explanations, but a pandemic similar to all other prior pandemics and lots of humans being exposed to lots of potential virus carriers with no protection _is_ a simpler explanation. The likelihood a lab accident is independent of "all other prior p…

When you hear hooves, think horses not zebras. All throughout history viruses have spread from close animal contact with humans. Including—and I cannot stress this enough—a novel coronavirus circa 2002 that spread from bat to intermediary host to humans in a wet market in the very same country. In comparison, for the lab leak you’re assuming a lab accident (rare), that it wasn’t noticed and quarantined immediately (e…

Lab accidents may be rare in general, but the lax safety at Wuhan had already [0] been noted two years prior.

The horse/zebra analogy is not so convincing within miles of a zebra breeding farm, with fences reported to be weak. Near this place, such assumptions don't carry their normal weight.

[0] https://www.voanews.com/a/covid-19-pandemic_chinese-lab-chec...

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

#216

Post by timr »

jpeloquin wrote: post #205
timr wrote: post #146

Earlier quoted context omitted.

> To your point however, could someone comment on the suitability of BsaI/BsmBI for the in vitro assembly of synthetic coronaviruses? These are very commmon enzymes. Perhaps the most common today. The GP comment is sort of misleading...you wouldn't just pick enzymes at random to do this analysis. You'd pick the enzymes in common use. These count. > Is it all just about finding sites in the genome at the right locatio…

> The GP comment is sort of misleading...you wouldn't just pick enzymes at random to do this analysis. I said pick blind, not at random. I recommend reading https://info.umkc.edu/drbanderson/p-hacking-and-the-problem-...

I know what p-hacking is. There's no reason to believe that they've done that here. The choice of enzymes was motivated by the logic they outlined in the paper, the enzymes chosen are some of the most popular today, and the authors are completely forthright that the choice might affect the outcome.

To fairly make a critique like that, you need to have at least some evidence that a selection bias was applied for no other reason than to affect the p-value. Otherwise, literally every study can be accused of "p-hacking". Here, there's a very good, obvious explanation for the choice that they made, and therefore all you can really say is that the results might be different if you looked at a different set of enzymes.

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

#217

Post by mikeyouse »

jhanschoo wrote: post #178
callesgg wrote: post #15

I Honestly thought it was common belief that corona come from that lab in china. But now after reading this, I searched a bit and read up on it and I guess it is still a somewhat honest debate on the topic. Even if it was lab made, it would be sort of stupid to dig in to it, due to the political nature of the matter. What happened happened, most likely the release would have been accidental, so why play blame games.

I originally didn't think that it came from a lab. Primarily because flu epidemics have happened before and they were of natural origin and there hadn't been good evidence that it came from a lab. But my opinion changed as more good evidence started to turn up that suggested engineering.

There's literally no evidence suggesting engineering. This is a deeply flawed paper (several cornaviruses of natural origin "rate" higher as artificial using their methodology) and essentially every other paper claiming to find some signal of engineering has been disproven or retracted.

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

#218

Post by mikeyouse »

misja111 wrote: post #166
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…

Exactly this. I'm completely stunned how everybody seems to be ignoring the fact that the closest relatives of the Covid virus are in Yunnan, which is 1500 km away from Wuhan, or even further, in Laos. So a zoonotic origin of the outbreak which started in the Wuhan market would have involved animals transported to the market over 1500km or more. Doesn't anybody ask themselves, why Wuhan? Why was there no outbreak in…

Everyone agrees that SARS1 was of natural origin, right? All of the same points you're making about Covid19 apply equally to the origin of SARS1.

First outbreak of SARS1: Foshan

Distance from cave containing progenitor virus in Yunnan to Foshan: 1,400 km

Doesn't anyone ask themselves why Foshan? Why not Qujing or Hanoi?

People don't take the location as some dispositive point proving the conspiracy because 15 years prior, a bat coronavirus from nearly 1,500km away infected an animal in the wildlife trade that started a pandemic in busy metropolitan area. So it doesn't seem especially unlikely for that to have happened again.

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

#219

Post by mikeyouse »

arisAlexis wrote: post #214
divided wrote: post #200

Earlier quoted context omitted.

Right, what I’m saying is we know The bats don’t need to be at all near the market, the theory is an intermediate host was in the market. A bat could infect the host population days prior or years prior. A long potential span of time. It might be illustrative to look at MERS. They found camel populations >3,000 miles away from the outbreak with antibodies to MERS. One potential explanation is the virus doesn’t sicken…

Because the theory of intermediate host hasn't Led anywhere after 3 years but we know for sure and as a fact that experimentos with bat coronaviruses did happen 1km from epicentro, I don't get why people insist so much. I think it's more like "I hope it's not true" thing.

No experiments with bat Coronaviruses happened "1 km" from the epicenter. WIV is 15km away.. so even if you were to believe it originated at the WIV, it's still odd why it took off at a seafood market 15km away instead of at the very busy campus or any market much closer to their research center.

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

#220

Post by mikeyouse »

tripletao wrote: post #175
mikeyouse wrote: post #171

Earlier quoted context omitted.

As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. And even more worrying than the false discovery rate are all of the missing genomes they should be comparing. I fear they've left them off because they punch big ole holes in the theory... e.g. https://twitter.com/zhihuachen/status/1583258714340892672

> As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. Where did you read that? Kinney explicitly asserts the opposite, but I can't figure out what he's referring to. Someone else linked to Figure S9 from their 2017 PLOS Pathogens paper, which indeed seems not to contain the site in the final assembly. I've edited my other comment here to reflect that.

Nope - the restriction sites aren't in the final assembly in that paper. These authors just don't understand the tools remotely well enough to have written their paper. It will never be published.

https://twitter.com/alchemytoday/status/1583361758903013376

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