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There was an episode the TWiV podcast a few months ago where they discussed the biology-based evidence for why SARS-COV-2 wasn't made in a lab. I think it was t

There was an episode the TWiV podcast a few months ago where they discussed the biology-based evidence for why SARS-COV-2 wasn't made in a lab. I think it was this one: https://www.microbe.tv/twiv/twiv-762/ https://www.microbe.tv/twiv/twiv-762/ One nice thing about the podcast is that because they're scientists by personality they tend to focus far more on the biology of it, which I really appreciate. I listened to it at the time, but I don't remember what they said, to be perfectly honest.

inciampati 5y ago
As a biologist (sorry for the appeal to authority, but it matches the tone of this thread), the evidence against a natural origin appears absolutely staggering. You have a viral clade that completely descends from a single introduction event inside a major city. The virus does not undergo a period of host adaptation, but instead infects many millions over nearly a year before phenotypic changes are observed. This is simply fantastic. I know of no case where a virus jumped species without a period of adaptation to the new host. The fact that the entire clade has a root in October 2019 (and we can see this even because the first viruses sequenced differed by only one or two mutations from their common ancestor) indicates that there was not slow community spread before the initiation of the pandemic period. There is no weaker progenitor virus. Considering as well the focus of research labs within the exact city where the pandemic arose makes any argument against the laboratory origin of the virus seem extremely weak. How does a serious and non-conflicted scientist explain all of these ultra-improbable coincidences?
- arbitrage 5y ago
  > sorry for the appeal to authority You don't need to apologize for your knowledge and experience. We are not engaged in a roman-style rhetoric class where the mandate is to build all arguments upon a set of rules we never agreed to. The wikipedia list of common logical fallacies is not a guideline to rational discourse in the 21st century.
  - ddxxdd 5y ago
    As far as I'm concerned, apologizing for the appeal to authority signalled that he was open to being criticized and challenged by layman, rather than choosing to belittle those who disagree with him without having his knowledge and experience. In short, he demonstrated that he wasn't an "elitist".
- michaelmrose 5y ago
  An appeal to authority is only inherently invalid insofar as the authority claimed is irrelevant authority or used to paper over weaknesses in the actual argument. Forums not entirely overrun with imaginary internet doctors and cranks can probably start with the polite presumption that you are actually a biologist and proceed with reasonable discussion from there without further ado.
- orwin 5y ago
  I agree with you for the begining, but this part: > The fact that the entire clade has a root in October 2019 (and we can see this even because the first viruses sequenced differed by only one or two mutations from their common ancestor) indicates that there was not slow community spread before the initiation of the pandemic period. There is no weaker progenitor virus. is hard for me to understand. Rural China in not rural USA. At all. I've hiked for a month in the Appalachian, another one in the Sierras, and spent two month in rural China. Rural china is as i used to imagine rural Africa. Rural china have two particularities: young, probably younger than you imagine. You have villages with a median age of 15, with no middle-aged inhabitants. And enclaved. You have villages where you have to use a jeep (that the village do not own) to get to. Is it possible, in you opinion, to have an early SRAS-Cov2 infecting a village, festing on the people for weeks or even months, then a parent coming back for his yearly vacations, getting infected, then going back to work in Wuhan? I'm not a biologist, so i don't understand how viruses works, but i _know_ rural China (and rural europe, and rural USA.)
  - bhickey 5y ago
    HIV is believed to have first infected humans in the 1920s where it traveled up the Congo before arriving in Kinshasa. From there it radiated across Africa carried by truckers. Like you say, I haven't seen evidence to rule out rural circulation before arriving in Wuhan. Granted, I don't think this is the most likely series of events, but the GoF lab leak hypothesis is lacking support.
    - tim333 5y ago
      The documents that the article is based on demonstrate the lab was doing GoF experiments to infect humanized mice with chimeras based on bat coronaviruses and got a grant to do further such research starting in 2019. And lo - we get a break out of something looking like a bat based chimera that infects human cells in 2019. Bit of a coincidence there.
