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Why the pandemic probably started in a lab, in 5 key points

nytimes.com

26 points by jashkenas 2 years ago · 30 comments

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robocat 2 years ago

I thought this was a great summary of the "debate":

https://www.astralcodexten.com/p/practically-a-book-review-r...

ethagnawl 2 years ago

I'm curious to know to what extent these sorts of data-rich stories are templatized. My guess is that they're to the point where the components used in this piece were pulled from an existing widget library. Otherwise, that'd be a lot of effort for ... such an opinion piece.

Also, the native reading experience on Android is surprisingly bad. The content was scrolling out from under me unexpectedly and other times -- reminiscent of the old FOUC on the web. I also felt "stuck" while trying to navigate through some of the dataviz components.

r721 2 years ago

>OPINION

>By Alina Chan

https://en.wikipedia.org/wiki/Alina_Chan

tim333 2 years ago

Jeffrey Sachs is quite entertaining on similar points https://youtu.be/JS-3QssVPeg?t=6500

He was Chairman of the Lancet Covid-19 Commission, and originally a believer that it didn't come from a lab, now flipped. Sorry the interview is with Tucker. Quite a lot more on the politics of the thing and why it would have happened than the nyt article.

yawpitch 2 years ago

And yet, shockingly, the consensus of the actually qualified remains that it didn’t start in a lab.

  • baja_blast 2 years ago

    And what is this consensus based upon outside of what is most beneficial for their field of study? As stated in the article we have not found any infected animals, no antibodies or samples pointing to infected animals, no precursor viruses found circulating in any animals species, no separate spillover events nothing. This is something we find for all spillovers and all of this evidence was uncovered almost immediately for SARS1/MERS. Take a look at the current bird flu situation cropping up, whenever we find a case, we find infected animals at the farm, we find the virus in animals during random sampling, we find the virus in raw milk, we observe many independent outbreaks etc.

    How is it that such an infectious virus no longer exists in any animal population? It's as if after the first human got infected the virus simply vanished off the face of the Earth like some sort of immaculate infection. Now how come when humans infected cats/dogs/deer etc. via reverse zoonosis that SARS2 didn't stop circulating in humans?

    • yawpitch 2 years ago

      Likely precursors have been known in both bats and pangolins since virtually the start of the pandemic (see below) and are widely found in those populations to this day; the entire catalogue of possible precursor genomes in both wild bats and pangolins is (and likely will remain) extremely undersampled (to the degree we barely see any of the current picture of the wild viral load of these animals), so your apparent expectation of them being found in anything like the population of almost entirely domesticated populations of Arabian dromedaries (MERS) and entirely domesticated commercial cattle (current H5N1 spillover risk) is quite simply ludicrous. As it’s entirely possible the spillover mutation was either within a single, long-eaten, animal sample or occurred in a single human post-infection there’s no reason to assume the original lineage of SARS-CoV-2 itself would ever be captured in any wild animal population.

      I don’t even know how to speak to the bizarre (but possibly simply badly communicated on your part) assertion that human -> animal re-transmission events either should (or even could) result in a magic cessation of circulation in humans, as that’s just nonsensical. Post human SARS-CoV-2 lineage infections still persist in animal populations (mink, for example) and likely will continue to do so essentially forever… there’s literally nothing immaculate about this entire situation.

      https://www.nature.com/articles/s41591-020-0820-9

  • tim333 2 years ago

    Citation might be needed on that one. I mean fair enough at the start but the evidence has been accumulating.

    Also in the Sachs video I linked elsewhere there's quite a nice bit on the consensus of the actually qualified from here for about 3 mins https://www.youtube.com/watch?v=JS-3QssVPeg&t=7205s

    • yawpitch 2 years ago

      Sachs (an economist) is not and never has been amongst the actually qualified to speak on virology. Formal graduate level research work in virology / epidemiology is the minimum qualification.

      • tim333 2 years ago

        True he's not a virologist but being chairman of the Covid-19 Commission probably gives him some qualification to talk about the goings on, if more on the political side. Here's his take on what happened there:

        In 2001 the US defence department changed and put it's entire research budget through Tony Fauci's NIH. Since then it's been doing secretive bio defence work.

        When covid broke out the scientists got together to write a paper about it and privately thought they couldn't see how it happened naturally and it was "so frigging likely it came from the lab" (Andersen). But they they met with Fauci, put out the Proximal Origins paper in Nature saying it was natural, after which Andersen got an $8m grant from Fauci.

        There was also a letter in the Lancet saying "We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin".

