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What happened to the lab-leak hypothesis?

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Re: What happened to the lab-leak hypothesis?

#391

Post by peteradio »

bayesian_horse wrote: post #340
uoaei wrote: post #313

Earlier quoted context omitted.

> "pandemicable" zoonotic virus (a VERY rare thing) has to somehow make it into a lab undetected. This is the opposite of what I understood the lab-leak theory to be: that an initially-zoonotic virus was identified and bred in a lab until someone working at that lab with lax security standards accidentally brought it out of the quarantine. This is plausible at face value. I think a lot of the really extreme vitriolic…

There's a spectrum... The zoonotic virus would need to have some rare "talent" to start with. Then there is the ominous "breeding" part, which many people describe as reckless or evil. In any case this isn't done in Humans but rather some kind of humanized model (and it's not clear that could work at all). Which is why it is quite a coincidence or accident that this process would end with a virus so well adapted to H…

> Gain-of-function research is medical research that genetically alters an organism in a way that may enhance the biological functions of gene products. This may include an altered pathogenesis, transmissibility, or host range.

Isn't the goal to end up with an infectious agent? I don't understand why it seems so implausible that they would succeed? Why would someone give a lab money for a truly impossible task?

Re: What happened to the lab-leak hypothesis?

#392

Post by lamontcg »

ChemSpider wrote: post #354
mikeyouse wrote: post #247

Earlier quoted context omitted.

You do realize that in opposition to my point about it being weird insinuation, you posted a bunch of weird insinuation promoted by some of the dimmest people in congress? There was a legitimate debate in 2020 about the origin of the virus, which the emails "released" by the House adequately demonstrate. Now nearly all of the people in those emails have updated their priors to favor zoonosis, which is given as eviden…

> all of the people in those emails have updated their priors to favor zoonosis, According the to released FOIA'ed emails, these scientists changed their mind within 1-2 days from "wow, could really be a lab leak" to "lab leak is a conspiracy theory" - why that? None of them can explain what made them change their mind on this short time frame in spring 2020. Was there new knowledge? A break thru experiment? They ref…

A lot of them thought that no sarbecoviruses had a furin cleavage site and when they were first exposed to the issue by the headlines they assigned an overly high estimate to the FCS as being evidence of human tampering.

Then other experts pointed out that isn't uncommon at all, and they all adjusted their thinking.

"Woah, that's a million to one odds, that can't be by chance!"

"No, it's actually really common, here's a pile of similar viruses with an FCS."

"Oh, nevermind."

Experts can leap to conclusions and run their mouths off just like everyone else, doesn't take some radical world-wide conspiracy that "got" to them (other than the radical conspiracy theory of "well-informed truthful information").

Re: What happened to the lab-leak hypothesis?

#393

Post by SiempreViernes »

gojomo wrote: post #384
mikeyouse wrote: post #346

Earlier quoted context omitted.

> "Two lineages" in rapid-succession is weird - but no better explained by two zoonoses (that left no hints in any animal population) than two lab-leaks. I mean, everyone can stop reading here... This is patently false. Multiple Spillover is a readily reproducible phenomenon that perfectly explains the dual lineages. Again, spell out specifically the route how two distinct lineages would be present at the market unde…

A lab worker who was careless (if not depressed/malicious) could just as easily carry out two variants as one. One animal shedded... two variants of virus? How did the animal get it, when no other nearby wild or market animals in the (lackluster) investigation around Wuhan, or since elsewhere, have shown candidate SARS-CoV2/precursor viruses? They proposed adding the FCS to existing viruses where FCS hadn't been seen…

> One animal shedded... two variants of virus

Maybe, but more likely two different ones out of the many millions of poorly documented animals in the East Asia animal trade. Certainly more plausible than a single lab engineering two very distinct linages for no good reason.

> That didn't mean that actually outracing nature to make the hypothesized worse viruses in accelerated lab processes was a good risk-reducing idea!

Presumably you can link to the papers published about how they did just such work, or evidence it in some other authoritative way since you make the assertion so boldly?

Re: What happened to the lab-leak hypothesis?

#394

Post by mikeyouse »

dekhn wrote: post #381
mikeyouse wrote: post #356

Earlier quoted context omitted.

It's a completely common technique - the same way we're tracing the current Monkeypox outbreak. https://www.ecdc.europa.eu/en/news-events/epidemiological-up... And is useful from an anthropological perspective on older outbreaks, also for Monkeypox; https://www.nature.com/articles/s41598-021-92315-8 The rate of mutations, especially for a virus as transmissible as Covid is a very strong signal.