  - inciampati 5y ago
    This process would leave traces that we would have detected by now. If this happened, we should see viruses that sit outside the Wuhan-rooted SARS-CoV-2 clade but are otherwise the same. The rate that this happens would be low, but it would have been observed. I would expect that the epidemic required to spread from rural to urban regions would be large enough to throw off daughter strains that would have been circulating after the main outbreak was discovered. These would have been detected by the mobilization to find the origins and scope of the pandemic. Of course we can make stories about a perfect chain of transmission leading from a bat cave in southwest China to a major population center, where each step never resulted in obvious illness or community spread. I also enjoy science fiction. Some things make for nice stories but involve staggeringly improbable series of coincidences. And if the same virus (remember: thanks to it's error correcting mechanisms it doesn't change very fast) were let loose in another community, why would it not take up residence there? We would have to explain why people in Wuhan and the rest of the world were so much more susceptible to a virus that was completely wiped out along it's entire chain of transmission from probable animal host to human.
- belter 5y ago
  Luc Montagnierd joint recipient of the 2008 Nobel Prize in Medicine for his discovery of the human immunodeficiency virus HIV has argued the virus was created in a lab. "French Nobel prize winner: ‘Covid-19 was made in lab’" https://www.connexionfrance.com/French-news/Disputed-French-Nobel-winner-Luc-Montagnier-says-Covid-19-was-made-in-a-lab-laboratory https://www.connexionfrance.com/French-news/Disputed-French-... https://en.wikipedia.org/wiki/Luc_Montagnier https://en.wikipedia.org/wiki/Luc_Montagnier Again, just another appeal to authority, to be analyzed further. I find curious his personal Wikipedia page still characterizes the controversy has him being accused of spreading a conspiracy theory, while today, its looking as one of the most likely causes.
  - bsaul 5y ago
    luc montagnier has a long list of insane public claims for the past decades (things about "water memory" comes to my mind , but there are others). He lost credit a long time ago, way before covid, so i would be really cautious about citing anything he has to say about the virus.
    - belter 5y ago
      After further research...I am inclined to agree with you. I just found he also claimed 5G was helping spread Covid.
      - inciampati 5y ago
        This phenomenon keep happening with old Nobel laureates. Linus Pauling for instance... For any public binary question with weak information, you'll find crazy people arguing both sides.
- bhickey 5y ago
  > The fact that the entire clade has a root in October 2019... indicates that there was not slow community spread before the initiation of the pandemic period. There is no weaker progenitor virus. SARS-CoV-2 has an error checking polymerase and a relatively slow molecular clock. Just because observed sequences have little divergence from our first observation does not imply that we actually observed the species jump. The preadaptation argument doesn't hold much water. SARS and MERS were deadly and high transmissible. That said, let's suppose we did observe cases shortly after it initially infected humans. Shi's lab regularly went caving in search of coronaviruses in bats. These expeditions have previously been described as reckless. The possibility that a lab worker became accidentally infected in a cave shouldn't be counted out by anyone advancing GoF origin claims.
  - native_samples 5y ago
    The distinction between "lab workers got infected whilst physically at a lab" and "lab workers got infected whilst doing remote work intended to benefit the lab" seems quite small.
    - bhickey 5y ago
      There's a huge gulf between getting sick attempting to make a virus more virulent and getting sick while gathering natural samples in the field.
      - inciampati 5y ago
        Both involve research that was specifically intended to reduce risk of pandemics. If either is true, our response here should be to conduct this research with extreme care or even stop doing it. If the lab origin hypothesis is not true, we should actually do more of exactly this kind of work. That's why it's important to understand and come to consensus about it. It's not just a curiosity or a chance to point the finger at countries and politics we don't like. The prescription for how we should behave is completely different depending on what we think happened.
