This is Alina Chan, one of the co-authors of Viral: The Search for the Origin of Covid-19.
In defense of a natural origin of Omicron, this study describes the remarkable evolution of SARS-CoV-2 during convalescent plasma treatment of an immunosuppressed patient for 3-4 months; the mutations also reduced sensitivity to neutralizing antibodies: https://www.nature.com/articles/s41586-021-03291-y
We know that there is a large immunocompromised population in Africa and that Covid-19 is rampant there. We also know that most hospitals, regardless of country, don't have the resources to track the evolution of SARS-CoV-2 in their immunocompromised patients. So it's not unexpected that a variant like Omicron could have evolved over an entire year in an immunocompromised individual before finally infecting others.
If there is any evidence that a lab in the region was serially passaging SARS-CoV-2 in neutralizing antibodies/patient serum, then I'd say there is something to go on for a potential lab origin. But at the moment, there is not even circumstantial evidence pointing to this happening in Africa. Maybe setting up a secure channel for whistleblowers with evidence of the above would be the most productive approach.
First detection is an indicator of that, when it was first detected, not a guarantee that it was first there. Only a very small fraction of RT-PCR positive samples are sent for sequencing under normal conditions.
> Omicron COVID was in Italy as early as 2021-10-13 – 7 weeks before alarm from South Africa.
7 weeks before the alarm, but only 10 days before in retrospective sampling, and even less in other places in Africa.
Saying it appeared in Italy but somehow it spread in Southern Africa first goes against normal epidemiological dynamics, especially given how contagious Omicron is. The chances are it started where the first cluster is detected, not where the first retrospective case is detected, because the possibility of it escaping in Italy, flying to SA, and somehow staying dormant in Italy while giving SA a head-start is extremely unlikely.
But Italy, hit extremely hard by early waves, and now with a much-higher vax rate than South Africa, could more easily miss a rising wave of mild cases in already-immune that don't seek treatment. There are plenty of factors in all directions, and only very spotty variant surveillance most places.
Thanks for referencing my tweet - & asking some questions I would!
I 1st learned of the referenced Italy antibody-escape gain-of-function paper via an HN post which appeared almost concurrently with the first reports of the (not-yet-named) Omicron variant: https://news.ycombinator.com/item?id=29359125
This is not to say either of those are the origin; just that this kind of research seems pretty common: within the capability & interest of many labs, who cheerfully report their creation, via selective pressure, of immune-escape variants in published papers.
Another thing that the blog post appears to be unaware of is that the absence of samples showing the step-by-step evolution towards omicron doesn't mean that this didn't happen. A lot of places in the world don't have the resources to do covid testing and genomic surveillance.
Absence of evidence is not evidence of absence, yes. But take another look at the phylogenetic tree. Those are huge gaps. See also this article describing how good South Africa is at spotting and sequencing variants."The reality is that southern Africa is a top international powerhouse of COVID-19 surveillance."
https://www.businessinsider.com/how-southern-africa-detected...
Consider this: days after the successful sequencing of Omicron, similar cases were reported in dozens of countries, having arrived there just before or just after the announcement. We know, that it's "just before," because references are being kept and re-analyzed in those cases, and none of the countries with the resources for genomic surveillance has any data on earlier strains in the phylogenic tree.
It is simply very unlikely (not impossible, but if you're in London and hear hoof beats, it's probably a horse, not a zebra), that Omicron could have developed over 33 N and a superset of S mutations without ever popping up in any surveillance. South Africa, especially, is a key surveillance player. They're often much more granular than even European key players like the UK, Germany, or France.
A strain with this level of infectivity doesn't linger in one hospital. From the looks of the genome, that part (infectivity) would have developed before immune evasion. Having a highly infective strain evolve would ring alarm bells in labs the world around.
I guess it's pretty non debatable that Omicron started its World Dominance Tour in October or November 2021. To get there, it had to undergo a massive sequence of events making it as far removed from α.7 as it is. So we can state, with some certainty, that it evolved in isolation and broke free shortly before being discovered.
If we now consider the possible origins, wild zoonotic, single origin immune compromised, or accidental leak from research, the latter doesn't sound so improbable anymore. Again, horse, not zebra.
But, the point is it was growling so fast you wouldn't expect it to show up in other places until the "knee" of the exponential showed up there as well. SA being just a couple of weeks ahead is a lifetime for Omicron.
100% agreed. Again, this is a possibility, not a certainty. But I'd be loath to dismiss it, just as I am not willing to dismiss a reservoir origin. In the end, the author does make a good point: we need mandatory disclosures of GoF research and a general ban on GoF financing of labs who aren't working in full disclosure mode.
Ideally, we should not have this discussion because the GoF leak is impossible. Sadly, as secretive as this research is, as much money as we funnel into labs in China and Russia, and as reluctant as oversight authorities (such as the WHO) are to even consider leaks, the best response would be a general ban on GoF and GoF financing.
There is a belief that Omicron originated in South Africa, but some growing evidence that it was present elsewhere earlier, but only either detected or first identified early on in South Africa.
And even if they did do genomic analysis - it's entirely plausible the results are sitting in a hospital database somewhere instead of uploaded to the international gene surveillance repository.
Plausible, yes. If the data exists, it should be made public. The article still mostly just makes a hypothesis and makes the argument that this is something that should be seriously investigated, not that the author has determined without a doubt that this is a lab leak.
Sure - but what are the chances that whichever hospitals did the sequencing even know they're in possession of the intermediate data? The OPs' method of "just asking questions" is really bad science and feels a whole lot like the God of the Gaps argument style that Creationists are so fond of using.
I'm not sure the best way to judge the quality of a scientific argument is whether it 'feels like good science.'
While the author is obviously only scratching the surface in an article targetted at non-scientists, the several PhDs he cites make decent arguments that are based on a little more than feelings. It would probably be more in line with the ideal of 'good science' to actually investigate the possibilities presented than dismiss them from emotional associations.
It is a worrying trend that the way science feels is increasingly more important than the actual evidence (or lack thereof). One could even describe the current attitude towards science outside of scientitific institutions as religious.
And the reason not all of these spread fast is obviously that one mutation (or combination) impacts the spread rate more than the 30+other mutations in isolation...
Although after enough conversations I've found this too needs spelling out in plain English...
The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa?
Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps.
> The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa?
You're pointing out distinctions that do not make any relevant or substantial differences to the argument.
> Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps.
With lack of information, ideas that have the less assumptions and concepts tend to be true than their counterparts who require many possible sub-hypotheses and concepts. GoF happen and lab leaks happen and the genetic histogram and the genes makes make this hypothesis the more likely one. The opposite require many hypothetical actors (mouses, immunosuppressed patients, back and forth between geographically distant places and all the combinations thereof) to account for it "hiding" since spring 2020.
> especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons.
Nobody blamed nobody here. GoF research happens everywhere.
> Give the science time and we might start to fill in the gaps.
Science is not beholden to your worldview. Filling the gaps is part of the scientific method, by the way.
All I'm saying is that my bias is towards this virus being a natural phenomenon and I think waiting for the full context will settle the case. Jumping to conclusions on the basis of flimsy evidence mainly serves political agendas. We simply will not know for a long time, months or years, where Omicron came from and that's uncomfortable, but we have to sit with that.
If you DO want to get conspiratorial, you can watch this 2001 Bush administration pandemic simulation where China blames the US for a smallpox lab leak. It's pretty amusing to me to watch the US administration astounded by their luck of COVID-19 first being identified in China try to flip the script on their simulated exercise. My feeling is this Omicron theory is trying to breathe life back into the original lab leak theory by proxy.
I don’t understand how natural origin is your “bias” while everyone else is “jumping to conclusions”. There’s a lack of conclusive evidence for either scenario. And politics aside, SARS has leaked before resulting in deaths… no conspiracy required!
That's true Delta leaked in Taiwan, but that was a preexisting natural strain. Smallpox's last fatality also was a lab leak. However, most gain of function experiments use test harasses that can't infect humans or can't replicate. It's not impossible, but it's hard to have any conclusion at all at this early date with very little evidence.
The virus is infecting so many people and changes so rapidly that a natural explanation will not be surprising in the least. New variants have been expected. I think people are surprised at how bad the new variants have been, but anyone following the scientific literature wouldn't be taken completely off guard.
You seem to have caught some memes which don't make you see things rationally.
> The opposite require many hypothetical actors (mouses, immunosuppressed patients, back and forth between geographically distant places and all the combinations thereof) to account for it "hiding" since spring 2020
If you ever implied that closeness of outbreak of the Wuhan variant to the Wuhan lab the same should make you incredibly suspicious about this being a lab leak, since there is such lab nearby. So it would require an actor in another country to "breed" this variant and import it into South Africa/have agents spread it world wide and someone funding and green lighting what would a be case of international bio terrorism or even bio warfare.
As for accounting for those factors. Africa is an incredible diverse places with Nomads and hyper dense slums, with untreated large scale AIDS and healthcare systems as South Africa has and also a poorly understood and explored flora and fauna.
Does it seem that implausible that some combination of immuno compromised tribes/rural human and animals caught the old variant and didn't interact with the new variants from western civilization for less than two years? I don't think so.
As for the low number of silent mutations. I can not imagine how the lab leak theory would account for that, if it was designed why would there a low number of silent mutations and not an average number or none and if it was due to GoF why would a lab environment have less silent mutations then a "natural" one?
AFAIK we have almost no data on variants in some African capitals let alone people in rural/tribal areas or surveillance of animals. Maybe along its evolutionary it was a variant that has an advantage in sparsely populated areas so we didn't notice a large part of its history because it wasn't competitive in cities with other variants.
There are many possible explanations but the lack of lab is kinda blow for a lab leak theory and your political goal of less GoF-Research is only compatible with a lab leak and not any other form of lab caused (philanthropist/evil government developing and releasing this variant) explanation.
Gaps can appear if there are (1) missing data or (2) a big change such as a transposition or elision event. Neither are the case for our coronavirus data. For (1) we have a good random sampling of the population as a whole so it is exceedingly unlikely we would not see intermediate changes and for (2) the overall structure has not changed dramatically--we are looking at the accumulation of point mutations over the course of 18 months. So while gaps can and do occur, we would not expect this to occur naturally in the situation we are observing today with coronavirus.
Gaps also appear because evolution is not a smooth process, and once in a while a large number of mutations are selected for. We see the same type of pattern even in vitro. Moreover, mutations are not always well described by gaussian processes: the rate of mutation can be seen as having a fat tailed distribution.
Mutations has to be incremental because most mutations are not viable or doesn't provide any reproductive gain. Having multiple functional mutations all at once happening in a very short amount of time and being naturally selected in big enough number of infections is very very improbable.
> mutations are not always well described by gaussian processes: the rate of mutation can be seen as having a fat tailed distribution
I'm sorry if I have to be blunt, but you have no idea of what you are talking about.
Sure and if it had arisen in Europe then those questions would have to be asked. But it's a safe assumption that very little analysis is happening in southern central Africa. It doesn't seem that outrageous that a parallel line has been percolating there for quite some time and only recently gained a mutation or two that allowed it to shoot to stratospheric levels.
Even in Europe I wouldn't find it all that difficult to believe. We see the same sort of pattern, qualitatively speaking, even in well controlled in vitro experiments.
"Omicron could have evolved over an entire year in an immunocompromised individual before finally infecting others"
Is it likely that this infected person would not have started any detectable cluster this whole time? How do you explain the ratio of functional vs silent mutations?
Evolution experiments in the lab mimic natural evolution. The ratio of functional vs silent mutations has also been used to characterize the evolution of viruses under natural selection.
