https://en.wikipedia.org/wiki/Biosafety_level#Biosafety_leve...
1. Gain of function research primarily uses samples collected from nature, and seeks to stimulate their evolution in as natural a way as possible to learn how viruses evolve in nature. If such viruses were to escape the lab, they would appear "natural"
2. It's not xenophobic for people from the US to suggest the possibility of a lab leak, because the US was itself funding gain of function research on novel coronaviruses in the Wuhan BSL4 lab
3. Lab leaks happen more often than most people realize[1]
[1]https://www.vox.com/future-perfect/2019/3/20/18260669/deadly...
Similar article which made the same case. This one provided a few more interesting stories about just how close we have come to potentially similar leaks in the past (and based in US labs).
Total deaths in WW2 estimated at approx 70 million. [1]
Johns Hopkins estimates COVID-19 deaths are approaching 3 million. [2]
It's also worth noting that even the leading experts can get these things wrong, as was the case with the Sverdlovsk lab leak.
Soviet authorities covered it up by blaming local meat markets, and leading US experts concurred with them, only to reverse their conclusion 6 years later.
https://en.m.wikipedia.org/wiki/Sverdlovsk_anthrax_leak#Acci...
> Valid ad hominem arguments occur in informal logic, where the person making the argument relies on arguments from authority such as testimony, expertise, or on a selective presentation of information supporting the position they are advocating. In this case, counter-arguments may be made that the target is dishonest, lacks the claimed expertise, or has a conflict of interest.
For example, if someone tells you that hydroxychloroquinea will cure COVID and cites a doctor, it is an ad hominem not but not a fallacy to counter that the same doctor also says that infertility, impotence, cysts, and various other reproductive medical problems are caused by witches and demons that have sex with people in the dreamworld, where they also gather sperm from people and use it on other people to produce more demons. (And yes, there really is a doctor who says all that).
It's not a fallacy because it is not offered to refute the claim that hydroxychloroquine cures COVID--it is offered to show that the person making the claim is not competent to make the claim.
Honest question: Is that a fair/accurate generalization to make? If Hell's kitchen episodes and accounts from food industry workers are any indication, sanitation practices in food handling establishments elsewhere are not necessarily always stellar either. And surely China has some equivalent of WholeFoods?
One ought to be careful not to attribute a characteristic differently depending on whether they belong to the class of people in question[0]. If it turns out that reality is that some chinese establishments have poor sanitation practices just like some US establishments do, and it just so happens that they got unlucky (perhaps partially due to not-so-directly-related aspects like zoning law differences or propensity for higher bat populations due to local fauna/flora ecosystems), the us-vs-them blaming game doesn't necessarily have as strong legs to stand on.
https://www.washingtonpost.com/context/read-the-state-depart...
Please note part (6) regarding WIV scientists studying human-disease causing SARS coronaviruses.
Also note this report with the science to back it ("The genetic structure of SARS-CoV-2 does not rule out a laboratory origin"):
https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.2020002...
https://www.washingtonpost.com/context/read-the-state-depart...
Note part 6.
https://www.npr.org/sections/health-shots/2021/02/03/9628119...
If you wouldn't mind reviewing https://news.ycombinator.com/newsguidelines.html and sticking to the rules when posting here, we'd be grateful. They include:
"Comments should get more thoughtful and substantive, not less, as a topic gets more divisive."
The term itself is somewhat ambiguous [https://en.m.wikipedia.org/wiki/Wet_market] in that it can cover both cases. However the style common in many places in China (and many other areas in east Asia) is one where there is no refrigeration or adequate sanitation. To avoid spoilage, animals are brought in live and slaughtered as needed to provide meat. It can be when a customer picks it, or when needed to stock a counter.
These styles of market are problematic disease wise because it brings many species of animals together in crowded and often unsanitary conditions, high stress, with humans in close contact with them, and lots of people and animals coming and going constantly.
If you’re looking for a way to encourage Zoonotic disease, it’s hard to do better.
Except nobody has been able to identify that animal. With SARS it was quickly determined to be civets, with MERS camels. With Covid, more than a year on, we still don't know.
https://www.technologyreview.com/2021/03/26/1021263/bat-covi...
If you wouldn't mind reviewing https://news.ycombinator.com/newsguidelines.html and sticking to the rules when posting here, we'd be grateful. They include:
"Comments should get more thoughtful and substantive, not less, as a topic gets more divisive."
Read the section in the WHO report on COVID19 and listen to the reputable international scientist that actually went and visited the lab and interviewed the people who worked there.
https://www.who.int/health-topics/coronavirus/origins-of-the...
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 country) to begin with. Even if China were to claim they've stopped we have no way of knowing.
Let's just assume China did have a lab accident. OK, then what? We tell them to stop doing it? Let's say they agree. In the future they decide to start doing it again. The entire thing is pointless to begin with. We can't get our own citizens to consistently wear masks and we think we're going to substantially change China's behavior here - hilarious.
I mentioned this in another comment, but here's the 2018 State Department warning.
Please note part (6) about human ACE2 coroniavirus:
https://www.washingtonpost.com/context/read-the-state-depart...
> with DNA showing it came from pangolins, in a place where pangolins
This is false. You can read the science here (note the "receptor binding studies of reconstituted RaTG13 showed that it does not bind to pangolin ACE2."
https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.2020002...
This is false. First of all it should be stated clearer that there has been parallel evolution across several branches of coronaviruses which have independently evolved a furin cleavage site (so there is evolutionary pressure and advantage for coronaviruses to follow this path):
https://www.sciencedirect.com/science/article/pii/S187350612...
And then the statement is just wrong. The related sarbecoviruses found in Thailand have similar furin cleavage sites:
> The RacCS203 S gene is most similar to that of RmYN02 (Supplementary Fig. 3a). The two viruses shared part of the furin cleavage site unique to SARS-CoV-2 (Supplementary Fig. 3b) and have an almost identical RBD aa sequence with only two residue differences out of 204 aa residues
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...
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"
Did you know that people use Bat Guano (literally bat shit) eyedrops to cure visual ailments in rural china? Among other risky practices. Bat guano is often handled with bare hands and used to fertilize fields without proper sanitary practices. The many tens of thousands of these events that happen everyday are a MUCH more likely scenario.
I have a PhD in virology and wrote a post all about this on Reddit a while back: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
Have you seen one in the last decade? It's changed dramatically, and ranges from an open-air grocery store to yes something more depressing like what is in that wiki article.
prima facie false.
https://en.m.wikipedia.org/wiki/1977_Russian_flu#Virology
“ it is widely believed that the virus was leaked to the public in a laboratory accident (may have been kept frozen in some laboratory beforehand).[4][5][10][11][12][13][17][19”
And on top of that, the original SARS leaked from Chinese, Taiwanese, and Singapore labs a minimum of 4 times.
So parent’s cited statement is false and does not apply.
We can emphatically not expect the experts to do their job. Those cited as having the most expertise (virologists who undertake gain-of-function research, symbolically under the auspices of HHS’ toothless P3CO regulation framework) have the most to lose from a finding that the pandemic’s source was a lab leak. They lose all the grants and public financial support, not to mention endure unending public scorn that will haunt the their careers for the duration.
