18 ms·

I feel like people are doing a poor job distinguishing between "engineered" and "leaked." There is, from my understanding, reasonable evidence to conclude the

I feel like people are doing a poor job distinguishing between "engineered" and "leaked." There is, from my understanding, reasonable evidence to conclude the virus was not engineered from the perspective of "we took genes from one virus and moved them to this virus," but there's no evidence disproving the idea that it was the result of gain of function research. My personal feeling is that these statements are true: * The virus is unlikely to have been engineered (in the way I described above) and leaked. * There is circumstantial evidence the virus was the result of gain of function research and it leaked. * There is circumstantial evidence the virus was a natural research sample and it leaked. * There is circumstantial evidence the virus was introduced by an animal/person who traveled to the wet market. Some of these are more likely than others, and an individual's own calibration for what is likely or unlikely will probably come into play more than evidence in the short term and possibly long term as well. I can say the vast majority of us are not qualified to answer the question either way though.

loveistheanswer 6y ago
>I can say the vast majority of us are not qualified to answer the question either way though. It's also worth noting that even the leading experts can get these things wrong, as was the case with the Sverdlovsk lab leak. Soviet authorities covered it up by blaming local meat markets, and leading US experts concurred with them, only to reverse their conclusion 6 years later. https://en.m.wikipedia.org/wiki/Sverdlovsk_anthrax_leak#Accident https://en.m.wikipedia.org/wiki/Sverdlovsk_anthrax_leak#Acci...
- AdamJacobMuller 6y ago
  Never heard about Sverdlosk, interesting story. > Russian Prime Minister Yegor Gaidar issued a decree to begin demilitarization of Compound 19 in 1992. However, the facility continued its work. Not a single journalist has been allowed onto the premises since 1992. About 200 soldiers with Rottweiler dogs still patrol the complex.
- eightysixfour 6y ago
  Absolutely, without multiple trust-worthy first-person accounts backed by evidence, the likely best we can hope for is an eventually-consistent story that we are "pretty sure" about. Considering the size of the impact on the world, that will take a long time.
- NineStarPoint 6y ago
  It’s worth noting that in both the Sverdlov case and in this one, world scientists are only being given access to the situation in an extremely controlled fashion. A primary reason we can’t say more on what happened in this case is the CCP’s tight control over access that could help clarify the situation. Which will always look suspicious, whether it was actually a completely natural virus or not.
  - lostinquebec 6y ago
    I don't understand how this works, so forgive my ignorance. Wouldn't the Wuhan lab be able to disprove this really easily? How often do they sequence viruses? Couldn't they show categorically that COVID-19 is not a descendant of a virus they were working with/on?
    - btilly 6y ago
      As long as they don't have an audited central database of all viruses that they sequenced, they have no way to demonstrate that they showed you all of their virus lines. And if they had such a central database, we'd have probably heard about it by now.
      - tripletao 6y ago
        I'm not sure about the "audited" part, but the WIV did have such a central database. It went offline in September 2019, they say due to repeated hacking attempts. It hasn't been back since, and access to that database has been a major point of contention between those who believe a forensic investigation (i.e., one that doesn't simply trust the WIV to report whether they were working with related viruses) is necessary, and those who do not. https://www.researchgate.net/publication/349073738_An_investigation_into_the_WIV_databases_that_were_taken_offline https://www.researchgate.net/publication/349073738_An_invest...
    - seoaeu 6y ago
      How would you know they provided a complete list of viruses they were working on? Couldn't they just leave off anything incriminating?
cameldrv 6y ago
I'm not sure you can rule out "engineered as you described above." WIV had recently published research on, and had an active grant to perform (at the time of the outbreak), chimeric Coronavirus research, and they were one of the two world leading labs in this. In that research, they were transplanting the spike gene from one virus to the "backbone" of another. You could call this "engineering" or "gain of function" depending on your perspective. The thing that raised people's suspicions about this is that the spike RBD strongly resembles a virus sequence they released recently (Pangolin-CoV), and the backbone strongly resembles another virus they recently published (RaTG13). That suggests that there was some sort of recombination event. That recombination could have occurred in nature, in an animal that was simultaneously infected with two viruses, or it could have occurred in the lab.
- andi999 6y ago
  Sources, please.
  - AndrewBissell 6y ago
    This article delves into the spike protein and its furin cleavage site which some have argued looks engineered: https://nymag.com/intelligencer/article/coronavirus-lab-escape-theory.html https://nymag.com/intelligencer/article/coronavirus-lab-esca... Incidentally (or perhaps not?), there is some evidence that the furin-cleavage site is what makes the virus resistant to hydroxychloroquine, which can be countered by combining it with a TMPRSS2 inhibitor: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009212 https://journals.plos.org/plospathogens/article?id=10.1371/j...
- selimthegrim 6y ago
  96% is strongly resembles?
- XorNot 6y ago
  They're viruses from the same family of viruses. "Strongly resembles" is not strong evidence. Which you note by pointing out that this is the exact thing we'd expect from a natural event.
Buttons840 6y ago
I like this presentation of evidence. Rarely do you see such a short acknowledgement that there are multiple contradictory theories, each having some evidence, and making no attempt to pick which theory is correct. Sometimes its wrong to present "both sides" like that. Like pretending the evidence against the moon landings is equal to the evidence for the moon landings. But if you're going to be wrong, this is probably the best kind of wrong.
