Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt • Hacker News Board

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#771

Post by lamontcg » Wed, Jan 12, 2022, 8:23 PM UTC

tim333 wrote: post #658

lamontcg wrote: post #309

Earlier quoted context omitted.

It isn't unusual at all. Many coronaviruses including MERS have a furin cleavage site and they're common and likely evolved independently multiple times, showing that this acquisition of an FCS is common: https://www.sciencedirect.com/science/article/pii/S187350612... The FCS in SARS-CoV-2 is NSPRRAR, we now know of sarbecoviruses like like the BANAL viruses in Laos which have NSPAAR, some other viruses like RmYN02 h…

You're answering why furin cleavage sites in general are not unusual. Not why this particular furin cleavage site is unusual from a natural evolutionary view. It's if you line up the related bat coronaviruses sequences they are all much the same in that region apart from Sars-Cov-2 which seems to have a clean insert of a PRRA sequence. Hence the "bothered by the furin site and has a hard time (to) explain that as an…

Here is that kind of thing: https://ibb.co/T1YtShy

That is from:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211627/#mmc1

Specifically the lower bit of figure 2:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211627/figure/...

If RmYN02 picks up the QTQT sequence from recombination with other bat coronaviruses (or RmYN02 is a deletion away from a common progenitor we haven't found yet -- and the QTQT deletion is seen in SARS-CoV-2 variants in humans) then it is one insertion away from PRAAR which would be an active FCS, which is then one substitution away from the PRRAR SARS-CoV-2.

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#772

Post by phh » Wed, Jan 12, 2022, 9:31 PM UTC

hosteur wrote: post #616

phh wrote: post #367

Earlier quoted context omitted.

> I remember vividly president Macron (a person that I respected before that) very serious in TV explaining to all the citizens of the republic that we should not buy nor wear masks. I don't remember this from Macron, but rather from Véran (Health Minister), but I could be wrong. anyway, at the time this was a more than reasonable request. Because the very first persons we had to protect were health professionals, a…

> anyway, at the time this was a more than reasonable request. Because the very first persons we had to protect were health professionals, and we didn't have enough masks for everyone. So that makes it ok for them to lie? I do not agree. And the trust is lost as a result. They should have explained that we should prioritize masks for health care professionals if that was their reasoning.

I don't see the lie. As I said, I don't remember them ever saying that it was safe without mask. They only said it was not useful.

I would actually say that at the time, it was counter-productive for the general public to wear masks, because it prevented protecting health professionals.

I agree there is a bit of conundrum that "not useful" is not exactly in between "counter-productive" and "useful", and here you could argue that the "not useful" in Véran's mouth meant "doesn't protect". I definitely wouldn't blame you for that, and yes I'm being very nice to them for my interpretation.

The reality is that had they said "yes masks are super important, but it's even more important to give them to health professionals", we'd have seen what we saw with hydroxychloroquine (which is that people who actually needed it couldn't get it), but 10 times worse. Could they have twisted their words 7 times more in their mouth before saying it, so that it's not factually a lie? Yes sure.

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#773

Post by largbae » Wed, Jan 12, 2022, 9:39 PM UTC

Maursault wrote: post #726

krisoft wrote: post #349

Earlier quoted context omitted.

Yes. Countries and people are two different thing and the expected and acceptable behaviours are different too. If you write an officially sounding letter to your neighbour demanding to know how they come to choose the paint to repaint their bikeshed you are a weirdo and they are in their right to ignore you. If you write the same letter to a city official about a public bikeshed you are sending a freedom of informat…

You missed GP's point, which apparently was equating personal privacy with China's national security. I didn't think twice about China's lack of transparency. It's normal and expected behavior from China, so I would never suspect it to mean they were hiding something that was actually salient to the global pandemic... they're just hiding everything, but all it amounts to is hiding whatever corruption comes with gover…

So just ignore it?

Wildfires occur naturally in a similar fashion. We still try to diagnose their causes and use that information to punish arson or otherwise come up with better strategies to prevent them.

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#774

Post by baja_blast » Wed, Jan 12, 2022, 9:43 PM UTC

tim333 wrote: post #693

baq wrote: post #247

Earlier quoted context omitted.

If you're approaching this with a western democratic frame of mind, yes. This is not suspicious behavior in China, as the GP said - it is standard operating procedure.

Some of the details are unusual though especially the Wuhan Institute of Virology taking down it's previously public pathogen sequence database before the thing kicked off.

They took it down in mid September of 2019, a previously public database. They still refuse to share the data with anyone, which is weird since the database was public to begin with.

