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I spent at least an hour reading through both the emails and the slack messages in this "expose", but I came away from it fairly certain that they are being por

I spent at least an hour reading through both the emails and the slack messages in this "expose", but I came away from it fairly certain that they are being portrayed unfairly, and I'm fairly surprised that Nate Silver has latched on to this. You have to both look at the time-line of the paper writing and the time-line of the conversations. By my reading, by the time the paper was being written, most of them had indeed come to the conclusion that (1) there was no evidence for an engineered virus, (2) that the data was consistent with both a leak from a lab (without engineering) or from exposure to animals, but that (3) the former was not as a priori likely, given what they knew about the kinds of research being done. You just can't take something someone says in Jan. 2020 at the start of their looking at the problem, and what they said in their paper written in Feb. 2020 on the same level. They started with concerns that it was an engineered virus and moved away from that view the more they learned.

Marazan 3y ago
[flagged]
jonnycomputer 3y ago
Also, paper writing is a collaborative effort, which does not imply that everyone on the paper agrees with every part of it 100%. e.g. if I get Jane on the paper because she knows the more than me about X, but we end up having a soft disagreement about X, I'm not walking away from the paper. Also ... authors have good reason to manage their interactions with journalists. They don't want to be used or misrepresented. Also, given the politics of the moment, they also had every reason to be cautious about what they said publicly.
aredox 3y ago
Nate Silver has been blatantly wrong several times during COVID, has been schooled by actual scientists and is now on a personal vendetta against them. He is ready to fan the flames of science-bashing because his fragile yet enormuous ego has been hurt. That tells all that you need to know about him. (Don't believe me? He has never apologised nor shown a little bit of humility after being corrected. That's who he is.)
- tekla 3y ago
  Provide links please.
  - Fomite 3y ago
    https://twitter.com/GermsAndNumbers/status/1634087467874947073?s=20 https://twitter.com/GermsAndNumbers/status/16340874678749470... This is a somewhat flippant take of mine, but is emblematic of a lot of Nate Silver's posting during the pandemic, which is that epidemiologists are all hyper risk adverse ninnies, and we're clearly at the end of the pandemic.
    - SV_BubbleTime 3y ago
      You could go to the 2016 election and see Nate Silver backtrack and never admit failure if you like. This guy came up out of nowhere and is a clown.
      - epups 3y ago
        How did he fail in the 2016 election? He produced one of the best prediction models.
  - aredox 3y ago
    I've quit twitter and that stupid website now won't allow people to see tweets if you're not logged in, so I guess you'll just have to search "Nate silver wrong" by yourself, big guy...
    - deleted 3y ago
      [deleted]
- hooverd 3y ago
  Superforecasteritis is the new Nobelitis.
- COGlory 3y ago
gptbore 3y ago
I agree with your description of what these correspondents consensus seemed to be at the time of writing. I don't see how this is at all consistent with that the paper claimed - "we do not believe that any type of laboratory-based scenario is plausible", nor how it was portrayed by the media - "COVID-19 coronavirus epidemic has a natural origin".
- jonnycomputer 3y ago
  The phrase "is not likely" imo should have been substituted for "is not plausible", though I am not sure everyone else interprets the phrase "not plausible" as meaning something like "almost certainly not true"; they could have meant it as, something like, "the least likely of all the possibilities, by a fair margin." Sure, I'd have preferred if they had been explicit, by giving their estimate of the probability of each possibility explicitly.
  - gptbore 3y ago
    "the main thing still in my mind is that the lab escape version of this is so friggin' likely to have happened because they were already doing this type of work and the molecular data is fully consistent with that scenario" As an understatement, I don't think the authors accurately conveyed what their priors on the origin really were, nor what data they encountered to so dramatically shift these priors.
    - jonnycomputer 3y ago
      My only response would be (1) to point to the date of when he said that compared to the date of the final manuscript, and the all the conversations that occurred n between. I think that was from sometime in January. (2) we shouldn't read over-much into an off-the-cuff slack message, ostensibly shared with a small number of individuals, with his impressions and thoughts at the time. The purpose of those discussions is to bang ideas off the wall. In any case, I don't expect good scientists to rigidly hang on to an idea. I expect good scientists to evolve their thinking as they learn. But you may be right that the published paper did not speak to what their particular priors were when they started out. I'm not certain that we should expect it to either. A lot of times you start off with ill-formed half-ideas, and while they may be where you started off from, the utility of sharing that starting point might cause more confusion--or even spread more misinformation--that do good.
stubybubs 3y ago
"Although the evidence shows that SARS-CoV-2 is not a purposefully manipulated virus, it is currently impossible to prove or disprove the other theories of its origin described here. However, since we observed all notable SARS-CoV-2 features, including the optimized RBD and polybasic cleavage site, in related coronaviruses in nature, we do not believe that any type of laboratory-based scenario is plausible. More scientific data could swing the balance of evidence to favor one hypothesis over another." Pretty standard scientific writing. I think the lesson is don't trust journalists and the general public to not blow what you're saying out of proportion and assign it more certainty than you intended. Lab leak is possible, sure. But keep in mind every horrible disease humanity has faced up until the early part of the 20th century came about before microbiology labs even existed. Historically, a zoonitic origin is extremely likely. Imagine if polio or smallpox or leprosy popped up today, you'd have every Joe internet theorizing how it came from a lab in whatever country it appeared in first. I guess back in the day they used to say it was punishment from God. The Spanish flu, God out there smiting the Spaniards.
- jonnycomputer 3y ago
  100% this.
- COGlory 3y ago
  >Historically, a zoonitic origin is extremely likely. Historically, there have been far, far more documented lab leaks of SARS-CoV than there have been animal-human jumps. People that wish to shutdown lab leak conversation are quick to mix in engineering. Lots of less educated people can't tell the difference. It is very possible that the virus was both zoonotic in origin, and leaked from the lab.
