Origins of SARS CoV-2 - split from: Covid-19 miscellany

[Elixir]

It does make sense.

No, it doesn't. The breadth of possible factors involved and the paucity of our actual knowledge of what happened conspire to make assigning greater than .5 probability to any cause that is not the simplest explanation, nonsensical. The simplest explanation is that what we know has happened before, happened again.

List of laboratory biosecurity incidents

indeed.
How many of those were novel coronavirii that caused an accidental/intentional pandemic?

 

[Bomb#20]

indeed.
How many of those were novel coronavirii that caused an accidental/intentional pandemic?

Special plead much?

 

[Bomb#20]

The fact that the China Virus BS is believed by a half dozen more suckers than the flat earth BS doesn't place it in the realm of reason. It's an extension of the brainless masses who also think the 2020 election was stolen. Not because there's any truth to it, just because the Mango Menace said so.

Not all of them. You might have convinced yourself without Cheato's encouragement, for instance.
But most of them. It is curiously just as well supported as massive fraud in the 2020 election. Assertions, innuendo, may even those affidavits that right wingers find so convincing...
We had plagues long before we had labs.
Plus, I'm feeling kindly toward China today because they slapped some banking restrictions on Uncle Vlad.

I know you said that. I said most people who think that do so because they were told to, not because there's sufficient reliable evidence to draw that inference.
I stand by my assertion just as you stand by yours. You're free to think I'm wrong, just as 90 something percent of trumpsuckers do.

Because most people who believe the Chyyyna Virus crap are trumpsuckers.
I thought I made that clear. Get it now?

Like we need more boogeymen.

Conservos and their halfwit cousins the trumpsuckers are furiously manufacturing them lest people fail to be terrified enough to vote against their own interests.

That doesn't make any sense, AM. Most trumpsuckers have no clue what >0.5 is, let alone grasp the concept of assigning probabilities.
You might as well call it the "lab leak theory" too, since they also have no idea what a theory is.

Keep it up, dude! Every time you post one of these you're just making it more and more blatant that you accept the natural origin hypothesis for political rather than scientific reasons.

 

[Angra Mainyu]

The probabilistic assessments under discussion only look at a few things. One thing that is not looked at is distance analysis from wet market, like in the paper I linked. In that paper it is interesting because they look at how robust their finding is to some alternatives such as that the epicenter was elsewhere.

If you are talking about my probabilistic assignments, as I said, I take a look at the information available to me and intuitively the assignment is made (I'm human after all). That includes information about papers who claim that the natural origin hypothesis is true due to the market stuff. Also, as I mentioned, I think the lab leak hypothesis is probable, but I do not assign as close to 1 as to say I'm convinced it is true. As I read more - new arguments, studies, etc., or old ones I haven't yet seen -, I will intuitively update in one direction or another.

 

[laughing dog]

The idea that a lab-leak origin of the SARS-CoV-2 is as unlikely as a flat earth is gaslighting.

It is not. You need to familiarise yourself with the definition of gaslighting:

psychological manipulation of a person usually over an extended period of time that causes the victim to question the validity of their own thoughts, perception of reality, or memories and typically leads to confusion, loss of confidence and self-esteem, uncertainty of one's emotional or mental stability, and a dependency on the perpetrator

It's gaslighting behaviour. bilby wants people to believe that the lab leak theory has about as much support as a flat earth or hoaxed moon landings. bilby's use of these as comparisons undermines people's confidence in the reasonableness of their own beliefs. He is publically trashing them. It is reasonable to believe SARS-CoV-2 might have emerged from a virology lab and specifically one in Wuhan.

Using your standard, you are engaging in gaslighting behavior because you are trying to undermine people's beliefs about bilby's credibility.

Non. Pointing out some truth to people is not gaslighting them.

Then why did you accuse bilby of gaslighting? After all, it is reasonable to believe bilby is correct.

It is not reasonable to equate the probabilities of a lab leak and a flat earth. It is entirely unreasonable.

I happen to think neither one of you is gaslighting under the normal interpretation, but you are gaslighting under your own standard.

