There was a period during the climate change debate—largely gone these days, I think—where skeptics were constantly coming up with new, scientific-sounding arguments against the idea of manmade warming. Typically, the claims were just technical enough that it was hard for lay readers like me to evaluate them, which meant they hung around in the air (and Fox News) until some climatologist took a break from real work to dive in and figure out what was going on. Almost without exception, these quasi-scientific arguments turned out to be wrong, usually egregiously so.
I wonder if we're entering a similar stage with proponents of the lab leak hypothesis? In the Wall Street Journal today, a pair of scientists argue that there's a specific location in the coronavirus genome that's often used in gain-of-function research. In this location, researchers splice in a code that generates two arginine amino acids in a row. There are six codes for arginine and therefore 35 possible combinations that will produce two in a row, and in the CoV-2 genome the combination turns out to be the rarest and least likely to occur in nature (a "double CGG"). It is, however, the most common in gain-of-function research because it's handy and easily available.
Is this true? How would I know? There are, of course, reasons to be cautious:
- This seems like fairly obvious stuff to a virologist. Surely someone would have mentioned this before if it were genuinely suspicious.
- The authors of the piece are a retired physicist and a physician/author who's been leading the lab leak hypothesis for a long time. No virologists signed onto this.
- The piece was published on the op-ed page, not the news pages.
So . . . there's probably nothing to this. But it will now swirl around among conservatives until it's conclusively debunked, and probably even after that. In any case, someone needs to get cracking on this.
Retired physicist should be a dead giveaway. They are the source of much of the mischief in the game of climateball. Even today Steve Koonin is out pimping his denialist book.
One thing I learned in following the climate wars was to never pay attention to a scientist talking outside his field. It should also be noted that early on there were several papers published which analyzed the genome of SARS-CoV-2 which found that there was no evidence of human manipulation of its genome.
An yes, Steve Koonin, your little Jewish fossil fuel lover and apologist
So we need the antisemitism?
That's Midgard. It's an experiment in Bayesian generative adversarial networks that's designed to demonstrate antisemitism regardless of context.
No matter what you do, Midgard is going to blame the Jews, because it's not an actual human being. It's a simulation of one that can't think or feel.
Obligatory movie reference: "They Saved Shootie's Brain".
Stop on
Agreed. In Spades. Because -- Ugh! -- ranking. By physicists, of course. Here's the usual XKCD reference: https://xkcd.com/435/
"One thing I learned in following the climate wars was to never pay attention to a scientist talking outside his field."
This. So much this.
It goes back way before the climate wars. I remember my father, a biochemist, speaking contemptuously of the efforts of Linus Pauling, a very good physical chemist, to promote megadoses of vitamin C as a prophylactic for the common cold. That was probably fifty years ago.
Let's not forget William Shockley, who pretty much wiped out his reputation in semiconductor research and as the Father of the Transistor, by his later life's obsession with eugenics-driven racism.
"a pair of scientists" leaves a lot to be desired (not your fault, Kevin). This guy Quay seems to be an oncologist with a company, and gives a lotta talks and such. Always suspect, since real scientists are too busy, y'know, working and stuff. His web page is a real hoot: real salesman, this guy. The Muller fellow, I can't track him down unless he's a theoretical physicist. In which case .... well, sure physicists like to pretend that everything else is stamp collecting; they're wrong about that.
That these guys are "scientists" doesn't count for much, unless they're different guys. I mean, I'm a "scientist": I'm a PhD computer scientist with a number of research fellowships and such, maybe I should be writing op-ends on covid!
You know how you can tell how someone's a working scientist (or at least a mathematician)? When you can verify that they're keeping abreast of current research. I know more than a few people who've taken the approach "All I need to know I learned at university" ... who graduated in '80 or thereabouts.
And, it doesn't need to have been the object of gain of function research to have escaped from the lab.
It's not clear to me that there has yet been any indication that "gain of function" research was being performed using Coronavirus backbones. The passages from the relevant funded grant proposals that I have seen quoted - for example, in the Nicholas Wade article - indicate only that spike proteins would be introduced into other viral vectors (meaning non-Coronavirus, and likely adenoviral), which is rather different.
Introducing spike proteins in adenoviruses is exactly how J&J's, AZ's, and Russia's vaccines were made.
Based on guidelines from Covid-19's blueprint.
Yes it does, because otherwise the "debate" is pointless. If it's a naturally occuring virus that escaped from a lab then it was already circulating outside the lab anyway.
Weeeeeell, there's a lot of stuff "circulating outside the lab" in animal populations that hasn't crossed over into humans; collecting wild samples of otherwise pretty isolated virus and culturing it in a lab could lead to an outbreak (if folks aren't careful) of something that would have been unlikely to cross over into humans otherwise. Covid-19 has killed millions of people and cost humanity trillions of dollars, so I think it's reasonable to up the safety standards at labs working with human-communicable virii regardless of what happened here.