For evidence that the relevant, oft-cited scientists act precisely this way, one need no more than to look at @BlockedVirology’s retweets: https://twitter.com/blockedvirology
Scientists are human - I would highly recommend disabusing oneself of the notion that they might act contrary to overwhelming human incentives in as weighty a context as investigating the origins of the greatest pandemic in a century.
The only alternative in the face of this embedded conflict of interest in our (society’s) ability to credibly investigate the pandemic’s origins is for technically-minded individuals (who don’t run multimillion dollar virology labs) to avail themselves of the findings gathered to date on the origins (there’s lots! Just need to take a look, the contributors to the above feed are a good place to start), and advocate to their representatives for a credible & even-handed origins investigation.
Failing that, expect no origin beyond all reasonable doubt to be credibly identified in our lifetimes.
[0] https://www.bloomberg.com/news/articles/2020-12-01/covid-inf...
According to the below video, eating exotic wildlife dates back to the starvation conditions of the Mao years and is now mostly practiced by the rich. The conditions in which these animals are kept are unsanitary, even by comparison to a market with live animals that you might be familiar with in the US.
There was a push to end the practice after SARS-CoV-1, but they came back a few years ago.
https://www.vox.com/platform/amp/videos/2020/3/6/21168006/co...
I have A) direct relationships with the people who study viral biodefense at USAMRIID and serve on the government panels, and they were very surprised to hear about these cables. They didn't find the authors credible at all. One is an entrepreneur and the other a career diplomat.
And for all those who don't have a PhD in the subject or know the people who know people, B) it's detailed closely in this washington post article who was there and what they wrote:
https://www.google.com/amp/s/www.washingtonpost.com/national...
https://www.washingtonpost.com/opinions/2020/04/14/state-dep...
There is one fascinating article I came across published by Nature in 2017 which has all sorts of innuendo given the state of facts on the ground today. https://www.nature.com/news/inside-the-chinese-lab-poised-to...
Doctors have escaped and claimed that it was lab engineered
https://bgr.com/2020/09/15/coronavirus-whistleblower-wuhan-l...
You can't do it in the time we've been able to handle viruses like this or modify them in the ways we can. You'd have needed to start a few decades ago, have tools that we've only just invented, and a huge number of willing test subjects.
I cover this in extreme detail in the post I linked under Q2 and Q3.
https://www.reddit.com/r/science/comments/gk6y95/-/fqpbt6o
https://www.reddit.com/r/science/comments/gk6y95/-/fqpc7c8
One of the most compelling pieces of evidence is the synonymous/nonsynonomous ratio of the genome and it's mosaic mutations.
That's not something you can just cook up over night, it takes many millions of viral generations which require A) diverse hosts (like you find in a natural ecosystem), B) many millions of hosts, like you find in nature, and C) decades of time.
The chinese virology labs don't have the resources, time, or space to do something like that. And maybe it would be kind of possible today with CRISPR and many thousands of oligonucleotides printed off of a desktop printer, but that technology hasn't existed for more than a few years. The timelines just don't add up.
Her government, not so much.
I am definitely not a fan of the Chinese government. But the scientists I've met at conferences and the papers I've reviewed from their labs have been of a very high quality.
Not saying such people could not commit atrocities or coverups like this. But I do find it personally less likely.
That isn't the evidence I rely on most in my personal assessment, though. The epidemiology and molecular clock data points to a zoonotic origin outside of Wuhan. Check out here to see what I mean: https://www.reddit.com/r/science/comments/gk6y95/-/fqpcfs2
Which makes the lab leak a whole lot less interesting of an idea since its' circumstantial evidence isn't actually the circumstance anymore.
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 number of years before SARS-CoV-2 made its appearance. While there's no proof that SARS-CoV-2 was created in a lab, there are quite a few studies describing the synthesis of different SARS-CoV variants, some quite dangerous.
From one of many papers on which he was a co-author (https://www.pnas.org/content/113/11/3048.full):
"Using the SARS-CoV infectious clone as a template (7), we designed and synthesized a full-length infectious clone of WIV1-CoV consisting of six plasmids that could be enzymatically cut, ligated together, and electroporated into cells to rescue replication competent progeny virions (Fig. S1A). In addition to the full-length clone, we also produced WIV1-CoV chimeric virus that replaced the SARS spike with the WIV1 spike within the mouse-adapted backbone (WIV1-MA15, Fig. S1B)"
EDIT: jeduehr, given your background in virology, I would be interested in any technical critique you may have regarding the Yuri Deigin article referenced in my post below.
> it really doesn't feel good to be a person from one of those locations.
I am from one of these locations and could not care less.
https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.2020002...
Like you, I don't enjoy when facts I post are de-railed without actually addressing any of them. It happens a lot, but I try my best to not let them be the last word.
There is plenty of factual information out there that makes an accidental lab-leak hypothesis strong.
Baric makes Chimeras. CoV-2 in comparison to the other closely related viruses in nature, is a mosaic. Lots of little changes all over the genome, not big copy and pastes.
See here for more detail on that distinction: https://www.reddit.com/r/science/comments/gk6y95/-/fqpbagf
Incidentally (or perhaps not?), there is some evidence that the furin-cleavage site is what makes the virus resistant to hydroxychloroquine, which can be countered by combining it with a TMPRSS2 inhibitor: https://journals.plos.org/plospathogens/article?id=10.1371/j...
But the epidemiological evidence points to covid-19 originating outside wuhan entirely, that's why I find that theory less likely, among other reasons. See here:
https://www.reddit.com/r/science/comments/gk6y95/-/fqpcfs2
Also if they had collected it in nature, it would have been in their freezers, or likely that people involved in that research would have been patient zero etc. See here:
https://www.reddit.com/r/science/comments/gk6y95/-/fqpcf33
https://www.reddit.com/r/science/comments/gk6y95/-/fqpce2z
Wuhan institute of virology also aren't the labs I'm worried about. They were built and designed by very reputable people in the virology community. Not saying you should trust them, but at least recognize that the people who are most qualified to distrust them think it's unlikely.
See here: https://www.reddit.com/r/science/comments/gk6y95/-/fqpccr1
>Does this imply covid-19 has been circulating in humans a long time?
No, it implies it was relatively stable passing amongst several species of bats (and other related mammals) before a single or a few crossover events into humans recently.
It's behaving exactly like we would expect a zoonotic transmission to behave. It's not very well adapted to bats, it's not very well adapted to humans. It's sort of "promiscuous" likely because it has infected several different species over several decades before arriving in humans.
