[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?