According to the blog post that we are commenting on, there is a strange ratio of silent to functional mutations. How can this be accounted for if it was a natural course of evolution?
Without looking more at the variants themselves and just going by the numbers in the post, it’s entirely plausible. It’s not likely, but plausible.
Mainly because we are talking rare events. If the level of success is 33/3.5 (9.42), we’d expect that 4 (or less) silent variants would happen with a probability of ~ 0.042 (Poisson X <= 4). So, a bit more than a 4% chance. But with millions of people infected, this ratio of S/NS variations would still happen at a pretty high absolute number.
Anytime you look at numbers like these, remember with a big denominator, even rare events are expected to happen.
If it was the case that the absolute number mattered, we would be able to sample different "Omicron-like" variants and observe various ratios such as 33N/10S, 33N/15S, etc. mutations. But according to the data presented, we don't: We only see a single (kind of) Omicron, the one with (about) 33N/4S mutations, presumably spilling over by a single event, so I don't see how your conclusion follows.
There are two different (and independent) forces at play here: mutation and natural selection.
The question is, given a known ratio of 3.5 NS/S, what is the likelihood that there would be only 4 non-silent mutations in any random strain (like omicron)? What the mutations are is irrelevant to this question. (I will use mutations and variants interchangeably below, but both mean a single change in the genetic code for the virus).
Because we are dealing with integer counts, you can’t really have 3.5 mutations. You can only have 1, 2, 3, etc. So, 3.5 is just the average of all ratios. When dealing with count data like this, the Poisson distribution is what you use. When you have 33 non-silent mutations, you could have 1, 2, 3, etc silent mutations. We’d expect to see 9.4 (33/3.5), but you can’t have 0.4 of a mutation, only integers. There is a specific probability associated with each possible value (1,2,3…), and that can be calculated using the Poisson distribution.
You are most likely to see 9 or 10, but all other values are also possible. To calculate how likely you are to see exactly 4 silent variants, you use the Poisson distribution. Again, we will expect that the rate should be 33/3.5 silent variants.
In R, you’d do:
dpois(4, 33/3.5)
[1] 0.02647255
So, if we had 33 nonsilent variants, we’d expect to see exactly 4 silent variants 2.6% of the time. To put this into context, the most likely number of silent mutations is 9, which is expected only 13% of the time.
We normally think in terms of “how likely is it that we’d see 4 or fewer mutations”, so we re-run the test for 0:4 and add them up:
sum(dpois(0:4, 33/3.5))
[1] 0.04211515
Which is how I got a probability of 0.042. And which answers the specific question — if we see 33 non silent mutations in a strain, how likely is it that we would be 4 or fewer silent mutations in the same strain? 4.2% of the time.
Given these numbers, I’d say it is plausible that you’d see this ratio of NS/S mutations occur naturally. It would be rare, but still somewhat expected to occur.
Now this says nothing about what the mutations are, or why the omicron strain is so prevalent. This is where natural selection takes over and this combination of mutations is out competing all others.
I was not taking an issue with the calculation of the 4% chance, but rather with this phrase: "But with millions of people infected, this ratio of S/NS variations would still happen at a pretty high absolute number."
I thought you were implying that since this was a 4% chance happening over millions of infection events, it was a virtual certainty, and thus the 4% factor made this highly probable. To which I counter argued, the 4% chance matters and should be accounted as a factor in a "natural vs lab leak" model, because everything seems to point that "a variant as infectious as Omnicron appears" was a single event.
It is a virtual certainty that a 4% likely event would occur given the millions of people that have been infected (and the subsequent mutations occurring within each of them). But that doesn't have anything to do with omicron specifically... and I certainly don't intend to suggest a correlation between NS/S and infectiousness. Mutations have a certain rate, but the events themselves are random.
I guess a different way to say this is -- It makes no sense to use the NS/S ratio as a rationale to claim that omicron was a lab-leak. The 33/4 ratio should be rare, but not unexpected. If you were going to claim that, the absolute increase in mutations would be a more compelling argument, but again, there are plausible reasons for how that could occur in the wild too.
We have very incomplete sampling data, so looking at a single strain and determining risk, or likelihood, is very difficult.
The sequence of mutations leading to Omicron is a one-off. Presumably, if there were a thousand variants with the same N mutations as Omicron, you'd see ratios like the ones you describe, but there's only one Omicron. The previous poster is pointing out it's plausible (~5% chance) that the path Omicron took has only 4 S mutations.
More simply, I don't think people tend to remain infected (and infectious) for a whole year (not saying they can't just that this seems a farcical assumption)
Yeah I agree with the going undetected too unless they're potentially asymptomatic (in which case why should we ever expect to find/treat them).
All leading to the same response of you can't control highly transmissible virus(vurii) once they have infected a large amount of the population. (aka a 0 covid strategy is self-defeating)
The mouse theory is interesting .... because omicron is more benign - one of the problems we have with covid is that because of all this modern medicine saving lots of lives (not enough though sadly) there's not a lot of evolutionary pressure to make things more benign.
But if omicron has been in a wild mammal population without vaccination or hospitals then there might be more evolutionary pressure to become more benign.
It's worth noting that some vaccines in the past have been 'live' vaccines - essentially viruses that get passed around with a sniffle or two but no more harm. This actually what we all hope omicron would be .... I can't see why we shouldn't give the virus a bit of a help along .... the right lab leak might be just what we all need
The Nature article you mention says, "These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals."
Fair enough. So is the hypothesis that this immune compromised person in SA was given a lot of antibodies over a long period of time, creating enough evolutionary pressure to create highly mutated forms of the virus? Such a person might end up with a highly mutated virus that is resistant to existing antibodies. Fair enough.
That explains one of the four weirdnesses, and leaves three unexplained. Where are all the missing silent mutations (Weirdness 2)? If someone is followed medically and receiving all these treatments, did no one around them ever get sick with an intermediate variant? (Weirdness 1)? And what about the mouse-related mutations? (Weirdness 4) Did the viruses in the immune compromised person develop those mouse-related mutations independently?
I find the "immune compromised person" hypothesis not a very parsimonious or compelling one, although if you can steelman it further, I'm all ears.
The other author of her book is Matt Ridley, the climate change skeptic.
But you know what they say, even a person who makes money by telling obvious lies about science is right twice a day, so we should probably evaluate this from first principals as if it wasn't coming from a professional serial liar.
That assumes the origin is Africa, but it could have just risen to prevalence there. We know the original COVID-19 was spreading around the world when at the time we thought it was mostly China. It needs only a 12-hour plane ride to get to the other side of the planet.
Thank you for visiting HN, Alina! And I agree, natural evolution seems to make more sense. It's natural to wonder about lab-driven adaptation before COVID was unleashed on the human race... but once it had the entire human race to run its own "gain-of-function experiments", a lab hardly seems necessary anymore.
The only question is why we didn't observe some steps on the way. And as you say, poorly monitored infections of the immunocompromised can easily explain this. It hardly seems necessary to posit nefarious secret labs when COVID is constantly spreading among billions of people, a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas.
"poorly monitored infections of the immunocompromised can easily explain this. It hardly seems necessary to posit nefarious secret labs when COVID is constantly spreading among billions of people, a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas."
How do "poorly monitored infections of the immunocompromised" explain weirdnesses 2 and 4? (Referring to the blog post under discussion)
Did the blog author "posit nefarious secret labs"? Not that I'm seeing. There are labs all over the world doing things with SARS-CoV-2, probably for what they believe to be legitimate reasons. "Nefariousness" and "secrecy" is not in the article. "Nefariousness" and "secrecy" are not part of the hypothesis.
"a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas": Contrary to people's seeming stereotypes about "Africa," South Africa monitors SARS-CoV-2 really well. The hypothetical immunocompromised person in Alina's discussion would not be someone untreated in some remote village, unnoticed for a year and a half. No, to get that level of immune evasion, Alina must be talking about someone who was being treated medically, with fancy treatments, and being monitored for a very long time.
Well, for one thing: My first question is "Who is it? Who is this person who received all the convalescent plasma and all the different monoclonal antibodies for a year and half, in well-monitored South Africa?"
But even if we don't know who this hypothetical person is, there are other problems:
That person apparently never infected anyone else. And...that person in a year and a half never had any _intermediate_ viruses that infected anyone else either, to account for the gaps in the phylogenetic tree. And...that person had a set of mutations that you might expect to see in a humanized mouse (Weirdness 4).
You see, then, that while this is all "possible" it's not very parsimonious. I think we do better to begin with parsimonious hypotheses and try to test those and rule those out.
The lab leak is a parsimonious hypothesis -- but instead, mainstream people, for whatever reason, are portraying it as so far-fetched as not to merit consideration -- they would dismiss it, rather unscientifically, as if the hypothesis were really wild and not meriting consideration, like "Space aliens from planet X did it." Then, instead, they put forward hypotheses that are in fact way more far-fetched because they don't account for the data neatly, like "it was an immune compromised person" -- but the set of circumstances in which that would be true, while kinda-sorta possible, is much more unlikely than the circumstances of "lab leak."
The failure of the scientific community to address this really makes no sense to me.
You misread that - there is no claim that delta was initially released by a lab, rather a the known fact that a lab studying delta had an accident. Read the links the author provided.
The claim wasn’t that Delta originated from a lab leak but rather that Delta happened to leak from a lab (after the point that it existed in the wild). Additionally, the phylogenetic points from the article would suggest that Delta is of natural origin
"[Edited, 5 Jan 2021, to add: Many people have been confused about the statement about delta, so I must have worded it poorly. I’m not saying delta originated in a lab leak. I’m saying delta escaped from a lab late in 2021 where it was being used in research. It’s an example of a research-related lab leak.]"
> We know that there is a large immunocompromised population in Africa and that Covid-19 is rampant there.
The fact that developed countries are hoarding vaccines, essential medications and are willing to let it go to garbage than to send it to those who need it there isn't helping either.
I'm open minded, but my bullshit detectors started going off around the point where it was casually implied that we all know and it is widely accepted that delta was leaked from a lab. I tried googling it but could find nothing. Then I looked at the two sources the author links:
Neither of these have nearly enough evidence or support for such a massive claim (the second doesn't even mention delta), as far as I can tell, and I can find no other reputable sources that make a similar claim. Heck, I can't even find un-reputable ones that mention this.
Am I missing something? I'm not going to continue with the article if this is how flimsy the sourcing is.
I think there is confusion on what the author meant by "leaked". The Delta variant was already spreading, yes. The author is saying - and the first link above essentially states this - that a lab worker was infected with Delta while in a lab. (Though it's not stated whether that worker was quarantined immediately, or if they could have possibly spread it to others.)
So what's the point? 1,000,001 people have Delta instead of 1,000,000? No. The point is to show that Covid infections are indisputably already happening in labs. And if there is a GoF lab that creates a new variant, it logically follows that it is possible for that new variant to escape. So instead of the not-so-bad 1,000,001 vs 1,000,000 Taiwan scenario, you could have a disastrous 1 vs 0 scenario.
I'm guessing it's impossible to get the lab leak rate down to 0.
And assuming there are currently thousands of labs studying covid, even with a low leak rate there could be some leaks. But of an already existing virus, so not so bad.
If it can happen in a lab studying an existing type, it can happen in labs studying GoF. The 1977 pandemic was a "leak" of sorts that seems to have originated from a prisoner camp known to give reduced sentence times to inmates willing to participate in medical research. The "leaking" doesn't have to happen from a vial or mouse, the avenues are numerous (Marburg "leaked" when African green monkeys, imported for non-viral research, were handled incorrectly without infectious precautions).