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#775

Post by baja_blast » Wed, Jan 12, 2022, 9:51 PM UTC

jacquesm wrote: post #768

tgv wrote: post #622

Earlier quoted context omitted.

Although they were hesitant at first, the Chinese government handled the SARS-1 outbreak differently.

The similarities vastly outweigh the differences. The biggest difference between SARS-CoV and COVID-19 is that the latter takes a bit longer before you get ill but you are already contagious. Other than that it's mostly the same old story. Note that if not for SARS-CoV this would have been a lot more serious because that served as a dress rehearsal and put a lot of mechanisms in place as well as suggested screening f…

Another major difference between SARS-CoV and SARS-CoV-2 is that SARS-CoV-1 took time to gain new adaptions to effectively spread between humans. These mutations that SARS-CoV-1 went through allowed researchers to find the intermediate animal host within months.

With SARS-CoV-2 there was no known mutation phase where the virus rapidly gained mutations to more efficiently transmit between humans. SARS-COV2 came out the gate perfectly adapted and did not start mutating extensively until many months after it spread globally. These lack of adaptations are also the reason why it's so hard to trace back to the original intermediate host species.

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#776

Post by denton-scratch » Wed, Jan 12, 2022, 10:03 PM UTC

chrishynes wrote: post #570

denton-scratch wrote: post #436

Earlier quoted context omitted.

> your a crazy person to believe there COULD have been a lab leak I'm not really bothered about the true origin of the virus, except inasmuchas scientists lying about their true beliefs is incredibly damaging to public confidence, and energises conspiranoids. Lying about the benefits of mask-wearing was bloody stupid. I no longer pay attention to statistics about infection rates and fatality rates. They are presented…

All of the lying and "nudging" and viewpoint policing is what made the "conspiraloons" so big (great word BTW). It was quite clear by March or April 2020 that a lot of lying was going on (wether "for the greater good" or some more nefarious reason) and also clear that everyone in media, politics, and science that should have been asking questions was instead giving a doe eyed acquiesce that the emperor was in fact we…

> great word BTW

Thanks, but not mine. At one time I used to read Indymedia, an open-posting forum. There were a lot of pretty conspiraloonatic posts, often about 9/11 and "chemtrails". This was the early noughties. The word's been around a long time.

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#777

Post by tim333 » Wed, Jan 12, 2022, 10:05 PM UTC

jacquesm wrote: post #766

tim333 wrote: post #697

Earlier quoted context omitted.

I think you are missing the context. It's not that it proves or disproves the lab leak hypothesis. It's that it shows the scientific authorities were deliberately misleading the public by saying it's a crazy conspiracy theory while in private believing it quite likely. And as to why that matters rather than "It shouldn't have been posted to HN" type suppression - we have millions dead in this outbreak and "At least 5…

> while in private believing it quite likely That's not what they said or believed. That's exactly why I have a problem with this whole exercise, it seems to me to be mostly a game of jump-to-conclusions.

Well "accidental release or natural event? I am 70:30 or 60:40." sounds like Mike Farzan thought it quite likely. And

>Before I left the office for the ball, I aligned nCoV with the 96% bat CoV sequenced at WIV. Except for the RBD the S proteins are essentially identical at the amino acid level – well all but the perfect insertion of 12 nucleotides that adds the furin site. S2 is over its whole length essentially identical. I really can’t think of a plausible natural scenario where you get from the bat virus or one very similar to it to nCoV where you insert exactly 4 amino acids 12 nucleotide that all have to be added at the exact same time to gain this function – that and you don’t change any other amino acid in S2? I just can’t figure out how this gets accomplished in nature. Do the alignment of the spikes at the amino acid level – its stunning. Of course, in the lab it would be easy to generate the perfect 12 base insert that you wanted. Another scenario is that the progenitor of nCoV was a bat virus with the perfect furin cleavage site generated over evolutionary times. In this scenario RaTG13 the WIV virus was generated by a perfect deletion of 12 nucleotides while essentially not changing any other S2 amino acid. Even more implausible IMO.

from Bob Garry sounds like he also thought it quite likely. Source https://republicans-oversight.house.gov/wp-content/uploads/2...

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#778

Post by finite_jest » Wed, Jan 12, 2022, 10:42 PM UTC

JohnTHaller wrote: post #731

jacquesm wrote: post #341

If this comment thread is the way the self proclaimed smartest forum on the web deals with articles like this then we're doomed. This article contributes zero actual evidence, is littered with out of context quotes (including of all places the title), doesn't appear to understand the science or the probabilities involved and finally is clearly written with an agenda. It shouldn't have been posted to HN in the first p…

This is The Telegraph, a conservative UK paper that published such Covid-19 misinformation as the common cold conveying immunity against Covid-19 and the lockdowns were dumb and herd immunity was the way. Being devoid of fact is a feature not a bug. Fluff pieces like this from biased news sources known for spreading misinformation have no place on Hacker News.