Fully agree with what folks are saying here, though--a WSJ editorial page piece by a couple of non-virologists talking out of their asses about gain-of-function is evidence of exactly nothing, and reads a lot more like infotainment for the crowd that wants to rehabilitate El Trumpo as somehow (a) tough on China and (b) wrongly persecuted by a close-minded deepstate of government scientists. "Grain of salt" doesn't begin to cover it.
Pffftt. Covid 19 is overrated in terms of pandemic scale. There is nothing to rehabilitate. Trump will be arrested and seen a invalid soon enough. A con man's con. Nursing home's problem.
Dude, without modern medicine - and by that, we mean medicine invented in the last decade - millions would have died. It would have made the 1918 flu look small.
Dude, right back. Look at 1889-94.
This isn't a end of the world type of thing.
Outside the lab can be a lot of places.
But you are obviously right in that the lab is situated where it is because that's the strategically best place for it to be.
The issue is simply that a final answer will never be determinable in the circumstances, and so those circumstances become the real issue.
Microbes may be in existence outside a lab (duh) but not in ways that bring them into close contact with humans. Yersinia pestis (plague) is in rodent flea guts all over the world but it's thankfully rare that the bug leaves its happy home and goes on a binge in the human bloodstream. A lab with poor protocols is not a bad place for a pathogen to get into a human system.
Please note I am NOT asserting the lab leak story is true.
"This seems like fairly obvious stuff to a virologist. Surely someone would have mentioned this before if it were genuinely suspicious."
Apparently you haven't been paying attention. Someone has mentioned this before. From Wade's article in the Bulletin of the Atomic Scientists:
"“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said. [1]"
The Baltimore comment is perplexing, mostly because it's BS. If you look around the Coronavirus family tree, furin cleavage sites are all over it. The Nicholas Wade article made a big deal about this and I couldn't figure out why either (that is, outside of dishonesty or ignorance, as per usual). The specific comparison was to the closest known relative to SARS-CoV-2, but "closest known relative" really doesn't mean much when, in terms of sequence divergence, virologists estimate that the most recent common ancestor with SARS-CoV-2 was extant something like 50 years ago, an eternity in viral evolutionary terms. Beyond that, of course, lateral transfer of sequences is common, and so the appearance of the furin cleavage site just isn't unexpected or surprising.
Double CGGs for 2 consecutive arginines may be unlikely, but far from impossible. That's a piece of information for which I'm afraid no proof either way will ever be forthcoming.
Well, now the Drum heuristic points the other way: internationally-recognized virologist versus anonymous internet commenter, saying contradictory things about a topic of which I know nothing. I'm tentatively backing the Nobel prize winner.
Hey, yeah, that's how evidence works, after all: the appeal to the highest authority must be right!
Anonymous, yes. Practicing molecular biologist, yes. Works professionally with engineered viruses and with sequence comparisons, yes. Practicing virologist, no.
Evaluate accordingly.
You're way cool! I often wish I had chosen a different career path, back in the day. Math is cool, but ... it only gets you so far and inasmuch as it's a useful description of the subject under consideration.
Also, maybe you should shop around a bit more. The Nobel prize winner is just one of a number of voices on this topic. He is currently in the minority. The balance of professional opinion at the moment is basically that a lab leak is possible, but there is no evidence for it. There is even less evidence for purposeful engineering of SARS-CoV-2. The zoonotic pathway is as yet not known, but it took several years to work out the pathway (from bats through civets) for SARS-CoV-1 and even now I don't think you could characterize that as a solid consensus.
For political purposes a lot of people want this answer RIGHT NOW. It won't work that way. Give it another 5 years.
".. but there is no evidence for it. .."
The fact that the origin of the epidemic was near the lab is in fact evidence that it came from the lab. Not conclusive to be sure.
"...Give it another 5 years."
So perhaps people shouldn't have been signing petitions last year declaring the case closed?
A great, another Jewish poster. Hopefully you are better than Guthman
One thing that perplexes me (and it’s the only aspect of the affair I’m qualified to opine upon) is the assumption that if the virus escaped from the lab that’s somehow exonerating for Trump. But this seems precisely backwards. During the Obama administration, the USA had its own experts based in the Wuhan lab itself. This obviously gave the USA its own ability to gather information and arguably could have provided even more advance notice and allowed our government to cut through Chinese obfuscation. But Trump shut down that program and blinded us to the danger.
More importantly, regardless of the origins of the virus, Trump had significant warnings and time to prepare. He deliberately downplayed the warnings and squandered the opportunity to prepare for the pandemic.
Truly, if the Chinese unleashed a bio weapon upon us, its name was Donald Trump.
Actually, the geographical origin of the COVID-19 pandemic is not evidence that it came from the lab. The viral research lab in Wuhan was placed there _precisely_ because the area around Wuhan was known as a source for novel viruses, particularly Coronaviruses. So your reasoning, such as it is, is circular.