  - inciampati 5y ago
- ksaj 5y ago
  Origin of Life is full of ultra-improbable coincidences. How do scientists in that field explain it? "There is no weaker progenitor virus." I've never heard a scientist dealing with any level of Complexity declare a negative fact before. Having not discovered a weaker progenitor doesn't preclude its existence. This type of statement ignores all comparisons made to the bat coronaviruses that have very much been part of the discussion. I read some of your other replies and agree with some, and can at least see the point of a lot of them. But the grander wide-brush statements weaken those points.

inciampati 5y ago

As a biologist (sorry for the appeal to authority, but it matches the tone of this thread), the evidence against a natural origin appears absolutely staggering. You have a viral clade that completely descends from a single introduction event inside a major city. The virus does not undergo a period of host adaptation, but instead infects many millions over nearly a year before phenotypic changes are observed. This is simply fantastic. I know of no case where a virus jumped species without a period of adaptation to the new host. The fact that the entire clade has a root in October 2019 (and we can see this even because the first viruses sequenced differed by only one or two mutations from their common ancestor) indicates that there was not slow community spread before the initiation of the pandemic period. There is no weaker progenitor virus. Considering as well the focus of research labs within the exact city where the pandemic arose makes any argument against the laboratory origin of the virus seem extremely weak. How does a serious and non-conflicted scientist explain all of these ultra-improbable coincidences?

arbitrage 5y ago
> sorry for the appeal to authority You don't need to apologize for your knowledge and experience. We are not engaged in a roman-style rhetoric class where the mandate is to build all arguments upon a set of rules we never agreed to. The wikipedia list of common logical fallacies is not a guideline to rational discourse in the 21st century.
- ddxxdd 5y ago
  As far as I'm concerned, apologizing for the appeal to authority signalled that he was open to being criticized and challenged by layman, rather than choosing to belittle those who disagree with him without having his knowledge and experience. In short, he demonstrated that he wasn't an "elitist".
michaelmrose 5y ago
An appeal to authority is only inherently invalid insofar as the authority claimed is irrelevant authority or used to paper over weaknesses in the actual argument. Forums not entirely overrun with imaginary internet doctors and cranks can probably start with the polite presumption that you are actually a biologist and proceed with reasonable discussion from there without further ado.
orwin 5y ago
I agree with you for the begining, but this part: > The fact that the entire clade has a root in October 2019 (and we can see this even because the first viruses sequenced differed by only one or two mutations from their common ancestor) indicates that there was not slow community spread before the initiation of the pandemic period. There is no weaker progenitor virus. is hard for me to understand. Rural China in not rural USA. At all. I've hiked for a month in the Appalachian, another one in the Sierras, and spent two month in rural China. Rural china is as i used to imagine rural Africa. Rural china have two particularities: young, probably younger than you imagine. You have villages with a median age of 15, with no middle-aged inhabitants. And enclaved. You have villages where you have to use a jeep (that the village do not own) to get to. Is it possible, in you opinion, to have an early SRAS-Cov2 infecting a village, festing on the people for weeks or even months, then a parent coming back for his yearly vacations, getting infected, then going back to work in Wuhan? I'm not a biologist, so i don't understand how viruses works, but i _know_ rural China (and rural europe, and rural USA.)
- bhickey 5y ago
  HIV is believed to have first infected humans in the 1920s where it traveled up the Congo before arriving in Kinshasa. From there it radiated across Africa carried by truckers. Like you say, I haven't seen evidence to rule out rural circulation before arriving in Wuhan. Granted, I don't think this is the most likely series of events, but the GoF lab leak hypothesis is lacking support.
  - tim333 5y ago
    The documents that the article is based on demonstrate the lab was doing GoF experiments to infect humanized mice with chimeras based on bat coronaviruses and got a grant to do further such research starting in 2019. And lo - we get a break out of something looking like a bat based chimera that infects human cells in 2019. Bit of a coincidence there.
