12 ms·

You don't understand biology. It is possible to date the divergence of genomes using a genetic clock. So they know if those spike proteins had been recombinated

You don't understand biology. It is possible to date the divergence of genomes using a genetic clock. So they know if those spike proteins had been recombinated. Serial passage in mice can't be ruled out but is quite out there. Lots of theories can't be completely ruled out, but wild speculation like that is not very productive. For the lab-leak theory to be true, a "pandemicable" zoonotic virus (a VERY rare thing) has to somehow make it into a lab undetected. Additionally and alternatively scientists have to undergo something like this "serial mice passage". Which is not proven that it could work. And then they would need to somehow let the virus escape through an accident even though they knew it could be dangerous. And it would have to accidentally be able to infect Humans extremely well (which is a tall ask still). It's just... highly improbable.

pbreit 4y ago
Less probable than such a coronavirus originating in Wuhan of all places?
- mikeyouse 4y ago
  The WIV was in Wuhan due to the proximity of coronaviruses and other bat-borne diseases like rhabdovirusus.. this line of logic is akin to blaming shark research centers in South Africa for nearby attacks.
  - emmelaich 4y ago
    I don't think so? The bats are generally from Southern China, Laos, Cambodia, .. Nowhere near Wuhan.
    - mikeyouse 4y ago
      There are tons of horseshoe bats in Hubei, that particular misunderstanding needs to go away.
      - mikeyouse 4y ago
        Too late to edit, but here's an article from 2018 following a group of scientists into a cave 60 miles from Wuhan to study horseshoe bats: https://www.sixthtone.com/news/1002326/how-chinas-bat-caves-hold-the-secret-to-preventing-epidemics https://www.sixthtone.com/news/1002326/how-chinas-bat-caves-... Unfortunately for us, tons of bats carry viruses of all types and some of them are literally found on the campus of the WIV: 18.5% of Japanese housebats sampled in one study had beta coronaviruses: https://pbs.twimg.com/media/FQ9ScdVXsAIZntp?format=png&name=900x900 https://pbs.twimg.com/media/FQ9ScdVXsAIZntp?format=png&name=... Those bats are regularly collected for study at the same academic complex that hosts the WIV: https://pbs.twimg.com/media/FQ9U624XoAAvQol?format=png&name=900x900 https://pbs.twimg.com/media/FQ9U624XoAAvQol?format=png&name=...
        tripletao 4y ago
        There are bats almost everywhere in the world, including Wuhan. The question isn't bats, but bats carrying sarbecoviruses related to SARS-CoV-2, not just betacoronaviruses. Dr. Shi herself has stated that she didn't expect such bats anywhere near Wuhan: > We have done bat virus surveillance in Hubei Province for many years, but have not found that bats in Wuhan or even the wider Hubei Province carry any coronaviruses that are closely related to SARS-CoV-2. I don't think the spillover from bats to humans occurred in Wuhan or in Hubei Province. https://web.archive.org/web/20201206204844/https://www.sciencemag.org/sites/default/files/Shi%20Zhengli%20Q%26A.pdf https://web.archive.org/web/20201206204844/https://www.scien... I've responded to you with this link before, and you didn't reply. It begins to feel like you are willfully disregarding all evidence contrary to your predetermined view, which is unfortunate.
      - kaitaincps 4y ago
        The WIV was not set up in Wuhan to study bats in Hubei. That is a total misconception. It was set up in 1956 with no connection whatsoever to bat-borne sarbecoviruses. That specialization arose later, but studies were made principally in Yunnan province. There is no connection between the bat specialization of the WIV and its location in Hubei.
  - kaitaincps 4y ago