There are oddities in the whole timeline which stand out to me. The social media videos of people keeling over in streets and buildings in Wuhan from the virus, which doesn't appear to be a genuine phenomenon of its pathology and therefore looks planted for psyop purposes. The CDC behaving so incompetently around testing and acknowledging the threat of the virus that it beggars belief (see: https://www.reuters.com/article/us-health-coronavirus-cdc-re...). No one from the global ruling class succumbing to the virus even as it claims multiple Covid-skeptical leaders in Africa where its impact is otherwise quite muted. Cuomo, Newsom, and Whitmer implementing policies which grossly amplified nursing home deaths in the early stages of the pandemic. Various maneuvers of public consent management, e.g. "15 Days to Slow the Spread" to get people to start lockdowns, followed by "we have to keep going until we get the vaccines" alongside zero investment in new ICU capacity and even reductions in hospital staff. The obvious wealth transfers and consolidation of the economy away from the middle class and small businesses which has occurred, along with the accelerated adoption of surveillable tech platforms as the primary means of interpersonal communication. Doctors reduced to begging on Twitter for people to run trials on repurposed generic treatments while all the stops are pulled out for the vaccines (even the Washington Post has recently acknowledged that financial incentives and political considerations are preventing cheap drugs from getting a fair shake: https://www.washingtonpost.com/health/2021/04/08/ivermectin-...).
But yeah, certainly nothing I can point to as hard proof.
https://drive.google.com/file/d/1vRbACWf90iBC35xNOwlI5bWcUq0... (Footnote 1)
Also, you can literally look around on this exact post and find people who believe that this virus was cooked up in a lab. There were also a lot of people on my original post who believed that.
As is often the case: never underestimate the intellectual overconfidence of people with little knowledge of the subject matter.
To draw a very clear distinction in the sand, I never said we can be 100% certain that this virus didn't originate in a lab. It's just really really unlikely. And there isn't any real evidence to support it. /Maybe/ some circumstantial evidence in the geographic proximity. But even that is probably irrelevant if the current epidemiological evidence is to be believed, which shows that the virus likely jumped into humans outside of Wuhan entirely. See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
In order of likelihood, based on all available evidence and expert consensus:
zoonotic release >>> accidental lab release of a wildly collected virus >>>>>>> accidental lab release of a "cooked up" virus > intentional lab release of a "cooked up virus"
[0]: https://www.francetvinfo.fr/sante/maladie/coronavirus/corona...
[1]: https://www.scmp.com/news/china/society/article/3074991/coro...
https://twitter.com/mlipsitch/status/1373978645560229890?s=2...
There was also never a consensus about masks, the US government and a few US virologists just felt that way. Asia and a lot of Europe definitely did not feel that way. I would urge you to be as non-America-centric as possible because the consensus that the virus is very likely not a lab leak is also global in character.
I actually know Dr. Lipsitch and have met him at a conference or two before, and he's not wrong in a lot of ways, it should be investigated to the fullest extent possible, I would absolutely agree with that and have never disagreed on that. China should allow in international investigators from unbiased third-party institutions with expertise in the relevant areas.
The problem, of course, is that it will likely be impossible to prove it either way. The closest we could get is identifying an extremely close relative of SARS-2 in nature, in bats or w/e, in an area where we also find Human seropositivity (antibodies in the blood).
On the other side, we could find a sample of SARS-2 frozen and old in a chinese lab that shows they had it before the outbreak.
I detail which things I would want to see to at least reassess my position in this part of my original post: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
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:
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.
Is that so inconceivable? The Chinese government has historically obfuscated facts and runs one of the largest media control operations in modern history. The WHO is also an organization of questionable trustworthiness and with suspicious subservience to China[1]. But the WHO wouldn't necessarily had to have been complicit. This could've easily been covered up by Chinese authorities during the many months of blocking external researchers into the country[2]. The research in the report you linked to started in January 2021.
As for the report itself, I skimmed a few pages and noticed some issues. My understanding is limited in this area, so please correct me if I'm wrong.
0. First of all, the conflict of interest of it being reported by WHO and Chinese researchers should be a factor in judging the validity of any of its claims.
1. From the arguments in favour of the intermediate host scenario (p. 115):
> Although the closest related viruses have been found in bats, the
> evolutionary distance between these bat viruses and SARS-CoV-2 is estimated
> to be several decades, suggesting a missing link (either a missing progenitor
> virus, or evolution of a progenitor virus in an intermediate host).
2. From the arguments against the intermediate host scenario (p. 116):
> There was no genetic or serological evidence for SARS-CoV-2 in a wide
> range of domestic and wild animals tested to date.
> Screening of farmed wildlife was limited but did not provide conclusive
> evidence for the existence of circulation.
3. From the arguments against the laboratory incident scenario (p. 119):
> There is no record of viruses closely related to SARS-CoV-2 in any
> laboratory before December 2019, or genomes that in combination could
> provide a SARS-CoV-2 genome.
The rest of the arguments that all labs complied with high safety standards, with no reports of illnesses or disruption are also coming from Chinese authorities, and should be taken with a grain of salt. Yet this is enough to consider this scenario "extremely unlikely".
4. China is praised multiple times for its "near-elimination of SARS-CoV-2", but the official data is comically suspicious[3]. A total of 4,851 deaths in a country of 1.4 billion people. That week of April 13, 2020 was rough.
Apologies if I sound inflammatory and conspiratorial, my disinformation senses are tingling.
Ugh and apologies for the formatting. HN please adopt Markdown.
[1]: https://www.youtube.com/watch?v=UlCYFh8U2xM
[2]: https://edition.cnn.com/2021/01/05/china/china-blocks-who-te...
1) Chimeric viruses (copy and paste) are what scientists make in the lab. They take a piece of one virus and paste it into the genome of another, en masse. This is very different from what SARS-2 is, which is more accurately described as a "mosaic" (lots of little changes all over the genome). This is much much more difficult (if not very close to impossible in the case of SARS-2) to make in the lab, at least not and have it be done and "cooked" by the time the pandemic started. See the part of my post here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
2) He makes it sound like the techniques Shi Zhengli uses in the lab could create SARS-CoV-2. This is not true. For the reasons I describe above in point 1, and others, this is not really a likely possibility. Modern virology just does not have the tools to do this. Only mother nature with its many millions of hosts and diversity of hosts (in different mammals) could do this in the span of time molecular clock analysis says it took to take similar viruses like RaTG-13 and mutate them into SARS-CoV-2. I go into extreme detail about this in this part of my original post: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
3) He also says things like "Considering the heights of user friendliness and automation that genetic engineering tools have attained, creating a synthetic CoV2 via the above methodology would be in reach of even a grad student." Yeah, in 2020. Not in 2000 when they would have needed to start doing this. We did not have these tools back then. We did not understand enough about viruses, and this is /before/ we even discovered SARS-CoV-1!
The molecular clock + the synonymous/nonsynonymous criteria + the mosaic nature of the virus together put constraints on how this virus could have evolved. The first says it takes about 50-70 years to evolve a virus like this, evolving as fast as it does in nature. The second says it evolved in a fashion that wasn't putting more selective pressure on it than nature usually does. The third says it happened in a semi-random way, the way natural mutations occur. All of these together (plus other stuff) mean that it's unlikely that anyone /grew/ the virus in a lab intentionally.
I go into extreme detail about the synonymous nonsynonymous stuff in 3.1.1 of my post.