> But of an already existing virus, so not so bad.
Millions of drivers every day. Hundreds of accidents. Many quite light. Still, the presence of light accidents outlines the possibility of heavy ones. And that's why "phew, got lucky this time" should lead to better protection not a "not so bad, nothing happened" attitude, IMHO.
You don't understand why I would challenge you to cite your sources in a thread discussing COVID-19 conspiracy theories and misinformation? Not to mention, I think it's pretty clear to both of us that this "well documented event" is not common knowledge to people who don't follow COVID conspiracy theories.
I think this event qualifies as “well documented” by any reasonable standard, there was official public disclosure and an open investigation.
As one quick example, here’s a news clip including an interview with the Taiwanese health minister discussing details of the (then) ongoing investigation:
I feel like you're unfairly biased. The author doesn't say what you think they do. All they're saying is that there was a lab leak of delta in 2021 as an example of lab leaks being possible. They do not argue that this was the source of delta, nor that this was the source of any other strain. Just that it happened.
Sorry, the hysteria on HN is ridiculous. At least read the damn thing and try to be objective about it.
Where to even begin with this. I'm unfairly biased because I misread what he said? After re-reading, I can see that he may not have been making the point I thought he was making. I'd argue he should make a point like that more clear, but fine, it's on me that I misinterpreted.
> the hysteria on HN is ridiculous.
"Hysteria"? How do you get hysteria from my response? Because I asked for citations for what I thought was an extreme claim?
> At least read the damn thing
I did. Reading it was a pre-requisite for posting my response, which cited specific links he included.
> and try to be objective about it.
Asking for high quality sources was my attempt to be objective.
--
Edit: Actually, you know what, I take it back. If you write a sentence like this, it's on you if it's misinterpreted:
"For example, we know that the delta variant of SARS-CoV-2 leaked out of a lab in Taiwan in late 2021."
Heck, I'm not even sure it wasn't the author's intent at this point.
"For example, we know that the delta variant of SARS-CoV-2 leaked out of a lab in Taiwan in late 2021." - is exactly (mechanically) true in that Delta did leak out of a lab in Taiwan in late 2021.
This statement does not declare that Delta’s origins were a lab leak, since late 2021 is a year after Delta was first detected in late 2020. Can’t have your origins in the future until time travel is invented.
Seems therefore more proper to interpret the statement exactly as written rather than add additional conspiratorial inferences.
Perhaps the audience for that blog isn't the regular hn reader because I read it the same way as d23. I get that an origin leak can't come after delta was already spreading but most of us aren't drawing a timeline on the side while reading either.
It’s also abundantly clear if you’re reading the whole article from the start, because the whole article is claiming Omicron is the second virus to originate from a lab, after the original strain.
Yes, s/he clarified it.
"[Edited, 5 Jan 2021, to add: Many people have been confused about the statement about delta, so I must have worded it poorly. I’m not saying delta originated in a lab leak. I’m saying delta escaped from a lab late in 2021 where it was being used in research. It’s an example of a research-related lab leak.]"
I don’t know the details of the Delta conspiracy theory, but the evolution of Delta looks abundantly natural, so whatever that theory is, seems unlikely.
I do see why you could have misunderstood that statement, but I at least understood it correctly on my first read, and didn't think anything more of it (except that I hadn't known about this particular leak before, and thought that was interesting) until reading your comment here.
So while I can see why you might have found that confusing, I also think the author could have believed the wording wasn't confusing, and is innocent of any accusations of bad intent. I think that's where the "hysteria" accusation comes from (though I agree that's a bit out of line): you seem pretty adamant about painting the author with a bad-faith brush, even after your misunderstanding was corrected. That's not ok either; just admit that you misunderstood and overreacted, and move on.
I'm not sure I buy this omicron lab leak theory, though I do think there may be better (if incredibly circumstantial) evidence for this than for the original virus being a lab leak from Wuhan. Under the assumption that the author is wrong, I'm willing to give the benefit of the doubt that the argument is sincere, if flawed.
I agree that phrasing it like that invites misinterpretation.
And when publishing on a subject with as much disinformation as this, it is your duty to be as clear and precise as possible in order to avoid misinterpretations and being misquoted.
This article indeed does not make any direct claim, it is just speculating, but expect to see a wave of disinformation from the usual offenders soon, linking to this and afterwards to eachother.
The author did not claim that Delta's origin was a lab leak. Just that there was one isolated case of it. And so it stands to reason, other lab leaks may also be occurring.
We should note you're talking about covered up lab leaks where all of the participants are conspiring to keep it secret because of convoluted motivations. It doesn't "stand to reason" that this happens at all, let alone is the normal case that we should all assume.
No, we're not talking about cover ups. We're talking about studying the virus and it escaping by accident. Also, there is a history of lab leaks so it stands to reason...
The title is "Lab Leak 2.0". The '1.0' is referring to the popular story about a covered up lab leak in China and the ensuing conspiracy to keep it all a secret.
Note that the article isn't suggesting that delta originated as a lab leak, just that some Taiwanese scientists were experimenting with delta in a lab (after delta had been seen widely in the wild), and a lab worker there was infected by delta in the lab (rather than getting it outside), and then brought that infection outside of the lab. That's a lab leak, but it's not the origin of delta.
"[Edited, 5 Jan 2021, to add: Many people have been confused about the statement about delta, so I must have worded it poorly. I’m not saying delta originated in a lab leak. I’m saying delta escaped from a lab late in 2021 where it was being used in research. It’s an example of a research-related lab leak.]"
I had the same reaction. Those articles don’t back up that claim one bit. And I cant make sense of the timings of the events described in those articles either and how that would line up with a supposed lab leak of delta.
Some of the other points made in this article were mildly compelling to me (though I don’t know enough on this topic to be able to poke holes) but that delta claim and lack of convincing data to back it up doesn’t help with credibility.
You misread because of a poorly worded sentence. She does not claim Delta's origin was a lab leak at all but that there has been a lab leak. Instead she implicitly compares Omicron and Delta showing that Delta did evolved naturally whereas it is unlikely of Omicron.
Which is funny because Delta's NS:S ratio is also very high. So by her own logic, the NS:S ratio -- what you called her "main" argument in the other thread -- has no predictive value whatsoever for the natural vs lab leak question.
The ratio is one of four "weirdnesses" laid out by the author, which a lab leak might parsimoniously explain, and which, so far, other hypotheses do not neatly or parsimoniously explain.
So for you to jump to "no predictive value" is a little odd.
Since you feel well-equipped to judge the validity of the various hypotheses for the origin of omicron, which hypothesis do you think explains the information and why?
I had never heard that before either. I remember multiple sources saying the discovery originated in India. I think an essay that represents surprising information as obvious is usually a good indicator of bias.
You misread because of a poorly worded sentence. She does not claim Delta's origin was a lab leak at all but that there has been a lab leak. Instead she implicitly compares Omicron and Delta showing that Delta did evolved naturally whereas it is unlikely of Omicron.
If the author actually had some kind of evidence that there was a lab leak source of Omicron, don’t you think it would be mentioned in the opening paragraphs of the blog? Instead we have a long list of connect-the-dots tweets, out of context quotes, and unsubstantiated speculation going on for 2/3s of the post before we even get to the Omicron stuff.
Have you actually read it ? Can you give your opinion about the ratio between silent/non-silent mutations ? Because it is the main and most compelling argument.
Another commenter pointed out that the probability of this ratio is around 4% (haven't checked the math on that, though; statistics was never my strong suit). While that sounds like it's unlikely, this virus is bouncing around and mutating in hundreds of millions of people. When your absolute numbers are that large, unlikely events should be expected to happen, and happen fairly often.
Not something I know much about but assuming there was a lot of selective pressure because the virus was in a new environment, likely a mouse, and one virus gets a silent mutation and another a non-silent, the non silent might zip ahead and take over?
The plot on Wikipedia looks to me like it has lots of variants with frequent branches coming off of each variant, except for Omicron, which went a great distance with no branches and then started branching rapidly again. This seems most consistent with a lab leak.
All of the GoF research procedures I've read stress natural evolution, but still rely on random mutations at the end of the day, which would still leave you with a natural looking count of silent mutations in the general case.
As a GoF researcher you don't want to cull 'silent' mutations because those are a major source of building blocks for useful mutations.
Damn this is the first comment contrarian to the article that acually addresses the main argument : Silent vs non-silent mutations ratio.
The article pretty much convinced me and I am not sure I am really unconvinced yet but I have to thank you.
It's also much more complicated to define "silent" in the context of a virus. In a larger-genomed organism there is a relatively clear (though still not completely clear) function of a coding region, where the change of a nucleic acid will have no effect on the protein made - but still might (subtly) effect regulation in some way.
In a virus, most nucleic acids have multiple, layered, and unknown functions - it's much much harder to assign any given nucleic acid as "silent", and be confident that that is the case from an evolutionary perspective.
As another posted, it's a good hypothesis that's straightforward to test statistically against all of the other variants. But on its own, it's not necessarily convincing here that the S/NS ratio is particularly concerning (and as above, doesn't speak to how directed evolution works either).
So, you take on faith that the s/ns ratio as described by "Eigenrobot" who is quoting "Brett" (who are they?) is correct, and the s/ns ratio described by many microbiologists and genome experts, identifiable on their Twitter accounts, is wrong?
I mean, we can find anyone on Twitter saying anything. I could create an account right now that says I'm an expert on time travel and tweet about it.
And of course now that omicron is circulating widely in humans, its pattern and ratio of mutations is occurring as one would expect. I wonder why something we know is a natural occurrence (mutation as it infects humans worldwide) looks natural. It makes me wonder why the original omicron looked so weird.
To me this is not a conversation about whether a lab leak occurred. It's a conversation about why the experts are not ruling out hypotheses that explain the information so they can (if necessary) move on to other hypotheses. Just dismissing hypotheses that explain the existing information is not very scientific, unless the hypotheses are untestable or are truly off the wall. This hypothesis is not truly off the wall.
Honest question : as a GoF researcher, wouldn’t I generate thousands (millions) of mutations from my 1st virus pool, which would each have a low number of mutation (s or n) compared to the original strain, then “select” the most resistant ones from that 1st pool of mutants, and use those to repeat the process ? I’d expect the result to be much richer in n mutation than in silent ones, just because I forced their selection. Am I missing something?
This may be the standard approach, but the question is how else it could have happened other than some GoF procedure. Any idea what the odds are of this ratio happening by chance?
Neither one of those hypotheses accounts for the four weirdnesses described in the article. So they don't seem like very good hypotheses.
Similarly "it came from an animal" that we've never found two years later is not a hypothesis that accounts for the information we have about the first COVID-19 outbreak either.
To me that sounds very much like OJ vowing to find the real killer, but somehow he never did.
The article is very well written, as was the last article on lab origin theory. Previous articles have already recognized that this mutation (technically 33 mutations) emerged from a strain prior to even the naming of the Alpha strain. That by itself had resulted in several theories, a few of which were mentioned: a lab leak, that this was mutating within a single population for over a year before spreading, that is was mutating within a single person, or that it traveled to another species where it spread rampantly and mutated then traveled back. This adds further data and it's great to see articles that use highly credible PHD sources like this, and the explains things in easy to understand ways. I feel it does move the probability closer to a lab origin but as the article states it is still only more likely in their opinion. Some articles or people have an odd level of conviction behind non-definitive data or an emotional attachment to the origin of the virus and I'm not seeing that in this article.
There sure is. I flagged it because it’s speculation and conspiracy stuff shouldn’t be on HN. Sure it could be a leak but armchair detective work can be dangerous.