    It was not. This is a widespread misconception. The local bat populations in Wuhan were negligible and their viruses were not being studied. Indeed, the local human population in Wuhan was used as a control in the WIV's studies because of their lack of any significant encounters with bats and their diseases. Shi Zhengli, the "bat woman" who conducted most of her research 1000 miles south, in Yunnan province, had this immediate reaction to an epidemic of bat-borne sarbecoviruses starting in Wuhan: “I wondered if the municipal health authority got it wrong. I had never expected this kind of thing to happen in Wuhan, in central China.” Her first panicked thought was that the outbreak might have started as a leak from her lab. Which is kind of curious, don't you think? She reported being relieved later when she found no evidence of this, but...why was that her initial thought?
    - bayesian_horse 4y ago
      There is no proof that the Virus was passed directly from bats. And as far as I recall there was evidence for at least one intermediate host. Which makes the bat-hunting rather pointless.
dekhn 4y ago
What does "date divergence of genomes using a genetic clock"? I am curious to learn about such a tecnology. If you mean https://en.wikipedia.org/wiki/Molecular_clock https://en.wikipedia.org/wiki/Molecular_clock that is highly non-quantitative.
- bayesian_horse 4y ago
  It is quite quantitative, just not very precise. Good enough to tell you if a Virus emerged more than a couple of years ago or not.
  - dekhn 4y ago
    Can you give me a link to a good example of that (ideally, non-covid)? my understanding is that it's only good for relative rates over evolutionary time so I'd like to see a counterexample.
    - mikeyouse 4y ago
      It's a completely common technique - the same way we're tracing the current Monkeypox outbreak. https://www.ecdc.europa.eu/en/news-events/epidemiological-update-monkeypox-multi-country-outbreak-15-june https://www.ecdc.europa.eu/en/news-events/epidemiological-up... And is useful from an anthropological perspective on older outbreaks, also for Monkeypox; https://www.nature.com/articles/s41598-021-92315-8 https://www.nature.com/articles/s41598-021-92315-8 The rate of mutations, especially for a virus as transmissible as Covid is a very strong signal.
      - dekhn 4y ago
        Thanks- personally, based on my experience in functional genomics, they have far too many assumptions to be trusted as "clocks", even relative ones. Here's the second paper's methods: a molecular clock signal was estimated on the ML tree using TempEst v1.532. BEAST v1.10.433 was used for Bayesian MCMC analysis to estimate temporal nodes. As recommended in Patrono et al., we selected the simplest model: strict clock and constant population size with a HKY substitution model and four Gamma categories7. An MCMC model was run with 50,000,000 generations and a burn-in of 25,000 sampled trees. All other parameters were by default. BEAST executions were completed checking chain convergence and sufficient sampling of the posterior space (ESS > 200) with Tracer v1.7.1. The final chronogram was generated using TreeAnnotator v1.10.433. I'd call these "time-scaled trees", not molecular clocks.
uoaei 4y ago
> "pandemicable" zoonotic virus (a VERY rare thing) has to somehow make it into a lab undetected. This is the opposite of what I understood the lab-leak theory to be: that an initially-zoonotic virus was identified and bred in a lab until someone working at that lab with lax security standards accidentally brought it out of the quarantine. This is plausible at face value. I think a lot of the really extreme vitriolic reactions to lab-leak theory are conflating it with the accusations that a secret cabal purposefully engineered and released this virus to sow harm and discord. But that's not at all the connotation of "leak" IMO -- leak implies a lack of intention.
- bayesian_horse 4y ago
  There's a spectrum... The zoonotic virus would need to have some rare "talent" to start with. Then there is the ominous "breeding" part, which many people describe as reckless or evil. In any case this isn't done in Humans but rather some kind of humanized model (and it's not clear that could work at all). Which is why it is quite a coincidence or accident that this process would end with a virus so well adapted to Humans that it is able to cause a pandemic. It's like winning a chess tournament after training for a Marathon. It's only plausible if you know very little about biology. Very few people who know a lot about viruses believe that this is possible and even those usually say the zoonosis hypothesis is more likely.
