Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out • Hacker News Board

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#481

Post by nyokodo » Sat, Apr 10, 2021, 5:54 AM UTC

spondyl wrote: post #470

Robotbeat wrote: post #401

Earlier quoted context omitted.

I assign non-negligible probability to each of them. I don't know. But I hate the stupid racism and hate around it. COVID-19 attacked every country. With the exception of, like, New Zealand (but it affected them as well... had to shut down their borders, etc). These viruses are a threat to all humanity. I just want us to fight them better and help everyone. I think it's super important that we both simultaneously hol…

> But I hate the stupid racism and hate around it. COVID-19 attacked every country. With the exception of, like, New Zealand (but it affected them as well... had to shut down their borders, etc). As someone who lives in New Zealand, we were still "attacked" by covid all the same. The only difference arguably is the coordinated response from our government compared to others. Some of that is presumably culture too (we…

There was a lot of luck too. Not being a major travel hub meant the virus hadn’t become widespread. The New Zealand government dragged its feet at first and clamped down just in time to prevent a much worse outbreak. If they had waited a few more days the cases likely would have gone exponentially vertical, possibly made it into more vulnerable populations and the death toll would have then increased considerably. I’m very grateful for the luck!

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#482

Post by fighterpilot » Sat, Apr 10, 2021, 5:57 AM UTC

tripletao wrote: post #478

fighterpilot wrote: post #471

Earlier quoted context omitted.

Anti-Chinese racism is stupid and toxic, yes, but you're missing the point. People here generally aren't blaming China because that's where COVID-19 originated. That would be stupid. No, they're blaming the CCP for covering it up in the early days, which allowed it to spread and become the global pandemic which it became. Big difference. It's not China's fault that COVID originated there (lab leak or otherwise). It i…

The article is about the earliest origins of SARS-CoV-2, whether that arose from the activities of the WIV or naturally. My comment is as well. Once the pandemic emerged, the CCP's response was certainly terrible in many well-known ways (e.g., their attempt to suppress Yan Limeng's initial alarm, and the disappearance of multiple citizen journalists from Wuhan), though it's impossible to know whether a better respons…

Agreed that it's a separate question.

I just don't think the anti-CCP sentiment is unjustified, though.

Whether it was a lab leak is important but a misdirection.

Their cover-up of the true scale of the problem (lab leak or not) made it hard for politicians in other countries to lock down quickly. It helped it spread intentionally to multiple countries and by then it was too late.

If they were blasting their sirens early in 2021 instead of covering it up we might have had swifter border closures etc.

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#483

Post by jeduehr » Sat, Apr 10, 2021, 6:06 AM UTC

COGlory wrote: post #468

jeduehr wrote: post #466

Earlier quoted context omitted.

> If memory serves, that was a single generation. An rdrp produces one error per thousand bases, which comes out to 30 mutations per generation, so we're talking 40 generations away? That hardly seems significant. Hi I made this exact calculation (as have others). You can find it here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did... Here's an excerpt of the important bit: >>>>>>>>>>>> SARS-CoV-2 is mu…

>We can't just focus on random mutation, we have to think about fixation. Because virus populations don't just evolve in one concerted direction. They evolve /outwards/ in a cloud. It's not simply A to B, it's A to B then back to A then over to C then to D, then back to B, then over to A again, then finally settled on C. A random walk. Fixation relies on selection, which is entirely different in a laboratory environm…

>Fixation relies on selection, which is entirely different in a laboratory environment than in a population with immune systems.

This is actually extremely controversial. There's a great deal of evidence that random walks are more important than selection in fixation events. Does selection play a role? Yes! Definitely! But the evidence is mounting and almost at consensus that random chance is actually what dictates most fixation events. It just can't be /deleterious/ but it does not have to be /helpful/ to fix. The evidence shows that most mutations, on median, are neutral or slightly deleterious. But the ones that are beneficial are so beneficial that the average is neutral-to-net-positive. A lot more of it is actually stochastic than you think! A lot of the transmission between hosts, for example, is stochastic and not selective.

See these reviews/studies from Bloom, Audino, etc:

-https://elifesciences.org/articles/35962

-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173453/

-https://www.cell.com/cell-host-microbe/pdf/S1931-3128(18)301...

-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372249/

-https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820....

-https://journals.plos.org/plospathogens/article?id=10.1371/j...

This is why it's less easy to maintain a virus at the proper S/NS ratio in the lab. It becomes too stochastic. too little selection. So your mad scientist would have to have extremely few viral genera.

You say every gene evolves more slowly than non-coding, which is true. but synonymous mutations happen at the same rate as one would expect it to occur in both.

Are you trying to say it isn't ever going to happen? From what I'm reading, there's actually no reason to believe the CGG in that site is fixed in any way. It's not always CGG. In fact, it rarely is in CoV-2 isolates. Maybe that was a fluke of the sequencer or the isolate?

Wow, now I'm starting to think Yuri just didn't do his homework.

This paper seems to suggest it uses codons extremely similarly to its neighbors, and that it doesn't use CGG often or at all. It says never: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173453/

but that's just in the isolates they're analyzing.