  - stubybubs 3y ago
    My point is that we don't have any documented anything for the first couple hundred thousand of years of humanity's existence, and we encountered the most horrific viral and bacterial infections, many of which caused unthinkable mass deaths. They were so awful we attributed them to God(s) as punishment for our bad behavior. None of them have documented microbiological origins. Some would have some from spontaneous mutation in humans and many would have come from animals. They are de facto not lab leaks, so the fact that we have some lab leaks documented in the last few decades isn't really convincing. There is nothing there that makes a zoonotic origin less likely. Here's a scientist who said we couldn't dismiss the lab leak, and asked for more research, which he did. https://www.npr.org/sections/goatsandsoda/2021/07/19/1016005828/new-data-leads-to-rethinking-once-more-where-the-pandemic-actually-began https://www.npr.org/sections/goatsandsoda/2021/07/19/1016005... The early cases are clustered around the market. I know the market and the lab are "close" on a global scale, but the details matter. They are 30km apart, about a 45 minute drive in traffic. Looks about as clear as John Snow's map of cholera outbreaks in London. That article is from 2021, but he stands by it in 2023: https://www.latimes.com/opinion/story/2023-03-08/covid-lab-leak-energy-department-fbi https://www.latimes.com/opinion/story/2023-03-08/covid-lab-l... "What is the chance that a big Chinese city like Wuhan would have a lab doing the kind of research that has come under suspicion? The answer is, the vast majority of the biggest cities in China have labs involved in such research. If COVID had emerged in, say, Beijing, there would be no fewer than four such labs facing suspicion." Edit: 2 things. It's important to rule out that the idea that this could only be engineered, which would imply a definite lab origin. That is why engineered viruses come up. A non-lab leak is certainly plausible, and a lab leak is not ruled out. There are labs all over China, there are markets all over China. The overlap of cities having both is significant. Viruses appear in larger, denser population centers. The "next thing" was very likely to appear in a city with a lab. The thing is, it's not very close to the lab. There's a large cluster around the market. Lab theory doesn't have much going for it. It's not actually that close to the epicenter. There are labs everywhere. SARS is widely studies. Sure some viruses have long incubation periods, but that would show as far less of a tight cluster around the market. Your hypothesis seems to be that it spread from lab distantly because of incubation time, then stopped spreading distantly once it reached the market? That does not make sense.
ayjchan 3y ago
The lead author of Proximal Origin wrote this in slack on April 17, a month after the letter had been published in Nature Medicine: "Okay, so about the current news. Is there any reason to believe that they might be onto something, or is it all smoke and mirrors? Eddie Holmes - any insights on the China side? The main things from my perspective: 1. Bioweapon and engineered totally off the table 2. If there is no engineering and no culturing, then it means that somebody magically found a pre-formed pandemic virus, put it in the lab, and then infected themselves. The prior on that vs somebody coming into contact with an animal source infected with the virus is as close to zero as you can get. Humans come into contact all the time with SARS-like CoVs, but the likelihood of somebody finding exactly that pandemic virus and infecting themselves is very very low (make no mistake - if they did find that pandemic virus. then they would get infected if they grew it in the lab - but the likelihood of them finding it in the first place is exceedingly small (or so one would hope - otherwise, good luck World avoiding future pandemic). 3. But here's the issue - I'm still not fully convinced that no culture was involved. If culture was involved, then the prior completely changes - because this could have happened with any random SARS-llke CoV of which there are very many. So are we absolutely certain that no culture could have been involved? What concerns me here are some of the comments by Shi in the SciAm article ("I had to check the lab" etc) and the fact that the furin site 1s being messed with in vitro. Yes, it loses it but that could be context dependent. Finally, the paper that was shared with us showing a very similar phenomenon (exactly 12bp insertion) in other CoVs has me concerned... I really really want to go out there guns swinging saying "don't be such an idiot believing these dumb theories - the president is deflecting from the real problems" but I'm warned that we can't fully disprove culture {our argument was mostly based on the presence of the O-linked glycans - but they could likely play a different role... We also can't fully rule out engineering (for basic research) - yes, no obvious signs of engineering anywhere, but that furin site could still have been inserted via gibson assembly (and clearly creating the reverse genetic system isn't hard - the Germans managed to do exactly that for SARS-CoV-2 in less than a month)." And: "Shi didn't do any GOF work that I'm aware of - but GOF work isn't the concern here. She did A LOT of work that involved isolating and culturing SARS-like viruses from bats (in BSL-2) and that's my main concerning scenario (we cite several of those in the paper - if you have a look at those original publications, it's definitely concerning work, no question about it - and is the main reason I have been so concerned about the 'culture' scenario)." I don't think much more needs to be said. The above messages are self-explanatory.
zzzeek 3y ago
Be surprised no more, there's an apparent garbage shute for lots of "journalists" and pundits where something unspoken about modern times bothers them enough that they just flip into being total nutjobs, riding on their previous respectability to keep eyes on them. Silver is part of a long tradition including Glenn Greenwald, Matt Taibbi, heck even the Dilbert guy of people who used to make sense, saw "something" that REALLY bugged them and they just threw it all away to become unintelligible cranks. Makes ya think.
- realjhol 3y ago
  There is absolutely nothing about Greenwald, Taibbi, or Adams that is in any way unintelligible or irrational.
  - jonnycomputer 3y ago
    Greenwald and Adams are cranks, imo. Don't know about Taibbi.
    - realjhol 3y ago
      What do you even mean by that? Their ideas are perfectly coherent and consistent within their own framing. Just because you look at the world through a different frame, doesn't mean that these people are saying things that are unreasonable
      - jonnycomputer 3y ago
        They consistently disregard evidence that contradicts their core beliefs.
        realjhol 3y ago
        So does literally everyone in the entire world