- beowulfey 6y ago
  well, often the benefit of listing out as much evidence as possible (basically, look at the facts on hand) is that it can help clarify WHICH theory makes the most sense
  - eightysixfour 6y ago
    I think this is one of those areas where our day-to-day probability heuristics do not align with the actual probabilities. So, as an individual, trying to decide which theory makes the most sense is a Sisyphean task. For example, I have seen a lot of comments that the closest natural COVID reservoir is 500 miles away, that sounds like a lot! But the average tractor trailer can cover that in a day no problem, so our heuristic needs to include how many trucks are moving between those areas, how many have come in contact with wildlife or are transporting it, etc. Since it only takes one transmission the problem rapidly becomes too complex. Fortunately the answer has no bearing on decisions being made in the here and now, so we can afford to wait and let experts do their jobs and hope we take the right steps long term if it was something that could have been avoided.
    - ricksunny 6y ago
      > we can afford to wait and let experts do their jobs We can emphatically not expect the experts to do their job. Those cited as having the most expertise (virologists who undertake gain-of-function research, symbolically under the auspices of HHS’ toothless P3CO regulation framework) have the most to lose from a finding that the pandemic’s source was a lab leak. They lose all the grants and public financial support, not to mention endure unending public scorn that will haunt the their careers for the duration. For evidence that the relevant, oft-cited scientists act precisely this way, one need no more than to look at @BlockedVirology’s retweets: https://twitter.com/blockedvirology https://twitter.com/blockedvirology Scientists are human - I would highly recommend disabusing oneself of the notion that they might act contrary to overwhelming human incentives in as weighty a context as investigating the origins of the greatest pandemic in a century. The only alternative in the face of this embedded conflict of interest in our (society’s) ability to credibly investigate the pandemic’s origins is for technically-minded individuals (who don’t run multimillion dollar virology labs) to avail themselves of the findings gathered to date on the origins (there’s lots! Just need to take a look, the contributors to the above feed are a good place to start), and advocate to their representatives for a credible & even-handed origins investigation. Failing that, expect no origin beyond all reasonable doubt to be credibly identified in our lifetimes.
Banyonite 6y ago
There is a rather detailed description of circumstantial evidence that leans towards the gain of function statement: https://yurideigin.medium.com/lab-made-cov2-genealogy-through-the-lens-of-gain-of-function-research-f96dd7413748 https://yurideigin.medium.com/lab-made-cov2-genealogy-throug...
- jeduehr 6y ago
  Hi, Yuri makes a few mistakes in this. 1) Chimeric viruses (copy and paste) are what scientists make in the lab. They take a piece of one virus and paste it into the genome of another, en masse. This is very different from what SARS-2 is, which is more accurately described as a "mosaic" (lots of little changes all over the genome). This is much much more difficult (if not very close to impossible in the case of SARS-2) to make in the lab, at least not and have it be done and "cooked" by the time the pandemic started. See the part of my post here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpbagf/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... 2) He makes it sound like the techniques Shi Zhengli uses in the lab could create SARS-CoV-2. This is not true. For the reasons I describe above in point 1, and others, this is not really a likely possibility. Modern virology just does not have the tools to do this. Only mother nature with its many millions of hosts and diversity of hosts (in different mammals) could do this in the span of time molecular clock analysis says it took to take similar viruses like RaTG-13 and mutate them into SARS-CoV-2. I go into extreme detail about this in this part of my original post: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpc7c8/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... 3) He also says things like "Considering the heights of user friendliness and automation that genetic engineering tools have attained, creating a synthetic CoV2 via the above methodology would be in reach of even a grad student." Yeah, in 2020. Not in 2000 when they would have needed to start doing this. We did not have these tools back then. We did not understand enough about viruses, and this is /before/ we even discovered SARS-CoV-1! The molecular clock + the synonymous/nonsynonymous criteria + the mosaic nature of the virus together put constraints on how this virus could have evolved. The first says it takes about 50-70 years to evolve a virus like this, evolving as fast as it does in nature. The second says it evolved in a fashion that wasn't putting more selective pressure on it than nature usually does. The third says it happened in a semi-random way, the way natural mutations occur. All of these together (plus other stuff) mean that it's unlikely that anyone /grew/ the virus in a lab intentionally. I go into extreme detail about the synonymous nonsynonymous stuff in 3.1.1 of my post. 4) Also, it doesn't actually look like a virus that was grown in a petri dish or one that was grown in a single species of animals. It has O-linked glycans on it that cell culture wouldn't add. See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpc9om/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... Also, if it were grown in a single species of animal, then the SARS-2 spike protein would bind most tightly to that receptor. That's not actually what it is. As best we can tell, the S from SARS-2 binds just ~okay~ to a lot of different ACE2 receptors, and it just happens to work to bind human ACE2 kinda well. It's not at all how anyone would have actually designed it if they wanted to make a virus that kills humans. If they were designing it that way, they were some really shitty super villains, let me tell you that. I go into some extreme detail about this in this part of my post: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpby1u/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... 