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"Either a zoonotic virus crossed over to humans fifteen miles from the biggest coronavirus laboratory in the Eastern Hemisphere."

As they say, 'you couldn't make it up'. Or, 'truth is stranger than fiction'. It does *seem* very suspicious co-incidence that a new virus that would turn into a world-wide pandemic just happened to pop up out of nowhere on the doorstep (as it were) of a specific institution dedicated to doing this kind of research, but there was no connection. And yet we seem to be forced to accept that this is so.

Congratulations and gratitude for sitting through 15 hours of video to produce this post! And I did appreciate the Linear B/Lineage B joke.

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Isn't it a reverse correlation issue though, the lab is situated there because it's an area where coronaviruses were found in the past.

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No. Wuhan is both far from bat habitats and far from south China, where wildlife consumption is popular.

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I would also add that concerns about a lab leak in Wuhan are not post hoc. There were concerns about lab safety in Wuhan in the scientific literature published from 2015 onwards. If you were to ask people in the know prior to the pandemic - where in the world would there most likely be a lab accident with a coronavirus, Wuhan would have been top of the list given that it has the world's largest collection of bat coronaviruses, and did incredibly dangerous experiments on them at BSL-2.

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Concerns about the wet market are not post hoc either. An Australian virologist posted pictures and video from visiting the HSM back in 2014, noting it would be an ideal breeding ground for coronavirus pandemic.

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Actually, Wuhan was used as a negative control for coronavirus antibodies in a WIV study prior to the pandemic. i.e. It was thought a v unlikely place for a spillover prior to the pandemic.

Shi Zhengli has said she never thought a spillover would occur in Hubei

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Also, the Australian virologist you refer to (Eddie Holmes) was in Wuhan because he was visiting the Wuhan Institute of Virology! He collaborated with the WIV on RatG13, one of the closest known relatives to covid, in 2018 (and then apparently forgot that he had done this_

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...and therefore... what? I don't understand your point here at all. I know he was visiting WIV. We already knew about RatG13. So?

Gonna combine 2 threads to reduce confusion:

> Shi Zhengli has said she never thought a spillover would occur in Hubei

Did she think a spillover would occur in the WIV? It's kind of weird to have this sentence right after your prior one... are we just cherry picking experts now? Some people identified wet markets, including HSM, ahead of time. Some people identified WIV ahead of time. Seems like kind of a wash to me.

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There's extensive bat populations in the cave systems of Enshi in western Hubei aren't there? And the whole province is within the range of the rufous horseshoe bat. There wouldn't be large populations in the area around Wuhan itself since it's heavily urbanized, but hunters would bring them into the city to sell them given that its the provincial capital and richest city in the nearby area by a far margin.

Also raccoon dogs are common across rural areas of central and eastern China and are another possible source.

Obviously I don't know what the internal reasoning of the Chinese CDC was for deciding where to put their research into coronaviruses. But Wuhan, as 7th largest city in China, fairly centrally located, and in the region of the relevant animals would seem a good choice. Chengdu is the only larger city in central China, but is much further west and has less tech sector, so presumably would be harder to get good people

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You also couldn't make it up that the virus appeared in a wet market that was identified years ago as a plausible place for a pandemic to appear. These kinds of coincidences are the rule, rather than the exception, for real-world events.

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Re-reading your comment, I realize you meant that as a joke, sorry.

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I was once at Disney World (over a thousand miles from my hometown of population 3000) and met a person from my hometown who also happened to be there that day. We had 0 idea the other was going.

This is a lot less weird than if I met them at a random gas station in rural Mongolia, but it's still pretty weird!

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While on a high school trip, my classmates & I ran into someone else from our class (not associated with the extracurricular organization that had arranged the trip) on the second level of the Eiffel Tower.

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Mar 31·edited Mar 31

I once was on random free city tour in another country ~5,000 from my home with maybe 10 people in total and met another person who lived within five miles of me back home (same suburb, so not like a city of millions either).

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Or as Jon Stewart put his perfectly natural skepticism:

“‘Oh, my God, there’s been an outbreak of chocolaty goodness near Hershey, Pa. What do you think happened?’ “Like, ‘Oh I don’t know, maybe a steam shovel mated with a cocoa bean?’ Or it’s the [expletive] chocolate factory! Maybe that’s it?”

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How many labs do coronavirus research?

I've seen the argument that it's suspicious that COVID appeared near one of China's only two BSL-4 labs, but in this debate the *proponents* of the lab leak hypothesis said that the WIV recklessly did coronavirus research in a BSL-2 lab, not in the BSL-4 lab. (The WIV has a BSL-4 lab as well as BSL-3 and BSL-2 labs.) It's less suspicious that COVID popped up near a coronavirus lab if dozens of labs do such research than if this is one of the few such labs in the world.

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Yeah, the emphasis on the pro-lab leak side puts less emphasis on the BSL-4 designation and much more weight on "there are/were two labs that were at the forefront of bat coronavirus research, WIV and one in North Carolina." Plus WIV seems to have been doing GoF research.

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15 miles is a long way away for it to travel without it being found first close to the lab or close to the families of the lab.