Marazan 3y ago

[flagged]

jonnycomputer 3y ago

Also, paper writing is a collaborative effort, which does not imply that everyone on the paper agrees with every part of it 100%. e.g. if I get Jane on the paper because she knows the more than me about X, but we end up having a soft disagreement about X, I'm not walking away from the paper. Also ... authors have good reason to manage their interactions with journalists. They don't want to be used or misrepresented. Also, given the politics of the moment, they also had every reason to be cautious about what they said publicly.

aredox 3y ago

Nate Silver has been blatantly wrong several times during COVID, has been schooled by actual scientists and is now on a personal vendetta against them. He is ready to fan the flames of science-bashing because his fragile yet enormuous ego has been hurt. That tells all that you need to know about him. (Don't believe me? He has never apologised nor shown a little bit of humility after being corrected. That's who he is.)

tekla 3y ago
Provide links please.
- Fomite 3y ago
  https://twitter.com/GermsAndNumbers/status/1634087467874947073?s=20 https://twitter.com/GermsAndNumbers/status/16340874678749470... This is a somewhat flippant take of mine, but is emblematic of a lot of Nate Silver's posting during the pandemic, which is that epidemiologists are all hyper risk adverse ninnies, and we're clearly at the end of the pandemic.
  - SV_BubbleTime 3y ago
    You could go to the 2016 election and see Nate Silver backtrack and never admit failure if you like. This guy came up out of nowhere and is a clown.
    - epups 3y ago
      How did he fail in the 2016 election? He produced one of the best prediction models.
- aredox 3y ago
  I've quit twitter and that stupid website now won't allow people to see tweets if you're not logged in, so I guess you'll just have to search "Nate silver wrong" by yourself, big guy...
  - deleted 3y ago
    [deleted]
hooverd 3y ago
Superforecasteritis is the new Nobelitis.
COGlory 3y ago

gptbore 3y ago

I agree with your description of what these correspondents consensus seemed to be at the time of writing. I don't see how this is at all consistent with that the paper claimed - "we do not believe that any type of laboratory-based scenario is plausible", nor how it was portrayed by the media - "COVID-19 coronavirus epidemic has a natural origin".