"Give it another 5 years" for figuring out the precise zoonotic pathway by which SARS-CoV-2 made its way into the human population. So don't misunderstand here. The case is practically closed as far as an artificial origin for SARS-CoV-2 (see the Robert Garry video someone else has posted below for a very long but cogent account of the evidence for this conclusion).
"The fact that the origin of the epidemic was near the lab is in fact evidence that it came from the lab. Not conclusive to be sure."
This point is worth dwelling on some more, because it also betrays a lack of knowledge about the city of Wuhan. In terms of population and area Wuhan is about as big as NYC. It is also a major hub, especially for the wildlife and meat trades in China. Your reasoning here is much better applied to these characteristics of Wuhan.
Really, this whole subject is just a chance for people on the left side of the Dunning-Kruger curve to clog up the discourse.
The city of Wuhan??? Coronavirus's are all over the world man. Your obsession with slant eyes is a big part of the issue. I would argue 2013, we saw covid-19.
"This point is worth dwelling on some more, because it also betrays a lack of knowledge about the city of Wuhan. In terms of population and area Wuhan is about as big as NYC. It is also a major hub, especially for the wildlife and meat trades in China. Your reasoning here is much better applied to these characteristics of Wuhan."
This all just relates to how strongly this points to a lab origin. If the first known cases were hundreds of miles away (with no known connection to the lab) people probably wouldn't be talking about a lab leak.
"This all just relates to how strongly this points to a lab origin."
No, it doesn't. Again, your argument is circular. The only reason there's a viral research lab in Wuhan is because that's where a lot of novel Coronaviruses are found, and can move from animal to human populations.
Regardless, very few of the people going on about "lab leak" are actually interested in the origins of SARS-CoV-2. Basically, anyone who isn't capable of sitting through the entire 2 hours of the TWIV video (posted by someone else, below) is simply worth ignoring, because "lab leak" is just a tool for another goal to them. It's veracity is not important.
"No, it doesn't. Again, your argument is circular. .."
My argument isn't circular. Consider this from a Bayesian perspective. Imagine yourself back in 2018. Someone tells you a novel corona virus will emerge in 2019 and end up killing millions of people. You will have some prior for the odds it was from a lab leak as opposed to a purely natural origin. Say 1 in 1000 or 1 in 1000000 but something.
You will also have priors for given that it was a lab leak or given that it was natural for where in the world the first cases are likely to be seen. Two heat maps. The lab leak map will presumably be concentrated around the labs doing corona virus research, the natural origin map will be more spread out.
Now you are told the origin and must update your prior about lab leak or natural origin. This will depend on the relative intensities of the heat maps in Wuhan. If the lab leak heat map was 10 times as intense as the natural origin heat map in Wuhan then the lab leak odds will improve by a factor of about 10. So now 1 in 100 or 1 in 100000.
You are arguing that given a natural origin the first cases are more likely to appear in Wuhan than in most places which is a good point (if true). But this will just affect prior up date factor. It in no way makes the argument circular.
Ya, thats fake.
There was some concern early on that it could have been from a lab, and rightly so. But that was effectively debunked fairly early on too.
Local officials tried to hide the outbreak early on, and the Central gov't there is afraid of outsiders, so that fosters all sorts of conspiracies.
Baltimore sadly is only one of a number of people afflicted with Nobel disease.
https://en.wikipedia.org/wiki/Nobel_disease
It's already up on Powerline as though it were fact. And as I was reading their post on this, I was thinking that this is a difference between true believers in God and religion and those who aren't. Those who believe think that there is a concrete explanation for everything - hence, there is no chance that the genome for the virus developed randomly. While those who don't believe except the possibility of randomness - hence, in a world of infinite possibilites, sometimes you roll snake eyes.
I would say that virologists working on other Coronaviruses could put this to rest fairly easily. Just look at the sequences for the furin cleavage sites in other Coronaviruses, and if single and/or double CGGs appear in any of them, that rather clearly indicates that this codon usage, however unlikely, nevertheless occurs naturally. There are plenty of other Coronaviruses that have furin cleavage sites and those sequences should be available.
So if you don't find this double-grouping in related species (I like reference in re viruses) does that mean that it doesn't occur in nature? Or does it mean that a naturally-occuring example hasn't been identified yet? As Sagan (quoting Rees) was fond of saying, absence of evidence is not evidence of absence. Or was that Sherlock Holmes who said it first 🙂
That's one conversation that needs to happen. The other is this: How would you make a differential diagnosis? That is, assuming a naturally-occuring example was found, how would you differentiate between 'just happened' and 'deliberately created'?
No, it's just evidence to be added to the pile for evaluation. The CGG codon for arginine is not as common as the others; finding two in a row may or may not be less likely depending on how the sequence originated (triplet repeats are common). But "less common" does not mean "never happens in nature," or "hasn't been observed in nature," or anything else that would rule out a natural origin. Notably, even when SARS-CoV-2 first emerged in Wuhan there were already 2 variants (A and B); the B variant was found at the notorious "wet market," while the A variant spread in a number of other markets in the area. They differ by 3 bp (out of a genome of ~30,000 bp) but not in the CGGs that encode the furin cleavage site of the spike protein. Any theory of the origins of SARS-CoV-2 has to account for the appearance of these 2 variants. It's significantly easier to do this with a natural origin, as opposed to a lab leak.
