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Culture War Roundup for the week of July 24, 2023

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Since my 'don't trust Science' threads were already toeing the line between 'Pepe Silvia!' and schizophrenic (fair!) (I didn't even touch the four-part follow-up), Nate Silver summarizes better than I can :

Here’s the scandal. In March 2020, a group of scientists — in particular, Kristian G. Andersen the of The Scripps Research Institute, Andrew Rambaut of The University of Edinburgh, Edward C. Holmes of the University of Sydney, and Robert F. Garry of Tulane University — published a paper in Nature Medicine that seemingly contradicted their true beliefs about COVID’s origins and which they knew to be misleading. The paper, “The proximal origin of SARS-CoV-2”, has been cited more than 5,900 times and was enormously influential in shaping the debate about the origins of COVID-19.

We know this because of a series of leaked and FOIAed emails and Slack messages that have been reported on by Public, Racket News, The Intercept and The Nation along with other small, independent media outlets. You can find a detailed summary of the claims and a copy of the emails and messages here at Public. There’s also good context around the messages here (very detailed) or here and here (more high-level).

((Silver's links carry the touchstones of conspiracy paranoia, like an emphasis on coverups and literally-by-the-minute analysis of claimed coordinated action, which would normally discourage me from pointing to them, except they also happen to be reasonable factual descriptions.))

To be clear, this isn't a case of some barely-related scientists from nearby offices in slightly-related fields being somewhat more open-minded. These documents demonstrate each and every single author of the paper held some of the exact same concerns about the proposed wet market origin as piles of shitposters and too-online dogs, often pointing to the exact same evidence... privately. In public, they named opponents giving these possibilities conspiracy theorists for naming options they were accepting privately, or drawing out a web that actually existed. Jeremy Farrar would send e-mails giving 50:50 odds on natural (and non-natural, mostly serial passage) origins at the same day he was shopping around early drafts of the paper; while he isn't on the author list, that's its own mess. To be fair, they do change positions in private, as information comes around and as debate occurred. But they remain far from as convinced as they pretended in public, not just during publication but months later, and it's exceptionally clear that the political and pragmatic ramifications drive that.

Nor was this filled with caveats and used or intended to be used solely as a small opinion piece. It contains a few limited cautions about available data's ability to discriminate from evolution at the wet market from cryptic adaptation among humans, but serial passage was actively dismissed by an incoherent mush that steps from animal models to purely in vitro considerations. The paper's authors and 'unrelated' academics (who had been heavily involved in discussions with the paper's authors behind closed doors) cited this not-a-paper at length to justify treating anyone even considering the possibility of just serial passage or an accidental lab leak to be a conspiracy theory that must be shut down, all the way from casual shitposters to federal politicians, including those who advocated specifically serial passage or a purely transport-focused accident. These private messages make clear that wasn't some unintentional side effect, but a if not the specific goal.

Nor was this limited to the broadest strokes: at best, these otherwise closely-knit scientists did mention important information not widely available to random shitposters to each other, such as the rarity of live pangolin trafficking, or the animal makeup of the wet market's official shipments, or a variety of information about possible serial passage techniques, all of which were carefully excluded from the final paper. Some writers received confidential notice of discovery of RmYNO2, and after finding that it wasn't itself more helpful to their point than other already-known genomes, decided to instead obliquely reference it as possible to make a 'prediction', because the Texas Sharpshooter's approach would have been too on the nose.

And that's the stuff that came through FOIA-able emails or broad and leakable Slack channels. The messages show many people involved transitioning to private e-mails, to phone calls, to unrecorded Zoom meetings, often dropping to very clipped wording during that transition: they knew this could eventually be public, and they knew other conversations would not.

None of this amounts, as many COVID skeptics are calling it, to research fraud; I'm not even sure it fits most definitions of academic misconduct. But that's mostly because the publication didn't have enough numbers or analysis to need to actively lie: this paper has no pixels to check for signs of photoshopping, nor specific population numbers to hit with GRIM. Silver has joined calls to retract the paper, but Nature's staff have already said that "Neither previous out-of-context remarks by the authors nor disagreements with the authors’ stated views, are, on their own, grounds for retraction." It ain't happening.

Silver proposes that the scientists were motivated by some combination of :

  • Evidence of a lab leak could cause a political backlash — understandably, given that COVID has killed almost 7 million people — resulting in a reduction in funding for gain-of-function research and other virological research. That’s potentially important to the authors or the authors’ bosses — and the authors were very aware of the career implications for how the story would play out;
  • Evidence of a lab leak could upset China and undermine research collaborations;
  • Evidence of a lab leak could provide validation to Trump and Republicans who touted the theory — remember, all of this was taking place during an election year, and medical, epidemiological and public health experts had few reservations about weighing in on political matters.