Please don't do this, our understanding of the world is not improved by censoring things we consider unplatable. It is not a "conspiracy" to consider various viewpoints. Everything speculated about in the article was backed up by real data. It may be true, or it may be false, but suppressing discussion is no way forward to determine the origins of the virus.
I'm an immunologist and molecular biologist, though I currently work on software-related things. I've worked in class 3 facilities in a medical school as a PhD and a postdoc. I've seen a fellow PhD student infect themselves with a tropical disease. I've seen my fair share of good and bad working practices. Scientists are not infallible, they are human. They make mistakes, they get sloppy, and they lose attention. The unfortunate reality is that lab leaks are commonplace. Most you never hear about because the consequences are minor.
Given the poor track record of labs worldwide to practice good biosafety, the real question here is whether we should have a complete worldwide ban on gain-of-function research. Is the risk really worth the benefit?
Over time, we'll gradually learn the real truth of the origins of all of the variants as we get more data, but attempting to suppress discussion of genuine avenues of investigation is about as anti-scientific as you can get. Please reconsider your attitude.
Also, everything that's unpleasant to consider isn't a 'conspiracy'. Labs have performed gain-of-function experiments that create nastier viruses fairly regularly, often proudly publishing their work. Those same kinds of labs, while they always try not to, sometimes leak dangerous disease-causing agents - typically by infecting a researcher who then infects others in the community.
So the speculated chain of events doesn't even require any malice – just known-to-happen events cooccuring at an inopportune time.
And how can "armchair detective work" like this be "dangerous"? Hackers love to engage in armchair detective work! Unless there are reckless accusations placing potentially innocent people in danger – not at all true of this article – there's no grounds for suppressing good faith discussion, at least not in any culture that values open discussion of ideas, including even suspect ideas, to confirm/refute/improve them.
If you're going to flag things that are "speculation", you're going to have to flag quite a lot of things that make it to the HN front page.
"Conspiracy stuff" means baseless, hand-wavy claims. While the author's hypothesis may turn out to be false, my reading of it suggests that the argument is made in good faith, and is supported by data. It may not be the right interpretation of that data, and the conclusions may be incorrect, but I don't consider this "conspiracy stuff".
Regardless of whether or not any of this turns out to have been one or more lab leaks, we need to keep talking about it, in an evidence- and data-based manner. We still have no idea where this virus originally came from, and we need to continue to explore all reasonable options until they are ruled out, or another option is proved to be true. You may not think a lab leak is reasonable, but I think that's short-sighted, and certainly hasn't been ruled out as an option.
It is a conspiracy because it does not fit into GPs world view and what they think is right. Apparently presenting citations and data is “speculation” these days…
If we're revisiting this subject, it's time to revisit these articles
"LEAKED GRANT PROPOSAL DETAILS HIGH-RISK CORONAVIRUS RESEARCH
The proposal, rejected by U.S. military research agency DARPA, describes the insertion of human-specific cleavage sites into SARS-related bat coronaviruses."
I posted this article on my Facebook feed and it was promptly auto-deleted by Facebook.
A sad state of affairs indeed.
*EDIT* it looks like it didn’t actually get deleted. When I went to edit the post my edit wouldn’t take and it said the post was deleted. But I am still seeing the post, so I think it’s “there” at least..
At this point I'm no longer sure if that'd be good or bad. It's highly speculative, and does a lot of cherry picking, and an informed reader can read it for what it is, but it dumbs down some things so far as to make it fodder for the tinfoil hat crowd. And it's especially ugly when it justifies the cherry picking as "it's because these people don't make their living with GoF research".
Substack is becoming YouTube for text at this point.
I'm not convinced that censoring ideas is healthy. Outright lies and attempts to generate panic and outrage might be an exception. But this isn't what's happening here: the article may be speculative and flawed, and may turn out to be incorrect, but it makes its case with actual real data, not with hand-waving and conspiracy theories. Even if none of the "popular" variants (or the original virus) came from a lab leak, this is an angle we need to be investigating, and silencing people who talk about it is counterproductive and dangerous.
Sure, the tinfoil hat crowd will likely take things like this and run with them in all the wrong ways. But that's going to happen regardless, and that's just the price of living in a society where we can and should be able to discuss ideas freely, even ideas many of us may vehemently disagree with.
Censoring ideas isn't healthy, but platforms that snowball bits of information into dangerous wackery for ad revenue aren't exactly healthy either.
It's funny how some people are swift to be against gain-of-function research because of its dangers, but when it's social media the one playing with petri dishes of information for (and I think I'm going to coin a new term here) "gain-of-engagement research", then for the same people free speech is paramount and social media blocking content is literally 1984. Not saying that's you or GP, but it's a common overlap in my experience.
Everyone should be able to read whatever they want. I can't argue with that, because I defend that.
What I disagree with is with corporations (or any institution, really) abusing their position to spoon-feed content only to maximize some function regardless the externalities of the spread of such content. That's not free speech, that's giving a megaphone to the loudest and most digestible yet polarizing ideas.
So, sure, I think GP should be always allowed to share that on his FB with their peers. But maybe feeding that content to people who will potentially misunderstand it just because it generates engagement isn't the best thing to do. How can FB know that? No idea, but it shouldn't be our problem.
Hmm, dunno, I thought it was a great article, with the main takeaway being that GoF research is unequivocally and inarguably dangerous AF, should be halted ASAP, if not forever then for a long period of time where we can proverbially have a breather such that the scientific community can engage in an official reassessment/reexamination upon its safety and viability.
It's great to oversee certain hypotheses, but as a whole it's largely clickbait, IMO.
Aside from what I said, for example, GoF research generally introduces silent mutations at about the same rate as natural evolution, because it's experimental evolution after all. Likewise, such research often implies loss-of-function, due to uneven selection pressure (unless you do GoF in humans, which isn't really needed in a pandemic scenario).
But on the other hand, he raises the point of the low level of silent mutations, which is more a case of genetic modification than GoF, and doesn't even mention the possible loss-of-function.
So even though the lab leak is plausible, she's using arguments that contradict each other, knowing that at least one of them is invalid (most certainly the GoF one).
This post takes many screens of text to get to the point: we don't know how omicron evolved from its last known ancestor in Spring 2020 to November 2021, when it burst into the world stage. Ergo, lab leak.
It's a great deal of throat-clearing for a one-sentence argument from ignorance. Alina Chan has pointed to a more plausible alternative in this comment https://news.ycombinator.com/item?id=29789480
The main argument is the ratio of silent vs non-silent mutations. So you are actually making a false presentation of her argumentation and I believe this is called... slander ?
Although the claim that there's little chance for Omicron to have developped resistance to antibodies in an immunodepressed patient (that is without antibodies) needs to be adressed to.
I would love to see a reasonable fact-based response to the article that actually take into account the points being made.
> The main argument is the ratio of silent vs non-silent mutations.
Incorrect. She claims four supporting lines of evidence and does not label any one of them as the "main" argument. The NS:S ratio is just the second of four presented. She is throwing everything at the wall and seeing what sticks, because she lacks the expertise to evaluate how strong any one of her arguments is.
> So you are actually making a false presentation of her argumentation and I believe this is called... slander ?
No, it's not called slander. I just didn't see it when scrolling through this poorly organized and low-information blog post to extract the 1-2% of text that contained novel or interesting claims. Honest mistake.
If we want to talk about this silent/non-silent ratio seriously, we need to look at the data a little more carefully and not just trust some random Twitter person's guesstimate. There is at least one other random Twitter person who doesn't agree with the ratio presented in the OP. This second person does a transparent calculation citing an authoritative source, so it's a lot higher quality claim than the first random Twitter person: https://twitter.com/TheBrettRGM/status/1471317205014900739
If you look at the counts of non-synonymous and synonymous mutations for each variant listed at https://covariants.org/variants, you will see that all variants have a very high NS:S ratio. So either the entire evolution of the virus is being guided by mad scientists in secret labs, or we armchair virologists are over-interpreting the NS:S ratio.
> Although the claim that there's little chance for Omicron to have developped resistance to antibodies in an immunodepressed patient (that is without antibodies) needs to be adressed to.
Immunocompromised people don't lack antibodies.
I think there is ample evidence at this point that this person is not an expert and the arguments made are probably much less strong than they may sound to a layman.
I don't like certain aspects of publishing with peer review, but if one is so confident with their lab leak theory, try go publish in journals or put it up in one of the preprint servers instead of substack. The key is to demonstrate not that your claims are based, but that you have tried various ways to invalid the conclusions but could not success.
Not regarding omicron, but SARS viruses have escaped the lab numerous times in the past… even killing people. It’s not like the lab-leak hypothesis is the whackiest idea, some might even say it has a “strong prior”.
What conflicts of interest? Big companies? The nations they are based in? None of that stopped, for example, the story about Volkswagen's Diesel fraud, or Boeing's troubles with the 757-MAX from finding a lot reputable publishers willing to print the story.
Conflicts on trying to appear politically neutral for PR pieces while 1) they are not (because research funding sources, public relationships etc), 2) it is not possible, so better off avoiding certain topics all together.
I still have faith in preprint servers though. Or self-publishing in the scientific writing form, instead of unorganized blog rant.
It's not like it was their first blunder, either. It's the same editor that needed more than a decade to retract Wakefield's fraudulent "vaccines cause autism" paper. He's very much an activist using the journal to further his political views [0].
I was unaware it was a requirement to have enough evidence for a peer-reviewed journal in order to begin even talking about something of interest.
I'm not sure I buy the lab leak theory -- and certainly not solely on the basis of the information presented in this article alone -- but I do believe it's worth further investigation.
And we know lab leaks do happen; safety processes in even highly-regulated labs seem to be severely lacking. Calling attention to that, as well as the dangers of gain-of-function research (especially when considered in context of poor safety processes) is IMO critical.
Then let me offer two informal "substantial" arguments. It's too long to question every point.
The author argued in section "weirdness 1" that the phylogentic tree implies the omicron strain is directly related to an ancestor genome from Spring 2020. I have the following concerns:
the tree is based on https://nextstrain.org/ , a database initially introduced in 2018 [1]. This is a great data source. However, for COVID, nextstrain naturally bias towards the more viable biosamples. In other words, COVID strains in wild animals such are going to be underrepresented, if represented at all. And if so, the large sequence divergence is surprising but not a direct indication of lab leak. The author can supply with a rough overview of sequencing sources of nextstrain to counter this. Or better, it would be good if the author can compare with, or cite existing literatures, phylogenetic trees of other epidemics and demonstrate that the sequence divergence is much larger than what we would expect from wild animal reservoir.
"weirdness 2" has a stand, but it should be accompanied by silent/functional mutation ratios in other COVID strains since synonomous mutation could be not entirely silent if translation efficiency is affected (correct me if I'm wrong).
Briefly on one other point, "weirdly it's exactly mice, not other animals": we use mice as lab animals for a reason. They are somewhat similar to human in terms of physiology. Therefore we can expect that they could be more prone to COVID infection, aren't we?
editted to add one more sentence: from a peer review aspect, this blog is beyond terrible and I'd probably have 10 major conerns listed if it comes in as a PR.
Adding one more clarification in case someone reads this text wall:
The "requests" I made was rather harsh, e.g. it might be impossible to check nextstrains's sequencing sources, if this is a real manuscript revision. I honestly probably won't question as harsh if it's a writting for a different topic.
