I thought we couldn’t trust virologists because they’re all going to lie just to keep their grant money coming?
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I’m not sure what to tell you if you think that, I certainly never said anything like that.
For the record I think Socrates (pronounced SO-crates) was mostly JAQing off and his method is dumb and annoying, but I carve out a special exemption for him as the original JAQ off.
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I should have clarified that my claim is strictly about science / scientists in practice and am not sure if it applies to philosophy. Answers (even bad / wrong ones) are the products that scientists make and are judged by. They are expensive and hard to get. It’s never questions. Sometimes it appears like the hard work was coming up with interesting or paradoxical questions but that’s never the hard part. Questions Guy is basically Ideas Guy.
Socrates: “Do you even know what love really is, exactly?”
Ancient dude: “Uh… I guess not?”
Socrates: “I are the greatest philosopher of all time!”
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Bump.
https://nicholaswade.medium.com/origin-of-covid-following-the-clues-6f03564c038
This is quite a long argument that COVID originated in a lab. I have to say that I found it quite convincing. I should warn that the author is a race-science bro, but I don’t think that’s relevant except insofar as it demonstrates a willingness to make unpopular arguments.
Please read the whole thing if you want to comment on it, but the argument is very briefly this:
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With the previous novel coronaviruses, the intermediate host species was identified and several variations of the virus were identified as it gradually became more infective in humans. SARS-CoV-2 emerges fully formed, there are no known previous iterations.
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In comparison to its closest known relative, SARS-CoV-2 has what’s called a furin cleavage site. Essentially this is an RNA sequence (P-R-R-A) inserted into the spike protein at precisely the right location to facilitate entry to human cells. Having this arise by random mutation is so low-probability as to be impossible.
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The other option for how it could naturally acquire the furin cleavage site is via recombination, except that no wild-type SARS related coronaviruses possess one, so where SARS2 would get one from is unclear.
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The coding for the furin cleavage site is very strange. Amino acids are encoded for by groups of three RNA base pairs. These groups are called codons. As there are more codons than amino acids, most amino acids can be coded for by several different codons. For arginine any of CGU, CGC, CGA, CGG, AGA or AGG are possible. However, different organisms prefer different codons, and only 5% of SARS2’s arginine codons are CGG. That codon is however commonly used in labs. For the furin cleavage site inserted into the spike protein of SARS2, both arginines are coded CGG.
“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.
- The Wuhan Institute was known to be working with novel bat coronaviruses and doing so called gain-of-function experiments:
“Since 1992 the virology community has known that the one sure way to make a virus deadlier is to give it a furin cleavage site at the S1/S2 junction in the laboratory,” writes Dr. Steven Quay, a biotech entrepreneur interested in the origins of SARS2. “At least eleven gain-of-function experiments, adding a furin site to make a virus more infective, are published in the open literature, including [by] Dr. Zhengli Shi, head of coronavirus research at the Wuhan Institute of Virology.”
There’s more. Like I said, read the piece.
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If you want to cut down on reading time, start at the section “Inside the Wuhan Institute of Virology” as everything before that is pretty pointless. Also skip the section about lab safety.
Race science bro? Let’s look into that more fully:
Wade writes about racial differences in economic success between whites, blacks, and East Asians, and offers the argument that racial differences come from genetic differences amplified by culture. In the first part of the book, Wade provides an account of human genetics research. In the second part of his book, Wade proposes that regional differences in evolution of social behavior explain many differences among different human societies around the world
Which… yikes. He’s a clown.
I’m not going to read a 40 minute piece from some racist piece of shit on medium of all places. However, I’ll point out that a lot of smart people in genetics/virology/biology all have looked at this and not come to that conclusion. I’ll believe them over the racist piece of shit.
Reading your post, I had to stop here (please note that the first bullet point is specious as well):
In comparison to its closest known relative, SARS-CoV-2 has what’s called a furin cleavage site. Essentially this is an RNA sequence (P-R-R-A) inserted into the spike protein at precisely the right location to facilitate entry to human cells. Having this arise by random mutation is so low-probability as to be impossible.
