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

[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.

 

[laughing dog]

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

1. He is not doing that, as the evidence is vastly stronger for one than the other. Purely for example, I will mentioned one big difference - but they're so different that this is merely a small example -:

In order for the existence of the universe we observe to increase the probability of design by a creator with properties P, Q, R in a significant manner - so that the ID argument works in that sense -, P, Q, R need to be specified in ways that make the prior of the existence of such creator astronomically low - so much so that the hypothesis of creation by that kind of creator remains very improbable even after considering the ID evidence. On the other hand, the probability of existence of virologists with the power to manipulate viruses is almost 1 (1 for all intents and purposes). Now if we could properly assign probability almost 1 to the existence of an entity who has the power to create universes, often does it, and really likes the very features we find in ours before we make the ID argument, i.e., before we factor in the features of our universe, then those features may very well provide the bases for a good argument to the thesis that our universe was indeed created by one such being, that is barring other difficulties that might or might not be present. But we can't - again, we can establish the existence of virologists with the relevant powers and dispositions before considering the properties of the virus that B20 mentioned.

2. Validity is a property of deductive arguments. ID arguments are arguments in the sense of 'arguing a case', and may or may not contain faulty logic. Some may contain only correct logic - so, no invalid arguments involved -, and terribly bad priors.

No.

I recommend you read the excerpt from the paper I posted to the thread. I also recommend that you do not snip the other sections of the post I made to Bomb#20 since the ID comment was in reference to dependency on those sections in light of the specific comment referred to later, i.e. don't snip or you won't get what I was talking about since you took it out of context.

I did not take anything out of context. Rather, your ID argument was not just the previous arguments. It was an addition to them. You were saying B20 was making an ID argument, and you were saying that even though he had not (and has not yet ) considered your other points in reply to him. And I pointed out why he was not at all making an ID argument. The rest of your points could not turn it into that, even if correct.

Please stop snipping.

Please stop saying I'm snipping. It's not true.

It is undeniably true. You even admit to it below in your attempt at justification.

I'm replying to parts of your post, properly. I don't have to reply to all of them, as long as I can make a proper case against the part I'm targeting. And I was doing just that.

 

[Angra Mainyu]

You did not properly address what you did not understand.

I did properly address what I did understand. Remember, you asked the rhetorical question "Do you really think ID is valid?", implying in context that B20's argument was valid iff ID is valid. I explained to you that validity is a property of deductive arguments not probabilistic ones like these, but leaving that aside, clearly you were implying that B20's argument committed him to accepting ID arguments as acceptable, even if not necessarily all of them, but in principle. I showed, however, that there was at least one key difference - namely, the probability of the existence of an entity with the relevant powers and dispositions before looking at the phenomena in question, in this case the details about the virus.

In doing so, I showed that your claim about ID would be incorrect regardless of how your two other claims fared, and also independently of what you meant in the part I did not understand, since I used the part I understood.

You are finding something not mentioned and arguing against it instead of what was meant in context.

No, I considered the context just fine. Remember your rhetorical question "Do you really think ID is valid?".

In biological context, I am obviously not discussing a non-existent scientist since scientists exist and further in context of the rest of my post I am obviously discussing ID vs evolution, the word "evolution" even being mentioned.

Well, obviously I am pointing out that that is a significant difference with the ID argument (well, more precisely, not just scientists, but specifically virologists with the power to modify viruses and make them more contagious and the motivation to do so). If you were aware of this crucial difference, your "Do you really think ID is valid?" was even more out of place than if you weren't aware of it.

You are prioritizing no discussion of value, just prioritizing semantic quibbling.

You are prioritizing attacking over discussing the content. It happens when you go on the offensive with "Do you really think ID is valid?", and then the "snipping" charge. And when you keep hammering on this. But I even posted another reply now, and it's about one of your substantive points!

 

[Angra Mainyu]

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

1. He is not doing that, as the evidence is vastly stronger for one than the other. Purely for example, I will mentioned one big difference - but they're so different that this is merely a small example -:

In order for the existence of the universe we observe to increase the probability of design by a creator with properties P, Q, R in a significant manner - so that the ID argument works in that sense -, P, Q, R need to be specified in ways that make the prior of the existence of such creator astronomically low - so much so that the hypothesis of creation by that kind of creator remains very improbable even after considering the ID evidence. On the other hand, the probability of existence of virologists with the power to manipulate viruses is almost 1 (1 for all intents and purposes). Now if we could properly assign probability almost 1 to the existence of an entity who has the power to create universes, often does it, and really likes the very features we find in ours before we make the ID argument, i.e., before we factor in the features of our universe, then those features may very well provide the bases for a good argument to the thesis that our universe was indeed created by one such being, that is barring other difficulties that might or might not be present. But we can't - again, we can establish the existence of virologists with the relevant powers and dispositions before considering the properties of the virus that B20 mentioned.

