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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?

#71

Post by ISL »

rlpb wrote: post #55
ISL wrote: post #43

Earlier quoted context omitted.

If it was released from a lab, no matter whether or not it was accidental, Covid would be the mother of all torts. The entire planet can show harm and will be very interested in recovering their losses from the entity that mis-handled a lethal virus.

It'd be much like trying to recover money stolen by a drug addict though. Instant bankruptcy and proportionally nothing recovered, to the point that it's not even really worth it.

A drug addict with a $14T GDP.

With ~7M deaths and a ~$1-10M value of human life [1], that's $7-70T in losses in lives alone, before lost productivity and economic value.

[1] https://en.wikipedia.org/wiki/Value_of_life#:~:text=In%20Wes....

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

#72

Post by rlpb »

ISL wrote: post #71
rlpb wrote: post #55

Earlier quoted context omitted.

It'd be much like trying to recover money stolen by a drug addict though. Instant bankruptcy and proportionally nothing recovered, to the point that it's not even really worth it.

A drug addict with a $14T GDP. With ~7M deaths and a ~$1-10M value of human life [1], that's $7-70T in losses in lives alone, before lost productivity and economic value. [1] https://en.wikipedia.org/wiki/Value_of_life#:~:text=In%20Wes... .

Only if liability transfers to the state. Even if state-owned, plenty of state-owned enterprises have limited liability.

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

#73

Post by [deleted] »

AnonymousPlanet wrote: post #63
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…

Studied and then escaped from a lab does not equal synthetic. Exactly nothing in your post supports a synthetic origin over a sample from nature that got studied in a lab. Jumping to these kinds of one sided conclusions should be a red flag.

[deleted]

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

#74

Post by Stevvo »

m0llusk wrote: post #18

There are at least a couple of suspicious points in this study: 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…

"the central claim is that 5 potential restriction binding sites versus 2 means that SARS-CoV2 is non natural"

That claim is not in the paper at all. The argument is based on the length of longest fragment and could apply to any number of restriction binding sites.

"the evidence for the wet market origin is trivialized."

It's a statistical analysis of viral genomes. The wet market evidence is unrelated.

Your third point is arguing in favor of ignorance and defeatism. "there is no clear and obvious way of systematically reducing risk" because we do not understand the origin. If we did, there may very well be; e.g. restrict trade in civet cats. Simple actions like this have controlled pandemics in the past.

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

#75

Post by stefantalpalaru »

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…

No post body was provided.

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

#76

Post by throwawaymaths »

iso1337 wrote: post #51
m0llusk wrote: post #18

There are at least a couple of suspicious points in this study: 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…

Their claims around Type IIS assembly are also suspect. eg in Golden Gate assembly, you choose Type IIS that reach over and cut, so the restriction site is absent from the final assembled product. "Additionally, because the final product does not have a Type IIS restriction enzyme recognition site, the correctly-ligated product cannot be cut again by the restriction enzyme, meaning the reaction is essentially irrever…

The argument is about the negative space of the RE. Regardless of what the article says, To do golden gate/Gibson/etc. best practice is to cut the template first (with RE) then assemble against the open ends, so to do this you must ablate the existing re sites. The alternative is to linearize by round the horn pcr. At 33kb, it's not impossible but why bother with the pain when it's much easier to snip.

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

#77

Post by RichardCNormos »

shikshake wrote: post #38
fdgsdfogijq wrote: post #17

True story, in early January of 2020, on an academic virology forum, which I wont link, it was known the virus was synthetic. Before the story hit the mainstream media, professors were sharing data about the virus fingerprint. There were concerns about the integrity of the data shared by the Chinese. One specific comment I will never forget by a Harvard professor when discussing the implications: "Should we turn on t…

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

No post body was provided.

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

#78

Post by chrisbrandow »

fdgsdfogijq wrote: post #17

True story, in early January of 2020, on an academic virology forum, which I wont link, it was known the virus was synthetic. Before the story hit the mainstream media, professors were sharing data about the virus fingerprint. There were concerns about the integrity of the data shared by the Chinese. One specific comment I will never forget by a Harvard professor when discussing the implications: "Should we turn on t…

This is super interesting but without any sort of substantiation it is indistinguishable from rumor-mongering.

I would truly love to hear more.

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

#79

Post by divided »

MockObject wrote: post #48
shadowgovt wrote: post #41

Earlier quoted context omitted.

That's going to come down to an individual observer's priors on probabilities of "pandemic virus being more closely patterned to every other pandemic in human history" vs. "pandemic introduced via a novel mechanism that has never become a pandemic before."

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 leak theory of course assumes a lab accident. Biolab accidents are fairly rare, some years have no recorded accidents, others a handful. They’ve all been successfully contained with no more than a couple fatalities each.

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.

Having said that, I’ve remained open minded and willing to consider both reasonable and unproven. Some pandemic will be the first from a lab leak, this may have been it. We will probably never definitively know.

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

#80

Post by kaneliomena »

m0llusk wrote: post #18

There are at least a couple of suspicious points in this study: 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…

Asserting that understanding the origins of a virus helps control its adverse impacts is completely bog-standard fare in the literature. Finding it suspicious in this case smacks of an isolated demand for rigor and unfamiliarity with the field. Even a cursory look at papers making a case for a zoonotic origin is likely to reveal statements to the same effect, here's just two for example:

https://www.sciencedirect.com/science/article/pii/S009286742...

>Failure to comprehensively investigate the zoonotic origin through collaborative and carefully coordinated studies would leave the world vulnerable to future pandemics arising from the same human activities that have repeatedly put us on a collision course with novel viruses.

https://www.nature.com/articles/s41591-020-0820-9

> Detailed understanding of how an animal virus jumped species boundaries to infect humans so productively will help in the prevention of future zoonotic events. For example, if SARS-CoV-2 pre-adapted in another animal species, then there is the risk of future re-emergence events.

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