@Soriek comments on "Culture War Roundup for the week of July 24, 2023

Culture War Roundup for the week of July 24, 2023

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Soriek 1yr ago · Edited 1yr ago

the existence of zebras in Kenya doesn’t mean zebras are super likely elsewhere which is what the scientist inferred.

Is this case we're not in a totally random elsewhere though. They haven't only demonstrated that zebras are a natural thing, and that the stripes don't look like human paintbrushes, they've also isolated the original zebra sightings to a safari/wet market, not the paint store/lab. Given this context, we would want some active evidence or rationale to consider that it's actually paint. Even so, in their paper they clearly note normal scientific limitations:

Although the evidence shows that SARS-CoV-2 is not a purposefully manipulated virus, it is currently impossible to prove or disprove the other theories of its origin described here. However, since we observed all notable SARS-CoV-2 features, including the optimized RBD and polybasic cleavage site, in related coronaviruses in nature, we do not believe that any type of laboratory-based scenario is plausible. More scientific data could swing the balance of evidence to favor one hypothesis over another.

Context

zeke5123 Soriek 1yr ago

They didnt isolate the findings to a specific wet market. They are relying primarily on the PRC’s claims regarding the spread which is highly dubious. They are basically taking at face value the claim of the paintbrushers about where the zebras started. This despite there is decent evidence that is not where zebras were first seen.
They privately noted serial passage was an easy way to make it look like humans and Wuhan knew of those techniques. So they knew the paintbrushers could’ve used technique A but publicly claim no.
This of course ignores all of the other evidence (including the furin cleavage site which was unknown to this particular family of coronaviruses but happened to be found in this coronavirus along with the only found in a pangolin sequence). Yet despite all of that they say lab leak isn’t plausible despite saying differently in private?

Soriek zeke5123 1yr ago

They didnt isolate the findings to a specific wet market. They are relying primarily on the PRC’s claims regarding the spread which is highly dubious.

No, the wet market samples are from two different international team of western scientists who went to Hanan market and found Covid samples on multiple different animals:

researchers swabbed walls, floors, metal cages and carts often used for transporting animal cages.

In samples that came back positive for the coronavirus, the international research team found genetic material belonging to animals, including large amounts that were a match for the raccoon dog, three scientists involved in the analysis said.

This was later matched with data reported by the Chinese CDC, as part of a study that specifically did not endorsed the market as the origin of the pandemic but rather just as a vector. Once the American scientists noticed a closer look suggested different conclusions, rather than signal boost this information the Chinese took the data down:

The swab taken from a cart there in early 2020, the research team found, contained genetic material from the virus and a raccoon dog.

“We were able to figure out relatively quickly that at least in one of these samples, there was a lot of raccoon dog nucleic acid, along with virus nucleic acid,” said Stephen Goldstein, a virologist at the University of Utah who worked on the new analysis. (Nucleic acids are the chemical building blocks that carry genetic information.)

After the international team stumbled upon the new data, they reached out to the Chinese researchers who had uploaded the files with an offer to collaborate, hewing to rules of the online repository, scientists involved with the new analysis said. After that, the sequences disappeared from GISAID.

It is not clear who removed them or why they were taken down.

For the case spread, what we consider the first cases are from their hospital system and were before anyone understood what Covid was, including the Chinese, and before the Chinese government claimed that the wet market was the origin. The bulk of it comes from WHO backdated assessments of patients that China explicitly did not report as "Covid cases" in their system, but that outside scientists have categorized by retroactively assessing symptoms.