Unfortunately, it works the other way around too. Finding CGGCGG in other Coronaviruses would be really good evidence for a natural origin in SARS-CoV-2, but in the end you can never fully prove a negative. It's always possible it got in there some other way. It's just that as scientists we go with the most likely explanation, not the politically expedient one, or the one we happen to like, or the one that would be the coolest and make for the better movie.
Why not go with no conclusion either way? The Scottish Verdict? Is that somehow impermissible? "We must do something, this is something, therefore we should do it"?
Something about that line of thinking doesn't seem quite right ... 🤔
Because that implies that the zoonotic origin and lab leak ideas have the same weight. They don't. Not having conclusive proof for one or the other is not the same as saying we do not have evidence that favors one over the other, and at the moment the balance of the evidence is pretty strongly on the side of an entirely natural origin.
A good scientist keeps an open mind, but is still capable of making judgments. New data could change that judgment, but that data does not yet exist.
That's ... not how it works. If you rolled double sixes three times in a row would you conclude the dice were loaded? Or that a coin was biased because it came up heads ten times in a row when you flipped it?
I hope not.
Actually...it is. Your analogy doesn't really apply regardless, but the probability of dual CGGs is quite a bit higher than the probability of 3 sixes in a row - and if any other Coronaviruses exhibit the same sequence, well, apparently those 3 sixes did happen.
Besides, we're talking about the totality of the evidence. There's too much that the lab leak theory doesn't do so well at explaining - the simultaneous emergence of 2 SARS-CoV-2 variants in Wuhan, the lack of a known ancestor, etc.
From a later thread on this blog, an explanation of the likely natural origin of the furin cleavage site, and the dual CGGs, from an actual virologist, thus someone with more expertise on this topic than I have:
https://web.archive.org/web/20210527162603/https://twitter.com/K_G_Andersen/status/1391507230848032772?s=20
Note that the two CGGs are not independent events in this analysis, and therefore the odds aren't really that stacked against them. The FCS likely arises from a frameshift mutation, which is a different story from what we've been considering here.
I repeat, this isn't how science works. You sound waaaaay out of your depth and there is no point in talking to you if you don't know or don't understand the basics.
Big hint here: This may come as a surprise to you, but we aren't in a court of law. Don't act as if we are.
I don't think I was trying to tell you how science works. I have cited a couple of virologists who were. Your argument is with them, but I have a feeling that they're all flooded with earnest diatribes from laymen telling them why their expertise in virology - or the actual evidence that they discuss - counts for nothing.
Chuckle. No, these virologists aren't telling anyone 'how science works.' This is me telling you how science works. You seem to be under the misapprehension that I'm arguing with you; I'm not. I'm giving you basic instruction. For free, as it turns out, which is not my usual rate. You're welcome to last word, because I'm not going to bother engaging with someone who insists on robotically repeating their talking points rather than responding to the discussion.
Here's something from a different pair of scientists.
Romeu, A.R.; Ollé, E. SARS-CoV-2 and the Secret of the Furin Site. Preprints 2021, 2021020264 (doi: 10.20944/preprints202102.0264.v1).
https://www.preprints.org/manuscript/202102.0264/v1
I think their main point is "The Arginine doublet is encoded by CGGCGG codons. Surprisingly, none of the Arginine doublet of other furin site of viral proteins from several type of viruses, are encoded by the CGGCGG codons. This makes it difficult to consider a virus recombination as mechanism for the PRRA acquisition. "
Or see this:
https://www.news-medical.net/news/20210217/The-origin-of-SARS-CoV-2-furin-cleavage-site-remains-a-mystery.aspx
A different view:
https://www.sciencedirect.com/science/article/pii/S1873506120304165
Nobody denies furin cleavage sites occur in other viruses. The question is how did SARS-CoV-2 get this particular sequence, given what other viruses in its subgenus are like?
From the paper you cite: "Moreover, SARS-CoV-2 is the only virus in subgenus Sarbecovirus having this feature, while even its closest relatives, bat coronavirus RaTG13 (sequence identity 97.7%) and pangolin coronaviruses (92.9%–90.7%), do not have furin site. "..... "The furin cleavage site of SARS-CoV-2 spike S1/S2 is formed by a insertion of PRRA in comparison to other Sarbecovirus including close relative RaTG13, showing it occurred very recently and independently. "
By random mutation in the amount of time ("very recently") is allegedly very unlikely. By recombination (i.e., obtaining parts from another virus) needs another virus to have a similar sequence.
The "closest relatives" to SARS-CoV-2 are the closest _known_ relatives. That tree is not fully characterized. The most recent common ancestor for RaTG13 and SARS-CoV-2 dates back something like 50 years ago, based on that level of sequence divergence. So unfortunately this is still an argument from ignorance.