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founding

Cities are designed to make distance and geography irrelevant. They aren't perfect about it, but the intent is that your interactions are defined by your social and economic network, and the physical infrastructure allows you to hop between those nodes without concern for what boring irrelevant-to-you terrain is between them. You probably barely notice that stuff when you're on the freeway, and you can't see it at all from the subway,

Again, that's only an ideal which is imperfectly approached. But what we need to know isn't "what's the distance from the WIV to the HWSM", it's "how many WIV lab techs have families with a taste for fresh seafood or exotic bushmeat?" If the answer is "lots", then the 15 miles won't stop them and/or their wives from schlepping their virus-laden selves over to the market.

Or maybe there's some class or cultural divide that means nobody working in the WIV's labs is going to shop at the HWSM; I don't know. That information, which would be very informative here, is hard to come by. The geographic distance, which isn't nearly as informative, can be read off any online nap; a few clicks and calculations, So that's what most people use; looking for their lost keys under the streetlight.

My prior, starting from ignorance, is that the odds of an average WIV lab tech('s wife) visiting the HWSM, is the same as the odds of an average Wuhan resident visiting that market. Which is something we can calculate.

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> Cities are designed to make distance and geography irrelevant.

They really aren’t. Cities are the slowest way to travel from A to B by car - which is what we are talking about with the 15 miles. It’s shorter as the crow flies. As for public transport we would have to look

Into it I suppose but if the lab Typhoid Mary was taking the infection to the wet market on a train then you expect the spread of the disease along the track of the line.

My belief is a zoonotic answer but if the virologists come out with a conclusive peridot that it’s artificial the lab leak isn’t the only game in town.

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Several recent papers challenge the core arguments relied on for Huanan Seafood Market origin in the Rootclaim debate. Also, Miller incorrectly claimed the N501Y mutation would result from passage in hACE2 mice (he mixed them up with BALB/c mice).

1. Samson et al (2024) estimate likely point of emergence between August and October 2019. Rendering the December 2019 cases and January 2020 market samples irrelevant to origins.

They refer to horizontal gene transfer of the spike gene from BANAL bat CoVs in Laos to pangolin CoVs occurred in mid 2018. "Horizontal gene transfer" can occur in the wild (rarely) or can be induced in he lab artificially "transgenic". In other words a nice code word for lab engineered virus leak.

Samson S, Lord É, Makarenkov V (2024) Assessing the emergence time of SARS-CoV-2 zoonotic spillover. PLOS ONE 19(4):

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0301195

2. Dietrich Stoyan, Sung Nok Chiu, Statistics did not prove that the Huanan Seafood Wholesale Market was the early epicentre of the COVID-19 pandemic, Journal of the Royal Statistical Society Series A: Statistics in Society, 2024;,

https://academic.oup.com/jrsssa/advance-article-abstract/doi/10.1093/jrsssa/qnad139/7557954

3. Lv et. al. (2024) found new intermediate genomes so the multiple spillover theory is unlikely (it was anyway given lineage A and B are only two mutations apart as François Balloux, Virginie Courtier-Orgogozo and Jesse Bloom have observed). Single point of emergence is more likely with lineage A coming first (as Nick Longrich points out below). The market cases were all lineage B so not the primary cases. Their findings are consistent with Caraballo-Ortiz (2022), Bloom (2021).

Jia-Xin Lv, Xiang Liu, Yuan-Yuan Pei, Zhi-Gang Song, Xiao Chen, Shu-Jian Hu, Jia-Lei She, Yi Liu, Yan-Mei Chen, Yong-Zhen Zhang, Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak, Virus Evolution, Volume 10, Issue 1, 2024

t.co/50kFV9zSb6

4. Jesse Bloom (2024) published a new analysis showing that genetic material from some animal CoVs is fairly abundant in samples collected during the wildlife-stall sampling of the Huanan Market on Jan-12-2020. However, SARS-CoV-2 is not one of these CoVs.

Jesse D Bloom, Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market, Virus Evolution, Volume 10, Issue 1, 2024,

t.co/rorquFs1wm

5. Michael Weissman (2024) shows a model with ascertainment collider stratification bias fits early Covid case location data much better than the model that all cases ultimately stemmed from the market. George Gao, Chinese CDC head at the time, acknowledged this to the BBC last year - they focused too much on and around the market and may have missed cases on the other side of the city).

Michael B Weissman, Proximity ascertainment bias in early COVID case locations, Journal of the Royal Statistical Society Series A: Statistics in Society, 2024;

https://academic.oup.com/jrsssa/advance-article-abstract/doi/10.1093/jrsssa/qnae021/7632556

6. Chen et al (2024) discuss how using the Grunow-Finke assessment tool lab origin looks at least as likely.

Chen, X., Kalyar, F., Chughtai, A. A., & MacIntyre, C. R. (2024). Use of a risk assessment tool to determine the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Risk Analysis, 1–11. https://doi.org/10.1111/risa.14291

7. The anonymous expert who identified coding errors in Pekar et. al. leading to an erratum last year has found another significant error. Single spillover looks more likely. t.co/GAPihZu51P

8. The argument that an engineer wouldn't make the furin cleavage site with the features of SARS-CoV-2 overlooks it resembles that of MERS in several structural and functional ways, and the sequence looks quite similar. In 2019 WIV researchers were involved in MERS research. Dr Andreas Martin Lisewski discusses similarities with a MERS infectious clone described in 2017 here. t.co/fAVUlJu0TK

9. Broad Institute biologist Alina Chan also observes the S1/S2 FCS PRRA insertion in SARS-CoV-2 generates a Class IIS restriction enzyme site (BsaXI). This was used by WIV and Ralph Baric at UNC previously. The full DEFUSE proposal available since the debate strengthens the argument of Bruttel et al. Specifically, the use of BsmBI, 6 fragments, and leaving the sites in). https://usrtk.org/covid-19-origins/scientists-proposed-making-viruses-with-unique-features-of-sars-cov-2-in-wuhan/

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What you say about raccoon dogs here is mistaken. Raccoon dogs are not a plausible intermediate host for sars-cov-2 on the basis of information that has been known since 2021. There are several considerations.