jonnycomputer 3y ago
The phrase "is not likely" imo should have been substituted for "is not plausible", though I am not sure everyone else interprets the phrase "not plausible" as meaning something like "almost certainly not true"; they could have meant it as, something like, "the least likely of all the possibilities, by a fair margin." Sure, I'd have preferred if they had been explicit, by giving their estimate of the probability of each possibility explicitly.
- gptbore 3y ago
  "the main thing still in my mind is that the lab escape version of this is so friggin' likely to have happened because they were already doing this type of work and the molecular data is fully consistent with that scenario" As an understatement, I don't think the authors accurately conveyed what their priors on the origin really were, nor what data they encountered to so dramatically shift these priors.
  - jonnycomputer 3y ago
    My only response would be (1) to point to the date of when he said that compared to the date of the final manuscript, and the all the conversations that occurred n between. I think that was from sometime in January. (2) we shouldn't read over-much into an off-the-cuff slack message, ostensibly shared with a small number of individuals, with his impressions and thoughts at the time. The purpose of those discussions is to bang ideas off the wall. In any case, I don't expect good scientists to rigidly hang on to an idea. I expect good scientists to evolve their thinking as they learn. But you may be right that the published paper did not speak to what their particular priors were when they started out. I'm not certain that we should expect it to either. A lot of times you start off with ill-formed half-ideas, and while they may be where you started off from, the utility of sharing that starting point might cause more confusion--or even spread more misinformation--that do good.

stubybubs 3y ago

"Although the evidence shows that SARS-CoV-2 is not a purposefully manipulated virus, it is currently impossible to prove or disprove the other theories of its origin described here. However, since we observed all notable SARS-CoV-2 features, including the optimized RBD and polybasic cleavage site, in related coronaviruses in nature, we do not believe that any type of laboratory-based scenario is plausible. More scientific data could swing the balance of evidence to favor one hypothesis over another." Pretty standard scientific writing. I think the lesson is don't trust journalists and the general public to not blow what you're saying out of proportion and assign it more certainty than you intended. Lab leak is possible, sure. But keep in mind every horrible disease humanity has faced up until the early part of the 20th century came about before microbiology labs even existed. Historically, a zoonitic origin is extremely likely. Imagine if polio or smallpox or leprosy popped up today, you'd have every Joe internet theorizing how it came from a lab in whatever country it appeared in first. I guess back in the day they used to say it was punishment from God. The Spanish flu, God out there smiting the Spaniards.

jonnycomputer 3y ago
100% this.
COGlory 3y ago
>Historically, a zoonitic origin is extremely likely. Historically, there have been far, far more documented lab leaks of SARS-CoV than there have been animal-human jumps. People that wish to shutdown lab leak conversation are quick to mix in engineering. Lots of less educated people can't tell the difference. It is very possible that the virus was both zoonotic in origin, and leaked from the lab.
- stubybubs 3y ago
  My point is that we don't have any documented anything for the first couple hundred thousand of years of humanity's existence, and we encountered the most horrific viral and bacterial infections, many of which caused unthinkable mass deaths. They were so awful we attributed them to God(s) as punishment for our bad behavior. None of them have documented microbiological origins. Some would have some from spontaneous mutation in humans and many would have come from animals. They are de facto not lab leaks, so the fact that we have some lab leaks documented in the last few decades isn't really convincing. There is nothing there that makes a zoonotic origin less likely. Here's a scientist who said we couldn't dismiss the lab leak, and asked for more research, which he did. https://www.npr.org/sections/goatsandsoda/2021/07/19/1016005828/new-data-leads-to-rethinking-once-more-where-the-pandemic-actually-began https://www.npr.org/sections/goatsandsoda/2021/07/19/1016005... The early cases are clustered around the market. I know the market and the lab are "close" on a global scale, but the details matter. They are 30km apart, about a 45 minute drive in traffic. Looks about as clear as John Snow's map of cholera outbreaks in London. That article is from 2021, but he stands by it in 2023: https://www.latimes.com/opinion/story/2023-03-08/covid-lab-leak-energy-department-fbi https://www.latimes.com/opinion/story/2023-03-08/covid-lab-l... "What is the chance that a big Chinese city like Wuhan would have a lab doing the kind of research that has come under suspicion? The answer is, the vast majority of the biggest cities in China have labs involved in such research. If COVID had emerged in, say, Beijing, there would be no fewer than four such labs facing suspicion." Edit: 2 things. It's important to rule out that the idea that this could only be engineered, which would imply a definite lab origin. That is why engineered viruses come up. A non-lab leak is certainly plausible, and a lab leak is not ruled out. There are labs all over China, there are markets all over China. The overlap of cities having both is significant. Viruses appear in larger, denser population centers. The "next thing" was very likely to appear in a city with a lab. The thing is, it's not very close to the lab. There's a large cluster around the market. Lab theory doesn't have much going for it. It's not actually that close to the epicenter. There are labs everywhere. SARS is widely studies. Sure some viruses have long incubation periods, but that would show as far less of a tight cluster around the market. Your hypothesis seems to be that it spread from lab distantly because of incubation time, then stopped spreading distantly once it reached the market? That does not make sense.