Exactly. Well that and the fallacy of false bifurcation. "It is a capital mistake to theorise before one has data. Insensibly one begins to twist facts to suit theories, instead of theories to suit facts.”, sez one S. Holmes 😉
So, suppose the scientific consensus at some point becomes that the virus was man made and likely accidentally released. Then what?
"... Then what?"
You try to reduce the chances of it happening again. By for example not performing dangerous experiments for no good reason. Which actually seems like a good idea in any case.
“ Which actually seems like a good idea in any case.”
Exactly. Should be doing that in any case. So why is this such a big issue? Seems like something scientists should be interested in no doubt
Does anybody think that’s why we are taking about it here? So for the people who see this as a political issue I again ask the question. If you are right, then what?
There is lots of money granted for virus research, publicly probably about 100m/year (https://www.nih.gov/news-events/news-releases/nih-establishes-centers-research-emerging-infectious-diseases). There are also research foundations like Gates and Wellcome that fund this stuff to a greater extent. If additional laws were enacted that restricted required public oversight, these institutions would get much needed sunlight on their activities. In particular, they also act as venture capital to fund startups with unique approaches to vaccines and other pharma.
I don't know about you, but I feel uncomfortable with the idea that they may be both funding the basic research which led to the lab leak and also profiting from the companies which created the vaccines.
It's unfortunate that the accident occurred at WIV, which looks like it was doing quality research. It would have been better if they were allowed to continue researching the origins of covid rather than shut down and evidence destroyed. I think the world will have to think twice about funding basic research in China as a result.
Neither the NIH, WIV or Gates Foundation are making profits from research that led to vaccines. They're two entirely different segements of an industry. What is this werid amalgamation of 101 conspiracy theories?
At the time of SARS, China was blamed for a lack of transparency and the sale of bush meat in its wet markets.
We can see that China hasn't changed all that much since SARS.
While they banned the sale of bush meat in wet markets, their enforcement slacked off considerably after a few years and they're not any more transparent now than they were 18 years ago.
So I guess the question might be moot as China won't change unless the rest of the world passes harsh sanctions against China for failures in its regulations, *regardless* of the origin of SARS-CoV-2.
Harsh sanctions will make "change" even less likely as even more shortcuts will be taken.
"... So why is this such a big issue? Seems like something scientists should be interested in no doubt"
Like it or not a hazard that has actually occurred and killed millions of people is going to be taken more seriously that one which is just hypothetical. Airplane regulations are sometimes said to be "written in blood" because often they are not enacted until after a fatal crash.
"By for example not performing dangerous experiments for no good reason."
So far there is no evidence that anyone was.
"So far there is no evidence that anyone was."
At this lab or in general?
At this lab.
The "gain of function" research you hear so much about is derived from funded NIH proposals that involved a component that was performed at the Wuhan lab. Those proposals, however, involved "gain of function" (at least as far as I can tell, from my own reading of the proposals) only so far as putting Coronavirus spike proteins into other viral vectors (most likely Adenovirus), which fairly routine for protein studies. There is nothing there about engineering new Coronaviruses; just collecting them in the field and analyzing their genomes.
The Chinese researcher who has thus far garnered the most notoriety is well known and respected in the field, and has dutifully published her results regarding novel Coronaviruses (again, collected in the field, not engineered) for many years.
"At this lab."
So how about elsewhere?
I'm not going to try to vouch for viral research everywhere else in the world. All I'm saying is that I have not yet seen any testimony or evidence to indicate that the viral research lab in Wuhan was performing "dangerous experiments for no good reason."
Suffice it to say that in my own work, when we just want to use viruses to move genes into cell lines for study, there are multiple regulatory steps to clear before we're allowed to work with the virus, and a slew of (well enforced) precautions that we follow.
Then what? You ask that as if the answer isn’t obvious: A US nuclear first strike on China. Duh!
Is that before or after they pay the $10 trillion in reparations?
How much of that ten trillion will go toward a blowout party for El Jefe's August 2021 reinstatement?
Well, adding President Donald J. Trump The Great to Mount Rushmore ain't going to be cheap, either.
It will be a big job, no doubt. First they will have to erase those other guys and then replace them with, oh, I suppose, an AR-15 and a big letter Q. Of course, Trump’s head will be at the center and 3 times the size.
Hmmm... sounds like repetitions of CGG is a standard mutation mechanism. See Fragile X Syndrome.
Something being rare but successful is not argument against natural origin.
Being successful is literally the only reason why natural origins work.
Very true. This type of argument was a favorite of evolution (as you note) denialists for quite a while - "The [pick your favorite complex structure] could not possibly have evolved naturally, therefore [pick your favorite god] had to have created it!" As far as I can tell, that's fallen out of favor because archeologists kept finding intermediate structures that showed [pick your favorite complex structure] iterating over time.
Something may be rare, but if variants are being constantly created by the billions and trillions and over relatively short periods of time, as happens (especially) at the level of bacteria and viruses, probability of any physically possible variation showing up closes rapidly on: "Yup, that's gonna happen, and real soon too!".