1. Xiao et al (2021) - https://www.nature.com/articles/s41598-021-91470-2%E2%80%8B%E2%80%8B%E2%80%8B , which includes a co-author of Worobey et al (2022), a leading zoonosis paper states in table 1 that the raccoon dogs were wild caught in Hubei, not farmed as you assert in the piece. This alone rules out raccoon dogs as plausible hosts for two independently sufficient reasons. Firstly, there is unanimity in the literature that the bat ancestral virus to SARS-CoV-2 is in southern Yunnan or South East Asia. Everyone agrees with this, including Shi Zhengli. If a species was wild caught in Hubei, then there would be no explanation of how it acquired the ancestral bat virus, given that Hubei is 1000 miles from southern Yunnan.

Secondly, a mystery of sars-cov-2 is how it acquired the furin cleavage site that makes it so transmissible. There are 850 known sars-like coronaviruses, and only one with a furin cleavage site. According to private messages exchanged by proponents of zoonosis, the furin cleavage site could not have been acquired in the market because the density of animals was too low (only 3-4 per cage). When avian influenza acquires a furin cleavage site that occurs on farms with thousands of chickens densely packed, i.e. not in the wild and not when there are a handful of animals in cages in a market. https://usrtk.org/covid-19-origins/visual-timeline-proximal-origin/

2. Wang et al (2022) https://academic.oup.com/ve/article/8/1/veac046/6601809 also confirms that the raccoon dogs were wild caught in Hubei. What's more, Wang et al (2022) tested 15 wild raccoon dogs of suppliers of Wuhan markets, including the Huanan market, in January 2020 and found them to be negative for SARS-CoV-2. On average, 38 raccoon dogs were sold across the four markets in Wuhan from 2017 to 2019. So, the 15 raccoon dogs likely comprised nearly the whole inventory of raccoon dogs that would have been supplied to the Huanan market at the time.

In short, the raccoon dogs supplied to the market were tested and were negative. It is very strange that the raccoon dog narrative has persisted for this long given this public information. Even the strongest proponents of the raccoon dog hypothesis have walked back their bold claims that raccoon dogs are thost.

Xiao et al (2021) has a list of species sold at the Huanan market. I would encourage you to read that list and suggest which animals you think are plausible, and I will tell you why they are not actually plausible.

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I don't think there's a consensus that the ancestral virus is from Yunnan or SEA. No plausible immediate ancestor has been found anywhere. For what it's worth, high seroprevalence for SARS-related viruses have previously been found in Hubei:

https://www.science.org/doi/10.1126/science.1118391

Second, the line between wild-caught and farmed animals in the wildlife trade is blurry. For instance, there was a wildlife farm in Hubei where SARS was detected in palm civets. The farm contained a mix of wild-caught and farm-breed civets:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1153763/

I am still not convinced that racoon dogs were the intermediate host, since SARS-CoV-2 evidently has a very broad host range.

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While it is true that Sarbecoviruses have a wide range, direct bat ancestors to SARS-CoV-2 have a much narrower range considering bat and viral dispersion patterns. Still under investigations though, and politically sensitive topic.

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My point was specifically about SARS-COV-2, which can infect mammals from several different orders. And we don't know whether the restricted bat lineages are descendent from an ancestral generalist lineage, or if SARS-CoV-2 is descendent from a more restricted lineage.

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Si et al has a preprint out (zhengli shi is a co-author as well) adressing some of it by analyzing what makes RBD have broad or narrow ACE2 tropism. Seems broad tropism is ancestral

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There are SARS-like coronaviruses in bats in Hubei, but they are too distant from sars-cov-2 to be the ancestor virus.

Shi Zhengli of the Wuhan Institute of Virology stated in July 2021:

“We have done bat virus surveillance in Hubei Province for many years, but have not found that bats in Wuhan or even the wider Hubei Province carry any coronaviruses that are closely related to SARS-CoV-2. I don't think the spillover from bats to humans occurred in Wuhan or in Hubei Province”. (Cohen interview)

This is confirmed by wider bat sampling efforts by the Wuhan Institute of Virology and EcoHealth Alliance prior to the pandemic. (Fan et al 2019 - WIV team; Hou et al 2010, Latinne)

The WHO Joint Study report noted:

“Tests on samples of more than 1000 bats from Hubei Province showed that none was positive for viruses related to SARS-CoV-2” (p106)

The samples tested had 74% to 90% sequence identity to SARS-CoV-2,(annex F table 4) compared to 96.1% for RatG13 (from Yunnan), and 96.8% for BANAL-52 (from Laos).(Temmam)

From January 7th to 18th 2020, Wang et al (2022) collected samples from 334 bats around Wuhan. All were negative for SARS-CoV-2 or its progenitors.

