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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?

#51

Post by iso1337 »

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 irreversible"

https://en.wikipedia.org/wiki/Golden_Gate_Cloning ----

The choice of focusing on a particular RE pair also smells of p-hacking. Their claim that BsaI/BsmBI makes for easy mixing/matching genomes doesn't make sense in this day and age, when you can use other techniques to make hybrids more effectively (eg, you are not restricted to the natural location of those restriction enzyme sites)

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

#52

Post by tripletao »

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…

> That argument points out that genetic drift is well characterized and the presence of two closely related SARS-CoV2 variants cultured from the wet market is extremely strong evidence that is where the virus initially appeared.

I assume you're referring to Pekar et al. here? The two lineages are literally just two SNPs apart, so it's near-impossible to distinguish whether they arose from two separate introductions, or just from two super-spreading events after cryptic evolution in humans from a single earlier introduction. Pekar builds an epidemiological model that purports to find that evolution in humans is p ~ 0.5% unlikely; but that result is highly sensitive to the assumptions in that model, most notably their choice of a scale-free infection network (and thus power-law distribution of number of other people each patient infects). Robustness to that infection network isn't studied.

The author of this endonuclease fingerprint preprint also has a preprint on Pekar's model,

https://www.biorxiv.org/content/10.1101/2022.10.10.511625v1

Note that I'm criticizing Pekar here, not endorsing the endonuclease preprint. I don't have a great sense of the correct Bonferroni correction (to borrow Prof. Balloux's framing) to apply to the latter's probabilities.

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

#53

Post by bequanna »

whydid wrote: post #28
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…

https://en.m.wikipedia.org/wiki/Sagan_standard Extraordinary claims require extraordinary evidence. This is why people are skeptical.

How is it an extraordinary claim?

It is by far the simplest and most obvious explanation.

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

#54

Post by sneak »

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…

“it was known” are weasel words on wikipedia.

Known by whom? Why? Based on what evidence? Can we know it, too?

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

#55

Post by rlpb »

ISL wrote: post #43
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.

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.

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

#56

Post by sneak »

navhc wrote: post #19
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 don't think it's all about blame, knowing it came from a lab would also pull into question the practice of engineering viruses and the safety and security standards required.

If it is possible that viruses of this type could be engineered, then lab safety needs to be upgraded anyway (or GoF research banned, or both) regardless of the origin of this specific virus.

It’s all about blame. Blame is a useful geopolitical tool.

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

#57

Post by kelseyfrog »

someuser54541 wrote: post #27
kelseyfrog wrote: post #23

Earlier quoted context omitted.

My Occam's razor says that every other virus has a natural origin, why wouldnt this one too? Maybe your razor needs sharpening?

> My Occam's razor says that every other virus has a natural origin, why wouldnt this one too? That's simply not true. There's an entire branch of virology dedicated to synthetic viruses; the first was made over 20 years ago.

No post body was provided.

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

#58

Post by swamp40 »

nl wrote: post #40
Dig1t wrote: post #24

Earlier quoted context omitted.

I really don't see how saying that the pandemic was a bad thing and that there is value in understanding its origin is "a dangerous level of sloppiness".

Well considering that's not what the OP said at all I guess it's ok you don't see that.

> third criticisms...show a dangerous level of sloppiness

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

#59

Post by iso1337 »

johnwdefeo wrote: post #8
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?

I sincerely hope not. From one of the authors: "Scientists publish papers not because the paper is the end of science, but because it is a unit of research that is valuable to share with others so that others can use this brick of knowledge and either build with it… or find its weakness and break it down...We wrote our entire analysis in R and shared our code with the world. I tried SO hard to check every single line…

Any publicity is good publicity. Sprinkle in some words about "this needs further study" and hope someone comes along to fund the next few years of your lab.

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

#60

Post by pencilguin »

danbtl wrote: post #39
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.

> why play blame games Because of the question of liability: If it was lab made and accidentally released, was it due to recklessness or criminal negligence? Is someone guilty of involuntary mass-manslaughter? Or if this was state-sponsored research, could they be found liable for the damage caused?

What court would usefully find this? What authority would enforce it?
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