4) Also, it doesn't actually look like a virus that was grown in a petri dish or one that was grown in a single species of animals. It has O-linked glycans on it that cell culture wouldn't add. See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
Also, if it were grown in a single species of animal, then the SARS-2 spike protein would bind most tightly to that receptor. That's not actually what it is. As best we can tell, the S from SARS-2 binds just ~okay~ to a lot of different ACE2 receptors, and it just happens to work to bind human ACE2 kinda well. It's not at all how anyone would have actually designed it if they wanted to make a virus that kills humans. If they were designing it that way, they were some really shitty super villains, let me tell you that. I go into some extreme detail about this in this part of my post: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
5) Yuri gets really hot and bothered about the furin cleavage site. But what he seems to misunderstand is that these cleavage sites have evolved in nature too. It's likely either A) a recombinatorial event between SARS-2 and similar viruses in nature or B) it mutated over a short period of time in a way similar to other "mutagenicity islands." We have actually seen this before in nature. See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
He even says it has been shown to be disabled in a relatively short period of time in lab animals, so why wouldn't it be able to show up in nature in 50-70 years in millions of wild animals? It's really not that unlikely when you consider that certain areas of viral genomes mutate a lot faster than others in the wild.
6) He even points out that the only viruses in nature that share the cleavage site share only 40% of the rest of their genomes with SARS-2. But that just shows it's likely that SARS-2 and one of these other viruses happened to infect the same animal at the same time, and their genomes had a cross-over event. This happens ALL. THE. TIME. in viruses in nature. It's basically how flu pandemics occur. See:
-https://www.nature.com/articles/nrg2053 -https://www.euro.who.int/en/health-topics/communicable-disea... -https://academic.oup.com/mbe/article-pdf/26/1/177/13640305/m...
Why is it not likely this sort of thing was involved in this coronavirus pandemic?
Honestly I can't keep going because I need to be studying for the most important exam of my career (USMLE Step 1) but I can tell you just from the first couple pages of this extremely long thing that Yuri is not a virologist and has never taken a formal viral genetics class. He is making fundamental mistakes in how viruses evolve and change over time. He clearly knows a lot about biochemistry and regular genetics, but viruses are a whole different ballgame.
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...
See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
I'm only gonna address the science in your post from here on out. I want to make it clear I never insulted you or attacked your character, I only said I had no way to know you were a virologist and only could go off of your word.
I get your hypothesis now that you have fully stated it.
And here are some questions that need answers.
Where did they get the virus? It's not anything like any coronavirus we know of before SARS-CoV-2 emerged in humans, it's 1200 away from RATG-13.
What experimental question were they trying to answer? We already know that the furin cleavage site is necessary for some aspects of pathogenicity, but not the ones canonically thought important (cell entry for SARS-1 for example, since furin doesn't actually cleave SARS-1 or MERS). Why would they test a random unrelated coronavirus' site? Why not try the SARS-CoV-1 site? Or the MERS site? Why was it a furin site in the first place? And why did they do it on the weirdly promiscuous SARS-2 ACE2 and not in a virus like RATG-13?
Re: cleavage site, I go into extreme detail about how possible it is for cleavage sites to evolve in nature here and here:
-https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
-https://news.ycombinator.com/item?id=26757881
It's really not that unusual for a cleavage site to evolve in nature, and especially not when we consider that furin cleavage sites are mutagenicity islands. It absolutely could have evolved from recombination with a distantly related coronavirus that has an extremely similar site.
Also, the cleavage site isn't even that long. Short stretches of nucleotides like that, upwards of 15-30 nucleotides, can absolutely evolve over the course of 50-70 years. Happens literally all the time. In influenza it happens on much shorter time scales. I provide evidence to that effect in the above posts.
Yes I actually address the idea of using recombinatorial cloning to make SARS-CoV-2 at several points in my post.
Nothing about the furin cleavage site makes it more likely to be unnatural than it is natural?
And so far, I don't see any compelling reason to believe that anyone would take a completely undiscovered and undescribed virus out of nature, not describe it or publish on it at all, and then start inserting random furin sites into it from random other coronaviruses.
Why would they be doing that? Is it technically /possible/? Yes, but I see no reason why it is more likely than a natural emergence.
Recombination can absolutely happen inter-genera and even inter-family.
There's some evidence that Ebola got its VP40 from bats, or vice versa. Meaning that an RNA virus somehow got its nuclear regulatory factor from a bat. We have no idea in science how that happened. But we know there is homology! I can't find the link at the moment, but when I do I'll add it here. It's not actually that important to my argument.
There are also examples of inter-family recombination in viruses that are much more down to earth.
See here: https://www.virology.ws/2016/10/27/genome-recombination-acro...
And you might be asking yourself, after reading that link "Why is it always bats?? Isn't that /suspicious/?" It's actually in keeping with everything we know about bats and their role as a viral reservoir. Lots of viruses cross paths in bats. See this other detailed post I wrote a while back: https://www.reddit.com/r/science/comments/gehvui/why_do_viru...
See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
Unfortunately that is impossible for two reasons:
1) Because you have inextricably tied your argument to who you are with lines like: >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.
2) Because you refused to present your argument here in a way that stands against my hypothesis, and instead relied on simply introduction of yourself and your credentials.
>Where did they get the virus? It's not anything like any coronavirus we know of before SARS-CoV-2 emerged in humans, it's 1200 away from RATG-13.
1200 mutations away from RATG-13 is how significant exactly? I will propose that it is not particularly significant. One virus I work with, I have 14 variants ranging from 300 to 500 base-pair differences. That is from passing in a laboratory only. I have one variant that has a 14000 BP deletion! (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217056/#mmi144... TABLE S2) However, it is noteworthy for that reason. That said, these are dsDNA viruses with comparatively much slower mutation rates. 1200-base differences are almost nothing.
>Why would they test a random unrelated coronavirus' site? That's a good question, and not one that I can answer suitably with this hypothesis. Perhaps because they were looking for a cleavable one?
>And why did they do it on the weirdly promiscuous SARS-2 ACE2 and not in a virus like RATG-13?
To me this is obvious. SARS-2 ACE2 is extremely promiscuous. That's a very good reason to study it - it has broad potential for cross-species jumps. If you are trying to narrow down what it is that causes the jump, you want to study on the virus that is most capable of making that jump.
>Re: cleavage site, I go into extreme detail about how possible it is for cleavage sites to evolve in nature here and here:
Again, I don't think that applies my hypothesis. Of course it had to evolve in nature. Otherwise there would be no furin site. The ability of a furin site to evolve in nature has almost no bearing on whether or not one could be inserted into coronavirus by humans, unless I'm totally misunderstanding what you're suggesting here.
>Also, the cleavage site isn't even that long. Sure, and again, this furin site likely did evolve in nature (at least in amino acid form). Whether or not it evolved in coronavirus is the topic here.
>Nothing about the furin cleavage site makes it more likely to be unnatural than it is natural? The two non-canonical arginines don't make it less likely?
>And so far, I don't see any compelling reason to believe that anyone would take a completely undiscovered and undescribed virus out of nature, not describe it or publish on it at all, and then start inserting random furin sites into it from random other coronaviruses.
I have some of viruses I work with I haven't published on yet, because I am either waiting to complete work, or they aren't significant enough compared to their peers for me to publish on them.