Hassanin et al (2024) reported the “the results of several field missions carried out in 2017, 2021 and 2022 across Vietnam during which 1,218 horseshoe bats were sampled”.(Hassanin) They conclude that “For SARS-CoV-2 however, phylogeographic indicators provided very high support for an origin in the zone covering northern Laos, southern Yunnan and north-western Vietnam”.

Pekar et al (2023) argue that the ancestral host for SARS-CoV-2 is ‘very unlikely’ to be from Hubei. *Pekar et al are the main proponents of the zoonosis hypothesis*

“Considering the large distance separating the closest-inferred bat virus ancestors from where SARS-CoV-1 and SARS-CoV-2 each emerged (Fig. 3i,j) and the high dispersal velocities necessary to traverse the aforementioned distance (Extended Data Fig. 18), it is very unlikely that the lineages descending from the closest-inferred bat virus ancestors of SARS-CoV-1 and SARS-CoV-2) (which reached, respectively, Guangdong Province and Hubei Province solely via dispersal of these viruses through their bat reservoirs.”

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Another point - If the animals came from a farm, why were there approx 1-2 spillovers only in Wuhan city sufficient to cause an ongoing outbreak? If the farm had hundreds of raccoon dogs, why were they not numerous spillovers at other locations the farm was supplying? This is much easier to explain on the lab leak hypothesis.

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What is the standard structure of exotic meat suppliers to wet markets? Are they usually big operations that supply many markets on a weekly basis, or are they usually small mom-and-pop operations that turn over their entire inventory in a single transaction to a single market? I'm sure I'm presupposing a million false things in the way I've phrased this question, but I think some of this information would be relevant to knowing how much and whether your question is a significant one to ask.

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Hello, farm size varies a lot - for SARS-1 civet farms had around 100 civets per farm, but some bamboo rat farms have tens of thousands of animals. So, a lot depends on what the intermediate host was and how big the farm was.

The go to source on the suppliers to the Huanan market in particular is this washington post article by michael standaert https://www.washingtonpost.com/world/asia_pacific/china-covid-bats-caves-hubei/2021/10/10/082eb8b6-1c32-11ec-bea8-308ea134594f_story.html

which is cited by Worobey 2022. They say that the suppliers of the Huanan market were farms in Hubei.

They reported that reported that authorities closed 290 farms in western Hubei that accounted for between 450,000 and 780,000 animals. This suggests that there were 1,551 - 2,689 animals per farm. The number of spillovers posited by zoonosis proponents is around 8. None of these spillovers have actually been ascertained, they are the product of a (bad) model, and none of the official confirmed cases in the wet market worked at wild animal stalls.

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Is there any reason to expect that the farms that were closed were relatively equal in size, rather than some being tens of thousands of animals and some being only a few dozen? Is there any reason to expect that the farms that were closed had a distribution of sizes that is representative of the set of all potentially relevant farms?

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There is a lack of information on this front. The farmed live animals sold at Huanan were mainly from Enshi and "A clampdown on Enshi's wildlife trade at wet markets began on Dec. 23, 2019, according to state media, eight days before China publicly acknowledged the new virus. The head start in Enshi doesn't mean officials found something amiss: It could have been preventive, as rumors emerged of market vendors falling mysteriously ill in Wuhan. But it means evidence regarding Enshi's wildlife trade was erased before the world was aware of the existence of a novel coronavirus."

It would be very nice to know what the specific farms supplying the market were, but we don't have much information. But certainly one has to posit that the farms could not have been very large, otherwise there would have been numerous zoonotic spillovers at other markets, which were not observed

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So, do you think the Wang et al (2022) and Xiao et al (2021) papers are fraudulent or mistaken? Have you thought about calling for a retraction. Wang et al literally sought out the suppliers of raccoon dogs to the Wuhan markets and tested the wild caught raccoon dogs. All negative.

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They only tested for viruses, not antibodies. If you tested 100 random humans today, your chance of finding any specific endemic virus (e.g SARS-COV-2) would be quite low.

They also only state that some raccoon dogs were wild-caught, not that all were.

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As noted above, they tested the entire inventory that would have been supplied to Wuhan and said they were all wild caught - they were not farmed. Xiao et al (2021) also says the raccoon dogs for sale at Huanan were wild caught. Xiao et al (2021) includes a co-author of Worobey et al (2022), the main zoonosis paper.

They tested their tissue and blood samples by PCR. Zoonosis proponents posit that the approx 20 raccoon dogs for sale at the Huanan market in the month of November 2019 caused approx 8 zoonotic spillovers, of which 2 led to an ongoing outbreak (per Pekar et al (2022). Despite testing of the suppliers to that market in January, they were all negative.

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There are, to recap, three independently sufficient reasons to rule out raccoon dogs (1) wild caught, so no explanation of FCS acquisition; (2) wild caught in Hubei, so ~impossible that they were exposed to the ancestral bat virus; (3) the animals at the market suppliers were tested and tested negative.