ayjchan 3y ago

The lead author of Proximal Origin wrote this in slack on April 17, a month after the letter had been published in Nature Medicine: "Okay, so about the current news. Is there any reason to believe that they might be onto something, or is it all smoke and mirrors? Eddie Holmes - any insights on the China side? The main things from my perspective: 1. Bioweapon and engineered totally off the table 2. If there is no engineering and no culturing, then it means that somebody magically found a pre-formed pandemic virus, put it in the lab, and then infected themselves. The prior on that vs somebody coming into contact with an animal source infected with the virus is as close to zero as you can get. Humans come into contact all the time with SARS-like CoVs, but the likelihood of somebody finding exactly that pandemic virus and infecting themselves is very very low (make no mistake - if they did find that pandemic virus. then they would get infected if they grew it in the lab - but the likelihood of them finding it in the first place is exceedingly small (or so one would hope - otherwise, good luck World avoiding future pandemic). 3. But here's the issue - I'm still not fully convinced that no culture was involved. If culture was involved, then the prior completely changes - because this could have happened with any random SARS-llke CoV of which there are very many. So are we absolutely certain that no culture could have been involved? What concerns me here are some of the comments by Shi in the SciAm article ("I had to check the lab" etc) and the fact that the furin site 1s being messed with in vitro. Yes, it loses it but that could be context dependent. Finally, the paper that was shared with us showing a very similar phenomenon (exactly 12bp insertion) in other CoVs has me concerned... I really really want to go out there guns swinging saying "don't be such an idiot believing these dumb theories - the president is deflecting from the real problems" but I'm warned that we can't fully disprove culture {our argument was mostly based on the presence of the O-linked glycans - but they could likely play a different role... We also can't fully rule out engineering (for basic research) - yes, no obvious signs of engineering anywhere, but that furin site could still have been inserted via gibson assembly (and clearly creating the reverse genetic system isn't hard - the Germans managed to do exactly that for SARS-CoV-2 in less than a month)." And: "Shi didn't do any GOF work that I'm aware of - but GOF work isn't the concern here. She did A LOT of work that involved isolating and culturing SARS-like viruses from bats (in BSL-2) and that's my main concerning scenario (we cite several of those in the paper - if you have a look at those original publications, it's definitely concerning work, no question about it - and is the main reason I have been so concerned about the 'culture' scenario)." I don't think much more needs to be said. The above messages are self-explanatory.

zzzeek 3y ago

Be surprised no more, there's an apparent garbage shute for lots of "journalists" and pundits where something unspoken about modern times bothers them enough that they just flip into being total nutjobs, riding on their previous respectability to keep eyes on them. Silver is part of a long tradition including Glenn Greenwald, Matt Taibbi, heck even the Dilbert guy of people who used to make sense, saw "something" that REALLY bugged them and they just threw it all away to become unintelligible cranks. Makes ya think.

realjhol 3y ago
There is absolutely nothing about Greenwald, Taibbi, or Adams that is in any way unintelligible or irrational.
- jonnycomputer 3y ago
  Greenwald and Adams are cranks, imo. Don't know about Taibbi.
  - realjhol 3y ago
    What do you even mean by that? Their ideas are perfectly coherent and consistent within their own framing. Just because you look at the world through a different frame, doesn't mean that these people are saying things that are unreasonable
    - jonnycomputer 3y ago
      They consistently disregard evidence that contradicts their core beliefs.
      - realjhol 3y ago
        So does literally everyone in the entire world