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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?

#221

Post by arisAlexis »

mikeyouse wrote: post #219
arisAlexis wrote: post #214

Earlier quoted context omitted.

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.

It's very clear that you really don't want to believe in the probability. You know nothing is 100%. If you assign 100% for no leak then your bias level is 100%. If you assign some probability then we just disagree on the probability level. Btw, people from the lab live there and shop there.

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

#222

Post by tripletao »

lamontcg wrote: post #213
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

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 re…

As far as I can tell, WIV (and other) researchers have left other restriction sites in final genomes, but not BsaI and BsmBI sites. That makes sense given the typical use of those two enzymes. So I'm inclined to agree there's nothing obviously special about that combination of restriction sites and spacings, which increases my concern that this is just a false discovery.

Jesse Bloom said he'd try reproducing with a wider range of natural viruses and potential synthetic assembly strategies. Unless and until that still gets an interesting p value, I'd agree this is oversold.

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

#223

Post by mikeyouse »

arisAlexis wrote: post #221
mikeyouse wrote: post #219

Earlier quoted context omitted.

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.

It's very clear that you really don't want to believe in the probability . You know nothing is 100%. If you assign 100% for no leak then your bias level is 100%. If you assign some probability then we just disagree on the probability level. Btw, people from the lab live there and shop there.

Of course there's the possibility - but the probability surely changes if the "market right next to the research lab" actually turns out to be a 20-minute drive away, no?

For people in the Bay Area, this is roughly equivalent distance-wise to a conspiracy theory about an outbreak at Twitter's HQ started by an "adjacent" lab in the Upper Mission that actually turned out to be in Jack London Square in Oakland instead.

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

#224

Post by tripletao »

mikeyouse wrote: post #220
tripletao wrote: post #175

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. 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

Yeah, I think Kinney is wrong here. Someone else found a survey paper noting the theoretical possibility of using BsaI and BsmBI in a way that leaves the sites in the final genome, but I haven't seen anyone who actually did that. So I'm leaning to a false discovery here.

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

#225

Post by arisAlexis »

mikeyouse wrote: post #223
arisAlexis wrote: post #221

Earlier quoted context omitted.

It's very clear that you really don't want to believe in the probability . You know nothing is 100%. If you assign 100% for no leak then your bias level is 100%. If you assign some probability then we just disagree on the probability level. Btw, people from the lab live there and shop there.

Of course there's the possibility - but the probability surely changes if the "market right next to the research lab" actually turns out to be a 20-minute drive away, no? For people in the Bay Area, this is roughly equivalent distance-wise to a conspiracy theory about an outbreak at Twitter's HQ started by an "adjacent" lab in the Upper Mission that actually turned out to be in Jack London Square in Oakland instead.

Again, bayesian priors. If there are only 4 labs worldwide messing with exactly these viruses, the combinatorics of this happening 20km from one of those 4 is infitesimal.

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

#226

Post by Fomite »

VagueMag wrote: post #138
Fomite wrote: post #135

Earlier quoted context omitted.

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.

One of the leading lab leak hypotheses (of which there are several) is that it was created as part of academic research - hence the fuss over PREDICT, the NIH and WIV.

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

#227

Post by Fomite »

BlueTemplar wrote: post #209
rleigh wrote: post #158

Earlier quoted context omitted.

It is not possible to be certain of this. You can't state that as an incontrovertible fact. Is it beyond reasonable doubt that a virus created as part of a gain-of-function research programme escaped? We simply don't know definitively one way or the other, and it's rather unscientific to make blanket statements about these things one way or the other in the absence of evidence to validate the claim. (I'm an immunolog…

In a way, the actual origin of Covid is a secondary matter at this point (because it's unlikely that China will give the required evidence to definitively disprove either the zoonotic or the lab leak hypothesis... am I wrong here ?). The more pressing matter is the conspiracies between some top level specialists and some governments that seem to have effectively pushed public opinion away from the lab leak hypothesis…

I know very few specialists, including those without a conflict of interest, who think the lab leak hypothesis is true.

From my perspective inside the field, a small number of specialists and a very enthusiastic lay readership have pushed the lab leak hypothesis in a way that presents far more disagreement than there actually is.

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

#228

Post by mikeyouse »

arisAlexis wrote: post #225
mikeyouse wrote: post #223

Earlier quoted context omitted.

Of course there's the possibility - but the probability surely changes if the "market right next to the research lab" actually turns out to be a 20-minute drive away, no? For people in the Bay Area, this is roughly equivalent distance-wise to a conspiracy theory about an outbreak at Twitter's HQ started by an "adjacent" lab in the Upper Mission that actually turned out to be in Jack London Square in Oakland instead.

Again, bayesian priors. If there are only 4 labs worldwide messing with exactly these viruses, the combinatorics of this happening 20km from one of those 4 is infitesimal.

I'm bored of this debate that happens every time one of these charlatans releases a paper that grabs a bunch of headlines and is disproven two days later (as already has happened with the original in this thread).

But "This happening" needs to be defined for Bayes to be of any use. State clearly what you think happened and it can be judged, because as has been proven over and over again, the virus is of natural origin. So the proximity to a lab studying Coronaviruses isn't nearly as interesting given China's history with these viruses.

This is long but in my opinion, worth reading regarding the Bayesian probabilities that actually matter here: https://protagonistfuture.substack.com/p/natures-neglected-g...

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

#229

Post by salawat »

_Wintermute wrote: post #185
fsh wrote: post #143

Earlier quoted context omitted.

It's incredible that the only sensible comments on this thread are this far down. The HN audience really has a massive Dunning-Kruger problem when it comes to science topics (especially true for COVID conspiracy theories).

As a pharmacologist reading the HN crowd arguing about hydroxychloroquine a year or so ago really highlighted 90% of this site regarding topics other than development or start-ups is at the same level as youtube comments, but with more arrogance.

Eh... That's why it's important to speak up and teach where you can. You never know who might learn something, and you may find yourself learning something in return.

Nobody gains anything in silence however.

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

#230

Post by salawat »

jonnycomputer wrote: post #206
b3nji wrote: post #202

Wasn't this a conspiracy theory at the start if this? I'm sure this kind of talk might have been squashed, suppressed, and some people might even people got banned for saying such things?

It is a conspiracy theory until you have good data and rigorous analysis. If you cannot see that people resisting jumping on an emotionally appealing bandwagon with racist undertones before careful evidence is collected on it, then I honestly don't know what to do for you.

>If you cannot see that people resisting jumping on an emotionally appealing bandwagon with racist undertones

It wasn't that back then, especially if you were following trends in that vein of research. We just had a cheeto in office, so people reached for the first shoe to dismiss it/discredit the cheeto instead of actually grappling with an intrinsically frightening, destabilizing possibility.

Also, treating anything as a conspiracy theory (a phrase coined, popularized, and cultivated during the Cold War/Vietnam era to discredit activists/leakers) by default is perhaps not the best starting point of a proper investigator. You should be going in with as few notions as can be supported by facts you can prove, or that can't be otherwise immediately disproven. The disprovable ones should only be thrown out if you are handed evidence that disproves it. Something you can't prove, bit you can't get cooperation to disprove is still on the table.

Once you have eliminated the impossible, whatever remains, no matter how improbable, must within it contain the truth. And you won't ever get there if you're putting out your eyes in the beginning.

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