5) Yuri gets really hot and bothered about the furin cleavage site. But what he seems to misunderstand is that these cleavage sites have evolved in nature too. It's likely either A) a recombinatorial event between SARS-2 and similar viruses in nature or B) it mutated over a short period of time in a way similar to other "mutagenicity islands." We have actually seen this before in nature. See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpbys1/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... He even says it has been shown to be disabled in a relatively short period of time in lab animals, so why wouldn't it be able to show up in nature in 50-70 years in millions of wild animals? It's really not that unlikely when you consider that certain areas of viral genomes mutate a lot faster than others in the wild. 6) He even points out that the only viruses in nature that share the cleavage site share only 40% of the rest of their genomes with SARS-2. But that just shows it's likely that SARS-2 and one of these other viruses happened to infect the same animal at the same time, and their genomes had a cross-over event. This happens ALL. THE. TIME. in viruses in nature. It's basically how flu pandemics occur. See: -https://www.nature.com/articles/nrg2053 https://www.nature.com/articles/nrg2053 -https://www.euro.who.int/en/health-topics/communicable-diseases/influenza/pandemic-influenza/how-pandemic-influenza-emerges https://www.euro.who.int/en/health-topics/communicable-disea... -https://academic.oup.com/mbe/article-pdf/26/1/177/13640305/msn238.pdf https://academic.oup.com/mbe/article-pdf/26/1/177/13640305/m... Why is it not likely this sort of thing was involved in this coronavirus pandemic? Honestly I can't keep going because I need to be studying for the most important exam of my career (USMLE Step 1) but I can tell you just from the first couple pages of this extremely long thing that Yuri is not a virologist and has never taken a formal viral genetics class. He is making fundamental mistakes in how viruses evolve and change over time. He clearly knows a lot about biochemistry and regular genetics, but viruses are a whole different ballgame.
Bukhmanizer 6y ago
My personal feelings are that all 3 are possible, but approximately 0.0001% of people will actually consider the likelihood of each one, but rather, most will choose whichever one is most convenient and comfortable to believe in. Of course as an Asian person, whatever people believe in will have a direct impact on me. I remember after 9/11, the amount of awful things that were said and done to the Sikh population in my city. It didn’t matter they had literally nothing to do with the attacks. People were angry and wanted someone to blame.
- anonymousisme 6y ago
  As a white American in Beijing during the 9/11 attacks, I experienced lots of not-so-surprising behavior from my Chinese hosts. Many Chinese felt that America deserved what they got. Tensions were still high from the "Hainan Island Incident" only a few months earlier. https://en.wikipedia.org/wiki/Hainan_Island_incident https://en.wikipedia.org/wiki/Hainan_Island_incident
  - redis_mlc 6y ago
    > Many Chinese felt that America deserved what they got. I don't see how their opinion matters, since they're misinformed and orchestrated by the CCP. The Hainan incident was caused by a Chinese fighter pilot running into a US surveillance plane. The former is agile, the latter is not, so that's the fault of the fighter. Also, a plane in distress doesn't need permission to land. For the CCP to make a big deal out of that when there's no other runway available shows their true nature - evil and authoritarian. The CCP has been at war with the US since the 1950s over ideology. If the US was not their enemy, the CCP would just pick another country. I've noticed that otherwise intelligent people seem to place significance in "man in the street" conversations with people who live in totalitarian countries and have no power. There's a phrase for that, useful idiot: https://en.wikipedia.org/wiki/Useful_idiot https://en.wikipedia.org/wiki/Useful_idiot
    - labawi 6y ago
      FWIW, when we heard of the incident, I think the prevailing sentiment was that America deserved it, and we are unrelated to China (in Europe). America has made a lot of enemies and inflicted a lot of damage and terror for what seems as both good and bad reasons. After all the one-sided "interventions", I find it hard to disagree that America (not the Americans affected) deserved something in return.
cdblades 6y ago
> but there's no evidence disproving the idea that it was the result of gain of function research. That's not a lens that can be used to usefully evaluate claims.
tootie 6y ago
Even the WHO report didn't rule out the possibility of a leak. They just said the evidence is weak and the evidence of animal to human transmission is stronger.
- jeduehr 6y ago
  Yes! And that is how most virologists (myself included) feel about this whole thing. Zoonosis is just a lot more likely.
bostonsre 6y ago
Yea, I'm not sure how some people can vehemently say any of the most plausible explanations are absolutely wrong or right. It seems like it's just not possible for anyone outside of a very small group in China to know the truth and also seems possible that no one at all knows exactly what happened. Without any smoking gun evidence, it seems like everything else is just guess work with some guesses a lot more educated than others.
- jeduehr 6y ago
  Hi, you're probably right it isn't possible to know 100% the origin at this point. All we can do is make probabilistic arguments. Inferences. Inductive reasoning. And that sort of analysis, occam's razor based on the least new assumptions necessary to conclude the mechanism, I think the zoonotic theory is more likely. The lab theory isn't impossible, it just requires a lot more untested and unknown assumptions.
roenxi 6y ago
And to a fair extent these questions are academic - say that it wasn't a lab leak and came from a natural reservoir. That doesn't change the fact that BSL-4 lab protections aren't perfect and there will be leaks of a similar magnitude of risk in the future. The biological research community are obviously playing with some much riskier toys than everyone else.
- gadf 6y ago
  So even if what we're saying if not true, we're still right. collateral racism bedamned. You're not going to take our legitimized bias say from us, so stahp trying!
trevelyan 6y ago