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You seem very focused on a very narrow scenario for zoonosis, that is very similar to the consensus position for the SARS-CoV-1 outbreak. If you accept any scenario for one hypothesis, but any scenario for another, of course you will end up favoring the second hypothesis. If you could prove definitively that it couldn't be raccoon dogs, that's evidence against a zoonotic origin. But it's far from devastating. There were plenty of other susceptible animals at the market. Additionally, it was a dense area with an unusual amount of traffic from people with close contact to wildlife. I think you really need evidence of engineering in order to believe in a lab leak, and I with a molecular biology background, find the evidence on that profoundly unconvincing.

I would also argue that since it's CCP policy that the outbreak didn't happen in Wuhan, we should be skeptical of statements from Chinese researchers working in China.

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Xiao does not seem to declare that all raccoon dogs sold at the market were wild-caught.

>Approximately 30% of individuals from 6 mammal species inspected (labelled W in Table ​1) had suffered wounds from gunshots or traps, implying illegal wild harvesting (Table ​1).

>Raccoon dog fur farming is legal in China; however, due to a drop in fur prices, raccoon dogs are now frequently sold off in live animal markets, augmented by wild-caught individuals."

If raccoon dogs in any specific population were subject to any particular viral epidemic that burned itself out due to herd immunity, it's possible that no virus would be sampled two months later.

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Xiao et al Table 1 marks them as wild caught on the basis of injuries and vendor interviews.

As noted above, on average, 38 raccoon dogs per month were sold across the four markets in Wuhan from 2017 to 2019. So maybe like 20 were sold at the Huanan market in November 2019, which is less than one per day. Wang et al 2022 states

"We immediately started a surveillance investigation on the

origin of SARS-CoV-2 during 7–18 January 2020. Consequently,

the lung, liver, and intestinal tissue samples were collected from

mammals, which were captured in the rural area (Changxuanling and Yaoji towns) of Wuhan by three local traders for

vendors at animal markets including Huanan Seafood market

during 7–18 January. "

I.e. these are locally captured wild animals. The 15 raccoon dogs likely comprised nearly the whole inventory of raccoon dogs that would have been supplied to the Huanan market at the time.

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"If a species was wild caught in Hubei, then there would be no explanation of how it acquired the ancestral bat virus, given that Hubei is 1000 miles from southern Yunnan." How often do viruses travel a thousand miles? I was under the impression it's common.

"Even the strongest proponents of the raccoon dog hypothesis have walked back their bold claims that raccoon dogs are thost." Who are these strongest proponents?

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It is true that viruses often travel more than 1000 miles, the point is that they do not do this via bats which do not migrate that far. e.g. it seems that SARS traveled ~1000 miles from Yunnan to Guangdong via the civet trade. But with SARS-CoV-2, for animals wild caught in Hubei, there is no explanation of how they would have been exposed to the ancestral bat virus.

eg Angie Rasmussen is in many ways the face of the zoonosis hypothesis and a co-author on many zoonosis favoring papers. She said to the Atlantic “This is a really strong indication that animals at the market were infected. There’s really no other explanation that makes any sense.”

Then she said this after the Bloom critique "As a co-author of the “raccoon dogs saga” report, it’s disappointing to see a journalist outright lie about our work. We never claimed to find infected animals."

https://twitter.com/angie_rasmussen/status/1651976430773731336

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> She said to the Atlantic “This is a really strong indication that animals at the market were infected. There’s really no other explanation that makes any sense.”

> Then she said this after the Bloom critique "As a co-author of the “raccoon dogs saga” report, it’s disappointing to see a journalist outright lie about our work. We never claimed to find infected animals."

I'm not sure what this is supposed to prove. There's no contradiction.

If I go into a bathroom and smell shit, there's a really strong indication that someone took a dump in there. There's really no other explanation that makes any sense. But that doesn't mean I found a turd in the toilet.

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I was responding to this: "Even the strongest proponents of the raccoon dog hypothesis have walked back their bold claims that raccoon dogs are thost." Who are these strongest proponents?"

She said "there is no explanation that makes sense apart from an infected raccoon dog". She then said that this doesn't imply that a raccoon dog was infected.

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No. She's saying that all signs point to an infected raccoon dog, and that they have not found an infected raccoon dog.

A detective finds a body. All signs point to a gunshot wound. He has not found a bullet or a gun. It doesn't mean he's changed his mind, or that it's now necessarily more likely that the guy lying on the ground with a big hole in his head died of strangulation.

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We might have to agree to disagree here.

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Except that animals were not all wild caught in Hubei. This may be part of what tripped up Saar during the debate -- lab leak supporters have spent the past four years repeating things that aren't necessarily true and creating an epistemic bubble for themselves.

In reality there are many ways a virus from southern China could have made its way to a market selling wildlife in central China. For instance the markets in Wuhan seem to have sourced raccoon dogs and civets from farms in a mountainous region called Enshi about 630km to the west of Wuhan, nearly halfway to Yunnan province. Enshi has some of the largest cave systems in the world and there's no testing of bats or farmed animals from there that's been released so far. This is the region, western Hubei, where animals were found infected with SARS-CoV-1 back in the early 2000s. https://www.independent.co.uk/asia/china/covid-coronavirus-bats-caves-hubei-b1940443.html

We also know that the Huanan Market also imported at least some animals such as bamboo rats directly from southern Yunnan province, as well as Guangxi. And these are only the sources we know about...it's unclear exactly where the raccoon dogs sold at the time of the outbreak came from.