I think I found the article you are referring to. [1] I don't think that's a good example of misinformation. Here's a recent report by Reuters on the same topic. [2]

I agree that The Telegraph is not the most reliable source of the news [3], but that doesn't make anything they report on automatically false.

[1]: https://www.telegraph.co.uk/global-health/science-and-diseas...

[2]: https://www.reuters.com/business/healthcare-pharmaceuticals/...

[3]: https://mediabiasfactcheck.com/daily-telegraph/

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#779

Post by bsder » Wed, Jan 12, 2022, 10:53 PM UTC

rhino369 wrote: post #123

bsder wrote: post #94

Earlier quoted context omitted.

Okay. China created it. Now what? I have yet to see anyone explain what they would do with the result that is somehow beneficial. Does knowing this help fight it? Does it help stop it? Does it help treat it? Does it help stop the spread? Let's say China even INTENTIONALLY did it. Then what? You gonna invade China? Exactly how are you gonna make someone like Apple pull out of China when they should already be doing th…

Ban gain of function research because it killed 20 million people? Your logic is like BP saying “hey it doesn’t matter how the oil spill started . . .”

> Ban gain of function research because it killed 20 million people?

And how do you plan on enforcing this on China? Or on Russia?

I'm still waiting for all the armchair geniuses to explain this one to me.

You can be ready for when some idiot does this research or not. Those are your options unless you've got some magic way to go to war with nuclear powers that I am unaware of.

All banning gain of function research does is leave you unprepared when it happens.

Unless you've got a way to enforce this on China, this is unactionable. It's simply propaganda to rile people up.

1) If it was an accident, what are you going to do? If there is anyone sane in the leadership of the lab with knowledge of how this occurred, procedures have already changed. What more do you want them to do? You're NOT going to get a gain-of-function ban without some form of strong coercion. What will it be?

2) If it was intentional (and I see no gain for China if it were), what do you plan to do? You will have to somehow do something to cause actual harm to Chinese leadership. What? China is already guilty of genocide, and all the West does is shrug.

Hell, it would almost be better if this were an intentional release if not for all the dead. The emergence of Omicron would demonstrate to the idiots worldwide who thought they could control a virus that the idea is laughable and that the virus will quickly evade whatever you think are your protection measures.

And all this ASSUMES that it actually was a lab leak, which the current hypothesis about jumping from mice back to humans decreases the Bayesian prior on dramatically. If Covid can jump that quickly from humans to mice and back, gain of function is suddenly frighteningly common. And the research into gain of function, rather than being banned, needs to be ramped up hard.

Re: Scientists believed Covid leaked from Wuhan lab, but feared debate could hurt

#780

Post by Maursault » Wed, Jan 12, 2022, 11:16 PM UTC

largbae wrote: post #773

Maursault wrote: post #726

Earlier quoted context omitted.

You missed GP's point, which apparently was equating personal privacy with China's national security. I didn't think twice about China's lack of transparency. It's normal and expected behavior from China, so I would never suspect it to mean they were hiding something that was actually salient to the global pandemic... they're just hiding everything, but all it amounts to is hiding whatever corruption comes with gover…

So just ignore it? Wildfires occur naturally in a similar fashion. We still try to diagnose their causes and use that information to punish arson or otherwise come up with better strategies to prevent them.

I'm not sure what you're referring to, re: ignore, but I don't think your analogy is remotely apt. I think you're saying a little fire is like a little virus, and a big fire like a pandemic. But anyone can light a fire, even animals cause wildfires, and thanks to lightning and fuel, fire doesn't need anyone to cause it. No one, I think, can "light" a little virus that could then spread like wildfire across the globe. Maybe a state actor, but not some individual and not accidentally. But this is mixing the two conspiracies, ordinary lab leak vs. engineered virus intentionally released. I just don't think China is up to it. I still return to the fact that lots of nasty things have escaped labs and the worst result was a very minor outbreak. Though genetics and microbiology has made incredible advances, it is all, all of it, on Nature's back. I think in a contest between Nature and any group of the smartest most knowledgable scientists with global resources to create the deadliest virus imaginable, Nature wins every single time, forever. And if COVID-19 was engineered for this, it sucks, it's an absurd and annoying failure. I think the reason why the source for COVID-19 can not be found is that it was fully consumed by one or more of the first 50 infected Wuhan residents that purchased it at the wet market and fully digested it before anyone had a hint of symptoms.