>Why would they be doing that? Is it technically /possible/? Yes, but I see no reason why it is more likely than a natural emergence.
OK so that's the crux of my argument. There's some interesting anomalies that point to it being a possibility. There's no way to rule it out. At the end of the day, it comes down to one opinion vs another, which is why statements like:
>The virus itself, to the eye of any virologist, is clearly not engineered.
...are so infuriating to me.
https://news.ycombinator.com/item?id=26757986
You don't have any molecular biology refutation that I can find.
You're comparing apples and oranges. 14 mutational sites across a virus with 17k ssDNA genome is not comparable to RATG-13 vs SARS-2, which have not just 1200 mutations different, they're spread out over HUNDREDS of SNPs.
That's the important comparator. And why it will take so long to mutate one into the other by natural mutation rates.
>The two non-canonical arginines don't make it less likely?
Not particularly. CGG exists in MERS 15 times. NL63, 29 times. It even exists twice in a row in Human coronavirus 229E. Throughout all of the known alphacoronaviruses (94 described) CGG exists 1575 times. In betacoronaviruses, it exists more times than my processor can count without hanging, and I believe it tops out at 9,999 events.
I just ran blastn to figure that out. Using these datasets: https://www.ncbi.nlm.nih.gov/datasets/coronavirus/genomes/
Why is it so unlikely that synonymous mutational drift over the course of 70 years of infections in millions of viral generations could create these arginine codons that are not the most optimized but still work in the mammals this virus infects? CGG works. It makes an arginine when this virus infects its host.
Why couldn't it be a recombination event between SARS-2 and one of the known coronaviruses with an extremely similar cleavage site? We know already coronaviruses have recombined with viruses totally outside of their family on occasion: https://www.virology.ws/2016/10/27/genome-recombination-acro...
There is strong tertiary evidence that patient zero was a Wuhan Institute of Virology researcher named Huang YanLing 黃燕玲, this has all been scrubbed from public memory. The wayback archive links still hold up. https://www.youtube.com/watch?v=bpQFCcSI0pU (links are at the bottom of the video description).
You understand the nuances better than most. I'm guessing you're self taught? I've never read the origin of species, but I feel like you might have!
The points you're making are a given in modern evolutionary theory.
https://en.wikipedia.org/wiki/Evolutionary_pressure https://en.wikipedia.org/wiki/Adaptation
>Actually, CRISPR/Cas is a fantastic example of lamarckian evolution.
This, however, is completely wrong.
>Lamarckism, also known as Lamarckian inheritance or neo-Lamarckism,[1] is the notion that an organism can pass on to its offspring physical characteristics that the parent organism acquired through use or disuse during its lifetime.
https://en.wikipedia.org/wiki/Lamarckism
CRISPR has nothing to do with use or disuse. Lamarckism is only relevant as an example of what evolution isn't.
I actually provided several links filled with sources above.
here is the main one you're referencing again: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
Thanks
https://yurideigin.medium.com/lab-made-cov2-genealogy-throug...
This absolutely shouldn't be China vs. USA, and it's deeply unfortunate that the Trump administration's early, characteristically unsupported rhetoric made it so. The WIV's safety was probably below American standards, but probably closer than a wet market is to American agricultural standards. So it's ridiculous to think a lab vs. natural origin makes it "more China's fault". If the CCP is currently covering up a lab accident, then they're probably quite unhappy that they've been "forced" to do so, and wishing in retrospect they'd instead decided a year ago to publicly blame the rogue, American-funded researcher.
Long before the pandemic, this was an obscure academic debate, between virologists who wanted to perform certain risky experiments and others who thought they presented an unacceptable risk:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097416/
With the possibility (absolutely not proven; but not disproven either) that such an experiment has just killed 2.9M people, that debate takes on a terrible new significance.
I'm talking about sources like major scientific journals and mainstream media here. It just takes some work to piece it all together.
The story is actually really fascinating and almost seems like a fictional thriller novel. It actually gave me chills. This is all heavily cited with credible sources, here's the story: https://followtheplot.org/covid19
-http://www.reddit.com/r/science/comments/gk6y95/covid-19_did...
-http://www.reddit.com/r/science/comments/gk6y95/covid-19_did...
I also address the statistical models you describe, here:
-https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
I go into detail about petri dish vs lab animals vs accelerated evolution and how implausible it is.
Re: sampling viruses in the wild this isn't necessarily my area of expertise, I'm a lab guy. But I do know a lil bit about it, re: ebola in bats mostly. Only that it actually takes much longer than you think, and it has to do with our sampling methods. RNA is really really really short lived outside the host, and our sampling methods aren't that good at finding it inside animal secretions, they're optimized for humans and humans want to be sampled. you don't need to squeeze a human to get them to pee in a cup, or spit in one, or hold still to swab them like you do bats. So sampling is much more difficult. And since it's out in the field, the RNA decays more quickly too. Some advances have been made in this but it still is quite difficult.
To give you an idea, here is a paper all about the vastly MASSIVE amount of estimated undiscovered viruses out there (figure 3 in particular): https://www.nature.com/articles/nature22975
I address the state department stuff also: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
Re: research mice, the mouse germination time from IVF to F1 (the first useful generation of mice) is about 12-16 weeks. Not that long on the global timescale, but really long in science. You can see a source for this here: http://ko.cwru.edu/info/breeding_strategies_manual.pdf
And that's from Case Western in Ohio, not a Chinese source. It really is that fast.
I'm sorry I'm not framing my arguments in precisely the way you want them, I framed them how I received the arguments out there having discussions in the real world with real skeptics. I then constructed the post to respond to those arguments I had been asked about.
I'm sorry, but that's just the way it is. Take it or leave it.
Let me restate my issue with the OP in a clearer way and then I'll get into the rest of the nuance and detail.
OP said:
>there is evolutionary pressure [...] for coronaviruses to follow this path
I interpreted this line as reading: "coronaviruses will likely evolve furin sites because <some external force/evolution> is causing them to". The issue I take with it is that coronaviruses don't know what to evolve to, they simply evolve, and if it works, great. If not, they die. I'm not sure there's a cause beyond random/stochastic factors. Otherwise, it would be Lamarckian. If I were to reword it myself, I'd say "evolution of furin sites will be selected for". The reason I make this distinction is because elsewhere in the thread, I commented that a lab leak is a real hypothesis, and one of the counterarguments of that seems to be that because coronavirus could evolve a furin site without human intervention means that they did evolve a furin site without human intervention, and I dislike the narrative that it was an inevitability. (To make my position clear, I'd give a personal weighting of a natural evolution of Covid as about 85%, and a lab leak at about 14.9999999999%, and a malicious lab leak at about 0.000000000001%. Those numbers could be wildly off. I just get upset when people try to say a lab leak was definitely not possible).
>You understand the nuances better than most. I'm guessing you're self taught? I've never read the origin of species, but I feel like you might have!
