Live data from Hacker News

Lab Leak 2.0?

bprice.substack.com

301–310 of 319 posts

Re: Lab Leak 2.0?

#301
post #165

Earlier quoted context omitted.

Yes, this is true. But it's also somewhat narrow. 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 ear…

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.

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.

This is the first link in a search for same:

https://www.cbsnews.com/news/omicron-variant-covid-in-europe...

Either way, it may be wrong to assume SA is point of origin, so any follow-on assumptions may be comparably flawed.

Re: Lab Leak 2.0?

#302
post #294
post #242

Earlier quoted context omitted.

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 co…

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.

That's not the way it works.

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.

Re: Lab Leak 2.0?

#303

Earlier quoted context omitted.

"... very well documented event"

Not sure what you mean by quoting that but there's not much controversy that Delta leaked from a Biosafety Level-3 facility in Taipei. https://fortune.com/2021/12/10/taiwan-investigates-covid-lab... https://www.taiwannews.com.tw/en/news/4371080 https://www.newsweek.com/taiwan-lab-worker-mouse-bite-covid-...

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.

Re: Lab Leak 2.0?

#304
post #278

Earlier quoted context omitted.

"it stands to reason" 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.

Re: Lab Leak 2.0?

#305
post #37

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…

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 infectio…

"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.

Re: Lab Leak 2.0?

#306
post #86
post #37

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…

Can you also comment on her claim that Delta was a lab leak?

S/he clarified it now.

"[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.]"

Re: Lab Leak 2.0?

#307
post #79

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: > https://www.taiwannews.com.tw/en/news/4371212 > https://www.taiwannews.com.tw/en/news/4382708 Neither of these have nearly enough evidence…

S/he clarified the delta thing:

"[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.]"

Re: Lab Leak 2.0?

#308
post #291
post #188

Earlier quoted context omitted.

"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 therefo…

FWIW, I read it incorrectly the first time too and had to do a double-take. I do think it's not written in the clearest manner.

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.]"

Re: Lab Leak 2.0?

#309

Earlier quoted context omitted.

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?

Thanks.

Re: Lab Leak 2.0?

#310

Earlier quoted context omitted.

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.

The S:NS ratio cited in the blog post also appears to be simply incorrect: https://twitter.com/eigenrobot/status/1471336024827568130?s=...

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.

Post reply on HN