  - chiefalchemist 4y ago
    > It's only plausible if you know very little about biology. Not trolling, series question: what would these same ppl say about the monkey pox outbreaks? Why now? Why so random?
    - bayesian_horse 4y ago
      As far as I know the experts say they don't know all that much. Also the awareness of such issues has shifted a lot...
  - peteradio 4y ago
dpbriggs 4y ago
> For the lab-leak theory to be true, a "pandemicable" zoonotic virus (a VERY rare thing) has to somehow make it into a lab undetected. That's not a necessary condition and it's ridiculous to think that's the only hinge by which the hypothesis stands. Another far more plausible idea is that a mistake occurred somewhere and it was covered up. This has occurred before in authoritarian regimes before. An input to a molecular clock is a mutation rate, which I imagine would be hard to quantify given the unknown source and the possibility of gain of function research.
- bayesian_horse 4y ago
  Of course it is a necessary condition. In order to leak from the lab, the virus has to be collected and be propagated in the lab. And all the rest isn't plausible if they knew the bat virus they had in their vials had the potential to cause a pandemic. But it must have had some rare "talent" that was as yet undiscovered. Otherwise nothing of the "lab leak" hypothesis makes sense. You can't "gain-of-function" just any virus and end up with a killer pandemic. You can interpret a molecular clock or a phylogenetic tree qualitatively, and you would expect to see multiple samples with the protein in question, but which have individually acquired so many mutations that they must have diverged before the dynamic. That would mean the protein sequence in question predates the pandemic by a long shot, unless you think the Wuhan lab tested the Virus in Laos...
  - dpbriggs 4y ago
    I guess the disagreement is around the word "undetected". It's possible some failure was covered up and I trust the Chinese government to be capable enough to do that. > virus has to be collected and be propagated in the lab That's a weaker statement than the one I replied to. I'm referring to the how it's necessary that it needs to a "pandemicable" virus that enters a lab "undetected" and I guess leaves the lab "undetected". There's several possible ways the virus could have made it into Wuhan: - Improper handling occurs somewhere in transporting the samples from bat caves (w/e) to the lab. - Improper handling of samples in the lab. - Improper disposal of samples in the lab. - Entering a more speculative area; bat samples are used in experiments and improper handling or disposal occurs. - Deeper into speculation: Improper handling/disposal of viruses used in gain of function research. And when any of the above occurs, use the state's staggering power to cover it up. > You can interpret a molecular clock or a phylogenetic tree qualitatively I'm sure that could work but I imagine the error bars are quite wide as otherwise that's definitive proof and we wouldn't be discussing this online. > unless you think the Wuhan lab tested the Virus in Laos Nice attempt at absurd rhetoric. Strengthens the argument doesn't it?
kaitaincps 4y ago
> has to somehow make it into a lab undetected Undetected? The lab was specifically searching for and storing pandemic-capable viruses, and had applied for grant money to insert furin cleavage sites into them!
- bayesian_horse 4y ago
  Nope. It was looking for bat viruses. There is no way to tell if such a virus is even able to infect Humans, without testing it out on Humans. The grant application is not proof that they either performed such experiments at all, that they did it on that particular virus nor that it worked. And there's still a long distance between a random bat virus with a "furin cleavage site" and something that is good at infecting Humans. All this theory is so far is wild speculation.