However, given that the author is trying to illustrate a not-very-likely scenario, which being, not only that there's a major lab leak, but also someone has engineered a not yet fully understood non-trivial virus genome to alter its function as desired (note that COVID doesn't have a well established animal model. It would be hard to test a engineered virus even if it exists. In this case, would you assume that it's continuous lab "leak" and only the omicron strain was a success? And if yes, how could all other strains went undetected at all in the past 2 years?), I think scrutiny is justified and should be expected. It is against several odds and you really need some strong evidences to rule out other possibilities.
Oh I genuinely mean that and nothing else. I'm remotely familiar with the topic, but I do not work with protein translation and viruses at all. My question about this silent/functional ratio argument could be completely wrong or in the wrong direction.
That original argument is interesting and is a surprising obervation to me, and I would love to read a well-written piece on that. Just keep in mind that "statistically unlikely" doesn't immediately mean "it's unlikely", you might have used the wrong presumption (in this case, silent mutation being not really silent).
This post had 40 points within 20 minutes, which is the reading time of the article at 200 WPM plus a minute or two for figures. How many of those upvotes were from people who didn't read or who skimmed the article?
I agree on the hostility, and I also hadn't flagged.
I wanted to see how the post evolved as I read the article and looked into each linked source's motivations, so I made a note of the points (14 after 10 minutes) specifically because I felt there would be a lot of biased discussion.
The instant popularity of the post could have three factors: multiple votes from one source, individuals already well-versed in disease propagation and clandestine government action who support more visibility in the post, and people who believe the post could have merit without actually putting a great deal of their own research into the sources.
I'm in the fourth camp: agnostics. That's why I haven't contributed to the popularity of the post. However, two years of hearing about this disease does a lot to build resent for armchair epidemiologists.
Here's a fourth factor: people upvoting before reading it (but possibly after skimming it or being aware of it's context) in order to keep it highly ranked (which is score + time sensitive) in order to trigger HN discussing the subject. I was in that camp before it got flagged.
I read, had a bunch things to argue about, and came back to find it flagged. IMO it's a terrible blog post and I regret reading it. But man, the flagging was... fast.
I often upvote articles I find interesting enough I want to see a discussion of them on HN. To me it doesn't mean every word of an article is perfect and above criticism, it just means it's IMO interesting and of substance enough to warrant discussion.
In this case I took my time fully reading it before posting it, but not being a biotech person I posted this here also because I was interested in criticism of flaws I would have no chance of not overlooking. But just flagging it isn't that. It doesn't tell me this article is bad, it tells me too many people aren't acting in good faith, so that raises the question why that is.
Trying to turn it around on others by speculating on what they might have done (i.e. why they upvoted it, if they read it), doesn't change what was definitely done (i.e. flagging it without any substantial criticism).
Same here. I skimmed parts of the beginning, then upvoted because I found it interesting. I don't feel we should be squashing everything that might challenge our existing beliefs just because. Then HN would just be like every other awful social media site out there. If people have substantive problems with the article, they should articulate them as comments instead of blindly flagging something and hoping nobody ever has the opportunity to think about it.
Agreed on this. I read the article before looking at comments (now 8-9 hours after it was posted), and thought "hmm, ok, I'm skeptical, but these seem to be pretty strong arguments". I was pleased to come here to the comments to find strong counter-arguments, many of which are things I wouldn't have considered due to lack of expertise here. So I'm glad it got enough votes and stuck around long enough for serious discussion.
(For the record, I still do believe the various lab-leak theories have legs, and should be discussed and investigated, even if this particular article ends up being unconvincing.)
Without wanting to or being able to contradict the article, some of it sounds like the creationists.
Because we cannot fully explain evolution, we do not know all the ancestors and the result is so complex, there must be a creator.
I hear exactly the same argumentation from creationists when it comes to the development of the human eye, for example.
Evolution occurs gradually, one base-pair at a time through replication error (or various other effects). Occasionally you get big changes through duplication, transposition or deletion of whole parts of a sequence. But the latter hasn't occurred here--we're looking only at the former. When we study evolution over time, we can look at the accumulation of silent and non-silent point mutations. And we can also pick up any larger insertions and deletions. From this data we can create a graph of the changes over time based upon relatedness (the phylogenetic tree). This is the data shown in the article.
When looking at a large sampling of data across an entire population, we would expect to see a gradual accumulation of point mutations over time. And very rarely, some larger insertion or deletion event. None of this is new. We had all the tools to do this for over two decades. I was using Perl for bioinformatics 15 years back.
So given the assumption that we would see a gradual accumulation of point mutations over time, if we see any big changes appear out of the blue, that's a flag to investigate more closely at what happened. That's not "creationism" of any sort. Given that the point mutations give a very clear fingerprint, we can immediately find the most closely-related genome, which is why it was found to match a sample collected in early 2020. That completely breaks our expectations of it missing a whole 12 months of natural accumulation of point mutations. We might not sample perfectly--we might occasionally see two or even three point changes because we failed to sample those intermediate states. But to have a jump spanning dozens of changes--that's just not matching our existing expectations, particularly when we tracked nearly every Delta change.
Now that might be real. But the probability of that being natural is very, very low. Almost nonexistent. But the chances that this was stuck in a freezer and pulled out, skipping over those 12 months of mutation-gathering while frozen in a tube, are unfortunately a much more likely possibility.
But we never have the full picture. 2020 was a year where several countries closed their borders and restricted domestic travel. Many countries were not sequencing the virus. It's not that far fetched that we'd see a descendent of an ancient variant if it had been in hiding in some remote isolated village in a poor country.
While what you say is certainly possible, it's not (IMHO) very likely. It doesn't matter that countries closed borders and restricted travel, or that not all countries were sequencing with the same rigour. That doesn't affect the eventual outcome as we randomly sample patients in the rest of the world.
If a country were hypothetically completely isolated and not sequencing, then we could have a new unknown variant develop. But from a given previously known origin genome, it would be mutating within that population over time at a fairly predictable rate, which would lead to a family of variants rooted at that known origin. We would see a spectrum of variants in a cluster branching from the origin. However, it clusters far from its origin, and this does raise a red flag.
It's possible that as we collect more data, we will "fill in the gaps" and get a better picture of how it evolved to the point it is at today. If there is a hypothetical country where this evolved naturally, those variants will still exist within the local population, and we will gradually sample a range of them in other countries over time as they too travel abroad where they can be detected.
If however it is not natural, then those intermediates will not exist, or will only exist as frozen down passages in a lab freezer. Maybe we'll identify the lab in time, if that's the case. They should be able to match it if they sequenced it.
Whichever hypothesis is correct, the data can't lie. We will know one way or the other fairly definitively in time.
You are confusing our lack of knowldege of the intermediate steps with the lack of interim steps.
They might simply have been lost in the crowd or not even noticed, depending on where they were posted. How carefully have we studied the variants in animals?
No, I'm not doing that. We might not yet have sampled the intermediate steps, if they exist, but it's inevitable that we will do so if it has a natural origin. Given the phylogenetic distance between the omicron cluster and its root in the phylogenetic tree, there should be several hundred to thousand intermediates if it's naturally occurring, of which we should be sampling many dozens (modulo selective pressure and sample availability biasing the sampling). Assuming that mutations occur randomly and with equal probability, then you would naively expect if the distance is between the cluster and the root is n base pair changes, then there would be n raised to the fourth power variants (assuming equal selective pressure). The reality is a bit more subtle than that, but I hope it illustrates the general scope and scale of what has taken place here. Given that scope and scale, the complete lack of any sequence data to date is astonishing. Particularly when we do see all those intermediate states for the other variants. Does that make sense?
As for variants in animals, that's a possibility. But it's more likely to be a red herring. Domestic animals will be infected with the same strain as their owners, and any reinfection would be very likely to be similar to the original. Transfer to a wild animal reservoir and back into the human population is so rare and unlikely that it is barely credible. Infection of humans from wild animal reservoirs is a rare event. To have it happen both ways within 12 months is not credible.
I could be wrong. This will only be answered by collecting more data to improve our understanding.
Why should it be inevitable?
How long do non dominant variants survive inside and outside a host?
We don't even know in which country omicron originated even less who was patient zero.
We could easily miss whole strains of the virus but because non of them lead to a new dominant variant we never know the even existed.
It's inevitable because even though one variant may become dominant, there will still be isolated pockets of the other variants. It's very unlikely that these variants will be entirely eliminated across the whole globe. Look at the epidemiology of HIV and the spatial distribution of variants as a point of comparison. Likewise for other viruses. Even if these other variants continue to evolve from the initial root, they will still be phylogenetically distinct from the current omicron clustering, somewhere intermediate between the root and existing omicron cluster. If it's out there in the wild, it will be picked up by PCR eventually. If it's not out in the wild, that big gap will remain, and a lab somewhere has questions to answer...
The starting point for the omicron cluster would be an interesting bit of information, but it doesn't necessarily have any bearing on where the intermediate strains are located. But none of that matters. If it's out there, it will eventually be picked up by PCR. We can use phylogenetic analysis to retrospectively reconstruct the evolutionary tree of every organism we have sequenced to date. Doing it just for the coronavirus variants is not hard (I have done it in the past including bootstrapping). Whether it's a month, a year or a decade from now, we will be able to answer the question by reconstructing the tree.
This is really basic bioinformatic analysis, in routine use for over two decades. None of this stuff is remotely new or groundbreaking.
The other questions you are asking are not really relevant to the problem. The virus does not survive long outside a host; it has no bearing upon the problem at all. The same applies to inside the host. All variants will continue to infect and propagate themselves to varying degrees within the host populations. It's endemic at this point.
One other point to bear in mind is that the mutation rate of the polymerase is effectively a constant, in terms of mutations per n kilobases. So we would expect all variants to accumulate a certain number of mutations averaged over time--the sequence will not remain static since the virus has to continually be passaged through mammalian epithelial cells to maintain and propagate itself. There will be some variation, but if it's been frozen down and manually propagated, it may have a dramatically different number of mutations compared with the other contemporary strains that have spent most of their time in living hosts.
It would be more credible if you knew for a fact that there are people manufacturing and studying eyes. Even if you don't know exactly how the eye you are looking at got there.
You might find the work of David Gelernter (computer scientist) interesting. He's not a creationist, but he has abandoned the theory of evolution.
> Suppose, then, that every bacterium that has ever lived contributes one mutation before its demise to the history of life. This is a generous assumption; most bacteria pass on their genetic information unchanged, unmutated. Mutations are the exception. In any case, there have evidently been, in the whole history of life, around 10^40 bacteria—yielding around 10^40 mutations under Axe’s assumptions. That is a very large number of chances at any game. But given that the odds each time are 1 to 10^77 against, it is not large enough. The odds against blind Darwinian chance having turned up even one mutation with the potential to push evolution forward are 10^40x(1/10^77)—10^40 tries, where your odds of success each time are 1 in 10^77—which equals 1 in 10^37. In practical terms, those odds are still zero. Zero odds of producing a single promising mutation in the whole history of life.
This is Intelligent Design dressed up in hand wavy math that builds on misrepresentation of cited studies and the fossil record. Read with a strong dose of skepticism.
The book is about Intelligent Design, but the reviewer (Gelernter) as far as I understand is only claiming that the theory of evolution doesn't hold. He is neither a creationist or proponent of ID
What kinda raised suspicions about Omicron for me is that it propagates considerably faster in the bronchial tissue, while being much slower in the lungs [0].
Given the current state of biotech, it is not possible to just edit the viral RNA achieving the desired clinical result, but is entirely feasible to keep applying minor edits and measuring the propagation rate in different tissues in vitro, effectively optimizing it to be more transmissible and less lethal. The snapshot of the phylogenetic tree, showing how Omicron "branched out" mid-2020 highly supports this assumption.