        Qualified virologist of the kind you mention are almost entirely funded from government or similar sources and letters like that pretty much say that if you say if came from the lab you are a conspiracy theorist and lose your grant and job.

        Science is supposed to be about the truth about nature found through experiment, not via politics. The whole thing is totally corrupted and Proximal Origins a fraud.

        • yawpitch 2 years ago

          > if you say if came from the lab you are a conspiracy theorist and lose your grant and job.

          And, absent actual hard physical evidence, not the slightest amount of which exists, you should be labeled a conspiracy theorist, because that is exactly what you are.

          Further if your job is in direct virology / epidemiology and you’re such a theorist — which, again, pretty much does not exist, hence precisely why the actually qualified write letters trying to counter the not-actually qualified — then you absolutely should lose your grant and your job. Science is about discovering the consensus on what the truth is… the truth is SARS-CoV-2 had animal origins in the wet market where all the original cases arose, full stop.

          But please, go on believing your conspiracy theory.

          • coupdejarnac 2 years ago

            You've bought into the propaganda. China orchestrated a massive disinformation campaign to deflect responsibility. They played the race card when flights to China were stopped. This all worked masterfully on left leaning people who know a lot less than they think.

            Science is about discovering consensus? Wtf is this garbage.

            I'm an avid China watcher, and the propaganda there started almost immediately, even before Wuhan was locked down. There were already stories being bandied about accusing the US Army of spreading a bioweapon in Wuhan etc etc.

          • tim333 2 years ago

            Well re "hard physical evidence" the Chinese ordered all samples destroyed, and the databases were taken down or erased, so I guess if the evidence is destroyed they must be innocent, right?

            I disagree about science being "discovering the consensus". It's like that Nazi book they brought out 100 scientists against Einstein. In my prefered definition of science Einstein was right and they were wrong even if the consensus there was that 'jewish science' was bad.

            Not sure about "conspiracy theory" - if there's a real conspiracy and the theory is correct does it still count?

            As to evidence of what actually happened, you can't get any more qualified virologist than Baric and it came out in his testimony to congress in January that he was the source of the idea to insert a furin cleavage site at the S1 S2 junction in sars like coronaviruses and was interested in the cleavage site in feline coronaviruses some of which are amino acid identical with the one in covid. (testimony 4720 on approx). There are something like 1000 natural viruses like covid and none in nature has been found with a furin cleavage site.

            Assuming covid was natural and came from the market isn't it a remarkable coincidence that Baric proposed a virus with that exact never before seen modification to be done at the lab down the road? I mean of course it's natural but what are the odds of that? Man's a genius.

            • yawpitch 2 years ago

              > […] the Chinese ordered all samples destroyed, and the databases were taken down or erased […]

              If the evidence doesn’t exist then, absent evidence, you’ve got no reason to believe that evidence was destroyed.

              > I disagree about science being "discovering the consensus".

              Nevertheless, it moves.

              > It's like that Nazi book they brought out 100 scientists against Einstein.

              IIRC, those 100 scientists were not actually qualified to speak on Einstein’s work. Listening to them on Einstein is precisely the same thing you’ve been doing with your sources.

              > if there's a real conspiracy and the theory is correct does it still count?

              You’re assuming the “if” and the “and” before the fact again.

              > As to evidence of what actually happened […] fhere are something like 1000 natural viruses like covid and none in nature has been found with a furin cleavage site.

              So, here’s how you do evidence:

              “86 diversified furin cleavage sites […] have been detected in 24 animal hosts in 28 countries since 1954. Besides MERS-CoV and SARS-CoV-2, two of five other CoVs known to infect humans (HCoV-OC43 and HCoV-HKU1) also have furin cleavage sites. In addition, human enteric coronavirus (HECV-4408) has a furin cleavage site and has been detected in humans (first in Germany in 1988)”

              Liu X, Wu Q, Zhang Z. Global Diversification and Distribution of Coronaviruses With Furin Cleavage Sites. Front Microbiol. 2021;12:649314. Published 2021 Oct 7. doi:10.3389/fmicb.2021.649314

              “Furin cleavage sites occurred independently for multiple times in the evolution of the coronavirus family”

              Wu Y, Zhao S. Furin cleavage sites naturally occur in coronaviruses. Stem Cell Res. Published online December 9, 2020. doi:10.1016/j.scr.2020.102115

              But, please, and again — and now despite direct contradiction of your own ”evidence” — continue to conspiracy theorize.

              • tim333 2 years ago

                By like covid I meant sarbecoviruses. I guess we are just going to differ on this stuff.

