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

biorxiv.org

201–210 of 250 posts

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

#201
post #10

Earlier quoted context omitted.

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...

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

No post body was provided.

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

#203
post #125

Earlier quoted context omitted.

Absolutely incredible to think that the national institute of allergy and infectious disease might fund research into infectious disease.

I think you’re committing a motte-and-bailey here. We are talking about research deemed so dangerous Obama banned it, not infectious disease research in general.

It looks like the US government stopped funding Gain of Function research for 3 years while working on handling guidelines, is that what you are referencing? That seems more like working out some details than burying the forbidden tomes in the desert.

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

#204

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 don't know that I believe that the answer to which one happened in the case of covid-19, is all that important It is when literally this week a version with an 80% kill rate but with the spread of the most transmissible was made in a lab for no good reason. How many would die if that leaked out and the only reason it’s been made is just so some academic can get their name in a paper and earn some grant presumably…

I don't know whether the research should have been done, but it wasn't done for no reason, and information it obtained seems quite useful. The hope, and general assumption, has been the same mutations that led omicron to be so transmissible also reduced its lethality. This research suggests otherwise (that it was happy coincidence). That would be very concerning (and makes me want to get the omicron variant vax)

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

#205
post #146

Earlier quoted context omitted.

> It's important to know whether or not the authors picked BsaI & BmBI blind, before looking at the genome. You could never convince me that these restriction enzymes were picked blindly, no bioinformatician I have ever met does science this way. There is a preliminary period of exploratory data analysis which is done before any hypothesis is put forward, and data dredging and leakage are rampant in the literature. T…

> 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-...

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

#206
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.

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

#207

"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…

I realized why this being based on simulation bothered me: this is a machine learning classifier that classifies viral genomes as synthetic or natural. The training set n = 72 (all negative, which is justifiable if you're ok with null hypothesis significance testing) the validation set n = 6 (only synthetic examples, which is less fine), and there's no test set. No effort was made to estimate true positive rate, false positive rate, etc. If this was published as a machine learning paper instead of a biology paper it would probably be held to a higher standard.

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

#208
post #79

Earlier quoted context omitted.

Wasn't the lab working with coronaviruses? So maybe some of it escaped. I really don't see how that's an unnecessary multiplication of entities. Is the objection simply that, pandemics have emerged from markets, but not labs? But we know that an escape of a coronavirus could lead to a pandemic. I see nothing needlessly complex here, and certainly not extraordinary.

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 pandemics", because it is not adjusted by whether there have been two natural pandemics, or two million of them. Rather, it's adjusted by the safety practices at the lab.

It's still not obvious that the wet market explanation is simpler than the lab leak. I don't see Occam's Razor making a selection here.

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

#209
post #158

Earlier quoted context omitted.

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.

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 (where they both can take a lot of blame) to the zoonotic hypothesis (less blame) - even though actual specialist opinion was (and still is) pretty split... (Not so much if you remove the specialists with a conflict of interest and the pressure they and the governments might have been able to exert ?)

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

#210

Earlier quoted context omitted.

> which I wont link Why not? HN promotes logical evidence-backed discussion. The least you can do is link the forum.

He's talking about virological and making up threads that never existed. There was a lot of discussion in the early days about how it seemed possible it was synthetic based on the binding site affinity but as scientists do, they researched the literature, conferred with their colleagues and almost all came around to the virus arising via natural origin. The early threads are super interesting in an anthropological se…

You can claim whatever you want, I'm just sharing what I discovered
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