There is little evidence to suggest a lab was involved. The vast scientific consensus at this time is that it did not come from a lab.
Once probabilities get to certain low value, there is no real distinction between them and zero.

Moreover, there is new report that seems to provide convincing evidence it came from a market. New report - Covid came from a market.

But hey, you continue to use double standards and fling those accusations.

 

[Elixir]

you’re just making it more and more blatant that you accept the natural origin hypothesis

“Accept?”

Among the numerous hypotheses I’ve seen, I consider natural origins to be most likely. I also consider “origin” a tertiary concern. It is what it is, and that’s what we have to deal with. So I ask myself “what is the most likely origin of the Chyyyna hypothesis, who is advancing it, and why?”
That’s how I come to provisionally hold that natural origins are most likely.
I am not married to the idea, and have no dog in that race. OTOH, I see a number of posters here who appear quite dedicated to finding malevolent actors to blame, in the typical manner of right wing fearmongers. I don’t see that being the least bit productive.

 

[Loren Pechtel]

What I don't understand is why the origins of C19 matter all that much.

Unless it was weaponized, either by a hostile government or pharmaceutical companies, it doesn't matter where it came from. What matters is how we respond to it.
Tom

There are a lot of people who are more interested in placing blame than in solving problems.

Placing blame is only useful for avoiding recurrences, it does nothing to solve the problem.

 

[Loren Pechtel]

I am not suggesting that this paper is correct, but it's new and I am sharing it:

Abstract

Despite strong epidemiological links and the documented presence of SARS-CoV-2 susceptible animals, the role of the Huanan Seafood Wholesale Market in the COVID-19 pandemic remains controversial. Using spatial analyses we show that the earliest known COVID-19 cases diagnosed in December 2019 were geographically distributed near to, and centered on, this market. This distribution cannot be explained by high densities of elderly people at greater risk of symptomatic COVID-19. This pattern was stronger in cases without, rather than with, identified epidemiological links to the Huanan market, consistent with SARS-CoV-2 community transmission starting in the surrounding area. By combining spatial and genomic data, we show that both the two early lineages of SARS-CoV-2 have a clear association with the Huanan market. We also report that live mammals, including raccoon dogs, were sold at the market in late 2019 and geospatial analyses within the market show that SARS-CoV-2-positive environmental samples were strongly associated with vendors selling live animals. Together, these analyses provide dispositive evidence for the emergence of SARS-CoV-2 via the live wildlife trade and identify the Huanan market as the unambiguous epicenter of the COVID-19 pandemic.

It's made at least two other zoonotic jumps that we are sure of and one suspected--and going back in time it's suspected in other situations. The idea that it once again did the same thing it keeps doing simply isn't surprising.

 

[Loren Pechtel]

1 in 400 means nothing here because there are so many rolls of the dice (mutations).

Sure, improbable things happen every day.

But probable things happen more often, so when a hypothesis implies an observation was improbable, it's rational to reduce one's estimate of the probability of the hypothesis, in accordance with Bayes' Theorem. But "reduce one's estimate" doesn't tell you how likely the hypothesis now is, because that also depends on how likely you thought the hypothesis was before you made the improbable observation, your so-called "prior probability". There is famously no objectively correct way to determine prior probabilities. So I'm not saying 1 in 400 means it didn't happen -- all I'm doing is backing up my earlier statement that natural origin hypotheses involve improbable coincidences, since blastula complained I hadn't shown any math.

My point is that you can't even assign a probability because you have no idea of how many rolls of the dice there were.

If one's prior probability estimate for natural origin is 99%, then some improbable coincidences like that one are enough to make it rational to reduce one's estimate to below 50%. If one's prior probability estimate for natural origin is 99.9999999%, then there are never going to be enough improbable coincidences to make it rational to reduce one's estimate to below 99%. So unless and until the Chinese government decides to make all the lab records available, rational people will continue to disagree -- and that's fine.