It is also quite obvious that an endeavor like this would be against all written rules and norms and would face backlash of epic proportion even if it wouldn't backfire, so it's safe to assume we won't hear an official confirmation of this theory from any of the governments.
And if this were the case, they don't seem to have done a particularly good job. People have already died of omicron, and that alone would be an indictment of the end result. "First, do no harm", and all that.
Re: the claim about the non-synonymous/synonymous mutation ratio (N:NS ratio): if you calculate this ratio for each variant listed on https://covariants.org/variants, you will see that all variants have a very high NS:S ratio. So either the entire evolution of the virus is being guided by mad scientists in secret labs, or we armchair virologists are over-interpreting the NS:S ratio.
I think there is ample evidence at this point that this person lacks expertise in virology, and the arguments they make are probably much less strong than they may sound to a layman.
Even then, the people working on this other planet/moon will probably want to come back home to Earth at some point. Maybe a leak that way is much less likely than a leak from an Earth-based lab next to a population center, but I would bet on humans still failing at perfect safety protocols, and bringing something nasty back to Earth regardless.
As the article states, we should be clearly weighing the benefits of gain-of-function research against its risks. It seems like that was the intent of the 2014 funding ban in the US, but we never actually did that work, and that's horrifying. And if the some/many/all of the benefits of GoF research can be realized through other means, even if those means are more difficult or costly, we should probably just do that anyway.
The sample distribution of viruses is incredibly important for this sort of analysis, and much of the argument here only makes sense through the lens of uniform virus sequencing. If you have imbalanced sequencing and imbalanced transmission you can also explain these differences.
The important thing is that mutations occur at a certain rate per virus per unit time. If you have an isolated population that's sequenced infrequently then (1) that strain will appear to evolve more slowly as there's a smaller population capable of mutating, and (2) once that strain is sequenced it's going to look far from what you've seen already since you haven't been tracking the intermediate mutations in this population.
The S/N ratio can be analyzed in terms of a random walk in high dimension. Variance in these walks grows over time (in terms of distance from origin, i.e. number of mutations), so the discrepancy doesn't seem super far from what's plausible under the null hypothesis. Perhaps someone can do the math on that.
The hypothesis merits further investigation, but the strength of the evidence presented here really requires some complex statistical analysis to determine if innocuous explanations fit. The analysis is far more complex than I would expect an epidemiologist or virologist to apply in the course of their work.
> “If a $1000 PhD side project could kill millions of people, we must end viral [gain-of-function research], or it may end us.”
This sentimental reminds me of a talk given by a government bomb expert where a naive student asked “why do we allow the ingredients for bombs to be sold in store, shouldn’t we ban them all?”
The answer of cause is that if we do that, then we suddenly don’t have gasoline, orange juice, basic electronics, fertilizer or even just basic sanitation products available anymore, but of cause anyone who wanted to make a bomb would still be able to do so easily.
If it really is the case as pitched that 1000$ gets you a virus that will bring down nations, why on earth would we leave the field only to bad actors? Would that not just make it ever so more important that such researched happened openly and under well funded, strictly controlled conditions so we know what to expect and so we can start to develop plans for counter measures for when the next 9/11-like fanatic driven attack comes along?
I don't know if this is truly the case (outside my area of expertise), but the article claims that most of the benefits of gain-of-function research can be realized through much safer methods. If true, the "good guys" don't really lose much by refusing to do what the "bad guys" might be doing.
That's a dangerous gamble which cannot be put back in the box in the event that it fails to be less dangerous. Like throwing a enormous amounts of sulfur in the atmosphere to take out CO2. It's the sort of decision that would have to be taken by isolated group or nation on behalf of the rest of humanity despite potentially catastrophic unintended consequences. Maybe the result will be that it's a "less dangerous than Delta collective immunizer", but I wouldn't be thrilled if it's an intended variant (even if a lab leak isn't much more reassuring).
I'm also unclear how such researchers could come to the conclusion that it is less dangerous and more contagious with humanized mice considering it is the result (AFAIU) of it contaminating and replicating in the airways rather than the lungs. I'd be curious for someone more informed than me (an ecologist with very superficial understanding of viruses and studies in mice), but if I'm correct that lung vs. airway contamination isn't quite replicable in humanized mice vs. humans, intentional "alter and release" seems dubious.
This is interesting, but even a brief discussion of selection bias would help it be more convincing. If you pick the most wildly successful mutation out of the thousands of available choices of course it is going to be an outlier in numerous ways. Isn't it perhaps even likely that the most widespread variant would have a low number of silent mutations and strong immune-evasion capabilities?
It's definitely likely that the most widespread variant would have strong immune-evasion capabilities, but I don't see how it follows that it it's likely that it would have a low number of silent mutations. The immune-evasion would be something that evolution would select for, but the number of silent mutations (low or high) would seem not to matter where evolution is concerned.
Why is a cover up necessary? SARS has leaked from the lab many times before, yet this fact is almost never mentioned in these discussions. The media does plenty of self-censorship.
People said the same thing about the government monitoring everyone's communications: "It could never be kept secret". Edward Snowden proved they were wrong, and this was kept a secret, for years.
To your point, it was even widely discussed in niche areas like tech blogs and HN. However, much the same way as this hypothesis it was dismissed as a conspiracy theory, widely debunked by “experts” and downplayed. Again, not claiming this makes lab leak a conspiracy, but the idea it needs to be 100% a secret does not need to be the case. The narrative just needs to be controlled to some extent.
I wonder if we need a better way to address safety related to research around potentially airborne diseases -- like maybe in the past things that could result in death are considered bad, but something that presently is not deadly, but being airborne and super contagious could mean it could mutate like crazy while in a large majority of the human population. Another not totally as crazy as it sounds now that we have things like long covid, what if we have something that basically has a minor, but real impact on people long term, but now apply that complication across a huge number of people and comparing the cumulative impact to say 1000 people dying of ebola is hard to compare.
So maybe respiratory diseases, no matter how dangerous they currently are should be heavily restricted to labs that can handle them, and then have international monitors at each of them with strict reporting rules not tied to any organization like WHO or UN or whatever, they are just there to report lab leaks no matter how small.
A cover up isn't very hard to execute if the involved parties all have aligned incentives - in this case, not ruining their careers, possibly destroying their entire professional field, and publicly accepting culpability for millions of deaths and other damages.
In a leak? Zero would be the minimum who would have knowledge of the leak. There is no law of the universe saying that anyone would be aware of what had happened or how, especially with an active disinterest and disincentives toward responsibility and accountability.
Not that many, probably 1, or maybe 3 to be conservative. Of course there are the institutional and governmental parties as well, but still not that many (1 lab director, maybe 1 executive above them, plus a handful of regulators with detailed knowledge of the labs operations). If it is the case that, say, the WIV leaked the initial virus, there's probably less than a dozen people in the world with positive knowledge of that fact.
I've seen fundings and positions related to COVID research popping up since at least mid 2020. Biorxiv submissions exploded. Certainly not a small group to deal with.
(on a serious note: the answer is, the scientists don't have to know about a leak for it to have happened, the important part is that they don't want to know. That is, China prefers if this question goes unanswered.)
How do they keep people from talking about something they'd rather not talk about? Why would they need to? Espcially since people tend to just scream "conspiracy theorist!", flag it off HN etc.
A couple handfuls, maybe a couple dozen? Seems not that hard to keep something like that quiet, especially when everyone involved would be strongly incentivized not to admit to being party to something like this.
Not saying it's true, but I don't think "they couldn't keep this a secret" is a particularly compelling rebuttal here.
If any of this is true, and I don't have enough brain power to decipher if it is or is not, would it be at least in the realm of possibility that Omicron was not an accidental leak; perhaps, rather, a deliberate one, to counteract the original (and Delta variant's) virulence and impact?
We know that the virus is likely to continue to mutate in the wild, on its own - and that the virus in the wild has upended our way of life with great economic costs. Is this a viable path way to introduce widespread natural immunity? Omicron introduces mutations with extremely high contagious properties but very mild virulence. In one swoop, you expose vaccine-hesitant and developing nations to a virus they're likely to survive, help inoculate them against future mutations and outcompete the dominate strains such that the human race is somewhat protected against future infections.
In effect, you kind of "undo" the original mistake.
Seems like a cheap shot to me. Does twitter as a communication medium somehow invalidate what was being said?
One quoted thread was from "Tony VanDongen, an associate professor of pharmacology and cancer biology at Duke"
Seems like a reasonably valid opinion from someone with a clue. He's addressing specifically why Omicron is weird, and doesn't look like a normal evolution of COVID-19.
Another is from "Scott Ferguson, a PhD in pharmaceutical sciences and a postdoc at the Harvard Center for Systems Biology".
3rd and 4th are: "Phillip Buckhaults, Ph.D., is a molecular biologist and cancer geneticist at the University of South Carolina" and "Valentin Bruttel, who received his PhD in 2016 at the University of Würzburg (Germany) where he studied tumor immunology, autoimmune diseases, and development of biologicals"
A key diagram used is a Phylogenetic Tree from Science.
Looks like a collection of valuable scientific info, collected to support an opinion. Not saying it proves COVID came from a lab leak, but it's not just random speculation. Seems like a pretty valuable discussion to me.
Wouldn't you want to know if a disease impacting billions of people looked inconsistent with a naturally evolved virus? The scientist involved mention possible other explanations, poor models, etc. But do seem to lean towards a likely explanation of artificially tweaks to get omicron.
So Twitter only for the Every Day Joe? This sounds like BS. How many scientists that you probably follow, have announced news around Covid, via Twitter. You've probably even re-tweeted them lol.
Hate to be the bearer of bad news but you're outdated on this point. Researchers & politicians of repute use Twitter to voice their opinion and share stuff with the public.
I didn't say these platforms are never used. In this context I don't regard the public as an entity where you have a meaningful engagement on a topic. An individual yes, but the public as a whole is broadcast to.
Hate to break it to you, trump likely never read your tweets...
It also cites Science, The Taiwan Times, and Forbes (shrug).
But more importantly, it's well reasoned. It's not "wild speculation". It's learned speculation based on history, opinions of experts, and independent sources, synthesized with deduction.
I understand the reflex to push back on claims of conspiracy. I find the mainstream meme conspiracy theories (flat earth, 9/11 was an inside job, etc) to be somewhere between laughable and terrifying. But this is a unicorn among conspiracy theories: both the initial conditions are plausible (that this was an accident, of a kind that has happened before, not a nefarious pre-planned event with dubious benefit), and the conditions of the conspiracy are plausible (the set of people with positive knowledge of a given leak would be quite small, and their incentives to keep it secret would be strongly aligned).
It links to a column on the Science website, and only to take a picture from it. The blog post doesn't discuss the scientific article that picture originally comes from or even he column that they link to. It uses the picture to say "omicron is weird" and jumps straight to speculation from twitter.
As for the news article from the Taiwan Times, it has nothing to do with omicron which is the main topic at hand.
It depends on what kind of media we're talking about.
A scientific article about the origin of omicron would be expected to provide citations and evidence behind everything it says. It would also be expected to discuss all the leading theories, as well as what additional information we need to figure out which theory is the one most likely to be correct.
A news article from a journalist might interview the experts to get their opinion and summarize the scientific consensus to the general public. Ideally it should also allow an interested reader to identify what scientific publications the news is talking about, should the reader desire to find more info.
This blog post is none of that. It ignores the leading theories in order to paint a biased picture that only a lab leak is possible. Their main "evidence" is someone on twitter. A close read reveals innumerable holes and red flags. For example, it when it says that omicron couldn't have evolved in an immunocompromised patient because they "don't have the antibodies". They actually do, it's just that they don't have as many! The whole point of the immunocompromised patient theory is that a long infection with a weak immune response provides selective pressure for immune evasion, while giving enough time for mutations to develop. Things like this demonstrate that this author has little idea of what they're talking about.