pbreit 4y ago

Less probable than such a coronavirus originating in Wuhan of all places?

mikeyouse 4y ago
The WIV was in Wuhan due to the proximity of coronaviruses and other bat-borne diseases like rhabdovirusus.. this line of logic is akin to blaming shark research centers in South Africa for nearby attacks.
- emmelaich 4y ago
  I don't think so? The bats are generally from Southern China, Laos, Cambodia, .. Nowhere near Wuhan.
  - mikeyouse 4y ago
    There are tons of horseshoe bats in Hubei, that particular misunderstanding needs to go away.
    - mikeyouse 4y ago
      Too late to edit, but here's an article from 2018 following a group of scientists into a cave 60 miles from Wuhan to study horseshoe bats: https://www.sixthtone.com/news/1002326/how-chinas-bat-caves-hold-the-secret-to-preventing-epidemics https://www.sixthtone.com/news/1002326/how-chinas-bat-caves-... Unfortunately for us, tons of bats carry viruses of all types and some of them are literally found on the campus of the WIV: 18.5% of Japanese housebats sampled in one study had beta coronaviruses: https://pbs.twimg.com/media/FQ9ScdVXsAIZntp?format=png&name=900x900 https://pbs.twimg.com/media/FQ9ScdVXsAIZntp?format=png&name=... Those bats are regularly collected for study at the same academic complex that hosts the WIV: https://pbs.twimg.com/media/FQ9U624XoAAvQol?format=png&name=900x900 https://pbs.twimg.com/media/FQ9U624XoAAvQol?format=png&name=...
      - tripletao 4y ago
        There are bats almost everywhere in the world, including Wuhan. The question isn't bats, but bats carrying sarbecoviruses related to SARS-CoV-2, not just betacoronaviruses. Dr. Shi herself has stated that she didn't expect such bats anywhere near Wuhan: > We have done bat virus surveillance in Hubei Province for many years, but have not found that bats in Wuhan or even the wider Hubei Province carry any coronaviruses that are closely related to SARS-CoV-2. I don't think the spillover from bats to humans occurred in Wuhan or in Hubei Province. https://web.archive.org/web/20201206204844/https://www.sciencemag.org/sites/default/files/Shi%20Zhengli%20Q%26A.pdf https://web.archive.org/web/20201206204844/https://www.scien... I've responded to you with this link before, and you didn't reply. It begins to feel like you are willfully disregarding all evidence contrary to your predetermined view, which is unfortunate.
    - kaitaincps 4y ago
      The WIV was not set up in Wuhan to study bats in Hubei. That is a total misconception. It was set up in 1956 with no connection whatsoever to bat-borne sarbecoviruses. That specialization arose later, but studies were made principally in Yunnan province. There is no connection between the bat specialization of the WIV and its location in Hubei.
- kaitaincps 4y ago
  It was not. This is a widespread misconception. The local bat populations in Wuhan were negligible and their viruses were not being studied. Indeed, the local human population in Wuhan was used as a control in the WIV's studies because of their lack of any significant encounters with bats and their diseases. Shi Zhengli, the "bat woman" who conducted most of her research 1000 miles south, in Yunnan province, had this immediate reaction to an epidemic of bat-borne sarbecoviruses starting in Wuhan: “I wondered if the municipal health authority got it wrong. I had never expected this kind of thing to happen in Wuhan, in central China.” Her first panicked thought was that the outbreak might have started as a leak from her lab. Which is kind of curious, don't you think? She reported being relieved later when she found no evidence of this, but...why was that her initial thought?
  - bayesian_horse 4y ago
    There is no proof that the Virus was passed directly from bats. And as far as I recall there was evidence for at least one intermediate host. Which makes the bat-hunting rather pointless.

dekhn 4y ago

What does "date divergence of genomes using a genetic clock"? I am curious to learn about such a tecnology. If you mean https://en.wikipedia.org/wiki/Molecular_clock https://en.wikipedia.org/wiki/Molecular_clock that is highly non-quantitative.

bayesian_horse 4y ago
It is quite quantitative, just not very precise. Good enough to tell you if a Virus emerged more than a couple of years ago or not.
- dekhn 4y ago
  Can you give me a link to a good example of that (ideally, non-covid)? my understanding is that it's only good for relative rates over evolutionary time so I'd like to see a counterexample.
  - mikeyouse 4y ago
    It's a completely common technique - the same way we're tracing the current Monkeypox outbreak. https://www.ecdc.europa.eu/en/news-events/epidemiological-update-monkeypox-multi-country-outbreak-15-june https://www.ecdc.europa.eu/en/news-events/epidemiological-up... And is useful from an anthropological perspective on older outbreaks, also for Monkeypox; https://www.nature.com/articles/s41598-021-92315-8 https://www.nature.com/articles/s41598-021-92315-8 The rate of mutations, especially for a virus as transmissible as Covid is a very strong signal.
    - dekhn 4y ago
      Thanks- personally, based on my experience in functional genomics, they have far too many assumptions to be trusted as "clocks", even relative ones. Here's the second paper's methods: a molecular clock signal was estimated on the ML tree using TempEst v1.532. BEAST v1.10.433 was used for Bayesian MCMC analysis to estimate temporal nodes. As recommended in Patrono et al., we selected the simplest model: strict clock and constant population size with a HKY substitution model and four Gamma categories7. An MCMC model was run with 50,000,000 generations and a burn-in of 25,000 sampled trees. All other parameters were by default. BEAST executions were completed checking chain convergence and sufficient sampling of the posterior space (ESS > 200) with Tracer v1.7.1. The final chronogram was generated using TreeAnnotator v1.10.433. I'd call these "time-scaled trees", not molecular clocks.