> There is circumstantial evidence the virus was introduced by an animal/person who traveled to the wet market. Not for this one. There were several cases we know preceded the wet market cluster. This was known in January 2020.
Robotbeat 6y ago
In some sense, it doesn't matter dramatically which of the 3 it was. All seem plausible because... 1) gain of function research is super risky and there have been lab escapes before. We need to do MUCH better about lab leaks. We should spend more on security and have greater transparency. We should also question whether it even makes sense to do that kind of research. 2) Same thing for natural research sample being leaked... 3) wet markets are probably a really bad idea. And we should probably keep a better eye on natural virus variants, HOWEVER... that's somewhat in conflict with the "maybe this research isn't worth it" line of thinking. So we have some somewhat hard trade-offs, here, but there are aspects where we can just do better. Like, whenever we do do research on viruses, we should probably be a LOT more careful about how and when we do it. And although it's very unlikely the virus was engineered, we should probably be careful with the technology that would let it be engineered. The technology that makes sequencing novel virus strains and developing novel vaccines using mRNA also makes it easier to engineer a virus. This is a tough one because if we had clamped down super hard on mRNA tech too early, we would've been perhaps unprepared to make a vaccine...
blablabla123 6y ago
> The virus is unlikely to have been engineered (in the way I described above) and leaked. Likely, unlikely, it's not really possible to attach probabilities to events that already happened. Also history is told chronologically, when told anti-chronologically we tend to make causal connections where there are none. I don't want to dismiss the lab theory completely but consider this: These kinds of labs are all over the world, in China, in the Netherlands, in the US and so on. They are mostly being built in metropole regions because that's where large science clusters tend to be. Coincidentally city centers are traditionally built around markets. These tend to be the densest areas of cities. Densest areas are where infection clusters are most likely to build up and get noticed. And now we find a case where all these 3 coincide. Really, that doesn't say much. Also there have been quite some hints about Covid19 cases before December 2019, outside of China even. [1] Statistics is a highly counter-intuitive discipline. If it wasn't maybe the virus would be already under control anyway. [1] https://www.bloomberg.com/news/articles/2020-12-01/covid-infections-found-in-u-s-in-2019-weeks-before-china-cases https://www.bloomberg.com/news/articles/2020-12-01/covid-inf...
f6v 6y ago
> but there's no evidence disproving... I don’t think that’s how legal system or science works(at least in statistics). We can assume that null hypothesis is that there was no leak/engineering of the virus, i.e. defendant isn’t guilty. Then it’s up to a prosecutor/someone with the evidence to reject that hypothesis. But you don’t start proving the alternative hypothesis when doing science, since it’s much more complicated. And again, the defendant doesn’t have to prove his innocence.
- eightysixfour 6y ago
  The circumstantial evidence exists though and I’m not making a claim to be a court of law, I’m claiming that these are how I view the probabilities, as a layman, and that anyone who doesn’t work on these things for a living that suggests they are more confident in one of these probabilities than another probably has some biases they need to check.
DebtDeflation 6y ago
For completeness sake, can we also say: * There is no evidence that the virus originated with imported frozen seafood. * There is no evidence that the virus originated with US Army personnel who were present for the Military World Games. * There is no evidence for the "multiple origins theory" that the Chinese government is currently promoting. The wet market origin theory would be more plausible to me if not for the fact that SARS-CoV-2 was found all over surfaces there but not in a single live or dead animal. That seems to indicate that it was merely the location of an early superspreader event and not the true origin.
- jeduehr 6y ago
  Yep, agreed on all 3 counts.
- jeduehr 6y ago
  Best epidemiological and genetic evidence suggests it originated somewhere outside Wuhan and then became a serious outbreak there as it's a major population center. https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpcfs2/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
pmiller2 6y ago
I agree that the virus is unlikely to have been engineered in the manner you describe. But, I'm wondering: where is this circumstantial evidence for the leak scenario, be it a natural sample or one that had some help evolving? (I also doubt the wet market scenario, but that one isn't nearly so contentious.) Here's the thing: in my mind, anyone who wants to claim the virus escaped the lab as a result of an accident needs to show how someone could have gotten infected with it while working with it in a lab using BSL-3 precautions. We're all just walking around wearing plain old surgical masks, and sometimes not even that level of protection, but literally a piece of cloth is enough to reduce transmission of this virus significantly. Now, tell me how someone wearing full body PPE gets infected with it. Even at BSL-2, any procedures that would create aerosols are done inside a containment vessel, so, I can't honestly see it happening there, either. And, it certainly wouldn't have been at BSL-1, as that's reserved for known non-pathogenic organisms. Basically, the criterion for a BSL-1 lab is "we grow bugs here, on purpose." Clearly, any of the bat coronaviruses they would handle at WIV would greatly exceed that level of precaution. With that in mind, IMO, the real interesting bit this article had to offer was to suggest the possibility that the virus snuck into the lab. Given the virus's relative inability to spread via surface contact and necessity of aerosolized droplet spread, you still have to answer the question of how it got out, but, it's at least an intriguing origin story. So, in summary, yes, the only correct answer we can really say for sure is "we don't know exactly where it came from, if it leaked out of a lab, and what might have been done with it while it was in the lab." But, I'm having a really hard time believing a virus that gets largely stopped by a simple mask could sneak out of a BSL-2+ lab.