If it is a lab leak it's unlikely the records would show anything--they wouldn't have known it happened. It also wouldn't disprove anything--there are a lot of hints that what we saw wasn't the original virus. Rather, there was something out there that was sometimes infecting humans but not sustaining transmission during Q4 and perhaps later Q3 of 2019. This would make what we see as the base version actually the first variant. If there was a lab leak it would have been that version with a human R0 below 1 and wouldn't match up with anything that has been identified in the wild.

 

[TomC]

There are a lot of people who are more interested in placing blame than in solving problems.

But I almost never hear anybody placing blame where it really is. Jet Travel. The transportation industry.

It doesn't really matter whether the C19 virus escaped a lab or jumped in an exotic food market. It spread around the globe at jet speed, while (and even before) governments and societies dithered about how to deal with it.

Placing blame is only useful for avoiding recurrences, it does nothing to solve the problem.

Avoiding recurrences is the only really useful reason for investing in the answer to this question.
But as long as travelers insist on spreading it and governments use it as a political football rather than stopping it, how it originated will remain an unimportant footnote to the story.
Tom

 

[Jimmy Higgins]

There are a lot of people who are more interested in placing blame than in solving problems.

But I almost never hear anybody placing blame where it really is. Jet Travel. The transportation industry.

It doesn't really matter whether the C19 virus escaped a lab or jumped in an exotic food market. It spread around the globe at jet speed, while (and even before) governments and societies dithered about how to deal with it.

Well that and people acting like plague rats when we knew it was a problem.

Placing blame is only useful for avoiding recurrences, it does nothing to solve the problem.

Avoiding recurrences is the only really useful reason for investing in the answer to this question.
But as long as travelers insist on spreading it and governments use it as a political football rather than stopping it, how it originated will remain an unimportant footnote to the story.

Origins is important because we can work to reduce the occurrences in the future. But the origin is being used as a distraction by some.

 

[repoman]

If there was rock solid proof that covid came from a lab and was mostly directly engineered with a bit of serial passage to top it off, how would that affect the dynamic going forward?

Would there be a bit of resentment like "We have to do this because these eggheads couldn't stop being curious and reckless?!?"

I think running through the hypothetical in full is interesting.

I don't know, even if did come from a lab and it was fully known by all, I don't see how gain of function research at that same level would ever be reined in. Things have to keep rolling, it is what we do as humans.

 

[bilby]

If there was rock solid proof that covid came from a lab and was mostly directly engineered with a bit of serial passage to top it off, how would that affect the dynamic going forward?

The same way that a rock solid proof that the Moon was made of cheese would.

Neither is going to happen, so speculation is at best pointless, and at worst harmful, in that it feeds the unreasoning paranoia of dangerous conspiracy theorists.

It's therefore both stupid and dangerous to speculate in this way. The evidence needs to come first, not the daft and dangerous "what if?"

 

[Elixir]

indeed.
How many of those were novel coronavirii that caused an accidental/intentional pandemic?

Special plead much?

Hard to find good fish an artificially created ocean full of red herring.

 

[Bomb#20]

How many of those were novel coronavirii that caused an accidental/intentional pandemic?

Special plead much?

Hard to find good fish an artificially created ocean full of red herring.

You wrote "The breadth of possible factors involved and the paucity of our actual knowledge of what happened conspire to make assigning greater than .5 probability to any cause that is not the simplest explanation, nonsensical. The simplest explanation is that what we know has happened before, happened again."

But how many previous cases have there been of novel coronavirii that caused a natural pandemic and left no trace of their evolutionary precursors? How many previous cases have there been of novel coronavirii that caused a natural pandemic where the intermediate host couldn't be found after two years of hunting for it? How many previous cases have there been of novel coronavirii that caused a natural pandemic in which the earliest known version of the virus was already well-adapted to infecting human cells? Zero. So the natural origin hypothesis postulates an event that's never happened before, just like the lab-leak hypothesis does. So you have no grounds for declaring that therefore yours is the simplest explanation.