Meanwhile the evidence at the market does seem to point to raccoon dogs. The store where they were sold appears to be the most likely source of the outbreak within the market. Positive samples were found on a cage used for holding them, as well as a tool used for stripping fur off the animals. That doesn't prove they were the species that spread the virus to humans but there's definitely not a good basis to rule it out.

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As noted above, there is consensus in the literature that the ancestral bat virus is not in Hubei. So, you are going against all of the scientific literature here, including Pekar et al (2023), who are leading proponents of zoonosis.

The bamboo rats you are referring to I believe were not live animals but frozen or refrigerated animal products. See the Gao teams' report - https://www.nature.com/articles/s41586-023-06043-2

Worobey et al cite the washington post article which says that:

“A person with knowledge of the Wuhan market supply chains, who spoke on the condition of anonymity to protect his contacts, told The Post that live animals sold at markets in Wuhan were sourced from Hubei, particularly Enshi and Xianning prefectures, as well as from Hunan and Jiangxi provinces.”

Further confirmation for this is provided by the fact that:

“A clampdown on Enshi's wildlife trade at wet markets began on Dec. 23, 2019, according to state media, eight days before China publicly acknowledged the new virus. The head start in Enshi doesn't mean officials found something amiss: It could have been preventive, as rumors emerged of market vendors falling mysteriously ill in Wuhan. But it means evidence regarding Enshi's wildlife trade was erased before the world was aware of the existence of a novel coronavirus.”

I don't understand why you think the raccoon dogs were not wild caught locally. Xiao et al Table 1 says this explicitly, as does Wang et al 2022

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Yes but did you read that Washington Post article? It's actually the same as this article I posted in the comment above: https://www.independent.co.uk/asia/china/covid-coronavirus-bats-caves-hubei-b1940443.html

It seems to be saying that many animals were from farms in Enshi where civets and raccoon dogs were raised. That's a significant distance from Wuhan and yet you're pointing to testing of the 15 raccoon dogs from within the Wuhan city limits itself.

As far as the ancestral virus not being from bats in Hubei that may be true but like I mentioned SARS-CoV-1 also somehow infected animals in western Hubei. So there are certainly some unexplained details but I don't think any of this makes a spillover to humans from raccoon dogs or civets impossible at all. Remember the zoonotic origin doesn't need to be something as simple as it spilling over from bats to one species of animal that then infects humans at the market. It could have spread between multiple species just as COVID did after infecting humans.

Also the reported shutdown of these markets in western Hubei a week before the Huanan Market was closed is interesting and that alone would seem to call the lab leak explanation into question.

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Mar 29·edited Mar 29

The 15 raccoon dogs were traced from suppliers of raccoon dogs in the Huanan market. It's not that they randomly sampled raccoon dogs in Wuhan. They did this over 11 days. Around 38 were sold on average per month. so, the raccoon dogs they tested likely accounted for the entire raccoon dog inventory in Wuhan at the time.

The wapo article is about the farms supplying the market, but Xiao et al says that not all of the animals sold at the market were farmed. Worobey et al also says this!

fwiw I think the infected animals for SARS in western Hubei is disputed though haven't looked into it.

Shutting down of the farms is not evidence against lab leak. Some parts of the government clearly thought it was a zoonosis and acted accordingly in Dec and Jan, which is eg why they disinfected the market in Jan.

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1) It's not clear if that report was indicating that ALL animals were wild-caught or just some. There was an interesting incident back in 2020 where a Chinese environmental NGO wrote to the Wuhan Forestry Bureau (responsible for regulating the wildlife trade in Wuhan) asking about animal sales at a single store at the Huanan Market: https://cbcgdf.wordpress.com/2020/05/31/breaking-news-cbcgdf-policy-and-research-department-received-a-response-about-the-dazhong-livestock-game-stall-at-the-wuhan-south-china-huanan-seafood-market/

The Forestry Bureau responded with a list of sources for the store -- which included raccoon dogs sourced from a farm where mink and foxes were also bred. So in at least some cases, they were sourced from farms.

2) This study doesn't say that all raccoon dogs were wild-caught and testing 15 animals from one location is a ridiculous number to draw a conclusion from.

Overall the wildlife trade in China is difficult to track with animals being raised on farms but also poached from the wild, often shipped long distances, with some such as pangolins trafficked illegally. We never got a full accounting of animal sales at the Huanan Market -- in spite of the post above by the Chinese NGO, this information was left out of the eventual WHO report. There was no mention of the sources for raccoon dogs and civets, two of the most-suspected species, and China denied there was any evidence live mammals had been sold at the market at all anytime in 2019.

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Mar 29·edited Mar 29

The article you link to refers to an advertising sheet from 2015. Xiao et al (2021) is a study from 2017-2019 involving observation of the animals and interviews with sellers.

15 is not a ridiculous number to draw a conclusion from. If the monthly sales were 38 per month across four markets in Wuhan, then the January testing by Wang et al (2022) of the supplier is half of the inventory that would be supplied to that specific market in a month.