loveistheanswer 6y ago

>I can say the vast majority of us are not qualified to answer the question either way though. It's also worth noting that even the leading experts can get these things wrong, as was the case with the Sverdlovsk lab leak. Soviet authorities covered it up by blaming local meat markets, and leading US experts concurred with them, only to reverse their conclusion 6 years later. https://en.m.wikipedia.org/wiki/Sverdlovsk_anthrax_leak#Accident https://en.m.wikipedia.org/wiki/Sverdlovsk_anthrax_leak#Acci...

AdamJacobMuller 6y ago
Never heard about Sverdlosk, interesting story. > Russian Prime Minister Yegor Gaidar issued a decree to begin demilitarization of Compound 19 in 1992. However, the facility continued its work. Not a single journalist has been allowed onto the premises since 1992. About 200 soldiers with Rottweiler dogs still patrol the complex.
eightysixfour 6y ago
Absolutely, without multiple trust-worthy first-person accounts backed by evidence, the likely best we can hope for is an eventually-consistent story that we are "pretty sure" about. Considering the size of the impact on the world, that will take a long time.
NineStarPoint 6y ago
It’s worth noting that in both the Sverdlov case and in this one, world scientists are only being given access to the situation in an extremely controlled fashion. A primary reason we can’t say more on what happened in this case is the CCP’s tight control over access that could help clarify the situation. Which will always look suspicious, whether it was actually a completely natural virus or not.
- lostinquebec 6y ago
  I don't understand how this works, so forgive my ignorance. Wouldn't the Wuhan lab be able to disprove this really easily? How often do they sequence viruses? Couldn't they show categorically that COVID-19 is not a descendant of a virus they were working with/on?
  - btilly 6y ago
    As long as they don't have an audited central database of all viruses that they sequenced, they have no way to demonstrate that they showed you all of their virus lines. And if they had such a central database, we'd have probably heard about it by now.
    - tripletao 6y ago
      I'm not sure about the "audited" part, but the WIV did have such a central database. It went offline in September 2019, they say due to repeated hacking attempts. It hasn't been back since, and access to that database has been a major point of contention between those who believe a forensic investigation (i.e., one that doesn't simply trust the WIV to report whether they were working with related viruses) is necessary, and those who do not. https://www.researchgate.net/publication/349073738_An_investigation_into_the_WIV_databases_that_were_taken_offline https://www.researchgate.net/publication/349073738_An_invest...
  - seoaeu 6y ago
    How would you know they provided a complete list of viruses they were working on? Couldn't they just leave off anything incriminating?

cameldrv 6y ago

I'm not sure you can rule out "engineered as you described above." WIV had recently published research on, and had an active grant to perform (at the time of the outbreak), chimeric Coronavirus research, and they were one of the two world leading labs in this. In that research, they were transplanting the spike gene from one virus to the "backbone" of another. You could call this "engineering" or "gain of function" depending on your perspective. The thing that raised people's suspicions about this is that the spike RBD strongly resembles a virus sequence they released recently (Pangolin-CoV), and the backbone strongly resembles another virus they recently published (RaTG13). That suggests that there was some sort of recombination event. That recombination could have occurred in nature, in an animal that was simultaneously infected with two viruses, or it could have occurred in the lab.

andi999 6y ago
Sources, please.
- AndrewBissell 6y ago
  This article delves into the spike protein and its furin cleavage site which some have argued looks engineered: https://nymag.com/intelligencer/article/coronavirus-lab-escape-theory.html https://nymag.com/intelligencer/article/coronavirus-lab-esca... Incidentally (or perhaps not?), there is some evidence that the furin-cleavage site is what makes the virus resistant to hydroxychloroquine, which can be countered by combining it with a TMPRSS2 inhibitor: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009212 https://journals.plos.org/plospathogens/article?id=10.1371/j...
selimthegrim 6y ago
96% is strongly resembles?
XorNot 6y ago
They're viruses from the same family of viruses. "Strongly resembles" is not strong evidence. Which you note by pointing out that this is the exact thing we'd expect from a natural event.

