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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?

#241

Post by BlueTemplar »

Fomite wrote: post #227
BlueTemplar wrote: post #209

Earlier quoted context omitted.

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.

Hmm, it's interesting that it's so different from my impression of specialist opinion...

Especially when the CNRS - (which would be partially guilty in the case of a lab leak !) - published the claim that the lab leak hypothesis could not be dismissed.

But you know how paradigms work, you have to be an anti-conformist to support what is going to become the new paradigm...

And sure, there most certainly is a very enthusiastic lay readership on the lab leak side... but why do you think there isn't one on the zoonosis side ?

And especially an even bigger fraction of specialists and lay readership that aren't rejecting either ?

(It bears repeating : I'm not anti-zoonosis, since I am not competent to judge either way anyway, I just find it very worrying that there seemed to be a campaign from quite early on, when social pressure wouldn't have had as much effect yet, to outright dismiss the lab leak theory, even though among the specialists gathered at the WHO in January 2020, there was no such consensus.)

I guess it only goes to show how bubbly the Internet (and your specific sub-field bubble ?) can be...

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

#242

Post by nil-sec »

_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.

I had the same experience a couple of years back when people started discussing AI. I try to keep this in mind but somehow I keep forgetting. It’s genuinely difficult to filter good from bad takes without expert level understanding of a topic unfortunately.

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

#243

Post by pantojax45 »

timr wrote: post #81
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…

> 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 of viral characteristics, only a comparison between wild and l…

> They also generated 100,000 random mutations to RaTG13 and BANAL52, and found that only ~1.2% and 0.1% of these

This could also be selection pressure - right? Ie imagine 99,000 yield viruses that are non viable… you’d see the same behavior of rare traits being common.

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

#245

Post by matkoniecz »

wnkrshm wrote: post #179
whywhywhywhy wrote: post #176

Earlier quoted context omitted.

> 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…

These kinds of experiments are going to be done either way - for example gain-of-function research on animal smallpox (which usually doesn't kill and can't infect humans) to make it lethal. Experts on the matter (I read a book recounting smallpox research, not a domain expert myself [0]) were concerned more about the publishing of that research than about the research being done, since proliferation is deemed very ea…

Stopping public funding of that would reduce risk.

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

#246

Post by matkoniecz »

farseer wrote: post #182
whywhywhywhy wrote: post #176

Earlier quoted context omitted.

> 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…

It could be a random lab in Cambodia, run by a professor with dreams and ambitions for fame and fortune. The point is you can't really regulate gain of function research. Pandemic preparation has to keep that in mind. That includes isolating countries immediately after a disease of unknown origin is found.

You can, in the same way as we regulate murder.

It will not be 100% efficient, but reduction can be achieved.

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

#247

Post by Fomite »

BlueTemplar wrote: post #241
Fomite wrote: post #227

Earlier quoted context omitted.

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.

Hmm, it's interesting that it's so different from my impression of specialist opinion... Especially when the CNRS - (which would be partially guilty in the case of a lab leak !) - published the claim that the lab leak hypothesis could not be dismissed. But you know how paradigms work, you have to be an anti-conformist to support what is going to become the new paradigm... And sure, there most certainly is a very enth…

So one key is to not that not thinking the lab leak hypothesis is true =/= thinking it can be dismissed.

Because showing a zoonotic origin of a disease like SARS-CoV-2 is the work of years, if not decades, and with the disruption of the pandemic to research + the political ramifications of that work, it may well already be beyond us.

I think the reason there isn't an enthusiastic readership on the zoonotic side is simply because that's how people are conditioned to think about these diseases. Everything from movies like Outbreak to Contagion, the current fuss about the emu YouTube woman, etc. primes people to think about that. It's hard to foster an enthusiastic readership for what people think they already know.

It's also not particularly...sensational. There's no smoking gun. No shadowy conspiracy. The problems that emerge from zoonoses are hard and dispersed. It makes for very bad SubStack material.

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

#248

Post by tiagod »

jhanschoo wrote: post #133
tiagod wrote: post #112

Earlier quoted context omitted.

We've seen horizontal gene transfer in fish, was it aliens or natural selection? Extremely unlikely events happen when an extreme amount of attempts are made, and natural selection amplifies them if they increase fitness

Your reply after reading the explanation is like you seeing a farm of branded cows and wondering if it was due to extreme natural selection that caused that. From the layperson article: > In wild viruses, these cutting/pasting sites are randomly distributed because there's no evolutionary pressure for the virus to be thusly cut and pasted in nature. In infectious clones, however, the humans behind the screen tend to…

The explanation given is based on some premises that I'm not qualified to assess, and others I am.

One of these premises is that their work properly models reality, there seems to be a lot of well informed doubt by subject-matter experts.

Another is that an event with a probability of 0.1-1% is exceptionally rare, its occurrence thus being most likely artificial, and with that I disagree, by looking at endless counter-examples nature provides.

Is the fact that humans found some optimization a proof that any occurrence of it is man-made? I believe most people would say it isn't.

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

#249

Post by timr »

pantojax45 wrote: post #243
timr wrote: post #81

Earlier quoted context omitted.

> 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 of viral characteristics, only a comparison between wild and l…

> They also generated 100,000 random mutations to RaTG13 and BANAL52, and found that only ~1.2% and 0.1% of these This could also be selection pressure - right? Ie imagine 99,000 yield viruses that are non viable… you’d see the same behavior of rare traits being common.

It was an in silico experiment.

But regarding your broader question: there's no reason to believe that thesse viruses experience any selective pressure for the number or location of cutting sites of the particular enzymes being investigated here. They're bacterial enzymes, entirely unrelated to coronaviruses.

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

#250

Post by timr »

tiagod wrote: post #248
jhanschoo wrote: post #133

Earlier quoted context omitted.

Your reply after reading the explanation is like you seeing a farm of branded cows and wondering if it was due to extreme natural selection that caused that. From the layperson article: > In wild viruses, these cutting/pasting sites are randomly distributed because there's no evolutionary pressure for the virus to be thusly cut and pasted in nature. In infectious clones, however, the humans behind the screen tend to…

The explanation given is based on some premises that I'm not qualified to assess, and others I am. One of these premises is that their work properly models reality, there seems to be a lot of well informed doubt by subject-matter experts. Another is that an event with a probability of 0.1-1% is exceptionally rare, its occurrence thus being most likely artificial, and with that I disagree, by looking at endless counte…

> One of these premises is that their work properly models reality, there seems to be a lot of well informed doubt by subject-matter experts.

The model is fine. There's no more "well informed doubt" than for any other paper. You can certainly debate the details of what they did, but none of this debate is substantial enough to invalidate the work.

What you're seeing is a group of people who have largely pre-judged the outcome, inventing reasons to reject an experiment that disagrees with their prior conclusions. This always happens, in any scientific domain. Nonetheless, there are also a large number of well-informed people who see this as an interesting result. If you don't listen to both groups, you will be misled.

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