When you typed the oddly specific phrase "novel coronavirii that caused an accidental/intentional pandemic", you were playing a rhetorical game: you were relaxing the criteria for classifying previous events as the same kind of event as the current one, and doing it in precisely the right way to make SARS qualify but past lethal lab-leak outbreaks not qualify. Anyone can play that game. You can relax the sameness criteria some different way to make some other event qualify and make SARS not qualify, and thereby make some other explanation pass the "It's simplest because it's happened before" test. Playing that game is a special-pleading fallacy.

 

[Elixir]

Playing that game is a special-pleading fallacy.

Your arguments are ALL based on ignorance. If we knew everything about where every coronavirus "came from" we wouldn't have pandemics. Oh - except the ones caused by organisms developed in secret for nefarious reasons that escape from labs, of course.

Hmmm. Must have been a lucky guess.

“When you look at all of the evidence together, it’s an extraordinarily clear picture that the pandemic started at the Huanan market,” said Michael Worobey, an evolutionary biologist at the University of Arizona and a co-author of both new studies.


Several independent scientists said that the studies, which have not yet been published in a scientific journal, presented a compelling and rigorous new analysis of available data.


“It’s very convincing,” said Dr. Thea Fischer, an epidemiologist at the University of Copenhagen, who was not involved in the new studies. The question of whether the virus spilled over from animals “has now been settled with a very high degree of evidence, and thus confidence.”

Forgive me if I don't immediately elevate your opinion over that of persons presumably better informed and better educated in epidemiology. That article is only 2 days old... so my earlier statements were probably lucky guesses, against all odds.
If my presumptions are incorrect and you consider your opinion as good as or better than theirs, I'll be happy to reconsider my position when you explain the transcendent nature of your expertise.
Meanwhile, color me unsurprised that these apparently expert folks have converged on what was OBVIOUSLY THE MOST LIKELY EXPLANATION FROM THE START.
At this point, the "special pleading" belongs exclusively to those laypersons who manage to irrationally deem the Chyyyna boogeyman hypothesis not only the most likely among many, but actually the PROBABLE source of SARS-CoV-2 despite the consensus of the plurality of epidemiologists. There is no reason to assign that kind of probability to something that can only be inferred from what we don't know - even before this "conclusive" study (I still withhold judgment pending its release and review by the broader scientific community). .

 

[Don2 (Don1 Revised)]

How many of those were novel coronavirii that caused an accidental/intentional pandemic?

Special plead much?

Hard to find good fish an artificially created ocean full of red herring.

You wrote "The breadth of possible factors involved and the paucity of our actual knowledge of what happened conspire to make assigning greater than .5 probability to any cause that is not the simplest explanation, nonsensical. The simplest explanation is that what we know has happened before, happened again."

But how many previous cases have there been of novel coronavirii that caused a natural pandemic and left no trace of their evolutionary precursors? How many previous cases have there been of novel coronavirii that caused a natural pandemic where the intermediate host couldn't be found after two years of hunting for it? How many previous cases have there been of novel coronavirii that caused a natural pandemic in which the earliest known version of the virus was already well-adapted to infecting human cells? Zero. So the natural origin hypothesis postulates an event that's never happened before, just like the lab-leak hypothesis does. So you have no grounds for declaring that therefore yours is the simplest explanation.

When you typed the oddly specific phrase "novel coronavirii that caused an accidental/intentional pandemic", you were playing a rhetorical game: you were relaxing the criteria for classifying previous events as the same kind of event as the current one, and doing it in precisely the right way to make SARS qualify but past lethal lab-leak outbreaks not qualify. Anyone can play that game. You can relax the sameness criteria some different way to make some other event qualify and make SARS not qualify, and thereby make some other explanation pass the "It's simplest because it's happened before" test. Playing that game is a special-pleading fallacy.

Speaking of arbitrary levels of criteria, relaxing or making stringent, the Wade article does that a few times. Did you notice?

 

[Elixir]

Speaking of arbitrary levels of criteria, relaxing or making stringent, the Wade article does that a few times. Did you notice?

That didn't jump out at me... it wouldn't, because this "origin" BS really isn't very important IMHO.
But I am disappointed that B20 is apparently quite committed to the right wing conspiracy theory that is the Chyyyna hypothesis.
I have found him to be the most - or at least one of the most - reasonable voices from the right on this board, and if he can get sucked in by this fearmongering invention, it does not bode well for us all.