These aren't exactly the most charitable framings for each possibility, if perhaps more charitable than focusing on Anderson's certainty this paper got him tenure. But with a more forgiving description, I get something along the lines of :

  • Prohibitions on gain-of-function and other virological research could undermine pandemic responses (and we wouldn't know about past prevented pandemics, after all), or drive research to locations with worse biosecurity or oversight (than BSL2?).
  • Bad relations with China could undermine future pandemic responses or escalate to a 'hot' war.
  • Trump and Republicans responding to a China with marginal scientific research could result in another Korematsu, undermine future pandemic responses, or escalate to a 'hot' war.

Perhaps @Chrisprattalpharaptor can do better. But even if these somewhat earnest reasons that business or political tribe might have controlled what these scientists were willing to say publicly, or if there was some more noble cause that they held above providing an accurate model of the world, it's still something other than providing an accurate model of the world. Which is what, supposedly, was their job.

Worse, few of these matters stop here. Trivially, a lot of academics and casual observers are saying that even if the Nature op-ed authors were playing fast-and-loose with the facts at the time, we since have a ton of evidence in favor the wet market/natural origin side and very little recently published in favor of serial passage or any intentional manipulation, and normally drawing big charts claiming almost all the experts in a field were conspiracy to hide The Truth would be the sorta thing you do shortly before the nice men give you a coat with extra-long sleeves and take you to get some anti-psychotics. Except all of the above.

The guys who authored the paper testified before a maximally hostile Congress last week. I was ready for them to get torn apart and surprisingly it left me less convinced of the criticisms against them.

The pangolin thing, as covered by the Public Substack and other places I've seen it repeated, seems to be misframed. The scientists never claimed that it was the actual origin of Covid; they explicitly says it's a different virus, just similar in structure. The argument is that no one (including any of the lab leak proponents, to my knowledge) seems to think the pangolin coronavirus variant, 600 miles away from the Wuhan lab, was also man-made, which raises the odds that a virus very similar to Covid-19 could arise naturally.

The distance in time between the scientists saying they weren't certain about how something like the Receptor Binding Domain in Covid-19 could manifest in nature, and them changing their minds and publicly supporting a natural origin theory, wasn't an abrupt turn around of a few days, as alleged, but rather forty five days. During that timeframe the pangolin samples with similar RBDs were discovered, raising odds that this kind of thing could be naturally evolved. In contrast, the site being studied in the EcoHealth proposal was genuinely different than that in Covid-19.

Beyond that, the main thrust of their argument is that the first samples were found in the Hanan market and the first cases in the area surrounding the market, not in the areas surrounding the Wuhan Virology Center. As far as I know nobody has contradicted this, though I don't really follow it and could be wrong.

I think the concerns about how the process was politicized, especially by bueaucrats worried about conflict with China, are still valid - welcome to government though. Claims of a vast Orwellian conspiracy on part of our neoliberal overlords I think are a little unconvincing given that our government has also argued that it probably was a lab leak. In fact, right now six agencies have weighed in and none agree - the DOE and FBI think a lab leak was most plausible, four other agencies plus the NSC suspect natural origins. Almost all of them have framed their results with "low confidence," but you can pick whichever result you like and still say the government agrees with you.

I personally consider the lab leak somewhere between possible and likely, but don't really care where Covid came from. Even if it was caused by research conducted by China and America, the two most powerful countries on earth are obviously not going to pay any kind of penalty.

The thing that frustrates me about the pangolin argument is that it is like reverse zebra with hooves.

As one of the scientist put it before, he was worried about the recombination as he hadn’t seen that before but then he found out it happened once in a pangolin so it is logical to assume it happened here. Sure, that raises the odds slightly. But if I studied horses and many times when I hear hooves I see horses but once I see a zebra doesn’t mean it is likely that on the 101th time I hear hooves I should suspect a zebra; especially when I am located in a place that is painting horses black and white.

Imo it's more like if we had only seen horses, then one day we saw a Zebra and were like "woah, what gives, the only explanation is some crazy guy must have painted that horse."

But then later we went to Kenya and saw a bunch of Zebras and were like "huh, I guess that is possible by the laws of evolution and doesn't require man-made intervention".

I don’t disagree with your conclusion. But at the same time, the existence of zebras in Kenya doesn’t mean zebras are super likely elsewhere which is what the scientist inferred.

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.

  1. 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.

  2. 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.

  3. 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?

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:

  1. 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.

  2. 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

Back to you:

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.

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