I'd prefer to avoid a conversation based on credentials because of recent bad experiences there, but yes, I have read it. However, I was thinking about "The Logic of Chance" by Eugene Koonin, who is fairly well respected in the evolutionary biology field. Particularly, in "The Logic of Chance", he defines Lamarckian evolution as the following:
>Lamarckian inheritance refers to nonrandomly acquired phenotypic changes, particularly those that are directly affected by the use of organs and are accordingly assumed to be adaptive (beneficial for the organism). The controversial French naturalist Jean-Bapteste Lamarck believed that directed changes are inheritable and constitute the basis of evolution
He also goes on to say:
>Lamarck was the author of the first coherent theory of the evolution of life, which he presented in his Philosophie Zoologique; “inheritance of acquired (adaptive) characters” played a key role in this theory.
He makes a good, and much more nuanced argument than I'll attempt to explain here (see "The Logic of chance: The Nature and Origin of Biological Evolution, Chapter 9 for the full argument) that the inability of Lamarckian evolution only applies to the central dogma (DNA -> RNA -> Protein) because the central dogma has no reverse mechanism (no way to transfer information from protein back to DNA). However, this scenario falls apart with the advent of things like proteins that can insert novel DNA into a genome, or reverse-transcriptases.
Specifically regarding CRISPR/Cas, Koonin has this to say: >The mechanism of heredity and genome evolution embodied in the CRISPR-Cas system seems to be bona fide Lamarckian (see Figure 9-2):
>• An environmental cue (a selfish genetic element, such as a virus) is employed to directly modify the genome.
>• The resulting modification (unique, element-specific spacer) directly affects the same cue that caused the modification.
>• The modification is clearly adaptive and is inherited by the progeny of the cell that encountered the selfish element.
He goes on to address your points about losing with disuse, as well:
>The CRISPR-mediated heredity appears to be short-lived: Even closely related bacterial and archaeal genomes do not carry the same inserts. The implication is that, as soon as a bacterium or archaeon ceases to encounter a particular agent (virus), the cognate spacer rapidly deteriorates.
While "Logic of Chance" was written in 2013, if I remember correctly, which was the nascent stages of CRISPR/Cas understanding, my personal experience in biology has proven that to be quite true. We know now that CRISPR spacers are inserted into the beginning of the spacer locus, directly adjacent the leader which is where spacer transcription is initiated, and this apparently serves an evolutionary function of ensuring that the transcription guarantees more transcripts of the most recently encountered viruses.
That said, there are some serious flaws in his thinking. See this rebuttal:
https://link.springer.com/article/10.1007/s10539-018-9662-y
As always, in large part, the phenomena is undisputed, and the fact that it breaks the central dogma is...mostly...undisputed, but the actual definition of the term "Lamarckian" is in hot dispute.
(See also Koonin's response to that rebuttal here: https://link.springer.com/article/10.1007/s10539-018-9666-7)
I appreciate the thoughtful discussion.
If you read the reddit comments, you'd also see ones like this:
-https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
-https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
-https://www.reddit.com/r/DepthHub/comments/gogzk0/u_shibbole...
-https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
all praising my tone and how I "kept my cool" despite the trolls and sealions. A few similar comments here as well. Sorry it wasn't to your taste. Better luck next time I guess
RaTG13 was such a virus (collected 2013, published post-pandemic), but it's very unlikely to be the ancestor for the reasons that you note. No one outside the WIV (and thus, no one beyond the physical control of the Chinese government) knows what other viruses they had in their freezer or database. Deigin has recently published an article claiming to have discovered a novel coronavirus in contamination of agricultural samples sequenced at the same facility:
https://arxiv.org/abs/2104.01533
To be clear, the new virus that he "discovered" absolutely is not an ancestor of SARS-CoV-2, and he absolutely isn't claiming that is; but it's (more) evidence that the WIV had unpublished coronaviruses.
The WIV took their database of viruses down from public access in September 2019. They say this was due to repeated hacking attempts. They haven't restored access, or provided their database in another format (e.g., a dump on a flash drive) that obviously presents no information security risk. Do you believe their claimed reason for taking it down? If not, why do you think they're lying?
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 mutating at the rate of about 2 changes/month (68,69,70,71), out there in society, circulating in millions of humans. 2/month in the overall population of millions of tiny viruses, among 30,000 letters in each genome.
So, at the fixation rate (~2 fixed mutations/month), with all the many billions of SARS-2 viruses making copies inside all those people, how long would it take to change RaTG-13 into SARS-CoV-2?
Answer: about 50 years. 30 years before the world even knew about SARS or MERS or any other pandemic-potential coronavirus. Before we knew these viruses even existed. Before we knew they liked to live in bats (72,73,74,75). And, for the record, they didn’t even build a BSL4 (the kind of lab you really need to handle this kind of virus in animals) in Wuhan until 2016 (76).
And that estimate (50 years) is with all the many mutations that are happening in all the many infected humans during a pandemic situation.
We know that with a smaller group of lab animals (or even human subjects), the virus is much slower at “finding” mutations that “stick around” (77,78). You have to picture it kind of like a big room full of millions of slot machines. Each machine is a virus, pulling the lever each time it makes a copy of itself. And you only win a payoff when you’ve found a change in the virus that A) makes it look different, and B) doesn’t screw it up, so it can still survive and do its job (infect people). A lot of these mutations screw the virus up, so they wouldn’t be a payoff. They wouldn’t be a “fixed” mutation.
>>>>>>>>>>>>
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.
That's why the population level data is so important.
> How many of those are in frame for an amino acid? How many of those are two in frame for arginine in a protein, next to each other?
Who said recombination events only happen in frame? Or that viruses only drift in frame?
> There are many reasons why it's unlikely. The first is pure statistics. But the statistics are almost certainly influenced by millions of years of biology.
I would respond to this if it contained any evidence other than 'statistics say it is so.'
> I don't think it's in the scientific spirit to discount other viable hypotheses.
Who said I'm discounting anything? I said it's just not very likely. Extraordinary claims require extraordinary evidence.
I don't see how their opinion matters, since they're misinformed and orchestrated by the CCP.
The Hainan incident was caused by a Chinese fighter pilot running into a US surveillance plane. The former is agile, the latter is not, so that's the fault of the fighter.
Also, a plane in distress doesn't need permission to land. For the CCP to make a big deal out of that when there's no other runway available shows their true nature - evil and authoritarian.
The CCP has been at war with the US since the 1950s over ideology. If the US was not their enemy, the CCP would just pick another country.
I've noticed that otherwise intelligent people seem to place significance in "man in the street" conversations with people who live in totalitarian countries and have no power.
There's a phrase for that, useful idiot:
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?
A gas cylinder exploded and prompted a fire in a Siberian research facility which houses samples of smallpox, SARS, Ebola and other potentially deadly viruses. Russian officials said there was no threat of contamination.
https://www.dw.com/en/russia-says-no-danger-after-blast-in-s...
Likely, unlikely, it's not really possible to attach probabilities to events that already happened. Also history is told chronologically, when told anti-chronologically we tend to make causal connections where there are none.
I don't want to dismiss the lab theory completely but consider this:
These kinds of labs are all over the world, in China, in the Netherlands, in the US and so on. They are mostly being built in metropole regions because that's where large science clusters tend to be. Coincidentally city centers are traditionally built around markets. These tend to be the densest areas of cities. Densest areas are where infection clusters are most likely to build up and get noticed.