This type of argument is common enough to be a named fallacy. Unfortunately I can't remember what it is. It's not the Gish Gallop, nor the God of the Gaps (or is it?) but it was employed for the same reason, to discredit the theory of evolution. Does anybody perchance know what it is?
God of the Gaps would describe it.
(The Gish Gallop is a different tactic where you spew nonsense arguments at a rapid clip, trying to overwhelm your opponent with sheer volume. It's more rhetorical technique than logical fallacy. The entire Trump Presidency was one epic-length Gish Gallop.)
The Gish Gallop is a standard sales technique, which that former guy employed for literally his entire life. Yet there are always more rubes...
Sorry about this digression. I'm trying to stick to my areas of relative competence.
Anthropomorphic projection, 'I have no idea why this exists therefore someone made it'.
...Which is precisely why we should keep up social distancing and masking until the population reaches herd immunity threshold.
The paper by Dr Quay that this article is based on, does have extensive analysis and references. If you have a couple of hours to spare, it's here:
https://zenodo.org/record/4477081/files/SQuay_Bayesian%20Analysis%20of%20SARS-CoV-2%20FINAL%20V.2.pdf?download=1
It's an odd argument that something shouldn't naturally exist, when in fact, it *can* exist. Even if the odds are 1:100M, someone's going to one day win the lottery, after all.
Yes, but if something is easy to produce by Method 1, and has a 1/100 million probability of occurring by Method 2, and it occurs, you should update your priors on which method was operating.
"you should update your priors on which method was operating."
So, let's take for instance the zoonotic transmission theory. It relies heavily on the argument that, because it's an exceedingly common (eg natural progression of viruses), therefore, zoonotic transmission should be the prior theory.
Put another way: If all we go by is probabilistic review, zoonotic transmission is the prior theory, is it not?
I certainly disagree that zoonotic transmission is the likely explanation.
I think that on weighing of the circumstantial (since there is no direct) evidence, the accidental release is the more likely case.
And directly, the rarity of a combination of amino acids found in a particularly important ORF section of a virus, does not in itself make it unlikely; all it does is make it a black swan/tail end event, probabilistically speaking, of course.
It's been pointed out time and again that evolution denialists refusing to change their position with new evidence to the contrary is _not_ a refusal to update priors. It's just the weight they place on those updates is very, very low. That's what I dislike about the sort of people who say they are taking a Bayesian approach on the grounds that arguments of implausibility when testing a hypothesis often come down to an arbitrary choice of significance level (that is, α): Their choice of priors stink just as bad if not worse.
The vast majority of practicing virologists disagree with you. Even just going with the human intelligence angle, as opposed to anything related to actual science, the researchers at the Wuhan lab were quite diligent about documenting and publishing the novel Coronaviruses they identified in the course of their work. Moreover, if they had the original SARS-CoV-2 or most closely related virus on hand, it would make more sense to release the sequence, if only to let the world know that they collected it in the field and didn't make it.
But the science weighs heavily against the lab-leak idea. There are a lot of strains to this, but to take one example: when SARS-CoV-2 first emerged in Wuhan there were already 2 variants (termed A and B; all subsequent strains are derived from one or the other of these); the B variant was the one found in the notorious "wet market," while the A variant was found in a number of other markets in the area. Any account of the origins of SARS-CoV-2 has to explain the simultaneous emergence of these 2 variants. This is a lot easier to do with a zoonotic origin than with "lab-leak."
MDB...
Your argument -- most virologists etc., -- is something of an informal logical fallacy. See: Appeal to authority.
Granted, a large part of why the accidental release theory feels like a long shot is because there has to be an alignment of the stars, so to speak. I fully acknowledge this point.
But, that's what happens in black swan -- tail end -- events. Probabilistic arguments survive until they fail, do they not?
And while it may seem on the verge of embracing fringe theory, an improbable outcome is nonetheless possible when the stars align.
Absent direct evidence (which seems unlikely to ever occur, given the opacity of Chinese authorities), the only answer is to collect as much circumstantial evidence on all sides of the issue, then weigh them.
As for finding the intermediate host, again, see Chinese opacity. If ever there was a motivation for the Chinese to find the intermediate host to clearly link SARS-CoV-2 to zoonotic transfer, one would expect them to be working furiously. Civets were linked within a year of SARS. So was MERS.
I'm just saying, you might be waiting for Godot. Maybe instead, do what I suggest and get everyone to collect as much circumstantial evidence on all sides.
Actually, the bats-to-civets-to-humans pathway wasn't really worked out for several years, and is still not really strong enough to qualify as a solid consensus in the scientific community.
I am not engaging in an appeal to authority. It is an appeal to expertise. Experts are, of course, far from perfect, and a reasonable scientist/expert will still have an open mind on this question. But the balance of the evidence at this time is heavily in favor of an entirely natural origin for SARS-CoV-2. To say otherwise would be the scientific equivalent of "both-sidesism." We cannot discount the lab leak idea, but the state of evidence for it has accurately been described as "...half-truths, misrepresentations, and tendentious conjecture."