 

[blastula]

Additionally, I look at the general trend among experts, as well as the assessments by people who are good or better excellent predictors, and so on. On that note, Bomb#20 made excellent points, and also provided in this post. Have you read it? Here is the link again:

The origin of COVID: Did people or nature open Pandora’s box at Wuhan?

If the case that SARS2 originated in a lab is so substantial, why isn’t this more widely known? As is now obvious, there are many people who have reason not to talk about it.

thebulletin.org

It's a very interesting read, but I am willing to listen to counterarguments...though perhaps, in addition to looking for counterarguments, you should read it and consider whether he has a point.

Why should anyone care what the hack non-expert Wade says about it?

Unwillingness to read an opposing argument and an ad hominem against the person who made it: the sure sign of an open mind.

Unless you're an expert, there's nothing wrong with pointing out his non expertise, it's just good epistemology. There are expert sources available to cite on the issue.

And Bomb didn't show his math neither to say this:

Double-standard much? You didn't show any evidence that Wade is a "hack".

I didn't give any pronouncements on probabilities like you did. But here is one example of why I call Wade a hack.

Something other than gain of function is remotely possible. Something other than gain of function involves a lot of improbable coincidences. Gain of function explains pretty much everything without relying on improbable coincidences.

Okay, just as a for-example, the two arginines in SARS2's furin cleavage site -- the novel insertion that makes the virus infectious in humans -- are coded CGG-CGG. Back of the envelope, the odds against that happening by randomly flipping RNA bases would appear to be four hundred to one. There are six different three-base RNA sequences that all code for arginine, and CGG is the rarest code for arginine in coronaviruses, used for only five percent of the arginines in SARS2. That would seem to imply likely formation by recombination rather than by point mutation. This raises the question, where were those CGGs copied from? CGG-CGG is a sequence that hasn't been found in any other beta coronavirus. But CGG is a very common code for arginine in humans. For a scientist trying to create a cleavage site in order to perform a gain-of-function experiment of the sort we know the Wuhan lab was doing, putting in two CGGs would be a natural choice.

Clearly, you're not an expert neither. You are describing some math, but you are not giving any background basis for what the inputs should be, because you don't have it. Don is right about it sounding like ID, this is no different than when Michael Behe comes up with some probability that proves evolution couldn't produce some protein. Just like Behe does, your .05 x .05 assumes simultaneous mutation. And a 1/400 number is hardly a big hurdle anyway when you consider a single covid infection produces billions of copies.

But how many previous cases have there been of novel coronavirii that caused a natural pandemic and left no trace of their evolutionary precursors? How many previous cases have there been of novel coronavirii that caused a natural pandemic where the intermediate host couldn't be found after two years of hunting for it? How many previous cases have there been of novel coronavirii that caused a natural pandemic in which the earliest known version of the virus was already well-adapted to infecting human cells? Zero. So the natural origin hypothesis postulates an event that's never happened before, just like the lab-leak hypothesis does. So you have no grounds for declaring that therefore yours is the simplest explanation.

You don't appear to know the answers to any of these. It comes off as tinfoil FUD, no different than "what's the melting point of steel?"

But the answers to some of that can be found in this review, which I've already posted here,

The origins of SARS-CoV-2: A critical review - Cell

And the question of what the precursor virus was is actually a bigger problem for your position, since there is no viable candidate known that was being studied by anybody.

Plus, just this past week, it so happens that a few more studies were released that lend further credence to a zoonotic origin.



Two of them are discussed here,

New Research Points to Wuhan Market as Pandemic Origin - The New York Times.

 

[Hermit]

Gee. I thought I was looking at the thread about COVID. WTF!

My apologies, Sohy, but he *points at some vaguely discernible point* started it.

So, back on topic. Angra Mainyu's assertion that the probability of the pandemic starting because the Coronavirus escaped from a laboratory in China is greater than 50% reminds me of this brief exchange: