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

[Angra Mainyu]

The probability that the pandemic originated in a lab (whether by the virus being engineered in a lab, or else by the virus being collected from the wild but scaping from a lab) is higher than 0.5, on the basis of the evidence I've seen

Show your math.

I don't have any math to show, but I did not give a specific number, just >0.5, i.e., it's probable. That's a probabilistic assessment on the basis of the available information, like humans normally do all the time. For example, I reckon the probability that I will persuade bilby to change his assessment "The probability that Covid originated in a lab is vanishingly close to zero, and no sane and well informed person could conclude otherwise.", is less than 0.5. The probability that most Western experts will give the lab leak theory >0.5 by 2030 is also >0.5; the probability that most Chinese experts will publicly do so is close to 0, and the probability that they will actually do so is still <0.5. But I don't have math for any of that. I'm just making human probabilistic assessments on the basis of the available information, and using numbers just to give bounds that give a bit more of an idea than 'probable', 'improbable', etc.

 

[bilby]

Bilby, Don2 who has a lot more knowledge than me, was spending time looking into details of the paper and you are spending your time and closed mind attacking us.

I am attacking your stupid and ill-advised rumourmongering and FUD.

I am not attacking any people.

Will you listen to what Don2 has to say if it clashes with your current mindset?

I have been listening to what Don2 says, and even to what you say.

I am keeping an open mind, but not so open that my brain falls out. This is a manufactured controversy, in which the weight of evidence MASSIVELY leans towards one side. To present the weak and illogical evidence against a natural origin for the disease over and over and over again in the hope that repetition will give it strength not presented by its content is simply dishonest.

You should stop promoting dishonest nonsense, lest people imagine that you are malicious, rather than just a patsy of the malicious people who originate this crap.

 

[bilby]

It is very easy to find virologists who assign high probability to the lab leak hypothesis.

But it is massively easier to find virologists who do not.

You can find small numbers of experts to support almost any position. But scientific consensus isn't made by small numbers of mavericks. And mavericks who were later shown to be right are so rare in science that you can probably name most of them, while scientists as a class - indeed, just virologists as a class - are so numerous that you couldn't name them all if you spent your entire life saying nothing but their names.

 

[bilby]

By the way, given that you are not a virologist, how are you assessing which virologists to listen to?

I am mostly using my education in molecular biology, and my experience in reading and interpreting biological research. It's fairly dated, but not completely obsolete.

How are you doing it?

In particular, how are you assigning those numbers to the probability that you keep bandying around? You surely must realise that they are utterly meaningless.

 

[Hermit]

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

 

[Hermit]

It is very easy to find virologists who assign high probability to the lab leak hypothesis.

Almost as easy as finding climatologists who deny anthropomorphic global warming.

 

[Metaphor]

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.

 

[Hermit]

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.

Pointing out that the idea that a lab-leak origin of the SARS-CoV-2 is as unlikely as a flat earth is gaslighting does not constitute psychological manipulation of a person. It is an assertion devoid of personal implications. You just project them into it.

Your take on what gaslighting means would make any assertion you disagree with an example of gaslighting unless it begins with "in my ever so humble opinion, and I am not sure this is true" or words to that effect.

 

[Angra Mainyu]

Almost as easy as finding climatologists who deny anthropomorphic global warming.

Or even easier, but more likely equally so. In any case, that is not a good reply. Take a look at the exchange. I said:

While not conclusive, the lab leak hypothesis ( whether by a genetically engineered virus or one collected in the wild and then leaked) seems to be probable.

bilby replied:

Not to anyone who has studied virology, genetics or molecular biology, it doesn't.

So, a single person who has studied virology, genetics or molecular biology would suffice to show that this claim is false. My reply does that. Your reply only confirms so: the claim is false.

 

[Angra Mainyu]

But it is massively easier to find virologists who do not.

It used to be so. Now I don't think so, since any google search will give you both right away, so it's about equally easy.
Also, in the beginning - well, not exacty in the beginning, but a while later -, the lab leak hypothesis was strongly condemned, laughed at, etc., so disagreement or even a request for evidence would likely have a huge social cost. Humans tend to avoid those instinctively, so that probably convinced many. But in spite of that, that has changed. Now it's not a fringe hypothesis, or laughed at - well, not by the community of experts at large. Still, the strong initial condemnation of the lab leak hypothesis by so many experts and their own research in the past will make it very hard for them to change their minds. Humans tend to be defensive and instinctively try to save face. But given the general trend and the evidence, in time, the lab leak hypothesis will probably gain more support.

I am mostly using my education in molecular biology, and my experience in reading and interpreting biological research. It's fairly dated, but not completely obsolete.

How are you doing it?

I'm human, so I look at the whole of the evidence and make an intuitive assessment.

In this case, I read the arguments I can understand, think about them, try to find counterarguments, and so on.