Someone else made a comparison to arguments from creationists, which I think is apt. They throw a bunch of things at the wall, hoping that something sticks. But they don't paint a coherent picture and if we look close it's a mess.
This is the perenial problem with all these poorly sourced "just asking questions" posts, in any topic (from covid misinformation to holocaust denial). By the time someone who actually knows their shit has a time to issue a proper response, the original wild speculation has already spread like fire on social media and landed in front of a bunch of eyeballs.
There are many things in the original article that raise red flags about how accurate it is (for example, barely even paying lip service to the non-lab-leak hypothesis, and using twitter as a primary source). Given that, I'm going to be less charitable about the questions it's asking.
And if they are right though? Are you going to apologize for suppressing different theses? As far as I know, Science lives of These and Anti-These, right?
I dislike Twitter, but if the people posting there have legitimate credentials and expertise in the field, that credibility doesn't disappear just because they've chosen to talk about this on Twitter.
That doesn't stop at least few "I Hate Ads" (read "I Hate Google") threads popping up every single day. For some reason this "tedious" tag only applies when it comes to Lab Leak or any China related threads.
It repeatedly asserts that immunocompromised patients cannot have antibodies ("weirdness" 3 & 4), but, immunocompromization is a spectrum. Many people can produce antibodies but not as many as normal.
If the piece hinges on getting this pretty basic element wrong, how wrong is it about some of the more sophisticated analyses?
Immunocompromised people, in order for their "omicron" to develop resistance to the various treatments available (the monoclonal antibodies) must have been exposed to those treatments. If they were exposed to those treatments, they were being followed medically. If they were being followed medically, and receiving long-term treatments, it's then odd that they didn't infect a single other person in a year and a half.
On the other hand, there's the somewhat bigoted implication that "oh there are a lot of remote people in Africa that don't come in contact with anyone else." Well, then how did their omicron develop resistance to all the fancy treatments?
Either it's an immune compromised patient who never came in contact with anyone else, and the specific resistance to monoclonal antibodies, which they never received, is not explained.
Or it's an immune compromised patient who received intensive treatments for a long time, in which case the lack of any intermediate variants ever being documented is not explained.
S/he didn't say immunocompromised people don't have antibodies.
S/he says mice don't have human antibodies, so if the "mouse hypothesis" is correct, how did the mice, unless they were lab mice, get the immunity to all these human treatments?
We have a record of successfully tracing viral origins. This is extremely detailed and difficult science. The last two coronavirus outbreaks took around fifteen years to understand. The previous pandemic was HIV which took even longer than that. Thinking that there is a quick and easy way to understand the origins of SARS-CoV2 variants based on narrative inference is essentially asserting that it is different this time. That might be the case, but it will probably take a long time to be sure. In the mean time we can be confident that we understand previous natural viral origins and also predict that there will be more coronavirus outbreaks no matter what people do in labs. Science and history did not suddenly change because there is an interesting hypothesis linked to a dramatic narrative.
I am in no way informed about this area but from just a layman/logical perspective:
> The last two coronavirus outbreaks took around fifteen years to understand.
Is it possible that because these diseases had less impact, less people worked on them? It seems like virtually every scientist in even a tangentially related field is working on Cov-2. Not to mention that we have made significant improvements in technology even over the last decade.
I am not saying that this proves or disproves your comment, but couldn’t it be said that more people, resources and technology could get us answers faster in 2019? Especially if we are building of research and knowledge we have acquired over the preceding 2 decades?
> "[A virus wouldn’t be expected to develop a bunch of resistances to the current human antibodies if it evolved in] An animal, because animals in natural circumstances don’t have human antibodies"
Animal antibodies would work just fine to put selective pressure on the virus.
I believe the theory for an accidental lab leak in Wuhan is more convincing, because it actually started near to a lab. Where is the evidence here that the first cases of Omikron were detected near a lab. Are there any labs in South Africa that could be responsible for such a leak?
I found it completely unconvincing, particularly when it came to discussing the "lab leak". From the article, where the author speculates about why the omicron variant is so genetically different from other variants of the virus:> "One parsimonious hypothesis is that some engineering has been done to it, in order to make its evolution look so unnatural. I have not heard another parsimonious hypothesis."
A New Scientist article from two weeks ago suggests two other hypothesis for the evolution of omicron: that it either evolved in a single immune-compromised person, or that it jumped to an animal population and then jumped back:
https://www.newscientist.com/article/2302268-how-did-the-omi...
I've been following COVID news the same way I do the weather during tornado season. That is to say, consistently and with an effort at personal awareness, but I'm hardly an expert. Yet I'm aware of several other "parsimonious hypotheses" which the author is not, and, worse, they apparently consider their own ignorance as evidence.
The author actually mentioned those two theory several paragraphs down in the article.
However, this actually made the article less credible to me, as this make me feel the article's purpose is to build a narrative and try to discredit everyone else, not to fairly evaluate all theories equally.
One thing I have been feeling about internet is there are too many experts on it, so one can always find enough quotes that support ones theory. However, as a reader, it's become impossible to determine whether particular expert should be trusted.
There is a figure 1 and the left side (A) which shows a maximum-likelihood phylogenetic tree. If you examine this tree, you can see that the highlighted piece is based off a recent (to the HIV patient's case) variant.
On the other hand, the linked article (https://bprice.substack.com/p/lab-leak-20) has a tweet by Jonatan Pallesen showing a tree for Omicron. This tree shows that Omicron is based off of a variant from a surpringly long time ago. This alone is bizarre.
That combined with the lack of silent mutations is extremely suspicious. I'm not saying this is concrete evidence or anything, but its very strange and doesn't appear to line up with a natural course of evolution
This virus is just too profitable and many folks at big pharma are unhappy that there are not yet in the top-10 billionaire list. Expect to see more variants and more 'booster' shots in the upcoming years. They will milk this opportunity for all its worth.
a coincidence which is almost always ignored is that China had huge Hong Kong protests with no resolution in sight until a global pandemic hit halting all and any street protests there.
I believe it's important to separate China and the Chinese Communist Party (CCP).
I don't doubt that the Hong Kong protests were a major problem for the CCP and that COVID allowed them to implement a series of restrictions and laws to stop protests. I also don't doubt the very real possibility of a lab leak in Wuhan (in fact, given how the CCP have responded, I find it very likely).
What I do doubt is that this virus was released to combat the Hong Kong protests. If it was on purpose, it was a huge self-inflicted wound, as the CCP's inability to contain the virus has made them look weak internally and externally. It's hugely crippled their own economic growth which was set to overtake the US, which has now been set back at least 5-10 years based on projections (if they are to be believed).
If I were an evil regime, I would probably fake terroristic plots from the protestors and then respond to them heavily. There were plenty of other options available too, such as "starving out" the protestors (a tactic I believe they employed).
What's more likely is that the CCP are very good at utilizing the current situation to serve their own means. They are surprisingly bad at it though and seem to completely misunderstand how they are perceived on the world stage.
Yes and no? In theory, the American government is "for the people, by the people", a feature not at all shared by the Chinese government. So actions taken by the American government should be the will of at least a majority of Americans.
(Of course, the reality is a bit different; the American government is run by people largely in the pockets of special-interest groups and lobbyists. But we'd like to think democracy works as well as we'd like...)
> Should other countries distinguish between the USA and the American government? That’s something I don’t see.
I think it's important when you are discussing some actions taken by a minority leadership - an unelected leadership at that. If Biden did something bad on behalf of the US, I would be tempted to say "Biden did X" rather than "America did X", especially if potentially speaking to an American.
I also think in terms of geopolitics, it's important to criticise the Chinese government rather than the Chinese people - especially with increasing nationalisation ongoing in China.
To participate in this intriguing line of inquiry,
It may be a case of aligned incentives. A new virus occurs (even CCP does not know whether it is lab-leaked), and it is allowed to exist for some time (doctors arrested for spreading rumors). Definitely prefer incompetence to malice here, but maybe a decision was made to "sit back and assess" while the problem grew more serious.
Faking terroristic plots and blaming protesters is old hat, and the outcome of cracking down on the free territories while you still have the #2 Navy in the world are predictable. Hong Kong is not alone in desiring independence, and Beijing is not willing to lose face. A re-run of Tienanmen Square was starting to look inevitable. What if instead of that well-trod path of war, they chose to boost the poll numbers by allowing a crisis to occur and saving the day?
The cost of an economic slow down, well it's a risky calculus, but if the pandemic becomes global, they will not be left that far behind the competition. In fact, a totalitarian regime may be better-able to enforce health mandates and become productive again sooner.
What's more, USA was also dealing with a kind of dueling rebellion between BLM and Trump-Forever types. Perhaps the two agreed that the world needed a cooling-off.
Indeed, we will likely never really know what the truth is here - even if the CCP dissolved tomorrow I imagine it would be years upon years before we start seeing anything emerge. A bit like the USSR.
> Definitely prefer incompetence to malice here, but maybe a decision was made to "sit back and assess" while the problem grew more serious.
I imagine that initially the CCP leadership was making decisions based on bad data. I.e. the classic "we have so much grain comrade we have to throw it away!", hence why the local government leadership in Wuhan were purged.
> Faking terroristic plots and blaming protesters is old hat [..]
I would say it's 'tried and tested'.
> A re-run of Tienanmen Square was starting to look inevitable.
I wouldn't yet rule it out. These protestors never vanished, the feeling of the people appears to still be strong (although nobody wants to be the nail that sticks out).
> What if instead of that well-trod path of war, they chose to boost the poll numbers by allowing a crisis to occur and saving the day?
How would that have looked like? I imagine it would have been achieved by keeping Hong Kong under zero lockdown to the point of collapse, and then rushing in with supplies, etc. Instead they were pretty quick to lockdown.
> In fact, a totalitarian regime may be better-able to enforce health mandates and become productive again sooner.
Not so long ago, their "5 year plan" entailed global medicine dominance, which you may argue they achieved during the pandemic. Pretty much all PPE was coming out of China. I think they made a mistake in restricting the export of PPE as other Countries suddenly saw them as a supply risk and begun to decentralise.
> What's more, USA was also dealing with a kind of dueling rebellion between BLM and Trump-Forever types. Perhaps the two agreed that the world needed a cooling-off.
I doubt that. The CCP are very interested in fuelling the political divides in the US. You get CCP officials Tweeting (despite Twitter being banned in China) stuff like "I can't breath".
I can't of course rule out that this was on purpose, but I think even the smartest of analysts couldn't possibly predict how this all would have played out. It was a massive gamble. I imagine the only sort of Country willing to take such a gamble is one with nothing to lose. If China's property market bubbles is really that bad (and they know it), maybe I would take it more seriously.
> > What if instead of that well-trod path of war, they chose to boost the poll numbers by allowing a crisis to occur and saving the day?
By this I meant to imply that, as opposed to being faced with rebellion, the government could allow (if not cause) the pandemic to take hold and then show competence vis-a-vis building hospitals and distributing vaccines. By doing a better job at it than democracies, the CCP could buy some praise from the public, but I'm unable to speculate whether the average Chinese citizen feels their government was heroic or not.
Agreed CCP is unlikely to co-operate with USA, but maybe we had the same idea, that division in the US population was a Good Thing, ie, what was that quote, maybe it was Martin Luther King Jr, that as long as poor white and poor black people are kept fighting, they won't notice that they're both being taken advantage of by the rich? That still goes on, but it is Red vs Blue as well, and as long as we keep voting our more radical representatives in, and being angry with the 'other side', the less likely we are to unite and overthrow the corrupt show of two-party politics.
