zlacker

>>todd8+(OP)
The evidence is circumstantial, but there has yet to be any evidence ruling it out. To be clear, the lab leak hypothesis is always possible. Things can always leak out of labs, let's not kid ourselves.

Some things (going by memory here) that seem to support the hypothesis:

1) Major point of differentiation for this virus is that compared to it's closest known relatives, it has acquired a furin site (eukaryotic protein cleavage site) that enhances its virulence.

2) That furin site RNA contains a non-canonical amino acid codon

3) That non-canonical codon contains a restriction site that could easily be used to track, whether, say, your added furin site is surviving multiple cell passages, by performing a restriction digest and running the fragments on a cell.

Like I said above, it's circumstantial, but this is all very normal. Both adding the furin site (how does coronavirus evolve into something more virulent?) and tracking it that way. Then all it takes is someone to get infected (EVERYONE working in biology has broken at least one lab safety rule in their life, even in BSL4) and either not be symptomatic and realize, or not say anything.

>>COGlor+lE
Furin cleavage sites very similar if not largely identical to this one have also been found in nature, and have been generated in nature in very short spans of time (on the order of a few decades, which is what is suspected to have happened with SARS-CoV-2).

I describe the evidence in detail in this detailed longform post I wrote on reddit a few months back: Hi, I have a PhD in virology focused on emerging viruses, and a few months back I wrote a very lengthy and involved piece full of sources.

And in there, I describe exactly how wrong your point 1 is. And how misguided your point 3 is.

The post also won a "best of r/science 2020" award!

You can find it here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...

See under "Addendum to Q2"

>>jedueh+u41
I read through your post and it was incomplete and hand wavy, although that makes sense because it was written for Reddit. The bias was also obvious, and remarkably unscientific in how you approached the "problems" in a deterministic manner. You cherry picked examples (for instance, saying we can detect Cas9 mutations) that make no conclusive point (for example, there are a variety of ways to add a furin site to a genome that don't involve Cas9) but are indistinguishable as proof by the Reddit audience. The bottom line is, though, you are cherry picking arguments that lay people are more or less too unaware of their cherry picked status to argue with.

As a virologist, who "engineers viruses", I also take some offense to this line: >The virus itself, to the eye of any virologist, is clearly not engineered.

I also suspect that the viruses referenced in the featured article would object to that line as well.

>>COGlor+Yf1
That's interesting, because of the scientists featured in the above article... None of them are virologists.

Petrovsky, for instance, if you look at his google scholar, hasn't published a paper in a virology journal in the 10 years that I looked. He's published in some predatory journals, ones I wouldn't be caught dead publishing in.

He's also gotten /close/, I guess, by publishing about tuberculosis. But it really is different and the man clearly has never done any viral biosafety work or worked or supervised work in any secure facilities working with viruses.

If he did, I think he might be more cautious about being so cavalier with the probabilities here.

David Relman studies the gut microbiome.

I have no reason to believe you're a virologist with any training other than your word, but that isn't actually all that important to my argument.

Using viruses in your research doesn't make you a virologist any more than using pens in an art school thesis makes you an expert in ballpoint pens.

All of that aside, the consensus among people who actually use or study dangerous viruses in biosafety labs (both those for and against gain of function research, btw) is that the virus likely came from a wild zoonotic crossover event.

Not a malicious lab leak.

>>jedueh+Xy1
I'm going to start off by pointing out that again, almost your entire argument is an appeal to authority, which is not a scientific argument. Oh and add gatekeeping to the list as well, in support of your appeal to authority.

As an aside to anyone that isn't a professional scientist reading this thread: I'd just like to issue a caution that any time some supposed "expert" is telling you that you should listen to them because of their credentials, and not the merit of their argument, you should promptly ignore them. Extra points if they tell you that the argument is too complex for you to understand. If they can't explain it to a highschooler, they don't understand it either.

>I have no reason to believe you're a virologist with any training other than your word, but that isn't actually all that important to my argument.

Actually, that's pretty much your entire argument. I'd rather not tie my HN identity to my real identity, as it's not unique to HN but all of my online life. All of my published work, with the exception of a single 1st author and a single 2nd author paper about CRISPR/Cas, is about viruses.

Here are some micrographs of viruses I work with that I took, today:

https://imgur.com/a/uDG51cN

Feel free to reverse image search them or whatever. Edit: removed reference to specific lab for sake of anonymity.

>All of that aside, the consensus among people who actually use or study dangerous viruses in biosafety labs (both those for and against gain of function research, btw)

Ah so now the goalposts have moved from "any virologist" to "people that use or study dangerous viruses in biosafety labs". Interesting.

>is that the virus likely came from a wild zoonotic crossover event.

I don't, and have never disputed that. You seem to think that the 3 points I laid out were some sort of thesis about the origins of the virus. They weren't and aren't. Just some interesting data that can be used to form a coherent hypothesis about the origins of the virus.

Similarly, none of the points in your "Reddit post of the year!" even remotely refute them. They cherry pick data.

Present an actual argument (here) and I'll engage on it based on the merits of the argument, not either of our credentials.

>>COGlor+4U1
....I presented a lot of extremely detailed arguments backed up by references in my original post and you just dismissed them by saying they "cherry pick" data.

How is that true about anything I said regarding S/NS ratios, molecular clock analysis, the mosaic nature of the virus, the presence of O-linked glycans, the promiscuity and non-species specific nature of the spike protein, etc.

You conducted the mother of all handwaves and then asked me to present "actual" arguments. What? You never even approached the detail of any arguments I have made thus far.

I'm not going to make new ones until you provide some actual factual responses to the ones I've already made, thanks.

In case you don't want to find the link, here it is again: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...