Buttons840 6y ago

I like this presentation of evidence. Rarely do you see such a short acknowledgement that there are multiple contradictory theories, each having some evidence, and making no attempt to pick which theory is correct. Sometimes its wrong to present "both sides" like that. Like pretending the evidence against the moon landings is equal to the evidence for the moon landings. But if you're going to be wrong, this is probably the best kind of wrong.

beowulfey 6y ago
well, often the benefit of listing out as much evidence as possible (basically, look at the facts on hand) is that it can help clarify WHICH theory makes the most sense
- eightysixfour 6y ago
  I think this is one of those areas where our day-to-day probability heuristics do not align with the actual probabilities. So, as an individual, trying to decide which theory makes the most sense is a Sisyphean task. For example, I have seen a lot of comments that the closest natural COVID reservoir is 500 miles away, that sounds like a lot! But the average tractor trailer can cover that in a day no problem, so our heuristic needs to include how many trucks are moving between those areas, how many have come in contact with wildlife or are transporting it, etc. Since it only takes one transmission the problem rapidly becomes too complex. Fortunately the answer has no bearing on decisions being made in the here and now, so we can afford to wait and let experts do their jobs and hope we take the right steps long term if it was something that could have been avoided.
  - ricksunny 6y ago
    > we can afford to wait and let experts do their jobs We can emphatically not expect the experts to do their job. Those cited as having the most expertise (virologists who undertake gain-of-function research, symbolically under the auspices of HHS’ toothless P3CO regulation framework) have the most to lose from a finding that the pandemic’s source was a lab leak. They lose all the grants and public financial support, not to mention endure unending public scorn that will haunt the their careers for the duration. For evidence that the relevant, oft-cited scientists act precisely this way, one need no more than to look at @BlockedVirology’s retweets: https://twitter.com/blockedvirology https://twitter.com/blockedvirology Scientists are human - I would highly recommend disabusing oneself of the notion that they might act contrary to overwhelming human incentives in as weighty a context as investigating the origins of the greatest pandemic in a century. The only alternative in the face of this embedded conflict of interest in our (society’s) ability to credibly investigate the pandemic’s origins is for technically-minded individuals (who don’t run multimillion dollar virology labs) to avail themselves of the findings gathered to date on the origins (there’s lots! Just need to take a look, the contributors to the above feed are a good place to start), and advocate to their representatives for a credible & even-handed origins investigation. Failing that, expect no origin beyond all reasonable doubt to be credibly identified in our lifetimes.

Banyonite 6y ago

There is a rather detailed description of circumstantial evidence that leans towards the gain of function statement: https://yurideigin.medium.com/lab-made-cov2-genealogy-through-the-lens-of-gain-of-function-research-f96dd7413748 https://yurideigin.medium.com/lab-made-cov2-genealogy-throug...

jeduehr 6y ago
Hi, Yuri makes a few mistakes in this. 1) Chimeric viruses (copy and paste) are what scientists make in the lab. They take a piece of one virus and paste it into the genome of another, en masse. This is very different from what SARS-2 is, which is more accurately described as a "mosaic" (lots of little changes all over the genome). This is much much more difficult (if not very close to impossible in the case of SARS-2) to make in the lab, at least not and have it be done and "cooked" by the time the pandemic started. See the part of my post here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpbagf/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... 2) He makes it sound like the techniques Shi Zhengli uses in the lab could create SARS-CoV-2. This is not true. For the reasons I describe above in point 1, and others, this is not really a likely possibility. Modern virology just does not have the tools to do this. Only mother nature with its many millions of hosts and diversity of hosts (in different mammals) could do this in the span of time molecular clock analysis says it took to take similar viruses like RaTG-13 and mutate them into SARS-CoV-2. I go into extreme detail about this in this part of my original post: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpc7c8/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... 3) He also says things like "Considering the heights of user friendliness and automation that genetic engineering tools have attained, creating a synthetic CoV2 via the above methodology would be in reach of even a grad student." Yeah, in 2020. Not in 2000 when they would have needed to start doing this. We did not have these tools back then. We did not understand enough about viruses, and this is /before/ we even discovered SARS-CoV-1! The molecular clock + the synonymous/nonsynonymous criteria + the mosaic nature of the virus together put constraints on how this virus could have evolved. The first says it takes about 50-70 years to evolve a virus like this, evolving as fast as it does in nature. The second says it evolved in a fashion that wasn't putting more selective pressure on it than nature usually does. The third says it happened in a semi-random way, the way natural mutations occur. All of these together (plus other stuff) mean that it's unlikely that anyone /grew/ the virus in a lab intentionally. I go into extreme detail about the synonymous nonsynonymous stuff in 3.1.1 of my post. 4) Also, it doesn't actually look like a virus that was grown in a petri dish or one that was grown in a single species of animals. It has O-linked glycans on it that cell culture wouldn't add. See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpc9om/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... Also, if it were grown in a single species of animal, then the SARS-2 spike protein would bind most tightly to that receptor. That's not actually what it is. As best we can tell, the S from SARS-2 binds just ~okay~ to a lot of different ACE2 receptors, and it just happens to work to bind human ACE2 kinda well. It's not at all how anyone would have actually designed it if they wanted to make a virus that kills humans. If they were designing it that way, they were some really shitty super villains, let me tell you that. I go into some extreme detail about this in this part of my post: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpby1u/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... 5) Yuri gets really hot and bothered about the furin cleavage site. But what he seems to misunderstand is that these cleavage sites have evolved in nature too. It's likely either A) a recombinatorial event between SARS-2 and similar viruses in nature or B) it mutated over a short period of time in a way similar to other "mutagenicity islands." We have actually seen this before in nature. See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpbys1/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did... He even says it has been shown to be disabled in a relatively short period of time in lab animals, so why wouldn't it be able to show up in nature in 50-70 years in millions of wild animals? It's really not that unlikely when you consider that certain areas of viral genomes mutate a lot faster than others in the wild. 6) He even points out that the only viruses in nature that share the cleavage site share only 40% of the rest of their genomes with SARS-2. But that just shows it's likely that SARS-2 and one of these other viruses happened to infect the same animal at the same time, and their genomes had a cross-over event. This happens ALL. THE. TIME. in viruses in nature. It's basically how flu pandemics occur. See: -https://www.nature.com/articles/nrg2053 https://www.nature.com/articles/nrg2053 -https://www.euro.who.int/en/health-topics/communicable-diseases/influenza/pandemic-influenza/how-pandemic-influenza-emerges https://www.euro.who.int/en/health-topics/communicable-disea... -https://academic.oup.com/mbe/article-pdf/26/1/177/13640305/msn238.pdf https://academic.oup.com/mbe/article-pdf/26/1/177/13640305/m... Why is it not likely this sort of thing was involved in this coronavirus pandemic? Honestly I can't keep going because I need to be studying for the most important exam of my career (USMLE Step 1) but I can tell you just from the first couple pages of this extremely long thing that Yuri is not a virologist and has never taken a formal viral genetics class. He is making fundamental mistakes in how viruses evolve and change over time. He clearly knows a lot about biochemistry and regular genetics, but viruses are a whole different ballgame.