> [..] building hospitals and distributing vaccines.
Eh, I remember those pop-up hospitals they boasted about which ended up being glorified cages. I remember the headlines were something like "China builds a hospital in a week!", and then we heard nothing more after they were forced to tear them down before they fell down. Turns out you can't actually build something to last in a week - the concrete won't even set.
Regarding developing and distributing vaccines, I really suspect this is why the WIV didn't share their latest COVID sequencing data and took their database offline. (They claimed it was due to hackers, but they could have easily sent the database on a shipped hard drive or hosted it in the Alibaba cloud.) It could only serve to incriminate them and it gives them a few weeks head start for generating a vaccine. (It ended up being awful anyway and the local people choose not to take it due to a loss of faith in the CCP - for the same reason they still import their baby milk powder from abroad.)
> By doing a better job at it than democracies, the CCP could buy some praise from the public, but I'm unable to speculate whether the average Chinese citizen feels their government was heroic or not.
If you control all external media, why even bother doing a better job? You can simply claim the rest of the world is awful outside of China and that the CCP is the best thing since sliced bread.
> [..] as long as we keep voting our more radical representatives in, and being angry with the 'other side', the less likely we are to unite and overthrow the corrupt show of two-party politics.
Right, the only thing that happens in a two-party system is that one side is slightly less disappointed than the other. You find yourself voting for what you perceive to be the lesser evil.
> Thanks for joining me under this aluminum tent
I think these ideas are worth probing out as long as everybody involved remembers which parts are fact and which parts are speculation. When we confuse the two it becomes less fruitful.
the reason why the coronavirus was developed in a Chinese lab and financed by Fauci is because China is in an advantageous situation for GoF research having humans for experiments at disposal. they use Falun Gong and Uighurs for that purpose. it's the same logic that applies to black sites operated outside of the US.
I’m flagging this as misinformation and surprised this is scoring so high on HN.
This author presumes every major VoC stemmed from a lab leak. From the wild strain to Delta to Omicron. This is sensationalist, unsubstantiated claims with weak supporting evidence.
Note that the author does not imply that Delta originated from a lab, but rather that Delta leaked from a lab at the end of 2021, and cites a supporting source.
In some ways this reminds me of the ill-fated flight MH370. It's not that there's compelling evidence that the pilot took deliberate action to divert the plane and assumedly land it in the Indian Ocean in a place where it would be hard to find because of the distance from land and depth of the ocean. It's that it's the only theory that fits the facts.
Likewise, it's not that there's compelling evidence of a lab leak (now or in 2019/2020). It's that we're sort of left with it by process of elimination. For example: if Covid-19 came from an animal population (eg via Wuhan wet markets) then why hasn't that population been found? The sources of SARS and MERS were, I believe, found relatively quickly.
Just like we shouldn't just accept the prevailing theory of MH370's disappearance as fact and we should continue to look for the plane and hopefully factually establish what actually happened, we shouldn't take the "lab leak" hypothesis as fact. Extraordinary claims require extraordinary evidence.
As for the articles claims about Omicron origins... I really don't know. I'm certainly no virologist so can't speak to the mutations. That's an odd-looking graph though.
I'm also wary of drawing conclusions from anything to do with statistics, just because it's so easy to make a mistake. My favourite example is the long-running idiocy about "natural immunity" being better than a vaccine. This is based on comparing two populations: vaccinated and unvaccinated. Except... those populations aren't equivalent. The vaccinated group includes people who would've died without the vaccine (and thus are more likely to have comorbidities). Those people are dead in the unvaccinated population.
> Likewise, it's not that there's compelling evidence of a lab leak (now or in 2019/2020). It's that we're sort of left with it by process of elimination. For example: if Covid-19 came from an animal population (eg via Wuhan wet markets) then why hasn't that population been found? The sources of SARS and MERS were, I believe, found relatively quickly.
there's a great deal of compelling evidence for alpha leaking from a lab; e.g. the director of the WIV publishing papers about introducing furin cleavage sites, which have otherwise never been detected in coronaviruses, into bat coronaviruses in the years leading up to the pandemic. if anybody has not read the nicholas wade essay in the bulletin of atomic scientists from last year that was mentioned briefly in the linked piece, i strong recommend it: https://thebulletin.org/2021/05/the-origin-of-covid-did-peop...
None of these Substack-based lab-leak hysteria pieces ever address "so what?" I see nothing here to convince me that Omicron is a lab leak as opposed to an animal reservoir, where the author includes "seems to have come from mice" as evidence for the former and not the latter, which is confused.
Regardless, there is nothing actionable about any origin theory aside from "be mad at some unnamed scientist" or, as some of these conspiracy-theory vendors would prefer, "be mad at science in general."
So, what is the call to action here? Stop researching gain of function entirely?
Yes, this was very explicitly stated. And this is nowhere near the first call to do so (a lot of very respected scientists were calling for a stop to GoF research before the pandemic).
Whatever claims GoF research had beforehand of helping w/ pandemic preparedness have evaporated, because none of the successful responses to the pandemic (vaccines, antivirals) have relied on GoF research whatsoever. It appears to a high risk with no reward.
Millions of people are dead. I think it's worth having an objective public debate about what steps would be appropriate to reduce the risk of this happening again. I don't see that "be mad at science" has anything to do with an insistence on an honest exploration and testing of hypotheses.
Neil deGrasse Tyson sums up the scientific approach as follows: "Test ideas by experiment and observation. Build on those ideas that pass the test, reject the ones that fail. Follow the evidence wherever it leads. And question everything."Cosmos (2014).
Why is that approach considered so anathema when it comes to hunting down the killer of millions of people?
I suspect you have a bit of a straw man in mind. The opposition would likely say something like: "GoF is the best means at our disposal to fight diseases much worse than COVID".
1. You don't know what my position actually is, as I haven't stated it
2. You are confusing assertion and evidence
In order to be even remotely convincing, you would have to show that the risk/reward ratio of GoF is stacked against GoF. Right now, you're just aggressively telling us that it is.
You'll note that no matter how bad you demonstrate COVID to be, the opposition could (rightly!) claim that there are potentially worse diseases. And no matter how bad you postulate a future GoF-related outbreak might be, they could postulate a scenario in which humanity were saved by GoF.
This is a hard question. It's literally a philosophical one. I really wish you wouldn't be so snarky.
Well you still didn't told us whats your position is, but maybe you can answer my question:
HOW GoF helped us to fight Covid? How the process that most likely played a huge role of creating the virus also helped us fighting it? Everyone how defends GoF tells us plebs, it helps us to fight future epidemics, but no one give us an example how it is helping the current one.
Friend, I think you maybe clicked the wrong reply link? I didn't say anything about GoF research at all.
Assuming that we ever get the honest and open public debate about COVID-19's origins, and if it was a lab leak from WIV and was related to GoF research, then certainly the potential benefits of GoF research would be weighed against the potential dangers. I don't take a position one way or another in that conversation at this point, because I think it's premature.
The fight we are facing right now is whether we're even allowed to have that debate or whether any discussion of the WIV as a possible origin is stamped out as anathema.
I find myself on the side of "follow the evidence" and "question everything" rather than "you're a conspiracy theorist if you even entertain this idea."
"Where did SARS-CoV-2 come from?" is a scientific question. It certainly could have ethical implications, granted, but that does not make it not a question suitable for scientific inquiry.
I think much of the interest in theories of lab leaks, or various other theories - credible or not, are mostly propelled with the same thrust as groundbreaking science itself: they want to find some truth about the world that's been unnoticed or less discussed.
This is what motivates conspiracy theories and scientific discoveries alike. It's even true about flat Earth kids, however misguided they may be.
The "so what?" is always an after thought, and often is irrelevant to the goal of simply finding something new.
There are a lot of implications if this is a lab leak, including:
- Are labs involved in this research sufficiently secure? Do we need to raise the standard of security?
- Is the cost-benefit of gain of research worth it?
- Should China be forced to pay reparations/ sanctioned for hiding the source?
All of these conversations depend on whether its a lab leak.
I would add to that: "is it an intentional means of destabilizing the West?"
To be clear: I see no evidence that Omicron is even a second lab-leak, much less that it's part of a sinister plot. My point is that there are immediate geopolitical implications, in addition to the scientific and public-health implications you have highlighted.
I'm confused. Is Dr. Ferguson and Dr. Vonagen's observations about s/sn ratio not decent evidence towards this?
It seems quite good statistically to me.
Which makes it even more ridiculous that random people on the internet are coming up with the lab leak theories and that American intelligence agencies, spanning 2 wildly divergent administrations, have not said anything to support this.
> IC analysts assess that a natural origin and a laboratoryassociated incident are both plausible hypotheses for
how SARS-CoV-2 first infected humans. Analysts,
however, disagree on which is more likely, or whether
an assessment can be made at all, given the lack of
diagnosticity of the available information. Most
agencies are unable to make higher than low confidence
assessments for these reasons, and confidence levels are
tempered by plausible arguments for the opposing
hypothesis. For these hypotheses, IC analysts consider
an exposure that occurs during animal sampling activity
that supports biological research to be a laboratoryassociated incident and not natural contact.
There's nothing hysterical about the article. Nor do they encourage the reader to conclude they should "be mad at a scientist/science in general". In fact they explicitly encourage the reader to believe and engage with scientists; just, you know, the ones that don't have obvious conflicts of interest around virology and specifically GoF research, who have been some of the most visible and vocal in speaking out against the Lab Leak theory. Also there's a clear call to action, which is to stop GoF research. Did you even read tfa?
Seriously. The incentive for these researchers is awful. Their goal is to take a virus that maybe isn’t a threat and find a way to manipulate it to see how it could be a threat if it somehow naturally mutated into some specific otherwise engineered form. It’s the only way to justify their job. No one will subsidize researchers who come up with “nothing to see here”.
> We need to make efforts to stay informed about what’s happening with these viruses and the status of GoF research. We need to tell our friends and families, to use whatever platform we might have, big or small, to promote the end of this research.
We need to get this in the public eye, so the public can demand change. We need to demand change, and not take no for an answer.
> So, what is the call to action here? Stop researching gain of function entirely?
I'd say it's this:
> We need to decide whom to believe: the people with a lot to lose and their not-very-parsimonious or plausible-sounding explanations, which receive almost all the media attention; or the people with expertise and parsimonious explanations who don’t have a dog in this fight.
In defense of a natural origin of Omicron, this study describes the remarkable evolution of SARS-CoV-2 during convalescent plasma treatment of an immunosuppressed patient for 3-4 months; the mutations also reduced sensitivity to neutralizing antibodies: https://www.nature.com/articles/s41586-021-03291-y
We know that there is a large immunocompromised population in Africa and that Covid-19 is rampant there. We also know that most hospitals, regardless of country, don't have the resources to track the evolution of SARS-CoV-2 in their immunocompromised patients. So it's not unexpected that a variant like Omicron could have evolved over an entire year in an immunocompromised individual before finally infecting others.
If there is any evidence that a lab in the region was serially passaging SARS-CoV-2 in neutralizing antibodies/patient serum, then I'd say there is something to go on for a potential lab origin. But at the moment, there is not even circumstantial evidence pointing to this happening in Africa. Maybe setting up a secure channel for whistleblowers with evidence of the above would be the most productive approach.
The above is not to say that I don't think there needs to be much more transparency and accountability from scientists working with pathogens. https://twitter.com/Ayjchan/status/1468582694007279616