And now we find a case where all these 3 coincide. Really, that doesn't say much. Also there have been quite some hints about Covid19 cases before December 2019, outside of China even. [1] Statistics is a highly counter-intuitive discipline. If it wasn't maybe the virus would be already under control anyway.
[1] https://www.bloomberg.com/news/articles/2020-12-01/covid-inf...
Turn on subtitles, then select automatic translation -> English in options.
And here also is an Australian strain from the beginning of the pandemic that does not have cggcgg: https://ncbi.nlm.nih.gov/nuccore/MT007544
https://www.frontiersin.org/articles/10.3389/fpubh.2020.5815...
Your comments on mutation rates confirm that RaTG13 is not closely related to COV (we knew that) and imply we should expect to find a closer relative. Yet we haven't. And the paper you share argues (again) against your conclusions by pointing out that neither Yunnan nor Wuhan are expected hotspots for missing zoonoses to emerge. We've also now spent more than a year hunting there and elsewhere in SEAsia and haven't discovered anything remotely related. But China won't let anyone look at or sample Tongguan mineshaft.
Your comments on the State Department factsheet don't say anything except express a vague chummy solidarity that would lead a reasonable person to believe that SOMEONE in your group of international scientists should be able to confirm or deny allegations the WIV was in fact shutdown for a week in September. If no-one cannot confirm or deny this direct and very specific allegation how can anyone take seriously your claim that international civilian researchers would have any clue who was doing what kind of research in the facility or with its materials elsewhere? And if your mouse answer is correct surely it should take significantly longer than 4 months to bootstrap a program that can do practical experiments on mice with human ACE2 receptors, if only because IVF is hardly the start of the process.
None of these things support your argument. They just raise further questions that you seem to have zero interest in flagging or asking, despite having a very keen interest in the conclusions that you want people to draw. Science does not work that way.
https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
But this event doesn't look anything like those other lab release events.
See here: https://www.reddit.com/r/science/comments/gk6y95/covid19_did...
It's not super likely, because we don't have the epidemiological data (increased deaths from non-influenza pneumonia at a large scale) to support that, to my knowledge.
It's certainly possible. And it is true that our methods of detection of viruses are ill-equipped so you can assume we're almost always behind the curve a bit.
But there also isn't much more than anecdote to support this. Lots of people get influenza-based pneumonia in the winter. Could you consider the possibility that your recollection is now tainted? And that you are primed to notice those events more? It was also already a very bad flu season. See here:
-https://time.com/5758953/flu-season-2019-2020/
-https://www.medscape.com/viewarticle/924728
Another kind of issue is that early reports of "SARS-2 positive serum!" were overblown, which colored a lot of news reports on this. They basically made the tests too "promiscuous" so they also detected antibodies against common cold coronaviruses. That was a big problem. If you're curious about how tests like this work, you can check out this other post I wrote on that! Antibody tests are actually my specialty!
https://www.reddit.com/r/medicine/comments/g1ty3g/are_immuni...
Why would this support either hypothesis? The cleavage site clearly has nothing to do with RATG-13 and it is probably one of the main drivers of SARS-CoV-2 pathogenesis. See here:
-https://www.nature.com/articles/s41586-021-03237-4
-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7457603/
But before you say "See! Gotcha! That means that the cleavage site is the smoking gun!"
It also looks, from a molecular perspective, like a natural recombination event. See here:
-https://www.frontiersin.org/articles/10.3389/fgene.2020.0078...
https://pubmed.ncbi.nlm.nih.gov/26654122/
https://pubmed.ncbi.nlm.nih.gov/30806904/
https://pubmed.ncbi.nlm.nih.gov/16940861/ (this one says wet markets, which probably are an issue, but not as big as initially thought, and probably not the origin of CoV-2)
https://pubmed.ncbi.nlm.nih.gov/27726088/
https://pubmed.ncbi.nlm.nih.gov/27426214/
That's called "sealioning," a term you may have heard. https://www.merriam-webster.com/words-at-play/sealioning-int...
If you did not believe in good faith the statements you made, or have substance behind the questions you asked as though you believed them to be true (CGG for example), that is very much insincere.
I am not going to be dragged into an endless debate with someone who wants to play devil's advocate. There are people with actual misunderstandings and misconceptions about science that are out there that need our help to understand the world around them.
Why waste time like this if we agree on the basic points? This is not a socratic discussion, you are not Socrates, and I am not Plato. This is not a PhD defense. It is not an academic conference.
I'm here to talk about this with people who have legitimate concerns that they actually believe about the subject matter at hand.
And please, I'm sorry if I mischaracterized your position or your actions thus far, but that's what it looks like. If you had said at some point "just playing devil's advocate here!" or "I don't 100% believe this but what about this thing I saw?" then if I had seen that, I would have engaged in a completely different way, and likely disengaged much earlier.
Thanks for the interesting ideas, but I have to go study for exams, and procrastinate in ways that are better for both of our mental health.
Have a great day, and I hope this hasn't taken up as much of your mental energy as it has mine. Because it took up a lot of mine.
"It is not possible to determine whether the potential SARS-CoV-2 infections suggested by this study may have been community- or travel-associated. A previous survey of blood donors, conducted to help understand travel practices, determined that less than 3% of respondents reported travel outside of the U.S. within the 28 days prior to donation, and of those reporting travel, only 5% traveled to Asia."
https://www.redcross.org/about-us/news-and-events/press-rele...
>4. China is praised multiple times for its "near-elimination of SARS-CoV-2", but the official data is comically suspicious[3]. A total of 4,851 deaths in a country of 1.4 billion people. That week of April 13, 2020 was rough.
Indeed, the same day China decided to censor all covid death counts was the same day Chinese activists who were reporting on covid deaths using Github were dissappeared.
https://github.com/Terminus2049/Terminus2049.github.io
https://www.hrw.org/news/2020/07/22/silenced-china-archivist...
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395678/pdf/bul...
And nothing requires accidents to happen the same way each time. If SARS-CoV-2 was a lab accident, then it's probably an accident involving a novel bat-origin coronavirus collected from nature. The WIV probably had the biggest program sampling such viruses in the world, and that's the database they made unavailable.
Why do you think that database is unavailable now? The WIV's stated reason could possibly explain why they took it down in the first place (though it would be a spectacular coincidence), but it doesn't explain why they can't bring it back up.
Note that I asked this in my previous comment, and you chose to ignore it, instead responding to the less substantive comment from another user. You likewise ignored my original question about the database until I asked it twice. You didn't discuss the possibility of an accident involving a novel, unpublished virus (which you consider the most likely lab accident scenario, I believe correctly) until others brought it up.
I don't think that's malicious, but that's not a comforting pattern. Virologists are supposed to be the experts, so they should be the ones presenting (and refuting where applicable) the strongest and most likely scenarios for a lab accident. Instead, they (and you) seem entirely focused on defending the profession, refuting easy and wrong arguments, and waiting to see how long it takes adjacent non-specialists to learn enough to discover the harder ones. You then dismiss their arguments, because they (David Relman, Alina Chan, Richard Ebright, I assume Marc Lipsitch too; the list is getting long) are mere molecular biologists or epidemiologists or whatever, and not specialist virologists.