Additionally, I look at what different experts say. When I find disagreement, I look at who assigns what probability to which hypothesis, whether the people who disagree address the position they disagree with or just generally laugh at others, I look at how they approach scientific evidence in this particular case, their commitments, conflicts of interest, etc. 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.

In particular, how are you assigning those numbers to the probability that you keep bandying around? You surely must realise that they are utterly meaningless.

No, they are not meaningless. I am human, so instinctively I make probabilistic assessments all the time. Things like >0.5 are easy. Precise numbers have the difficulty of the imprecision of the assignment itself (...still, there are prediction markets for example and other similar prediction sites; a working approximation can be given at least).

Unfortunately, in my experience most humans do not realize they are doing that all the time - just not giving numbers, but words like 'probable', 'very probable', 'very improbable' and so on - and if someone explicitly says what they are doing, they tend to unfortunately think the person in question is not being rational.

 

[bilby]

Almost as easy as finding climatologists who deny anthropomorphic global warming.

Or even easier, but more likely equally so. In any case, that is not a good reply. Take a look at the exchange. I said:

While not conclusive, the lab leak hypothesis ( whether by a genetically engineered virus or one collected in the wild and then leaked) seems to be probable.

bilby replied:

Not to anyone who has studied virology, genetics or molecular biology, it doesn't.

So, a single person who has studied virology, genetics or molecular biology would suffice to show that this claim is false. My reply does that. Your reply only confirms so: the claim is false.

"Not to anyone who..." is vernacular language. It's not a claim that literally not one single such person exists, merely that they are a trivial variation from the norm.

If you want to be pedantic, that's your choice; But you are unwise to expect or demand equal pedantry from others.

There are always exceptions in any sufficiently large group. Their existence is completely irrelevant to my point.

 

[Hermit]

Almost as easy as finding climatologists who deny anthropomorphic global warming.

Or even easier, but more likely equally so. In any case, that is not a good reply. Take a look at the exchange. I said:

While not conclusive, the lab leak hypothesis ( whether by a genetically engineered virus or one collected in the wild and then leaked) seems to be probable.

bilby replied:

Not to anyone who has studied virology, genetics or molecular biology, it doesn't.

So, a single person who has studied virology, genetics or molecular biology would suffice to show that this claim is false. My reply does that. Your reply only confirms so: the claim is false.

I did not claim that nobody who has studied virology and assigns a high probability to the lab leak hypothesis can be found. I claimed that it is almost as easy as finding a climatologist who denies anthropomorphic global warming.

 

[Metaphor]

Pointing out that the idea that a lab-leak origin of the SARS-CoV-2 is as unlikely as a flat earth is gaslighting does not constitute psychological manipulation of a person. It is an assertion devoid of personal implications. You just project them into it.

Your take on what gaslighting means would make any assertion you disagree with an example of gaslighting unless it begins with "in my ever so humble opinion, and I am not sure this is true" or words to that effect.

The idea that that a lab leak origin for SARS-Cov-2 is as likely as a flat earth is ludicrous, and bilby knows it, and you know it.

 

[Don2 (Don1 Revised)]

Bilby, Don2 who has a lot more knowledge than me, was spending time looking into details of the paper and you are spending your time and closed mind attacking us.

Will you listen to what Don2 has to say if it clashes with your current mindset?

I have an open mind on "lab leak hypothesis," but there are multiple hypotheses, including loose kind of association with lab to more direct involvement to more deliberate stuff. I am definitely not in favor of an hypothesis of a leak being deliberate or Great Reset conspiracy. Some of those hypotheses deserve derision, some are political propaganda, some are not. I definitely think finding the virus at the location ("district" or whatever terminology is correct) is an improbable event. I do wonder if that could be correlated to something else such as great care in the area to sequence respiratory illnesses and infrastructure to do so. For example, when I had a respiratory thing pre-pandemic, go to a walkin clinic, if they do a strep test or pneumonia xray or whatever, I don't think they were ever like "hey, let's sequence this thing. Look, it's a virus of unknown origin!" But that seems to be a feature of that narrow area of China. In any case, still suspicious, but I am unsure how to quantify all the gaps of untested and untestable alternatives.

Regarding the paper, it doesn't actually advocate strongly a lab leak hypothesis, but does propose that the change at spike protein is from a human as host. I don't know that is true and am a little skeptical of the math as I think it ought to be not as significant as the probability they give--I gave some reasons last post(s). Btw, I did throw the 12nt sequence into NCBI BLAST but I wasn't getting results. It could be because BLAST is very glitchy for small sequences, not meant for those by design. Blasting the 19nt sequence, on the other hand, gives a bunch of results. It's probably not worth it to spend hours analyzing further because not getting results means there are tons of untestable ideas, not to mention blast databases available are very biased toward human.