"All human coronaviruses analyzed in this study did not use two synonymous codons (CGC, CGG) for arginine as well as CCG for proline and UGA for stop codon at all"

The money shot is in figure B. I think Yuri in his write up is just using a random one-off sequence of SARS-2 that showed up /later/ in the pandemic. It isn't in the earliest released sequences from Korea or Wuhan or Iran (https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2) (https://www.ncbi.nlm.nih.gov/nuccore/MT126746.1) (https://www.ncbi.nlm.nih.gov/nuccore/MT121215.1). It only shows up in later sequences. It could be a result of adaptation to humans for the weird non-human cleavage site.

I couldn't find CGG in the cleavage site sequence anywhere in the early pandemic. Not in any of the earliest papers.

I could only find it in clinical sequences from later on in the pandemic, suggesting it may have been a random mutant that fixed /after/ the emergence into humans. Which pokes a big ol hole in the idea that it represents a smoking gun of genetic manipulation:

-https://www.ncbi.nlm.nih.gov/nuccore/MW269555.1 -https://www.ncbi.nlm.nih.gov/nuccore/MW672572.1

I shouldn't have taken it as a given that CGGCGG was actually there in the beginning. Looks like it wasn't It certainly isn't in the refseq.

And the thing I'm asking here is: Are you really saying you think the lab leak is /as probable/ as the zoonotic crossover? Given that the A) the CGGCGG wasn't even there when the crossover happened, B) the probabilistic arguments I've made above, and C) the fact that you can't provide any actual evidence of a mechanism? I gave you lots of mechanisms and examples of how it would happen in nature. Why is one not more likely than the other?

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#484

Post by nyokodo » Sat, Apr 10, 2021, 6:07 AM UTC

Robotbeat wrote: post #401

Bukhmanizer wrote: post #151

Earlier quoted context omitted.

My personal feelings are that all 3 are possible, but approximately 0.0001% of people will actually consider the likelihood of each one, but rather, most will choose whichever one is most convenient and comfortable to believe in. Of course as an Asian person, whatever people believe in will have a direct impact on me. I remember after 9/11, the amount of awful things that were said and done to the Sikh population in…

I assign non-negligible probability to each of them. I don't know. But I hate the stupid racism and hate around it. COVID-19 attacked every country. With the exception of, like, New Zealand (but it affected them as well... had to shut down their borders, etc). These viruses are a threat to all humanity. I just want us to fight them better and help everyone. I think it's super important that we both simultaneously hol…

> But I hate the stupid racism and hate around it.

What is most astonishingly stupid about this particular racism is that while the CCP doesn’t come off looking great in significant ways, Taiwan comes away looking spectacular! Japan, Korea and Vietnam also have a lot to be commended for major aspects of their responses! Asians in the United States have on average done an excellent job of staying safe and therefore keeping our communities safer! The rest of us should be studying their policies and behaviors with a mind to adapt and emulate not having racist delusions.

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#485

Post by fighterpilot » Sat, Apr 10, 2021, 6:12 AM UTC

endisneigh wrote: post #139

disambiguation wrote: post #102

Earlier quoted context omitted.

> It's impossible to conclusively prove no it's not. it might be impossible to prove the negative, but if it did come from the lab there should be physical records and first hand witnesses. > so what so maybe we make it a point to have the lab shut down so this doesn't happen again? maybe we publicly acknowledge there are secret teams working on secret science and viruses that can kill people en masse? but you have a…

You have a misunderstanding of reality. The USA has done the exact same research before, and we have (also) had accidents around pathogens being mishandled, and we have had a consequent ban. However we ended up unbanning it and we still do it now. If the goal is to simply stop this type of research in its entirety, there's still no point of trying to get China to stop as we have no authority in China (or any other co…

Maybe we'll end up banning it again and stopping international funding of it?

It's pretty absurd to say that it makes no difference whether or not the virus was a lab leak or not. The answer to that question changes the posterior risk estimates of such research and therefore our international funding and domestic regulatory priorities.

There's also such a thing as soft, diplomatic nudges. Not everything is "force X to do Y when they want not-Y".

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#486

Post by philliphaydon » Sat, Apr 10, 2021, 6:21 AM UTC

jeduehr wrote: post #381

philliphaydon wrote: post #367

Earlier quoted context omitted.

Is everyone forgetting china tried to sweep that under the rug initially?

Source? As far as I know, the government may have tried, but the scientists themselves were not down with it. This sort of culture of the openness of science is why the Chinese government distrusts scientists inherently. And also why Shi Zhengli has maintained an extremely consistent story with the pandemic despite the government's changing its story like 3 times. Also why they've since silenced her. They don't trust…

It's common knowledge that the CCP tried to cover up the SARS outbreak initially, and then later changed course. Just like they tried to fly under the radar with covid-19, the WHO changed the timeline last year admitting China never informed them. Then China tried to silence anyone who spoke out about it. It makes you wonder what would have happened if Taiwan never requested information from the WHO, effectively informing the WHO to begin with.

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#487

Post by tripletao » Sat, Apr 10, 2021, 6:23 AM UTC

fighterpilot wrote: post #482

tripletao wrote: post #478

Earlier quoted context omitted.