Regardless of what we eventually learn about the origin of this pandemic, that's not the behavior of a profession that can be trusted to regulate itself, and I believe the world is realizing that now. It would be unfortunate if important virological research gets banned because the regulations are drafted by half-informed outsiders; but if virologists themselves don't seriously engage with the possibility that their work just killed 2.9M people, that's what will happen.
Of course that's not all virologists. Étienne Decroly has been pushing quite openly for an investigation of a possible lab accident, though mostly in French-language media and perhaps you'll find something wrong with his resume too.
And just so you don't miss it: Why do you think that database is unavailable now? Please feel free to ignore everything I've written except that question.
Maybe per capita but not per se. The US had 241 million international air passengers in 2019[1]. The UK had >160 million[2]. The US has two land borders with significant traffic and the UK had 21.5 million Chunnel passengers in 2019[3]. The volume of passenger shipping is also vastly higher in both countries. NZ also has almost no illegal border crossings.
NZ has a much smaller risk profile than these and many other countries. And this is born out by events. By the time the world became aware of what was happening the virus had already been spreading in Europe and the US for months. While it had been introduced to NZ it was still in much earlier stages.
[1] https://www.bts.gov/newsroom/final-full-year-2019-traffic-da...
[2] https://www.statista.com/statistics/303654/number-of-arrivin...
[3] https://www.statista.com/statistics/304968/number-of-passeng...
https://www.preprints.org/manuscript/202005.0322/v2
Of course that's not evidence of anything malicious; the renaming and failure to reference might have just been inadvertent. But it's still a bit weird, and it unquestionably shows at least a 2.5 year delay between sampling and publishing even a fragment of the genome.
That delay isn't evidence of anything malicious either. Research takes time, and any group in any discipline has a backlog of unpublished work. The WIV didn't stop sampling in 2013 though, and no one outside China's physical control knows what else might be in their collection.
https://www.globaltimes.cn/content/1181292.shtml (USA, misidentified as vape lung)
https://www.globaltimes.cn/content/1183658.shtml (something with Fort Detrick)
https://www.globaltimes.cn/page/202101/1214376.shtml (not the Huanan market, maybe imported seafood)
I guess you could try counting up and comparing the total lies implied by each origin, but the volume is so high that seems pointless to me. Their strategy seems more like a general fog of confusion to me than a particular story intended to be believed.
I don't have time to address the rest of your comment I'm sorry, I have already sunk so much time into this post that I should have spent studying. This is the exam I have in 3 weeks: https://en.wikipedia.org/wiki/USMLE_Step_1 Pay particular attention to the section marked "effect on matching residency." I never should have responded or brought myself into this post in the first place.
Sorry, but I need to exit now. I hope you find the certainty you're looking for, either way. I hope you find the solace in "holding virologists to account" that you are looking for, although I'm not sure it will happen the way you are suggesting.
If that's true, then why has the WIV removed public access from their database? It serves only to remove a valuable scientific resource, and to cast suspicion on China; so why would they do such a thing? Do you genuinely believe that even with the international importance of the topic, no one in China can figure out how to keep a simple database-backed website up?
And again, Deigin et al. report assembly of the genome of a novel coronavirus from contamination in other published reads sequenced in the same facility:
https://arxiv.org/abs/2104.01533
As far as I can tell, this virus wasn't previously known outside the WIV. Am I mistaken? I emphasize again that their novel virus is relevant not because it's an ancestor of SARS-CoV-2 (it's not), but because if the WIV had one unpublished virus, it gets harder to claim it's ridiculous that they might have had others.
https://fivethirtyeight.com/features/why-did-the-world-shut-...
One of the first things done by the Trump administration was close borders with China, but it was not enough.
This is the worst idea I've ever heard. [1]
[1] https://www.newyorker.com/humor/daily-shouts/l-p-d-libertari...
> The reemergence was probably an accidental release from a laboratory source in the setting of waning population immunity to H1 and N1 antigens
https://www.nejm.org/doi/full/10.1056/NEJMra0904322
About 700k people died worldwide. That's more than a typical flu season but not grossly so, and it's impossible to say with certainty what kind of flu season would have occurred naturally without the escape.
https://nouvelles.umontreal.ca/en/article/2018/01/19/you-re-...
SARS-CoV-2 is certainly worse. The 1977 flu pandemic is still a lot of deaths, though, and surprisingly little-known.
https://www.researchgate.net/publication/349073738_An_invest...
https://twitter.com/Rossana38510044/status/13806444823669841...
> the scientists among us should be trying to properly falsify it to the best of our ability.
This is precisely why I am bothered this has been placed into "conspiracy theory" land, due to a lot of political reasons and a whole lot of online pressure with those "hand-wavy" arguments. The same type of arguments you originally did not accept. I get them constantly when I post facts, and the are meant specifically to try to steer the discussion away from anything I was pointing out, to get that last word in.
Did SARS-CoV-2, with its affinity for human ACE2, leak from a lab in Wuhan that was doing known gain of function experiments dealing with CoV and human ACE2?
Or did it somehow show up in a market right next to the lab, with "hand-wavy" explanations as to how that happened?
The science seems to strongly point to one of those. Since access to the lab has been completely shut down, and historical information on the web has been systematically being removed, finding a smoking gun is difficult. But I feel an extremely strong case can be made with circumstantial evidence.
"The first practical use of the test system for the detection of antibodies to COVID-19, developed by the Novosibirsk State Research Center of Virology and Biotechnology" Vector ", was held among the employees of the FSBI" National Medical and Surgical Center. N.I. Pirogov" Ministry of Health of Russia. Testing was carried out in 204 employees of the center, who had no symptoms of acute respiratory viral infections in the previous two months. According to the results of testing, antibodies to coronavirus were detected in 30 employees of the Center working in the" red "zone and at the entrance to it", - the message says.
https://news.rambler.ru/community/44036116-immunitet-k-koron...
Here is fresh evidence (< 1 wk ago) that labs in Wuhan have worked on unpublished coronaviruses:
https://arxiv.org/abs/2104.01533
The above findings are replicable by any bioinformatician operating on published sources. This preprint was reviewed by one of the authors of the Human Genome Project’s landmark 2001 paper having served as an HGP sequencing team leader at the Whitehead Institute:
https://twitter.com/kevin_mckernan/status/137939900576396083...
The findings critically undermine Western zoonotic scientists’ (Daszak of the WHO-convened study particularly) claim that they knew what viruses WIV researchers were working on.
The CCP prohibited the virus's genetic sequence from being published. After a lab published it, it was shut down.
>On 11 January, Edward C. Holmes contacted Zhang for permission to publish the virus's genome. Zhang granted permission, and Holmes published the genome on virological.org that day.[1][3] The Chinese government had prohibited labs from publishing information about the new coronavirus, though Zhang later said he did not know about the prohibition.[3] The next day, the Shanghai Health Commission ordered Zhang's laboratory to close temporarily for "rectification".
https://en.m.wikipedia.org/wiki/Zhang_Yongzhen#COVID-19_pand...