2. Validity is a property of deductive arguments. ID arguments are arguments in the sense of 'arguing a case', and may or may not contain faulty logic. Some may contain only correct logic - so, no invalid arguments involved -, and terribly bad priors.

No.

I recommend you read the excerpt from the paper I posted to the thread. I also recommend that you do not snip the other sections of the post I made to Bomb#20 since the ID comment was in reference to dependency on those sections in light of the specific comment referred to later, i.e. don't snip or you won't get what I was talking about since you took it out of context.

I did not take anything out of context. Rather, your ID argument was not just the previous arguments. It was an addition to them. You were saying B20 was making an ID argument, and you were saying that even though he had not (and has not yet ) considered your other points in reply to him. And I pointed out why he was not at all making an ID argument. The rest of your points could not turn it into that, even if correct.

Please stop snipping.

Please stop saying I'm snipping. It's not true.

It is undeniably true. You even admit to it below in your attempt at justification.

I'm replying to parts of your post, properly. I don't have to reply to all of them, as long as I can make a proper case against the part I'm targeting. And I was doing just that.

Let me get this straight. So, you think replying to some parts of a post and making a proper case against them is what Don meant by "snipping" ? Well, then, in that sense of the word, there is nothing wrong with snipping. And it's often interesting. So go snipping!

 

[laughing dog]

Let me get this straight.
So, you think replying to some parts of a post and making a proper case against them is what Don meant by "snipping" ? Well, then, in that sense of the word, there is nothing wrong with snipping. And it's often interesting. So go snipping!

Nope. I doubt you will ever understand it, and frankly, I do not wish to waste my time dealing with someone who thinks there is a greater than 50% probability covid was developed in a lab.

 

[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.

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.

 

[TomC]

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

 

[ZiprHead]

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

Yes, it's a dangerous plague released upon us by Dr. Fauci but it doesn't really exist and if it does it's not that bad.

 

[repoman]

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

If it did and it happens again in the next few years, then it doesn't matter now and it won't matter then /s

 

[Angra Mainyu]

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

Well, when people are accused of bad/irrational/etc. behavior, laughed at, etc., for assessing it probably originated in a lab, it usually matters to those people to defend themselves. That seems to be human instinctive behavior. And to those who strongly condemned people who said it probably originated in a lab - or just said it was a reasonable hypothesis, etc. -, it usually matters to them to defend their accusations to save face. That seems to be human instinctive behavior. So, the fight will likely go on independent of other considerations, as the opponents are all human.

All that aside, if one intends to take measures to reduce the chances of another pandemic, knowing how it started is probably important.

 

[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.

 

[Don2 (Don1 Revised)]

Since you insisted so much, here's one more point of yours:

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.

And yet, that sort of copying has not happened in any other known beta coronavirus. So, that sort of copying would seem to be rare, if it happened.

I don't think it is true that it hasn't happened, but regardless since it doesn't matter one way or the other, since you say it "would seem to be rare," you should be informed that this scenario you are claiming to be rare is the scenario that repoman's paper he submitted to the thread is suggesting. It is suggesting the possibility of recombination between a human cancer gene and a SARS-like virus, i.e. NOT a synthetic insert.

Additionally, no intermediate host has been found despite two years of searching with a lot of resources.

It was discussed in thread that in another case, it took many more years than two to identify an intermediate host while searching with a lot of resources.

Another hypothesis is that it was designed in that manner, by an entity that we know (with probability 1 for all intents and purposes) exists, and had the powers and very probably the dispositions to make such a virus.

That hypothesis in its full context is a wacky conspiracy theory. The different hypothesis which is being implicitly proposed in the paper that repoman referenced in the thread is that the initial SARS-like sequence, say the RaTG one for example--made its way to a human with cancer gene that had the 19nt and these were combined in a complex recombination process.

 

[Jarhyn]

Since you insisted so much, here's one more point of yours:

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.

And yet, that sort of copying has not happened in any other known beta coronavirus. So, that sort of copying would seem to be rare, if it happened.

I don't think it is true that it hasn't happened, but regardless since it doesn't matter one way or the other, since you say it "would seem to be rare," you should be informed that this scenario you are claiming to be rare is the scenario that repoman's paper he submitted to the thread is suggesting. It is suggesting the possibility of recombination between a human cancer gene and a SARS-like virus, i.e. NOT a synthetic insert.

Additionally, no intermediate host has been found despite two years of searching with a lot of resources.

It was discussed in thread that in another case, it took many more years than two to identify an intermediate host while searching with a lot of resources.