Worobey et al said of the raccoon dogs photographed in Dec 2019 "“appear to be local, wild-caught common raccoon dogs rather than farmed raccoon dogs and that their plush coats are consistent with those observed in the winter”. edit - reference is the worobey preprint - https://zenodo.org/records/6299600 fig 3

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No the article I linked involves an environmental NGO asking the Wuhan Forestry Bureau about that advertising sheet, which lists nearly a hundred species for sale, far exceeding the total number of species you're allowed to sell in China.

The Wuhan Forestry Bureau responds by giving a list of sources for that store at the market, and it includes raccoon dogs from a specific farm. This is the ministry that was responsible for regulating the animal trade in Wuhan.

Meanwhile the Xiao study you mentioned simply indicates that some of the animals observed appear to be wild-caught. So this is a good example of why it's important not to draw such a strong conclusion when there are all these different facts swirling around. Let's at least wait until China gives a source for the raccoon dogs that were sold on the western side of the market -- they've never provided this information amazingly.

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Ah I see, that's interesting I hadn't seen that.

Still, the referenced farm is in the east of China, which is even further from the relevant bats than Hubei. In general, fur farms in China are overwhelmingly in the east of China.

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Yeah I agree but this particular store, located on the east side of the market, was already less likely to be the origin. The question is why this information, sources for the most suspected species, was left out of the WHO report. There are no sources listed for raccoon dogs or civets at all, in spite of them clearly having been sold there and in spite of China already having both sampling data and seemingly also sales records showing they were.

WHO investigators later said CCP officials pushed them to exclude any mention of these animals from the 2021 WHO report and denied there was any evidence of any live mammal sales at the market during 2019. So China seems to have censored almost all of the information (beyond the 15 locally tested animals you mentioned) about the most likely intermediary species.

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Roko (the one infamous for the basilisk) has argued that what might have appeared as a shift in expert consensus is in fact "manufactured consensus." This is worth considering. Link: https://www.lesswrong.com/posts/bMxhrrkJdEormCcLt/brute-force-manufactured-consensus-is-hiding-the-crime-of | I also believe an algorithm somehow sorting, weighting evidence cleverly could solve the problem of "too much evidence." The CIA, in fact, at least has used one such algorithm, invented by Richard Heuer.

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I think the fact that the expert class went out of their way to suppress the lab leak hypothesis, and that lab leaks of this nature have occurred in the past, is probably damning enough. My impression is that Roko hasn't really introduced any new arguments that Peter didn't cover in the debate, and Peter isn't being funded by the CDC, to my knowledge.

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Everybody plays "Cover Your Ass" whether they're innocent or guilty. So that's not a viable argument. Nobody likes to be accused of having made a mistake, whether they have or not.

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Is this supposed to excuse any possible degree of pre-emptive collusion and fraud to cover up for institutional incompetence?

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No, it's supposed to say that suppressing a hypothesis is not damning evidence of the hypothesis being correct. The hypothesis might be correct or incorrect, suppressing it is bad anyway.

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I agree. That's why I'm saying it's a 'damning' indictment of our reigning technocrats.

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I regret to inform you that technocracy is unusually *good* on this point. If you can reliably find a strain of human that doesn't reflexively hide their misdeeds, we sure could use them!

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Everyone? Some naive people talk to cops believing they will get their side of the story out there

Destroying evidence, like oh idk dna sequences the wuhan insitute were working on at the time; suggests a estimation that they expected they couldve been at fault, I would expect innocent people to hide the evidence and do a very private ananlysys and ask a lawyer if it helps them.

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>So [playing "Cover Your Ass"] is not a viable argument.

It *is* a viable argument in the sense that it dampens and modulates the strength of other arguments.

Arguments about what the WIV can or cannot do, arguments about the number of cases centered around the wet market, and arguments about which DNA sequences were found and when they were found, all need to have their Bayesian impacts divided by a selection-bias-from-a-Maoist-Totalitarian-Government factor.

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OK, but you've got to include EVERYONE, not just the people you don't like. It wasn't *just* the various segments of the government of China, it's also the investigators, people who have a public positions ahead of time (and "public" can be a argument with another expert).

Just about everyone who made a public statement on any factor related to COVID during the early days had at least one mistake that they wanted to "de-emphasize". There were "public experts" in the US claiming that we could keep COVID out after it had already been circulating for months. And the border closings were a farce. The quarantines were not really enforced, and lots of people were allowed to essentially skip them. (Not that it really mattered since COVID was already circulating.)

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This would be the perfect placement for the Peter Parker-Harry Osborn meme.

I already distrust the FDA, the CDC, the WHO, and the CCP. You don't need to sell that distrust to me.

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founding

The expert class went out of their way to suppress the lab leak hypothesis in part because Trumpist Republicans were promoting the lab leak hypothesis and the expert class is reflexively opposed to anything associated with Donald Trump. And in part because discussion of the lab leak hypothesis, regardless of its factual basis, would imperil the funding and prestige of themselves and their colleagues.

Neither of these depend on the lab leak hypothesis being true or probable, so the fact

of the suppression carries little information regarding the truth of that hypothesis.

More generally, innocent people reflexively engage in coverups often enough that "Coverup, thus Guilty!" is a weak argument at best. The bit where innocent people welcome thorough investigation of every accusation made against them because they are confident it will prove their innocence, is sadly disconnected from reality.