Bukhmanizer 6y ago

My personal feelings are that all 3 are possible, but approximately 0.0001% of people will actually consider the likelihood of each one, but rather, most will choose whichever one is most convenient and comfortable to believe in. Of course as an Asian person, whatever people believe in will have a direct impact on me. I remember after 9/11, the amount of awful things that were said and done to the Sikh population in my city. It didn’t matter they had literally nothing to do with the attacks. People were angry and wanted someone to blame.

anonymousisme 6y ago
As a white American in Beijing during the 9/11 attacks, I experienced lots of not-so-surprising behavior from my Chinese hosts. Many Chinese felt that America deserved what they got. Tensions were still high from the "Hainan Island Incident" only a few months earlier. https://en.wikipedia.org/wiki/Hainan_Island_incident https://en.wikipedia.org/wiki/Hainan_Island_incident
- redis_mlc 6y ago
  > Many Chinese felt that America deserved what they got. I don't see how their opinion matters, since they're misinformed and orchestrated by the CCP. The Hainan incident was caused by a Chinese fighter pilot running into a US surveillance plane. The former is agile, the latter is not, so that's the fault of the fighter. Also, a plane in distress doesn't need permission to land. For the CCP to make a big deal out of that when there's no other runway available shows their true nature - evil and authoritarian. The CCP has been at war with the US since the 1950s over ideology. If the US was not their enemy, the CCP would just pick another country. I've noticed that otherwise intelligent people seem to place significance in "man in the street" conversations with people who live in totalitarian countries and have no power. There's a phrase for that, useful idiot: https://en.wikipedia.org/wiki/Useful_idiot https://en.wikipedia.org/wiki/Useful_idiot
  - labawi 6y ago
    FWIW, when we heard of the incident, I think the prevailing sentiment was that America deserved it, and we are unrelated to China (in Europe). America has made a lot of enemies and inflicted a lot of damage and terror for what seems as both good and bad reasons. After all the one-sided "interventions", I find it hard to disagree that America (not the Americans affected) deserved something in return.

cdblades 6y ago

> but there's no evidence disproving the idea that it was the result of gain of function research. That's not a lens that can be used to usefully evaluate claims.

tootie 6y ago

Even the WHO report didn't rule out the possibility of a leak. They just said the evidence is weak and the evidence of animal to human transmission is stronger.

jeduehr 6y ago
Yes! And that is how most virologists (myself included) feel about this whole thing. Zoonosis is just a lot more likely.

bostonsre 6y ago

Yea, I'm not sure how some people can vehemently say any of the most plausible explanations are absolutely wrong or right. It seems like it's just not possible for anyone outside of a very small group in China to know the truth and also seems possible that no one at all knows exactly what happened. Without any smoking gun evidence, it seems like everything else is just guess work with some guesses a lot more educated than others.

jeduehr 6y ago
Hi, you're probably right it isn't possible to know 100% the origin at this point. All we can do is make probabilistic arguments. Inferences. Inductive reasoning. And that sort of analysis, occam's razor based on the least new assumptions necessary to conclude the mechanism, I think the zoonotic theory is more likely. The lab theory isn't impossible, it just requires a lot more untested and unknown assumptions.

roenxi 6y ago

And to a fair extent these questions are academic - say that it wasn't a lab leak and came from a natural reservoir. That doesn't change the fact that BSL-4 lab protections aren't perfect and there will be leaks of a similar magnitude of risk in the future. The biological research community are obviously playing with some much riskier toys than everyone else.

gadf 6y ago
So even if what we're saying if not true, we're still right. collateral racism bedamned. You're not going to take our legitimized bias say from us, so stahp trying!

trevelyan 6y ago

> There is circumstantial evidence the virus was introduced by an animal/person who traveled to the wet market. Not for this one. There were several cases we know preceded the wet market cluster. This was known in January 2020.