uoaei 4y ago

> "pandemicable" zoonotic virus (a VERY rare thing) has to somehow make it into a lab undetected. This is the opposite of what I understood the lab-leak theory to be: that an initially-zoonotic virus was identified and bred in a lab until someone working at that lab with lax security standards accidentally brought it out of the quarantine. This is plausible at face value. I think a lot of the really extreme vitriolic reactions to lab-leak theory are conflating it with the accusations that a secret cabal purposefully engineered and released this virus to sow harm and discord. But that's not at all the connotation of "leak" IMO -- leak implies a lack of intention.

bayesian_horse 4y ago
There's a spectrum... The zoonotic virus would need to have some rare "talent" to start with. Then there is the ominous "breeding" part, which many people describe as reckless or evil. In any case this isn't done in Humans but rather some kind of humanized model (and it's not clear that could work at all). Which is why it is quite a coincidence or accident that this process would end with a virus so well adapted to Humans that it is able to cause a pandemic. It's like winning a chess tournament after training for a Marathon. It's only plausible if you know very little about biology. Very few people who know a lot about viruses believe that this is possible and even those usually say the zoonosis hypothesis is more likely.
- chiefalchemist 4y ago
  > It's only plausible if you know very little about biology. Not trolling, series question: what would these same ppl say about the monkey pox outbreaks? Why now? Why so random?
  - bayesian_horse 4y ago
    As far as I know the experts say they don't know all that much. Also the awareness of such issues has shifted a lot...
- peteradio 4y ago

dpbriggs 4y ago

> For the lab-leak theory to be true, a "pandemicable" zoonotic virus (a VERY rare thing) has to somehow make it into a lab undetected. That's not a necessary condition and it's ridiculous to think that's the only hinge by which the hypothesis stands. Another far more plausible idea is that a mistake occurred somewhere and it was covered up. This has occurred before in authoritarian regimes before. An input to a molecular clock is a mutation rate, which I imagine would be hard to quantify given the unknown source and the possibility of gain of function research.

bayesian_horse 4y ago
Of course it is a necessary condition. In order to leak from the lab, the virus has to be collected and be propagated in the lab. And all the rest isn't plausible if they knew the bat virus they had in their vials had the potential to cause a pandemic. But it must have had some rare "talent" that was as yet undiscovered. Otherwise nothing of the "lab leak" hypothesis makes sense. You can't "gain-of-function" just any virus and end up with a killer pandemic. You can interpret a molecular clock or a phylogenetic tree qualitatively, and you would expect to see multiple samples with the protein in question, but which have individually acquired so many mutations that they must have diverged before the dynamic. That would mean the protein sequence in question predates the pandemic by a long shot, unless you think the Wuhan lab tested the Virus in Laos...
- dpbriggs 4y ago
  I guess the disagreement is around the word "undetected". It's possible some failure was covered up and I trust the Chinese government to be capable enough to do that. > virus has to be collected and be propagated in the lab That's a weaker statement than the one I replied to. I'm referring to the how it's necessary that it needs to a "pandemicable" virus that enters a lab "undetected" and I guess leaves the lab "undetected". There's several possible ways the virus could have made it into Wuhan: - Improper handling occurs somewhere in transporting the samples from bat caves (w/e) to the lab. - Improper handling of samples in the lab. - Improper disposal of samples in the lab. - Entering a more speculative area; bat samples are used in experiments and improper handling or disposal occurs. - Deeper into speculation: Improper handling/disposal of viruses used in gain of function research. And when any of the above occurs, use the state's staggering power to cover it up. > You can interpret a molecular clock or a phylogenetic tree qualitatively I'm sure that could work but I imagine the error bars are quite wide as otherwise that's definitive proof and we wouldn't be discussing this online. > unless you think the Wuhan lab tested the Virus in Laos Nice attempt at absurd rhetoric. Strengthens the argument doesn't it?

kaitaincps 4y ago

> has to somehow make it into a lab undetected Undetected? The lab was specifically searching for and storing pandemic-capable viruses, and had applied for grant money to insert furin cleavage sites into them!

bayesian_horse 4y ago
Nope. It was looking for bat viruses. There is no way to tell if such a virus is even able to infect Humans, without testing it out on Humans. The grant application is not proof that they either performed such experiments at all, that they did it on that particular virus nor that it worked. And there's still a long distance between a random bat virus with a "furin cleavage site" and something that is good at infecting Humans. All this theory is so far is wild speculation.