Coronavirus thread

[Spotted Horses]

I would not place much stock in how much "confidence" a government agency has in a particular assessment, and the evidence in favor of the lab leak theory is not entirely circumstantial.

I've been following a very interesting discussion on one of the AAAS forums. According to one gentleman on that forum, a biotech entrepreneur, the presence of a furin cleavage site in the SARS CoV-2 genome is extremely unlikely to have come about except by human manipulation, because no closely related coronavirus has such a site, and because if it developed somehow in a mammal other than man, it would reduce, rather than enhance, the virus's transmissibility.

The strongest argument against the lab leak theory is the fact that samples of the virus itself were found in stalls that housed the most susceptible species at the Wuhan market. The only way the lab leak theory can explain that finding is by a worker at the market who was infected by exposure to someone infected at the lab, and then transmitted the virus to an animal - reverse zoonosis, another possible but very unlikely event.

So it seems that whichever theory you prefer, the other theory's proponents have an argument that seems to rule out your favored theory.

I'm highly skeptical of both arguments since each relies on an intuitive notion of "very unlikely" or "extremely unlikely", and human intuition about probability is famously unreliable - most beliefs in the paranormal are a consequence of that fact.

(Of course, one possibility is that the furin codon found its way onto the virus inside a HUMAN host, perhaps an immunocompromised person who was infected with a different virus that does have the furin codon. That theory doesn't involve a lab, but also requires reverse zoonosis to explain the findings from the market stall samples.)

I don't think we have enough evidence to draw a firm conclusion about the virus's origins, and very likely we never will.

These are articles in respected, peer-reviewed scientific journals:

Furin cleavage sites naturally occur in coronaviruses

https://www.sciencedirect.com/science/article/pii/S1873506120304165

SARS-CoV-2 furin cleavage site was not engineered

https://www.pnas.org/doi/10.1073/pnas.2211107119

There is a history to this. When the SARS-CoV-2 sequence was first published some self-appointed "experts" who had no detailed knowledge of coronavirus claimed that the Furin cleavage site was proof it was engineered. Then the Coronavirus community collectively replied, "WTF, all Coronaviruses have Furin cleavage sites!" Of course, that didn't prevent conspiracy theorists to latching on the the initial mistake.

[Todd]

People sure seem to need to believe in something.

[Spotted Horses]

People sure seem to need to believe in something.

And some people seem to need to believe in nothing.

[Todd]

And some people seem to need to believe in nothing.

When one relies on verified facts only, belief is not needed.

[Spotted Horses]

When one relies on verified facts only, belief is not needed.

Pointing out that a claim made about the SARS-CoV-2 is contrary to established evidence (that furin cleavage sites are a common feature of coronavirus) is not "belief."

[Todd]

Pointing out that a claim made about the SARS-CoV-2 is contrary to established evidence (that furin cleavage sites are a common feature of coronavirus) is not "belief."

The science on the origin of the disease is not settled at this time.  That is a fact. 

[Spotted Horses]

The science on the origin of the disease is not settled at this time.  That is a fact.

I didn't say the origin of the virus is settled. I said that that claim that a furin cleavage site is not found in coronavirus and had to be engineered is demonstrably false.

[Todd]

I said that that claim that a furin cleavage site is not found in coronavirus and had to be engineered is demonstrably false.

You are not qualified to make that assessment, even after having read several articles. 

[Spotted Horses]

You are not qualified to make that assessment, even after having read several articles. 

How do you know that?

[Todd]

How do you know that?

You would have broadcast your bona fides and you would have referenced technical jargon much sooner.  You also would have referenced academic articles, typically with limited access to the general public, with more robust evidence supporting your claims.

By all means, if you are a virologist or specialist in a related field that would provide you with qualifications to offer more than a hobbyist's knowledge, enlighten everyone here.

[Dry Brett Kavanaugh]

Just to point out that this is not new, independent evidence, but another article detailing the same evidence that has been mentioned here before (including by yours truly this weekend).

The RNA evidence from the market is the strongest evidence for the zoonosis theory yet, but even this article concedes that it is not conclusive:

For topics like this, I like reading scientific/academic publications (that's why I don't read this thread). In natural science, and more in social science, conclusive/perfect evidences are effectually impossible even if a correlation is 0.93. Only non-professionals claim "conclusive" evidence.

[Madiel]

Todd is always good at pointing out the supposed lack of expertise of others.

Todd never draws attention to his own total lack of expertise.

PS I majored in biochemistry at university. I at least know what the fuck a cleavage site is.

[Karl Henning]

Only non-professionals claim "conclusive" evidence.

Oh, and I have a theory about that ....

[Madiel]

Also... I can scarcely begin to unpack all of the things that are so utterly wrong with suggesting that only experts are allowed to read other experts.

Not that Todd actually believes this. I mean, he merrily reads all sorts of things and then posts them here, clearly with the intention that other people read them and derive "beliefs" from them. It's just that when anyone else does the same (and does it with a lot more intelligent narrative and effort rather than pasting a link and maybe uttering a one line quip) that suddenly Todd wants to put someone in their place.

This is because Todd is a hypocrite. As well as a troll. Those aren't quite synonyms but one is definitely a characteristic of the other.

[Spotted Horses]

You would have broadcast your bona fides and you would have referenced technical jargon much sooner.  You also would have referenced academic articles, typically with limited access to the general public, with more robust evidence supporting your claims.

