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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?

#91

Post by jpeloquin »

"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 the multiple comparisons problem and the p-values aren't reliable. I guess it depends on how many other commonly used type IIS endonucleases there are. The authors use 214 to generate their null hypothesis distribution for the CoV restriction maps but say only 6 are specifically amenable to BAC cloning.

The "wild type distribution" null distribution for fragment length (Figure 3C) being a simulation (permutation of known CoV genomes, split at randomly selected restriction sites) bothers me. On the first read I thought it was a distribution of fragment lengths in real viruses. Does synthesizing virtual genomes by permutation produce a realistic distribution of fragment lengths?

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

#92

Post by abledon »

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.

i wonder what % of damage it caused to economy, compared to WW2 reparations.

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

#93

Post by tgsovlerkhgsel »

s1artibartfast wrote: post #61
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…

>Thirdly, this paper emphasizes the strong impact of the COVID pandemic and asserts that understanding the origins of the virus would necessarily aid in preventing future pandemics. I strongly disagree. If of natural origin, there are a plethora of simple controls that could be implemented. Control doesn't necessarily need to be perfect. Some simple controls could be restrictions or bans on Commercial trade or transp…

I believe the research on the bat viruses was being done under BSL-2 conditions, which basically means normal lab practices, an autoclave for waste, and some of the work needs to be done in a biosafety cabinet. Of course, that assumes the procedures are strictly followed.

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

#94

Post by alchemist1e9 »

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…

Lazy question. Is there a git url for the code?

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

#95

Post by alchemist1e9 »

kelseyfrog wrote: post #57
someuser54541 wrote: post #27

Earlier quoted context omitted.

> 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.

Quoted post unavailable.

Does your razor include a previous pandemic originating from a Soviet lab leak?

https://en.wikipedia.org/wiki/1977_Russian_flu

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

#96

Post by thunky »

astrange wrote: post #84
guelo wrote: post #66

I've seen several papers with the opposite conclusion. Why do we only see the lab leak hypothesis front paged on HN?

Cynical engineers are required to believe in it because it's 1. "the opposite of the current thing" 2. contains more rationality than the other leading hypothesis (i.e. more of what happened was planned, rather than an accident) 3. and lets them blame a person rather than a bat. An ironically fitting end for them would be that it is true, they get all similar research banned, and then the next virus is zoonotic and n…

That's pretty dark.

A nicer thing to wish for is that it leads to better safety an accountability protocols.

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

#97

Post by steve76 »

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.

No post body was provided.

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

#98

Post by kens »

alchemist1e9 wrote: post #94
johnwdefeo wrote: post #8

Earlier quoted context omitted.

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…

Lazy question. Is there a git url for the code?

To save you the two clicks, the code is at https://github.com/reptalex/SARS2_Reverse_Genetics

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

#99

Post by samatman »

beiller wrote: post #29
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…

I have the opposite Occam's razor thoughts. My opinion is we are not capable of developing in a lab a virus that is so transmissible and survivable in human species only. I think the complexity of the virus machinery and its interactions inside of our bodies and immune system is beyond astronomical in complexity. It's laughable to suggest that we are so intelligent as to invent a better version of the machinery that…

The lab in question was doing gain of function research.

The existence of gain of function research shows that you are wrong.

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

#100

Post by xupybd »

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…

>Thirdly, this paper emphasizes the strong impact of the COVID pandemic and asserts that understanding the origins of the virus would necessarily aid in preventing future pandemics. This does not clearly follow. Especially if the virus had natural selection origins there is no clear and obvious way of systematically reducing risk. Simply living or traveling where host populations like bats live could be enough to generate exposures and it is not simple to clear people off of rural habitations.

Exterminating all the bats is an option. It would be our first purposeful extinction and would no doubt cause many problems. We need to at least weigh up the possibility. Then we can run the risk benefit analysis.

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