- inciampati 5y ago
  This process would leave traces that we would have detected by now. If this happened, we should see viruses that sit outside the Wuhan-rooted SARS-CoV-2 clade but are otherwise the same. The rate that this happens would be low, but it would have been observed. I would expect that the epidemic required to spread from rural to urban regions would be large enough to throw off daughter strains that would have been circulating after the main outbreak was discovered. These would have been detected by the mobilization to find the origins and scope of the pandemic. Of course we can make stories about a perfect chain of transmission leading from a bat cave in southwest China to a major population center, where each step never resulted in obvious illness or community spread. I also enjoy science fiction. Some things make for nice stories but involve staggeringly improbable series of coincidences. And if the same virus (remember: thanks to it's error correcting mechanisms it doesn't change very fast) were let loose in another community, why would it not take up residence there? We would have to explain why people in Wuhan and the rest of the world were so much more susceptible to a virus that was completely wiped out along it's entire chain of transmission from probable animal host to human.
belter 5y ago
Luc Montagnierd joint recipient of the 2008 Nobel Prize in Medicine for his discovery of the human immunodeficiency virus HIV has argued the virus was created in a lab. "French Nobel prize winner: ‘Covid-19 was made in lab’" https://www.connexionfrance.com/French-news/Disputed-French-Nobel-winner-Luc-Montagnier-says-Covid-19-was-made-in-a-lab-laboratory https://www.connexionfrance.com/French-news/Disputed-French-... https://en.wikipedia.org/wiki/Luc_Montagnier https://en.wikipedia.org/wiki/Luc_Montagnier Again, just another appeal to authority, to be analyzed further. I find curious his personal Wikipedia page still characterizes the controversy has him being accused of spreading a conspiracy theory, while today, its looking as one of the most likely causes.
- bsaul 5y ago
  luc montagnier has a long list of insane public claims for the past decades (things about "water memory" comes to my mind , but there are others). He lost credit a long time ago, way before covid, so i would be really cautious about citing anything he has to say about the virus.
  - belter 5y ago
    After further research...I am inclined to agree with you. I just found he also claimed 5G was helping spread Covid.
    - inciampati 5y ago
      This phenomenon keep happening with old Nobel laureates. Linus Pauling for instance... For any public binary question with weak information, you'll find crazy people arguing both sides.
bhickey 5y ago
> The fact that the entire clade has a root in October 2019... indicates that there was not slow community spread before the initiation of the pandemic period. There is no weaker progenitor virus. SARS-CoV-2 has an error checking polymerase and a relatively slow molecular clock. Just because observed sequences have little divergence from our first observation does not imply that we actually observed the species jump. The preadaptation argument doesn't hold much water. SARS and MERS were deadly and high transmissible. That said, let's suppose we did observe cases shortly after it initially infected humans. Shi's lab regularly went caving in search of coronaviruses in bats. These expeditions have previously been described as reckless. The possibility that a lab worker became accidentally infected in a cave shouldn't be counted out by anyone advancing GoF origin claims.
- native_samples 5y ago
  The distinction between "lab workers got infected whilst physically at a lab" and "lab workers got infected whilst doing remote work intended to benefit the lab" seems quite small.
  - bhickey 5y ago
    There's a huge gulf between getting sick attempting to make a virus more virulent and getting sick while gathering natural samples in the field.
    - inciampati 5y ago
      Both involve research that was specifically intended to reduce risk of pandemics. If either is true, our response here should be to conduct this research with extreme care or even stop doing it. If the lab origin hypothesis is not true, we should actually do more of exactly this kind of work. That's why it's important to understand and come to consensus about it. It's not just a curiosity or a chance to point the finger at countries and politics we don't like. The prescription for how we should behave is completely different depending on what we think happened.
- inciampati 5y ago
ksaj 5y ago
Origin of Life is full of ultra-improbable coincidences. How do scientists in that field explain it? "There is no weaker progenitor virus." I've never heard a scientist dealing with any level of Complexity declare a negative fact before. Having not discovered a weaker progenitor doesn't preclude its existence. This type of statement ignores all comparisons made to the bat coronaviruses that have very much been part of the discussion. I read some of your other replies and agree with some, and can at least see the point of a lot of them. But the grander wide-brush statements weaken those points.