By all means, if you are a virologist or specialist in a related field that would provide you with qualifications to offer more than a hobbyist's knowledge, enlighten everyone here.

It would be pretty ridiculous for me to tout my credentials or use technical jargon on a non-specialist discussion site like this. I think it serves a purpose when unsubstantiated "conspiracy theories" are pushed to point out reliable sources of information that reflect the most reliable scientific evidence. A thoughtful non-specialist can probably get the gist of these studies from the abstracts, although a specialist would want to pour over the text, supplemental material and references. And I would hope that a thoughtful person would recognize that an article published in, for instance, The Proceedings of the National Academy of Science, carries more weight than something that a self-described expert posted on a discussion board. If my comments carry any weight it is because of the nature of the sources I cite, not because I have puffed myself up as an "expert."

[Todd]

It would be pretty ridiculous for me to tout my credentials or use technical jargon on a non-specialist discussion site like this. I think it serves a purpose when unsubstantiated "conspiracy theories" are pushed to point out reliable sources of information that reflect the most reliable scientific evidence. A thoughtful non-specialist can probably get the gist of these studies from the abstracts, although a specialist would want to pour over the text, supplemental material and references. And I would hope that a thoughtful person would recognize that an article published in, for instance, The Proceedings of the National Academy of Science, carries more weight than something that a self-described expert posted on a discussion board. If my comments carry any weight it is because of the nature of the sources I cite, not because I have puffed myself up as an "expert."

It's OK to be a hobbyist.

[ritter]

There has been some great, nuanced, intelligent discussion in this thread recently. Let's make sure to keep it that way and not get personal. Thanks!

[krummholz]

These are articles in respected, peer-reviewed scientific journals:

Furin cleavage sites naturally occur in coronaviruses

https://www.sciencedirect.com/science/article/pii/S1873506120304165

SARS-CoV-2 furin cleavage site was not engineered

https://www.pnas.org/doi/10.1073/pnas.2211107119

There is a history to this. When the SARS-CoV-2 sequence was first published some self-appointed "experts" who had no detailed knowledge of coronavirus claimed that the Furin cleavage site was proof it was engineered. Then the Coronavirus community collectively replied, "WTF, all Coronaviruses have Furin cleavage sites!" Of course, that didn't prevent conspiracy theorists to latching on the the initial mistake.

First, I am NOT arguing in favor of the lab-leak theory, just to make that clear. I am saying that both leading theories have been criticized in ways that seem to make them equally implausible, yet there are really no other possible ways the virus could have emerged. My main point was that all of these criticisms rely on notoriously unreliable, intuitive notions of probability and appeal to the same kinds of arguments that have been used to defend claims of paranormal phenomena, and should (IMO) inspire extreme skepticism on those grounds alone.

However... labeling all arguments that further the claim that the virus was the product of gain-of-function research as "conspiracy theories" because a paper that refutes one of them appeared in a peer-reviewed journal is not really a relevant argument, either. (Peer review is not a guarantee of correctness.) The gentleman I paraphrased was NOT by any means saying that furin cleavage sites were rare in coronaviruses, or even in sarbecoviruses. He was saying that the specific 12-nucleotide insertion at S1/S2 did not exist in the most closely related coronaviruses, something the paper at your first link also states in an early paragraph. He further argued that while it could have occurred naturally, in most non-human mammals that codon would have been an evolutionary disadvantage. Again, I am not saying that this argument is necessarily correct - it may well be dead wrong, I am not qualified to assess it in detail - but it is a carefully nuanced argument and not a conspiracy theory.

Also, the idea that the furin codon on SARS-CoV-2 was a "smoking gun" for human engineering came originally not from some anonymous, self-anointed expert, but from Nobel laureate biologist and virologist David Baltimore. Baltimore has since backed off that assessment a little, but even his most recent comments drip with skepticism that the virus could have emerged entirely naturally. I've lost the link to that interview and don't have time at the moment to look for it, but I'm sure I could dig it up tomorrow if anyone is interested.

[Madiel]

You posted the link previously, because I remember reading it. In my view he had backed away from his previous comments a heck of a lot. EDIT: Found it again, he basically seems to have moved to saying he has no opinion one way or the other.

Also, one of the articles Spotted Horses posted says that a 12-nucleotide insertion isn't involved, only 4 nucleotides. It also points out things about the sequence that aren't logical for a human-engineered sequence.

I think it's very easy for people to reason that if something looks significant to humans, it must have been GIVEN significance. The reality is that shuffling of genetic sequences is happening constantly, and the great majority of them do absolutely nothing in practice and so we ignore them, or simply never see them.

The microbiological world is a bit like that room full of monkeys with typewriters, only typing much much faster than the monkeys ever could and the room is huge. And some of this feels a bit like people think it's not possible that one of the monkeys could have managed to accidentally type the word "beach".  When of course no-one is going to comment on the many, many times that the same monkey generated nonsense.

Meanwhile, generic shuffling has kept going since the virus jumped to humans, and as far as I know no-one is claiming THAT process has been engineered even though it led to strains that were much better at infecting humans.

[Spotted Horses]

Sorry if I read more into k.'s post than was intended.

The fact that the novel coronavirus deviated a lot from the most closely related virus we know of is a very weak statement because we know of a very limited subset of the viruses that are out there. It presumably evolved from a viral strain we have no knowledge of.