MDB...
I mentioned this previously, but even while bats had not been identified as the original source reservoir, civets (and camels in the case of MERS) were immediately identified as the intermediate (closest) hosts, from whence the virus jumped to humans. I do not want to give anyone the sense that we should stop looking for an intermediate host, mind you, but that we should not be so focused on just looking for an intermediate host.
But anyway, been meaning to ask you *why* you think that the A/B split adds to the circumstantial natural zoonotic transfer.
I understand the timeline required to produce the split, but it seems quite possible that one could force the timeline by serializing infections, whether through culture or animal testing (or obviously, by directly manipulating the coding).
I also understand that a natural virus reservoir in an intermediate species would be expected to have multiple (maybe hundreds or thousands) of such splits -- bat caves after all produce hundreds of variants -- but the same is true of a lab of several thousand viruses cataloged and cultured, is it not?
Because a lab leak has to happen twice, with each of the 2 variants present in the lab (for whatever reason). Zoonotic origin takes care of all of this, because multiple variants are naturally present in whatever reservoir this virus came from, and likely in a single animal.
It's academic regardless, given that there is absolutely no evidence for a lab leak, at least on the scientific side of things. Even the notorious FCS/dual-CGG has a ready explanation:
https://web.archive.org/web/20210527162603/https://twitter.com/K_G_Andersen/status/1391507230848032772?s=20
(This is from a later thread on this blog, and represents a Twitter summary from an actual virologist, who is therefore someone with more expertise than I have on this topic. Note that the dual-CGGs do not represent separate events, and likely arose from a single frameshift mutation that has been observed in other Coronaviruses).
It's really an Occam's Razor sort of thing, at this point. The state of evidence for the lab leak is accurately described as "...half-truths, misrepresentations, and tendentious conjecture." Virologists in general don't see anything unusual going on here.
Motherfuckers still denying the many worlds theory.
Don’t forget the targeted audience. Including a real expert in this theory would make it suspect to the Trump crowd. They believe the real scientists are in on the conspiracy.
The Trump crowd??? Doesn't exist. The theory has holes in it due to virus itself being very natural in its structure. You know, this isn't the first time a coronavirus has gone global and led toward a pandemic. See 1889-94. The Napoleonic era sweating sickness are 2 strong contenders for previous coronavirus outbreaks which focuses on the elderly. I had a coronavirus virus in 2009 fwiw. Something I probably mentioned to forget mentioning before. I mean they are everywhere, people usually think it is a "really really bad cold".
"Something I probably mentioned to forget mentioning before."
Silly bot! Your algo is showing!
Bots can't get colds!
Then East Asia will blame "the west" and create a alternative theory(China is already blaming Europe for "covering" up its fall 2019 outbreak. Liberalism as burst from the enlightenment really needed functioning capital markets and the huge debt to growth machine called the industrial revolution to keep the plebs at arms length. Between government bailouts in the 30's and information boom echo between 1960-00, it kept things down. 21st century capitalism is a fraud. Advantage East Asia.
"(China is already blaming Europe for "covering" up its fall 2019 outbreak...." Where's that parenthetical end?
Classic Bayesian error. Bot doesn't appear to know that every opening bracket has a matching closing bracket. Need to expand the scope of its proximity weightings.
Muller is a known contrarian. He is a legitimate, well published, retired Professor of Physics at UC Berkeley. For many years, he was a vocal skeptic of global warming. He received a Koch Bros funded grant to expose the liberal "lies". To his credit, his team "discovered" what the IPCC has reported for many years: global warming is real, man-made, and accelerating. A true global threat. He actually changed his tune after he did real research into the subject. Once again, he is proclaiming in the pages of the WSJ the Trumpist claim that a Chinese engineered virus escaping the Wuhan lab is the likely source of covid. Once again, he is outside of his subject matter expertise. Take with a VERY large grain of salt. ANY argument from statistics requires independent verification. If I flip a coin 100 times in a row and get heads 100 times, is it a miracle or a crooked coin? Statistics CANNOT answer that question. Muller's contrarian viewpoint history is on display here: https://en.wikipedia.org/wiki/Richard_A._Muller
Lol,the IPCC covered up and lied about man made global warming. They reduced the severity and gave energy companies cover for denials.
IPCC is a consensus document, and as such, is very conservative estimate. Even at that, it concludes that man made global warming is real, and accelerating. Your accusation (offered without proof) is irrelevant.
Actually, global warming has been around ever since earth developed something approximating its current nitrogen/oxygen/CO2 mix. Good thing too - otherwise we'd be a LOT furrier than we currently are and a haircut would be a very expensive full body experience.
