[barnacled]

There is now evidence firmly against lab leak and firmly in favour of natural origins, covered in depth by a domain expert here - https://twitter.com/angie_rasmussen/status/15519378265808240...

I feel like this isn't publicised enough. The lab leakers are louder and people definitely seem to want it to be true more than natural origins and they are not being honest in their attempts to dismiss these papers.

[null_object]

> There is now evidence firmly against lab leak and firmly in favour of natural origins, covered in depth by a domain expert here...

A counter:

https://ayjchan.medium.com/evidence-for-a-natural-origin-of-...

As for Angie Rasmussen - she is hardly the dispassionate scientist that you seem to want to portray her as, in your post[0]

[0] https://disinformationchronicle.substack.com/p/a-toxic-milie...

[barnacled]

The 'counter' is incredibly weak sauce and she's been rebutted several times. Again, as I said, if you just ignore rebuttals you can keep acting like you have a point.

The second post is a scurrilous and nasty smear job from a thoroughly unpleasant individual and I'm quite appalled you posted it. Shameful.

[kgarten]

Did you read the thread? The counter just takes the first paper she cites into account ... Not the second: https://www.science.org/doi/10.1126/science.abp8337

Both of them are interesting reads. I find a natural cause now more plausible after reading them.

Yet, of course nobody knows and we might not for a long time (or never).

[tripletao]

The "two lineages" argument has been grossly oversold. They're just two SNPs apart, making it near-impossible to distinguish whether they evolved in animals (implying two introductions into humans) or in humans (after one introduction). If they were more different, then we could exclude evolution in humans, since it's unlikely the virus could spread for that long without causing enough sickness and death for someone to have noticed earlier. With just two SNPs, that's much harder--SARS-CoV-2 picks up something around 1/3 of an SNP per transmission, so it's not even that unlikely that the lineages formed in a single human-to-human transmission (p ~ 1/9). It's also possible that an intermediate lineage existed but went extinct before it could be sampled, as most lineages do.

Pekar et al. do some complicated phylogenetic modeling that purports to show the MRCA in humans is too recent for a single introduction. That result is unintuitive, and I believe their model is highly suspect, per my comments and links at

https://news.ycombinator.com/item?id=32740568

I agree that "of course nobody knows", and so do Ebright and Chan; they are careful to assert only that further investigation is required, if necessary by subpoena (e.g. for any sequencing data potentially containing early genomes of SARS-CoV-2, whether as the deliberate target or from contamination like those Antarctic soil samples).

The author of the thread that you're praising does not though; she considers the question closed, and has viciously attacked those calling for such investigation, including Chan, whom she called "an intellectually dishonest, manipulative conspiracist". (Ebright gets rather unpleasant himself, so perhaps one could excuse her behavior to him as tit for tat; but Chan does not.) I find both those attacks and the overselling of Pekar's result to be deeply unfortunate. Don't you?

[kgarten]

agree with some of your statement, not with your sentiment. I find your comment slightly off topic. I asked the original commenter if they read the thread, because they answered with a link to a horribly weak rebuttal of the first paper and a even worse personal attack on the author of the tweets. so I should care if she attacks somebody "viciously" yet not if she is attacked in an even worse manner? Interesting.

[tripletao]

In your comment, you linked to Pekar's paper. You said that after reading it, you found a natural cause more plausible. I've also read that paper, and I'm much less convinced. That's what I wanted to discuss, and I don't see how it's off-topic. If anything I wrote came across as a defense of Ebright's tone or any aspect of that Thacker piece, then I expressed myself unclearly; for the avoidance of doubt, I think they're bad too.

Have you looked at Pekar's full model, as set out mostly in the supplementary materials? This isn't any standard molecular clock approach. It's a byzantine stack of plausible but somewhat arbitrary assumptions, ending in a simulated phylogenetic tree. The shape of that tree with one introduction doesn't match the shape of the actual tree constructed from the earliest real samples in Wuhan, so Pekar concludes there were two introductions. But I'm not aware that such an approach has ever made a successful prediction, and there's no circumstance in any field where I can imagine trusting a model of such complexity without validation. Their sensitivity analysis is meaningless, varying some irrelevant parameters but keeping what seems intuitively like the main determinant of that shape (the connectivity of their contact network) fixed.