                • yawpitch 2 years ago

                  Given that furin cleavage sites have been found naturally occurring on other, earlier in the phylogenetic tree of coronaviruses, viruses than SARS-CoV2, the natural assumption is that such a site is not only possible to develop, but likely to develop, in wild sarbecoviruses. Shifting the goalposts in no way whatsoever implies or allows the idea that this furin cleavage site tack of yours is evidence of anything but natural selection.

                  • tim333 2 years ago

                    But it's about probabilities and timing. No sites seen naturally. Then in 2018 or so there is a proposal from a guy who works with the WIV:

                    >We were interested in it because most other coronaviruses in family had those sites. Why didn't sarbecovirus? So the way the grant was designed... ... The third thing was we would probably build virulent viruses and study pathogenesis...

                    And lo the next year (approx) a virus just like that pops up by the WIV. Bit of a coincidence?

                    Same guy by the way who after the breakout when Daszak said BSL 2 research at the WIV was ok emailed back

                    >...don't insult my intelligence by trying to feed me this load of BS

                    Which doesn't seem to show great confidence is the goings on there.

                    • yawpitch 2 years ago

                      > Bit of a coincidence?

                      On the balance of probabilities and with plenty of evidence of the first human infections being in the market and absent any evidence whatsoever of the first infections being in the lab then, yes, absolutely, just a coincidence.

                      These viruses are always mutating, in situ, and the fact other coronaviruses have these sites means it’s only a matter of time and iterations before one of these sarbecoviruses both develops the mutation and infects a human host, given proximity between bats / pangolins / civet cats + humans. That wet market was, effectively, trying to create and release this thing millions of times a day, way faster than any lab could hope to do the former, and way more often than any lab would accidentally attempt the latter.

                      The entire reason anyone would be interested in trying it in a lab is to see if that, again more or less inevitable, wild mutation would actually be a problem for humans. It very likely would be, hence the interest in finding out… but absent evidence of both intentional genomic intervention and a vector of release (and you are very absent evidence of either) that interest correlation very much does not equal any substantive reason to believe in a causation event.

                      You don’t have a smoking gun. You don’t have a gun. You don’t have smoke. What you have is a guy asking if maybe it would be a good idea to check if pulling a trigger on a bullet by your head is a bad idea while a few miles away an endless parade of people were playing Russian Roulette over and over and over, millions of times every day, and you have the first dead bodies and the shell casing there, not where your supposed antagonist worked.

  • mharig 2 years ago

    Who are the "actually qualified"?

    • daly 2 years ago

      Vincent Racaniello https://microbiology.columbia.edu/faculty-vincent-racaniello

      He does not think this started in a lab.

      • mharig 2 years ago

        So you refer to a consensus of the thinking of one person?

        I estimate the probability that the virus is 100% of natural origin to 3.21 ×10−11. And I am backed by one widely ignored article:

        https://www.frontiersin.org/articles/10.3389/fviro.2022.8348...

        • RecycledEle 2 years ago

          Help me understand your math:

          3.21 ×10−11

          Do you mean 3.21*(-1)=-3.21

          Do you mean a number between 32,100,000,000 and 321,000,000,000?

          Do you mean odd between 3.21:10 and 3.21:11?

          Thanks

          • mharig 2 years ago

            Sorry. Copy'n'paste crap. But it should be obvious, and from the linked article clear, that it should be 3.21*10E-11.

    • yawpitch 2 years ago

      Virologists and epidemiologists, as opposed to a molecular biologist with no particular specialized training in either of those topics.

      Well, that was easy.

    • whatthesmack 2 years ago

      The people who claim to be "actually qualified" are the same people who run (ran?) the show at the NIH that have been actively covering up their own opinion that the lab leak of the research they were funding is the most likely source of COVID-19.

      • HelloNurse 2 years ago

        What about actually fun conspiracy theories? Wouldn't any plot trying to reduce population with an artificial coronavirus push lab leak theories in order to depress virus research? If you prefer Big Pharma as the bad guys, wouldn't Western pharmaceutical cartels attempting to earn billions selling vaccines attempt to discredit China as a diversion?

    • lazyeye 2 years ago

      Im guessing its people with vested interests.

    • defrost 2 years ago

      You may or may not enjoy reading through a full and lively debate that was well refereed with clear rules in advance with all the known and verified facts from all sides to hand in advance.

      It went down like this:

      Lableak truther loses $100,000 in his own debate

      https://www.protagonist-science.com/p/lableak-truther-loses-...

      Sure, a lableak origin is "possible" .. just very very very unlikely.

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