Of the initial 41 people hospitalized with unknown pneumonia by 2 January 2020, 27 (66%) had direct exposure to the Huanan Wholesale Seafood Market (hereafter, “Huanan market”). These first cases were confirmed to be infected with a novel coronavirus, subsequently named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and were suffering from a disease later named coronavirus disease 2019 (COVID-19). The initial diagnoses of COVID-19 were made in several hospitals independently between 18 and 29 December 2019. These early reports were free from ascertainment bias because they were based on signs and symptoms before the Huanan market was identified as a shared risk factor (5). A subsequent systematic review of all cases reported to China’s National Notifiable Disease Reporting System by hospitals in Wuhan as part of the joint WHO-Chinese “WHO-convened global study of origins of SARS-CoV-2: China Part” (hereafter, “WHO mission report”) showed that 55 of 168 of the earliest known COVID-19 cases were associated with this market...

The 2021 WHO mission report identified 174 COVID-19 cases in Hubei Province in December 2019 after careful examination of reported case histories (7). Although geographical coordinates of the residential locations of the 164 cases who lived within Wuhan were unavailable, we were able to reliably extract the latitude and longitude coordinates of 155 cases from maps in the report (figs. S1 to S8).

Although early COVID-19 cases occurred across Wuhan, most clustered in central Wuhan near the west bank of the Yangtze River, with a high density of cases near to, and surrounding, the Huanan market

It goes on to list other ways they approached the data, non-Covid social media check ins to control for population density, downloads of Covid apps, etc.

Perhaps China was so ahead of the curve they before they recognized they had a viral disease and took any steps to respond to its containment they preemptively censored a bunch of hospital records from nearby to the lab and carefully left lists of symptoms concentrated around certain areas such that they would produce statistical signifigance across a variety of tests in order to lead researchers down the wrong path, but combined with finding the samples at the Hanan market it seems less likely.

To be clear though, this paper does not even say that Covid originated from the market. The point of the paper is to show that what were considered non-natural characteristics of Covid requiring human-intervention-based explanations actually do have examples occuring in nature. This is the sum total of what they have to say on the market:

As many early cases of COVID-19 were linked to the Huanan market in Wuhan, it is possible that an animal source was present at this location.

Back to you:

This despite there is decent evidence that is not where zebras were first seen.

What evidence?

They privately noted serial passage was an easy way to make it look like humans and Wuhan knew of those techniques. So they knew the paintbrushers could’ve used technique A but publicly claim no.

Nobody, especially including the authors, argues that it is outside the realm of literal scientific capability for Covid to be man-made. I think your comment is blurring two things though:

Are we able to 100% determine whether it Covid was natural or man-made? The answer is of course no, which is why our research has focused on determining whether covid's human-binding characteristics (the RBD and polybasic furbin cleavage site) are novel characteristics that would suggest human creation, or whether they appear naturally which suggests a more parsimonious explanation.
Do the things we can observe about Covid show signs that would suggest human intervention or natural evolution? The answer seems to be the latter:

As noted above, the RBD of SARS-CoV-2 is optimized for binding to human ACE2 with an efficient solution different from those previously predicted. Furthermore, if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone

This of course ignores all of the other evidence (including the furin cleavage site which was unknown to this particular family of coronaviruses but happened to be found in this coronavirus along with the only found in a pangolin sequence).

They did indeed cite research demonstrating that polybasic furin cleavage sites can arise naturally. They also point out that polybasic furin cleavage sites are unlikely to come about via laborotory cultures without being inculated in living hosts. Is there other evidence you're thinking of?

Yet despite all of that they say lab leak isn’t plausible despite saying differently in private?

You're responding to my parent comment where I pointed out that their main uncertainty was that they had never seen an RBD site like Covid-19's in nature, then more research emerged showing exactly that, then a month and a half later they came with a stronger stance incorporating the new relevant evidence.

I honestly don’t have time to respond to you in full right now but the basic problem is you are talking about data from early 2020 after covid had been spreading in Wuhan for at least one month. That doesn’t show anything re origination.

Intelligence communities seem to believe the leak occurred in perhaps October near Wuhan.

As for China being ahead of the curve, remember all of this videos of a seemingly healthy person walking in the street and then collapsing from covid? That suggests the Chinese government was aware and started bullshiting.