The phenomenon wasn't suspected until a little over 200 years ago, depending on exactly when Joseph Fourier started investigating solar heating affects and came to the conclusion that even then, the earth was warmer than an airless rocky body at our distance from the sun should have been. Later research by others identified possible heat retaining gases, including CO2, and then fingered CO2 as the primary culprit. (Other gases, including water vapor and methane are also heat trappers, but CO2 comes first and the others "pile on".)
By the 1890s, Arrhenius had even come up with a pretty good calculation of the relationship between CO2 and temperature and (with Arvid Högbom) did a remarkably good prediction of what would happen if we continued "evaporating" our coal mines into the atmosphere. Arrhenius and Högbom also doubted it would happen - although by 1908 Arrhenius recognized that we were burning through coal more quickly and shortened his prediction of a rise of 5-6 degrees celsius from 3000 years to a few hundred years. Of course, we kept burning coal and then added oil on top of that, so...
Check out history.aip.org/climate/co2.htm for a nice synopsis.
Yes, Fourier, Tyndall. But the Swedes were the one that really got the ball rolling which became the keeling effect.
Man-made global warming (driven by CO2 emissions) began with the industrial revolution and really took off after WW2. Natural global warming happens on geological time scales. Not relevant to this discussion.
Reread the last paragraph ^-^ DButch buries the lede, methinks, in history ^-^
The TWIV crew host fellow virologist Robert Garry and discuss the lab-leak hypothesis at length in TWIV 762. Garry was one of the first to publish on Cov2 origins.
https://www.microbe.tv/twiv/twiv-762/
https://medicine.tulane.edu/departments/microbiology-immunology-tulane-cancer-center-tips-advisory-committee-tips-mentor/faculty
I think it would be helpful if, going forward, we just didn't listen to anyone incapable of sitting through the entire two hours of this video. I just finished it and it was highly enlightening. Anyone not interested enough to watch the entire thing isn't really that interested in the origins of SARS-CoV-2. They have other agendas.
I’m content to give the lab leak theory a chance because, well, it really doesn’t matter. It doesn’t change anything. The Chinese would never admit it. And even if they did, there is nothing to do about it. Maybe we can re-think the wisdom of some of this research but we won’t.
On thing is certain, the Chinese government is pretty awful. I wouldn’t put anything past them. They have a warped value system as do most governments these days, but theirs is particularly noxious. There is little reason to give them credit for anything.
But that has nothing to do with the Chinese folks I work with or with the chines owners of my favorite restaurant. They are fine.
The Chinese system is based on tribalism. The problem is, muttering dialectical nonsense ain't gonna cut it. Just yelling lab leak without proof is lolz. Why even bother???? Justin, what do you think will happen when East Asia is cut off from US debt financing??? Pooof to capitalism, that is. The value of the $$$$ will collapse bringing us forced debt liquidation that 2008 wanted. Oooooooooowwwwwwww!!!!! Maybe the black man will be at peace then, watching white unemployment surge to meet his.
I don’t think it matters so all the awful things you suggest don’t really follow from my opinion. So indeed, why bother? I’m not bothering.
Also, 'tribalism' is the last thing the Chinese government resembles.
Also, you're not allowed to say "tribalism."
https://reason.com/2021/06/04/journal-of-hospital-medicine-tribes-tribalism-apology/
I have one for you....
SARS-CoV2 wasn't a lab leak....
It was a different virus that was leaked from the lab the recombined with SARS in the wild. A "no fingerprints" release.
Let the conspiracies commence!
More evidence Trump totally wazzed himself Saturday,
he goes on Fox today to say something outrageous enough to divert attention from it,
https://www.rawstory.com/trump-facebook-phony-lockboxes/
More evidence that . . .
No thanks. I'm enjoying the ****-free silence.
Arguments for the origin of this virus based the supposed implausibility of scenario vs another leave me cold. Especially when they're about People Doing Things. TL;DR: the only person who could tell you why Hiroshima was nuked is Harry S Truman himself (Or more philosophically, the difference between the past is the future is that you can't predict the former, nor read about the latter.)
These arguments won't be settled by expert opinion; they'll be confirmed or ruled out based upon documentation and personal testimony, and say, why can't people simply say they don't know and leave it at that? People giving you directions when in fact they haven't the faintest clue as to how to get there from here aren't doing you any favors. Quite the contrary.
If they handed these out at vaccination sites you'd drag in a huge number of the junior dingbats who think they're immune,
https://old.reddit.com/r/pics/comments/nubx3p/i_made_a_biker_style_covid19_vaccination_patch/
This makes it 'edgy', like a tattoo, because now they think they're taking a huge risk getting the vaccine.
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From Laurie Garrett, a virologist's take on origin of COVID-19, fur trade in China and bats by way of raccoon dogs.
Laurie Garrett
@Laurie_Garrett
·
Jun 6
Germany's immensely popular virologist Christian Drosten has a #COVID19 podcast admired across the nation. He has worked in the field directly with #SARS #SARCCoV2 #MERS & bat #coronaviruses. Here's what he has to say about the "lab leak" theory.
https://bit.ly/3uWcmMa