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What happened to the lab-leak hypothesis?

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Re: What happened to the lab-leak hypothesis?

#381

Post by dekhn »

mikeyouse wrote: post #356
dekhn wrote: post #351

Earlier quoted context omitted.

Can you give me a link to a good example of that (ideally, non-covid)? my understanding is that it's only good for relative rates over evolutionary time so I'd like to see a counterexample.

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 and constant population size with a HKY substitution model and four Gamma categories7. An MCMC model was run with 50,000,000 generations and a burn-in of 25,000 sampled trees. All other parameters were by default. BEAST executions were completed checking chain convergence and sufficient sampling of the posterior space (ESS > 200) with Tracer v1.7.1. The final chronogram was generated using TreeAnnotator v1.10.433.

I'd call these "time-scaled trees", not molecular clocks.

Re: What happened to the lab-leak hypothesis?

#382

Post by dekhn »

voakbasda wrote: post #370
dekhn wrote: post #109

Earlier quoted context omitted.

Let us know when you have an "unambiguous truth detector" so we can start to revoke credentials. In the meantime, let's understand that scientists frequently allow their personal biases to leak into their papers.

I’m not talking about absolute truth. I am pointing my finger at those “scientists” that falsify or cherry-pick data sets, do not publish results that contradict their organization’s agenda, and similarly commit flagrant acts of dishonesty.

Ah, well, the best you can do is read RetractionWatch and see that a subset of those scientists have been identified, and fired.

Re: What happened to the lab-leak hypothesis?

#384

Post by gojomo »

mikeyouse wrote: post #346
gojomo wrote: post #329

Earlier quoted context omitted.

The prior linked post is a gish-gallop of overconfident motivated reasoning. "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. Worobey et al's analysis is at the mercy of Chinese data sources, and even if all early cases were exclusively in the market, and even the live-animal section, that doesn't disprove lab origi…

> "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 before – and yes, the motivation was because that was considered a potential natural risk. But that doesn't mean it was a natural inevitability. Isn't the proximity of the proposal, "add FCS to a bat coronavirus to see how much worse it makes it", to the appearance of SARS-CoV2 at least a little suspicious?

They & others have published lots of work that specifically made existing viruses more transmissable, or more severe – often in labs with a history of leaks. This can be done via evolutionary pressures – serial passage forced-evolution – or via explicit engineering of new chimeric viruses.

Coronavirus crossover was theorized to be a major risk, after SARS/MERS. That didn't mean that actually outracing nature to make the hypothesized worse viruses in accelerated lab processes was a good risk-reducing idea!

Re: What happened to the lab-leak hypothesis?

#385

Post by dekhn »

throwawaymaths wrote: post #210
dekhn wrote: post #185

Earlier quoted context omitted.

Do what math now? I spent 10 years as an academic doing bioinformatics, with deep expertise in BLAST (I helped demonstrate that BLAST E-values accurately represent homology). If you look, he shows some pages with resuults where the E-value is 282. Normally, an evalue should be 1e-2 or better (ideally 1e-6) before you start making ANY claims. I've seen hundreds of examples where a person did the math, convinced everyb…

But this is not a homology exercise with natural selection. I can show you where I did a blast search, panned for "select amino acid substitutions of interest" and from the library out popped out a more efficient enzyme.

Sure, show us.

Re: What happened to the lab-leak hypothesis?

#386

Post by booleandilemma »

VoodooJuJu wrote: post #372

The lab-leak hypothesis has been suppressed because it is a politically unauthorized thought. If the hypothesis is investigated and proven true, powerful people stand to face justice, which is of course unacceptable to these very people, and so the idea has been banned by way of media silence and by way of association with other unauthorized politics, i.e. with those who are right of center.

Not to mention you’d see a rise in anti-Asian hate crime as disturbed people take out their frustrations.

Re: What happened to the lab-leak hypothesis?

#388

Post by trhway »

dang wrote: post #359
trhway wrote: post #344

Earlier quoted context omitted.

Quoted post unavailable.

Could you please make your substantive points without name-calling and swipes? It's against the site guidelines. It's also not in your interest, since it weakens your case. https://news.ycombinator.com/newsguidelines.html

thank you, i appreciate it, overwatching Big Brother :) Sometimes one just gets carried away.

Re: What happened to the lab-leak hypothesis?

#389

Post by mikeyouse »

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…

> 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 refuse to say.

Again, this isn't true. Plenty of them have explained it. Just not up to the standards of the conspiracy theorists. This goes beyond the "lab leak vs. natural origin" debate and is now, what, including American scientists in covering up the lab leak to aid the Chinese?

Spell out specifically what you are implying here.

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