Thanks- personally, based on my experience in functional genomics, they have far too many assumptions to be trusted as "clocks", even relative ones. Here's the second paper's methods: a molecular clock signal was estimated on the ML tree using TempEst v1.532. BEAST v1.10.433 was used for Bayesian MCMC analysis to estimate temporal nodes. As recommended in Patrono et al., we selected the simplest model: strict clock a…

Their accuracy is completely subject to stable mutation rate and frequency of sample -- with that second paper, they were working with ~10 samples from 15 years ago vs. thousands of samples with hourly granularity and entirely traceable transmission chains in the early days of Covid. Completely different capabilities arise with Covid-level specificity.

Re: What happened to the lab-leak hypothesis?

#395

Post by lamontcg »

mikeyouse wrote: post #307
gojomo wrote: post #249

Earlier quoted context omitted.

Overfocusing on the market cluster is an error. First, because viruses travel easily – so even if 100% of early cases were around the market, it could have reached the market via a lab worker. And second, early overemphasis on the market cluster caused authorities to search for every case there, and ignore cases elsewhere – just as in the US, authorities missed early community spread because they didn't even consider…

Both of your points are directly and conclusively addressed in the post.. > First, because viruses travel easily – so even if 100% of early cases were around the market, it could have reached the market via a lab worker There were two distinct lineages at the market with a cluster of positive environmental samples in the wild animal section. I would love to hear a plausible theory on how two unrelated lineages came t…

> There were two distinct lineages at the market

No there were two distinct lineages in two separate crossover events, the market was just one of them.

Which is even worse for the lab-leak hypothesis.

Re: What happened to the lab-leak hypothesis?

#396

Post by tim333 »

status200 wrote: post #338

I have tried to get a biologist / someone with more scientific knowledge than me to either help peer review, confirm or debunk this paper by Steven Quay: https://zenodo.org/record/4642956 It seems so scientific and created a buzz when it came out, it has been the most thorough explanation of the lab leak theory, but I never saw a decent discussion that either helped confirm or debunk the ideas within.

I think it's kind of rubbish but 140 pages long and most serious scientist have better things to do than going through all that.

But at a glance he seems to be using bayesian analysis in a not very valid way.

Re: What happened to the lab-leak hypothesis?

#397

Post by Closi »

qbasic_forever wrote: post #280
eric_cc wrote: post #271

Earlier quoted context omitted.

> we cooked them up When you say “we”, who do you mean exactly? How did they cook them? Can you explain why you believe the pandemic is not over?

> When you say “we”, who do you mean exactly? How did they cook them? The entire population of the western world. Every time COVID-19 infects a person and replicates it has the chance to mutate or introduce errors. If those errors in replication increase the fitness of the virus it will evolve to become a more powerful variant (i.e. gain of function). By continuing to allow hundreds of thousands of new cases and infe…

Ah yes, is this the old "let's lock down the planet forever" solution?

Re: What happened to the lab-leak hypothesis?

#398

Post by cameldrv »

mikeyouse wrote: post #350
thereddaikon wrote: post #342

Earlier quoted context omitted.

Scientists aren't going to prove lab leak one way or the other because the evidence isn't going to be in the virus itself. The for or against lies with the lab and the staff working there and the PRC is not going to allow an open and honest investigation to either prove or discount it. So unless it can be proven to have come from somewhere else, you are likely never going to settle whether it was lab leak.

But we've pretty much established that it was a virus of natural origin - all of our molecular techniques leave signs, so an honest discussion would foreclose that possibility. That doesn't eliminate the possibility that it was a natural virus which had been collected and subsequently escaped due to bad lab technique but the former is too attractive a conspiracy theory to let go..

This is not true. Ralph Baric developed (and patented) a seamless technique to assemble coronaviruses in 2002 [1]. Baric was a close collaborator of the Coronavirus group at WIV.

Since then there has been even more progress. Since 2015 or so it's been possible to "print" DNA of any sequence.

In fact as COVID started to spread in China and the sequence was released, a Swiss lab used this technology to print the genome of SARS2, inject it into some yeast cells, and voila, you have the virus. They wrote this up in Nature [2].

If you wanted to change a naturally sampled virus using this technique, say, to insert a Furin site, swap out an RBD, whatever, you can literally do it with a text editor and copy and paste.

[1] https://patents.google.com/patent/US7279327B2/en

[2] https://www.nature.com/articles/s41586-020-2294-9

Re: What happened to the lab-leak hypothesis?

#400

Post by SiempreViernes »

dehrmann wrote: post #256
theptip wrote: post #45

I think the important point is not whether this outbreak was in fact a lab leak, but that it is entirely plausible due to gain-of-function research. Even if this one wasn’t a lab leak, the next one very well could be. The risk/reward profile of that sort of research is insanely unfavorable.

As someone in tech, what bothers me is all the attention AI gets for possible ethical problems, while biologists are doing some pretty scary experiments with potentially large-scale negative consequences, and they've gotten relatively little attention.

Biologists have well developed frameworks for judging the ethics of experiments that has been built up over a century of horrifying missteps.

AI is at the "hire and fire until they get a sycophant" stage in the development of proper ethical review methods.

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