That is nonsense. Positing that a four residue mutation is ‘impossible’ is nonsense. Furthermore, I’ve seen discussion of exactly that sequence. It’s been known to be important for quite some time, and I can find discussion among various molecular bio types about it going back to Feb 2020. The consensus is clear - it’s not artificial.
The specifics of the science of this is beyond me, but I think we can avoid medium articles from known racists well outside the mainstream on the topic.
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Wade might be overplaying the existence of the furin cleavage site. Derek Lowe, who writes the excellent In The Pipeline pharma blog I’ve linked a few times, says this:
I’ll eventually have to write about this. I think Wade overestimates the “smoking gun” potential of the furin cleavage site, but on the other hand the lab-escape theory is definitely still on the table. And the actions of the Chinese government are doing nothing to take it off.
Wade wrote this:
Viruses have all kinds of clever tricks, so why does the furin cleavage site stand out? Because of all known SARS-related beta-coronaviruses, only SARS2 possesses a furin cleavage site. All the other viruses have their S2 unit cleaved at a different site and by a different mechanism.
But this is carefully phrased. No other “SARS related” beta-coronaviruses have the site, but other beta-coronaviruses do. There’s an article here which has them occurring independently in the genomes of various branches of the coronavirus tree.
https://www.sciencedirect.com/science/article/pii/S1873506120304165
This means the virus could have acquired it via recombination while circulating in bats. Wade also asserts that SARS2 is poorly transmitted in bats but this assertion also seems suspect, as this article has several bat species susceptible to it.
I read a paper by, I think, the Stephen Quay quoted that made the same points about the spike protein a few weeks back.
My problem with this is just that the science is far beyond me so I have no way of assessing the claims about how surprising or unlikely it is, and that when I googled about that paper (not anything linked above) one of the first things I found was that it used uncritically the stuff that came out early in the pandemic about similarities between COVID and HIV, which everyone seemed to agree was nonsense. At which point I just had to shrug.
I did read something last week about trying to model COVID evolution, which I think suggests it was circulating and evolving in humans widely prior to Wuhan.
From the abstract:
We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient. This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the USA harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China.
Lol? How is that possibly not relevant? But yeah, tell me more about how the China lab created virus theory isn’t racist please. It’s just a total coincidence that the theory is supported by all these racists.
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I thought this part was interesting considering the loud chorus of people yelling about how viruses don’t escape labs and they were taking such extreme precautions. Most of the gain of function work they were doing on bat coronavirus was done with the same safety precautions as a dentists office.
I read the piece after seeing it on Twitter and looked up the author afterwards. Probably wouldn’t have read it if I did it in the reverse order, but I thought it was a good synthesis of the lab leak argument, which tbh I still find pretty likely (although I have no idea how to quantify the likelihood).
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I’m not nearly informed enough to have a strong opinion, but it’s weird to me how often people seem to be conflating “lab-created” and “escaped from a lab”. Those seem very different to me.
That is a lab created argument he posted though
Yeah, that was a “lab-created” article written by a race science proponent, posted unironically, on unstuck politics.
Fair enough, I obviously wasn’t reading the whole thing and only saw this:
so it wasn’t obvious to me that the article was supporting a lab-created theory. I still think that this thread has occasionally blended the “lab-created” and “lab-escaped” theories in an unhelpful way, but maybe I overreacted in this case. mea culpa.
I mean nobody is disputing that they were doing gain of function research on bat coronavirus in the lab. NIH issued a grant for them to do it! They were 100% creating SARS-like viruses there. The only point in dispute is whether our specific coronavirus came from the lab or the wild.
Honestly the condescending attitude about this is really bizarre to me.
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The research they were doing in this lab involved manipulating the viruses they were studying. If anything escaped from there, it’s overwhelmingly likely that it was “created” in some sense of the word.
I had never heard the phrase “gain of function” until this week when Rand Paul fought with Fauci about it. Does that mean taking something and trying to soup it up by genetically modifying it or something?
I’ve been interpreting “lab created” as “intentionally designed to infect humans, and potentially intentionally released”, which is why I’ve been viewing “lab created” and “lab escaped” as being so different. And why I think “lab created” is much more of a racist theory than “lab escaped”. But maybe the two phrases aren’t as different as I had been thinking.