Robotbeat 6y ago

In some sense, it doesn't matter dramatically which of the 3 it was. All seem plausible because... 1) gain of function research is super risky and there have been lab escapes before. We need to do MUCH better about lab leaks. We should spend more on security and have greater transparency. We should also question whether it even makes sense to do that kind of research. 2) Same thing for natural research sample being leaked... 3) wet markets are probably a really bad idea. And we should probably keep a better eye on natural virus variants, HOWEVER... that's somewhat in conflict with the "maybe this research isn't worth it" line of thinking. So we have some somewhat hard trade-offs, here, but there are aspects where we can just do better. Like, whenever we do do research on viruses, we should probably be a LOT more careful about how and when we do it. And although it's very unlikely the virus was engineered, we should probably be careful with the technology that would let it be engineered. The technology that makes sequencing novel virus strains and developing novel vaccines using mRNA also makes it easier to engineer a virus. This is a tough one because if we had clamped down super hard on mRNA tech too early, we would've been perhaps unprepared to make a vaccine...

blablabla123 6y ago

> The virus is unlikely to have been engineered (in the way I described above) and leaked. Likely, unlikely, it's not really possible to attach probabilities to events that already happened. Also history is told chronologically, when told anti-chronologically we tend to make causal connections where there are none. I don't want to dismiss the lab theory completely but consider this: These kinds of labs are all over the world, in China, in the Netherlands, in the US and so on. They are mostly being built in metropole regions because that's where large science clusters tend to be. Coincidentally city centers are traditionally built around markets. These tend to be the densest areas of cities. Densest areas are where infection clusters are most likely to build up and get noticed. And now we find a case where all these 3 coincide. Really, that doesn't say much. Also there have been quite some hints about Covid19 cases before December 2019, outside of China even. [1] Statistics is a highly counter-intuitive discipline. If it wasn't maybe the virus would be already under control anyway. [1] https://www.bloomberg.com/news/articles/2020-12-01/covid-infections-found-in-u-s-in-2019-weeks-before-china-cases https://www.bloomberg.com/news/articles/2020-12-01/covid-inf...

f6v 6y ago

> but there's no evidence disproving... I don’t think that’s how legal system or science works(at least in statistics). We can assume that null hypothesis is that there was no leak/engineering of the virus, i.e. defendant isn’t guilty. Then it’s up to a prosecutor/someone with the evidence to reject that hypothesis. But you don’t start proving the alternative hypothesis when doing science, since it’s much more complicated. And again, the defendant doesn’t have to prove his innocence.

eightysixfour 6y ago
The circumstantial evidence exists though and I’m not making a claim to be a court of law, I’m claiming that these are how I view the probabilities, as a layman, and that anyone who doesn’t work on these things for a living that suggests they are more confident in one of these probabilities than another probably has some biases they need to check.

DebtDeflation 6y ago

For completeness sake, can we also say: * There is no evidence that the virus originated with imported frozen seafood. * There is no evidence that the virus originated with US Army personnel who were present for the Military World Games. * There is no evidence for the "multiple origins theory" that the Chinese government is currently promoting. The wet market origin theory would be more plausible to me if not for the fact that SARS-CoV-2 was found all over surfaces there but not in a single live or dead animal. That seems to indicate that it was merely the location of an early superspreader event and not the true origin.

jeduehr 6y ago
Yep, agreed on all 3 counts.
jeduehr 6y ago
Best epidemiological and genetic evidence suggests it originated somewhere outside Wuhan and then became a serious outbreak there as it's a major population center. https://www.reddit.com/r/science/comments/gk6y95/covid19_did_not_come_from_the_wuhan_institute_of/fqpcfs2/ https://www.reddit.com/r/science/comments/gk6y95/covid19_did...

pmiller2 6y ago

I agree that the virus is unlikely to have been engineered in the manner you describe. But, I'm wondering: where is this circumstantial evidence for the leak scenario, be it a natural sample or one that had some help evolving? (I also doubt the wet market scenario, but that one isn't nearly so contentious.) Here's the thing: in my mind, anyone who wants to claim the virus escaped the lab as a result of an accident needs to show how someone could have gotten infected with it while working with it in a lab using BSL-3 precautions. We're all just walking around wearing plain old surgical masks, and sometimes not even that level of protection, but literally a piece of cloth is enough to reduce transmission of this virus significantly. Now, tell me how someone wearing full body PPE gets infected with it. Even at BSL-2, any procedures that would create aerosols are done inside a containment vessel, so, I can't honestly see it happening there, either. And, it certainly wouldn't have been at BSL-1, as that's reserved for known non-pathogenic organisms. Basically, the criterion for a BSL-1 lab is "we grow bugs here, on purpose." Clearly, any of the bat coronaviruses they would handle at WIV would greatly exceed that level of precaution. With that in mind, IMO, the real interesting bit this article had to offer was to suggest the possibility that the virus snuck into the lab. Given the virus's relative inability to spread via surface contact and necessity of aerosolized droplet spread, you still have to answer the question of how it got out, but, it's at least an intriguing origin story. So, in summary, yes, the only correct answer we can really say for sure is "we don't know exactly where it came from, if it leaked out of a lab, and what might have been done with it while it was in the lab." But, I'm having a really hard time believing a virus that gets largely stopped by a simple mask could sneak out of a BSL-2+ lab.