The article is about the earliest origins of SARS-CoV-2, whether that arose from the activities of the WIV or naturally. My comment is as well. Once the pandemic emerged, the CCP's response was certainly terrible in many well-known ways (e.g., their attempt to suppress Yan Limeng's initial alarm, and the disappearance of multiple citizen journalists from Wuhan), though it's impossible to know whether a better respons…

Agreed that it's a separate question. I just don't think the anti-CCP sentiment is unjustified, though. Whether it was a lab leak is important but a misdirection. Their cover-up of the true scale of the problem (lab leak or not) made it hard for politicians in other countries to lock down quickly. It helped it spread intentionally to multiple countries and by then it was too late. If they were blasting their sirens e…

I don't think we disagree? There's plenty of reason to dislike the CCP, in relation to their handling of SARS-CoV-2 and otherwise. I just don't think SARS-CoV-2 originating in a WIV lab accident would add to that.

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#488

Post by arcticbull » Sat, Apr 10, 2021, 6:27 AM UTC

refenestrator wrote: post #465

arcticbull wrote: post #423

Earlier quoted context omitted.

And SARS escaped from a lab twice. In China. The government at the time admitted it. So I’m not 100% that’s the example I’d go with haha. It’s important to split this in two: one thesis is that it was invented or created or synthesized at a lab in China. This I’m far less bullish on. The other separate thesis is regardless of origin, man made or wild, it accidentally or intentionally found its way through the doors o…

The point is it didn't start in a lab. Look, if the point here is blame, have at it. It started in China, blame China, feel great about that and don't worry about our government's performance or theirs. But if the point is truth, it probably came from agriculture->society. Labs are not necessary for that story, and China was blindsided anyways.

Define "start in a lab" -- are you talking about "created in a lab" or "accidentally released from a lab in which it was being studied causing a pandemic"?

If the latter, I don't think you have any evidence to say the pandemic didn't begin as a result of an accidental release from a lab in the literal epicenter of the pandemic. It's not possible to prove a negative in general, although in this case, it would have been pretty easy to prove by allowing international inspectors into the facility and turning over records.

Of course labs are not necessary. However, there's a precedent for labs causing outbreaks.

Were it indeed a totally spontaneous wild situation that occurred, why would I blame China? Diseases start all over the place, there's no fault for that. Any more than I blame the Congo for Ebola (named after the Ebola River) or America for Lyme disease (named after Old Lyme, CT). Even if it was an accidental release from a lab, I don't think China as an entity bears responsibility for that.

If it was an accidental release from a lab (an if), then they bear the responsibility for the coverup that led to insufficient efforts towards containment.

America has done a dreadful job to be sure, but that's more whataboutism.

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#489

Post by jeduehr » Sat, Apr 10, 2021, 6:50 AM UTC

tripletao wrote: post #459

jeduehr wrote: post #456

Earlier quoted context omitted.

Hi, I address this idea in this comment over here: https://news.ycombinator.com/item?id=26758597

Thanks. That comment doesn't address the database, though. Do you believe their stated reason for taking it down? If not, why do you think they're lying?

Hi, I have no way to verify if that is the true reason, but also no reason to doubt it.

I will say DDOS attacks on scientific databases are not that uncommon. This is the same reason that a lot of scientific publication data are now hosted by the publisher and not the scientist.

It's rarely actually a malicious "hacker," though. Usually it's some grad student somewhere pulling a really crappily made wget script out and accidentally using all the bandwidth.

Scientists aren't actually that great of programmers, yours truly included. Have I done this before with an independently hosted database? I can neither confirm not deny. Lol.

But seriously I have no idea. I get why you find this suspicious, but to me it is extremely circumstantial and I can think of a lot of mundane reasons for it.

For one, I don't know that the translation of DDOS and hacker or idiot script kiddie is nuanced enough between Mandarin and English.

Re: Scientists who say the lab-leak hypothesis for SARS-CoV-2 shouldn't be ruled out

#490

Post by jeduehr » Sat, Apr 10, 2021, 6:52 AM UTC

Banyonite wrote: post #244

jeduehr wrote: post #209

Earlier quoted context omitted.

Actually a lot of virologists are also critical of GOF. Just look at public health people, epidemiologists. Folks like Andrea Sant, Michael Osterholm, David Topham, etc. These folks criticize GOF all the time, and are a big part of the group that helps write regulations to make Virology research safe. But you know what these same virologists also don't believe? That SARS-COV-2 was cooked up in a lab. That should tell…

> That's why when consensus exists about something, you should respect it. There is quite a large consensus about this one. Respecting a consensus is reasonable. That having been said, I would be interested to hear what the virologists to whom you refer think about Ralph Baric's work. Ralph Baric is a very well-known virologist specializing in corona virology. His group synthesized quite a few SARS-CoV variants, a nu…

Wow I also describe elsewhere how his understanding of the CGGCGG codon usage is truly flawed. It looks like these codons weren't actually there in the earliest sequences of the pandemic, but evolved over time as the virus adapted to us as a host. Really not the smoking gun he thinks it is. If you wanna see what I mean, just search this page for "CGGCGG"