[The other thing there which is only a few words in the paper is I think the paper referenced the human codon optimization, but I am not sure that is always a thing with every single function of each gene--i.e. sometimes the function may make re-using the typical codon suboptimal. In any case, there are probably quite a few organisms we do not know the codon usage for, but one that we do and that also matches as an alternative to human is Chinese hamster. I am sure that will also generate conspiracy talk, but my understanding there is that they are much less used in labs these days than before and further these are both found in the wild in China and as domestic pets.]

 

[Hermit]

Pointing out that the idea that a lab-leak origin of the SARS-CoV-2 is as unlikely as a flat earth is gaslighting does not constitute psychological manipulation of a person. It is an assertion devoid of personal implications. You just project them into it.

Your take on what gaslighting means would make any assertion you disagree with an example of gaslighting unless it begins with "in my ever so humble opinion, and I am not sure this is true" or words to that effect.

The idea that that a lab leak origin for SARS-Cov-2 is as likely as a flat earth is ludicrous, and bilby knows it, and you know it.

Where did you find words by either of us that might suggest that "a lab leak origin for SARS-Cov-2 is as likely as a flat earth". bilby, wrote:

I am not viscerally, emotionally invested in a flat Earth not being possible; Nor in the Moon landings being a hoax not being possible; Nor in vaccines not causing autism.

Not the same thing as your take of what he did write, is it?

As for me, I objected to your mistaken use of gaslighting while ignoring your erroneous take on what bilby actually wrote.

 

[blastula]

The probability that the pandemic originated in a lab (whether by the virus being engineered in a lab, or else by the virus being collected from the wild but scaping from a lab) is higher than 0.5, on the basis of the evidence I've seen

Show your math.

I don't have any math to show, but I did not give a specific number, just >0.5, i.e., it's probable. That's a probabilistic assessment on the basis of the available information, like humans normally do all the time.

Just show whatever evidence you're relying on to make this 0.5 assessment.

For example, I reckon the probability that I will persuade bilby to change his assessment "The probability that Covid originated in a lab is vanishingly close to zero, and no sane and well informed person could conclude otherwise.", is less than 0.5. The probability that most Western experts will give the lab leak theory >0.5 by 2030 is also >0.5;

Oh brother, even more numbers out of thin air.

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

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.

 

[repoman]

A perfect person or group of people to honestly look into the lab leak possibility would need as many of the following as possible:

Professional credentials in virology and genetics

A low level of conflicted interest - (can the need for grants be thought of as this?)

Not too old, or at least not demented (aging sucks) or out of this fast moving field for too long

Not have a messiah complex or be an asshole with an axe to grind

Not be a grifter literally out for money

Someone who can debunk their own interesting theories based on coincidences that SHOULD be investigated by seeing these in a bigger context.

----------------------------------------------------------------------------------------------------------------------------------------------------

So, are there any scientists who are doing good work now on the bounds of possibilities of the lab leak? If the papers are not trying to steel man the lab leak, even if only to shoot it down, they are not doing the right job.

The initial Daszak led paper on it does not meet this bar.

 

[Rhea]

The probability that the pandemic originated in a lab (whether by the virus being engineered in a lab, or else by the virus being collected from the wild but scaping from a lab) is higher than 0.5, on the basis of the evidence I've seen

Show your math.

I don't have any math to show, but I did not give a specific number, just >0.5, i.e., it's probable. That's a probabilistic assessment on the basis of the available information, like humans normally do all the time. For example, I reckon the probability that I will persuade bilby to change his assessment "The probability that Covid originated in a lab is vanishingly close to zero, and no sane and well informed person could conclude otherwise.", is less than 0.5. The probability that most Western experts will give the lab leak theory >0.5 by 2030 is also >0.5; the probability that most Chinese experts will publicly do so is close to 0, and the probability that they will actually do so is still <0.5. But I don't have math for any of that. I'm just making human probabilistic assessments on the basis of the available information, and using numbers just to give bounds that give a bit more of an idea than 'probable', 'improbable', etc.

Wait - you made a probabilistic assessment to >0.5 without using any math?
I mean, I get making intuitive assessments. Humans do that all the time. "I bet it won't," "I expect so," "I think it will," etc.
But you don't get to use statistical notation to do it, dude. That just raises questions about your competency, which is now rightly questioned.

Just stick with, "I've been convinced."

 

[Bomb#20]

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.

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".

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.

 

[Don2 (Don1 Revised)]

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.

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".

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.

Mutations are non-random and a single event could explain the insertion rather than conceiving it as a series of independent events.

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.

It is probably common in many other untested possible intermediate hosts on the planet. We have limited info on codon optimization relative to number of species on the planet. One alternative out of many alternatives most of which are unknown is Chinese hamster. Additionally, even if either of these is an intermediate host in the case of Chinese hamster or final host in the case of human, that doesn't necessarily connect to a gain of function experiment as opposed to recombination or evolution.

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.

You are making an intelligent design argument through implication. Do you really think ID is valid?