You are correct that Alina Chan's thread doesn't address that aspect of Pekar's argument. Others have though, per the Twitter threads I linked. What do you think?

[chrisan]

Hope this gets more upvotes. Kind of dismaying the number of people relying on tweets with no source(s).

Haven't we learned enough over these years of misinformation and "fake news"?

TLDR the tweet string from the actual Dr of Virology: evidence so far points to natural but more info is needed

[barnacled]

Ah I expected to get downvoted into oblivion, I know it's a cliche to say it but HN isn't what it once was.

A key point to take away is that the fact there are 2 lineages means that lab leak is super unlikely. It would require somebody from the lab to come to the same relatively small market to give lineage A, then somebody else who got infected through a totally different evolutionary route at the lab to happen to come to the market just after and both to not spread it anywhere else.

Of course lab leakers are working hard to try to deny this or claim the data is wrong or yada yada. It's an ongoing battle and they have several highly dedicated 'independent scientists' (lol) working on it seemingly 24/7.

It's quite dispiriting to see.

[null_object]

> Of course lab leakers are working hard to try to deny this or claim the data is wrong or yada yada. It's an ongoing battle and they have several highly dedicated 'independent scientists' (lol) working on it seemingly 24/7.

I think the downvotes are because of this type of statement, which suggests that people who have read the papers, and thought about the conflicting evidence, and finally come to a conclusion that differs from your viewpoint, dislike the implication that they are simply nutty conspiracy-theorists tirelessly and obsessively working to undermine rational science.

[barnacled]

You do realise there are countless people who have 'read the papers and thought about the conflicting evidence' about climate change right?

The reality is unfortunately that these people ARE nutty conspiracy theorists. They are not 'thinking about the papers' and providing a reasonable push back, they're reiterating long debunked points (did you read the thread I posted?).

Ebright already claimed the papers were scientific fraud until he thought better and deleted the tweet. This is the kind of person you're dealing with.

I'm not going to both-sides something which now has very clear evidence in one direction and not a shred of evidence in the other, I'm sorry I'm just not.

Hacker news of old would be more open to that. Again,this is why I no longer post here.

[tripletao]

The two lineages are literally just two SNPs apart. SARS-CoV-2 averages ~1/3 of an SNP per human-to-human transition, so ~1/9 of such transmissions generate "two lineages" at least that different. So intuitively, it seems easy to believe those lineages could have evolved in just a few weeks of early cryptic (unsampled) human spread.

Pekar et al. did some complicated modeling that purports to establish that the MRCA in humans is so recent that the two lineages must have arisen in animals, implying two introductions into humans. I believe that's highly suspect though, per my explanation and links at

https://news.ycombinator.com/item?id=32740568

[ripper1138]

They aren’t mutually exclusive though right? We can say the initial outbreak was from the wet market. Does that mean the virus itself is of 100% natural origin?

[kgarten]

why is this downvoted? this is an excellent thread with links to a paper that seems to show strong evidence against the lab leak ...

[peyton]

> there is insufficient evidence to define upstream events, and exact circumstances remain obscure

From the paper.

[kgarten]

I was talking about the second paper she mentions in the twitter thread:

https://www.science.org/doi/10.1126/science.abp8337

[_86sk]

What I saw is that it started in SW Indonesia, in a jungle near the coast, in 2008. That was its first appearance:

  covid-19 origin's

i see this coronavirus first originated in South West India

And first jumped to human in coastal Bengkulu/West Sumatra in Indonesia

I'll try to get time on these events

end of 2008: origination in SW india near Mangalore

1Q2013: first jumps to humans in BGK/WSU indonesia after an animal outbreak on the coast in late 2012

first substantial human outbreak: Mid 2013 slightly inland from outbreak location.

but of course there's no political capital to be made by blaming these poor places ....

feel kind of sad to consider how much of the crazy blame game is actually driven by knowledge, desire for truth and competence, and how much of it is just driven by political competition....i guess the motivation doesn't matter...the result matters. the output is not about truth it's about politics and narrative ... so sad....