With respect to furin cleavages, read what Wuhan lab were proposing! It was what occurred.

Finally, the whole recombinant point was according to one author of the paper when he appeared on the Megyn Kelley podcast something that cane out after he spoke with Fauci (well before the paper was finalized). That was, it was a matter of a few days. Maybe you are right but that means there was yet another lie in the timeline.

Soriek zeke5123 1yr ago · Edited 1yr ago

This would be true of samples but not of our case tracking. It's fine to say all data should be taken with a grain of salt, but you overstate our reliance on China given we are not using their reported cases. Saying "everything is a lie" does not bring us closer to having evidence for a lab-oriented origin.

It wasn't what occured though right? EcoHealth has multiple coronavirus grant proposals; the only one to my knowledge that proposed a furin cleavage site was rejected, and was supposed to have happened not in Wuhan but North Carolina.

The argument - not just from Andersen et all but most scientists I've seen weigh in - is that human molecular engineering has some established, effective ways to create a cleavage site. If the goal is to intentionally create a virus that can latch on to humans then you use one of the most effective ways to do that. Instead Covid has a distinctly suboptimal cleavage site that is more likely to have evolved randomly rather than have been used by a University of North Carolina scientist with better tools at their disposal, and furthermore that it would be hard to sustain a laborotory environment. I cited them writing on that in the study but here's from the Congressional testimony:

I mean, again, there would be certain -- again, if you insert the site into the virus, which has been done for all the viruses, including coronaviruses, then typically people use what we know to be a good furin cleavage site.

There are multiple versions of a furin cleavage site, right? There's optimal ones and there's sub optimal ones. And when research have done this in the past, they do with, like, we know that this is an optimal furin cleavage site. We know it will definitely be cleaved by furin. That's what people insert.

This is not that, right? It's a sub optimal site. It is good enough to be cleaved by furin, but it's not a great site and, in fact, has since evolved to become a beta site in things like Omicron and alpha and other variants, right...

Q -- is it possible, or has it been done before -- two separate questions -- to gain it in a coronavirus just through either culture or animal passage?

A I don't believe so. So, again, this is where, you know, my early thinking was this, that I thought it was possible, but I just think that -- because, again, I've looked, you know, everywhere for a reference that would suggest that it can be gained during passage, for example, and I just haven't found anything. And, again, what's important here for SARS 2, specifically we know that it has a tendency to actually lose it as its passage in tissue culture.

if it loses it in a laboratory, then it ain't going to gain it, right? It's one or the other. The fact that it even loses it is interesting because -- and it probably has to do with the fact that furin cleavage sites are probably important for respiratory transmission of a virus, which is probably also why they're pretty rare in bats, right, because bats don't transmit viruses between themselves in the respiratory route. They do this with the good old fecal-oral route. And that's different than that in mammals. That's why a lot of coronaviruses in rodents, for example, have furin cleavage sites because that's a respiratory route. In bats it's not a respiratory route, so there the furin cleavage sites are rarer, although still present.

When you're in tissue culture, that's a totally artificial selection environment, right? It's nothing to do with a respiratory route, for example. The furin cleavage site itself probably makes the virus less stable, and that's probably detrimental in tissue culture. And that means that if there is a version of the virus that emerges in this tissue culture experiment that doesn't have the furin cleavage site, then they'll out-compete all the other viruses in the same cell, and very quickly you'll end up with basically having viruses that -- viral particles that don't have that furin group,

Given that argument for the lab origin seems to rest on cleavage insertion that wasn't funded and wasn't going to happen in Wuhan, probably we stick with the simpler explanation.

No idea what you mean. The email expressing uncertainty is from Feb 1st, the finalized paper was released March 17th. They testified under oath to that timeline and a panel of politicians trying to embarass them couldn't find anything closer in time that would reflect significant doubts.

Throughout all this I've said that I fully consider politicization of this study to be a concern and that I personally consider a lab leak possible. But the arguments people are making against this study are pretty weak.

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