Another hypothesis is that it was designed in that manner, by an entity that we know (with probability 1 for all intents and purposes) exists, and had the powers and very probably the dispositions to make such a virus.

That hypothesis in its full context is a wacky conspiracy theory. The different hypothesis which is being implicitly proposed in the paper that repoman referenced in the thread is that the initial SARS-like sequence, say the RaTG one for example--made its way to a human with cancer gene that had the 19nt and these were combined in a complex recombination process.

that is honestly one of the most terrifying ideas. Ever.

A virus that gives you cancer if you haven't been immunized, and maybe even if you have?

It's the Tasmanian Devil but to humans.

 

[Don2 (Don1 Revised)]

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.

 

[Angra Mainyu]

I don't think it is true that it hasn't happened, but regardless since it doesn't matter one way or the other, since you say it "would seem to be rare," you should be informed that this scenario you are claiming to be rare is the scenario that repoman's paper he submitted to the thread is suggesting. It is suggesting the possibility of recombination between a human cancer gene and a SARS-like virus, i.e. NOT a synthetic insert.

I wasn't discussing the paper submitted by repoman's, but your reply to B20's post. And I did not claim it hasn't happened. The point is that the natural origin theory requires things that are less probable - even together - than the lab leak theory. Yes, I know you disagree, and a much more detailed analysis of the different possibilities can be found in Wade's article. But my reply was precisely a way of pointing out the improbability of one of the alternatives you were proposing.

It was discussed in thread that in another case, it took many more years than two to identify an intermediate host while searching with a lot of resources.

I don't have the links at the moment, but it seems improbable that there were resources on the same scale, given the motivation in this case. However, in any case it is another piece of evidence. Failure to identify the host only decreases the probability that there is such host, which was already improbable.

That hypothesis in its full context is a wacky conspiracy theory.

That is nonsense, but just in case, when I say it was designed, I do not mean it was done gene-by-gene. There are different ways of designing a virus, even ways that would give those results without leaving specific traces, if that is what you're getting at.

 

[Don2 (Don1 Revised)]

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.

 

[Bomb#20]

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. 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.

(Of course, saying rational people can disagree is not to say that all the people who disagree are rational. The folks here comparing the lab leak hypothesis to bioweapon/flat-earth/fake-moon-landing/greenhouse-effect-denial/Trumpism etc. have left the realm of rational discussion and are trying to settle a wide-open scientific question by character assassination of the skeptical. It's an intellectually dishonest rhetorical tactic and it's unbecoming in a forum for infidels.)

 

[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.

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.

 

[Bomb#20]

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

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.

Yes. That's what I said! Exactly which part of "That would seem to imply likely formation by recombination rather than by point mutation." didn't you understand?

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.

Certainly. And if Chinese hamsters really are a good candidate host, but in spite of this nobody has checked yet to see if they were the intermediate host, and pre-furin-cleavage-site-insertion "SARS1.9" was infectious in Chinese hamsters, and CGG turns out to be common in Chinese hamsters, that's an improbable coincidence too. Hardly impossible, but that doesn't make it sensible to take for granted that it must have happened. Absence of evidence is not evidence of presence.

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.

So who the heck said "necessarily"? (And of course gain of function isn't "opposed to" recombination -- people have been doing gain of function experiments by means of recombination for thousands of years.)

There was apparently a single insertion event -- twelve RNA bases got spliced in together. The information content -- which twelve bases they are -- arose in that event, or before it, or after it. That the bases changed to their current form afterwards is unlikely per the 1/400 consideration. For T-CCT-CGG-CGG-GC to have originated in the insertion event itself is 1 in sixteen million if it was a natural event but pretty likely if it was a GOF experiment -- that a coronavirus would become infectious to humans if it were to acquire a furin cleavage site there had been discussed in the virology literature for years prior to 2019. So a natural origin theory pretty much needs to assume the information arose before the insertion event: that the bases evolved into that order somewhere else and then were copied in -- i.e., natural recombination.

So if the sequence evolved naturally somewhere else and then got copied into SARS1.9 to create SARS2 in a natural recombination event, where was it copied from? Can you propose a hypothesis that doesn't involve improbable coincidences? Contrariwise, can you exhibit an improbable coincidence that the lab leak hypothesis depends on?

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?

Um, the Wuhan Institute of Virology reported that they were doing gain-of-function experiments on viruses with the potential to turn into viruses deadly to humans, in a Biosafety Level 2 lab. They appear to have been doing this because getting career-advancing scientific papers published was a more significant consideration in their minds than the possibility of accidentally killing people. So no, I am not making an "intelligent design" argument. Whether or not their creations include Covid, what Dr. Shi and her staff designed there was not intelligently designed.

 

[Bomb#20]

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