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Agree on the second part but scientists also dismissed the lab leak hypothesis because they genuinely found it to be less likely than zoonotic origin. The private Slack messages everyone likes to cite where scientists initially discussed the possibility it came from a lab end with them saying that. https://jabberwocking.com/i-read-the-entire-slack-archive-about-the-origin-of-sars-cov-2-there-is-no-evidence-of-improper-behavior/

Also important to realize that the idea of lab origin was pushed by a number of different groups, not just Trump Republicans. The first version of it was actually from the CCP themselves, who tried to claim SARS2 was a bioweapon the USA attacked them with at the Wuhan Military Games. From there it was picked up by anti-CCP groups in the Chinese diaspora, which had a surprising degree of influence on certain Trump officials, and the storyline changed to focus on the Wuhan Institute of Virology. Other governments such as Iran and Russia came up with their own versions blaming the USA.

So there's really an ocean of BS on this topic and you can't blame scientists for saying it's less likely when it actually does appear to be less likely. None of this resulted in the idea itself being suppressed. It's probably gotten something like a hundred times or more coverage in the media as the animal trade origin. Governments and other groups are incentivized to promote some version of this storyline for geopolitical reasons -- in China's case to evade responsibility for the pandemic, in the USA's case to more directly blame China. Meanwhile the real origin gets lost in the confusing back and forth of competing claims and accusations.

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Mar 30·edited Mar 30

"It's probably gotten something like a hundred times or more coverage in the media as the animal trade origin"

Really? You want to dig into the archives of NYT and show me a hundred-to-one ratio of articles propounding the lab leak theory vs. zoonosis?

I also think 'Biorealism' made a fair point at the end of the comments section-

"There is at least one argument they used knowing it was misleading. They used Ron Fouchier's argument (without acknowledgement) that WIV would have used a well known reverse genetics system despite Andersen saying that wasn't the case on at least two occasions. He noted they had been created "on a whim" and on 20 Feb if anyone thought these were hard to create from scratch a group of researchers had just created one in a week. They should have acknowledged this.

The Nature reviewer clearly took too hard a line as well. Their initial manuscript was far more balanced. Moving from lab origin was not "necessary" to "not plausible" was not justified. As David Relman emailed Francis Collins there need to be an impartial assessment which acknowledged the lack of evidence either way. A Dept of Defense Working Paper dated 26 2020 noted their conclusions were based on "not on scientific analysis but, on unwarranted assumptions"."

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Just doing a quick search on Google, even NYT, which has been criticized by lab leak supporters for their supposed biased coverage, has about twice as many stories that mention "Wuhan Institute of Virology" vs "Huanan Market." And overall in the media the number of articles on the animal trade origin -- i.e. looking into the animal trade in China in relation to the outbreak -- is almost nothing vs. those covering the lab leak controversy.

This is strange because even if you think it leaked from a lab there are specific people in China, vendors and workers at the market, who could tell us much more about what happened, and yet the focus has shifted almost entirely to American scientists and politicians. You then have to think about the fact that many experts believe the lab leak never happened at all!

As far as the Proximal Origin paper I think it's fine to say the conclusion should have been less strong, maybe they should have said "lab origin is less likely" rather than "not plausible." But what's funny is you can also find a quote from Richard Ebright from the same time period (but before Proximal Origin was published) where he says "Based on the virus genome and properties there is no indication whatsoever that it was an engineered virus."

So clearly this was not an unreasonable conclusion to come to, unless you are saying Ebright has no idea what he's talking about, and where it falls apart IMO is this idea that in writing this paper scientists were somehow suppressing the lab leak theory. Just weeks after the paper was published the president of the USA was repeating stories about how someone at the lab had started the pandemic. The State Department launched an investigation that resulted in the stories about "sick WIV scientists with COVID symptoms." Steve Bannon ran a PR campaign to promote Li-Meng Yan's bioweapon allegations. Congress issued multiple reports and held hearings about it. We're now going to see yet another investigation by Rand Paul, who doesn't exactly seem neutral. You can't say this idea was really suppressed that much...instead there's a narrative people repeat over and over about how it was suppressed.

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"Just doing a quick search on Google, even NYT, which has been criticized by lab leak supporters for their supposed biased coverage, has about twice as many stories that mention "Wuhan Institute of Virology" vs "Huanan Market.""

If you use those exact terms, yes, you get 450 results vs. 170 in favour of the Wuhan lab being mentioned. If you search for "wet market" vs. "lab leak", you get ~40,000 results for the former vs. ~16,000 for the latter, so the balance of coverage flips. If you search for the same terms on google outside of the NYT website, you get about 3 times more mentions of the Wuhan lab or 'lab leak' than you do for the wet market, but on the other hand, "chinese animal trade" returns 89 million results as opposed to 274,000 for "chinese biolab". So I'm not sure the zoonotic origin story is being downplayed, precisely.

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Mar 30·edited Mar 30

My argument is not "cover-up, therefore lab leak is true". My argument is "cover-up, therefore untrustworthy"- that the effort to suppress the lab leak hypothesis was a crime in itself, and the expert class are still 'guilty' in that sense.

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My understanding was that the Proximal Origins paper was already published by the time Trump made a public statement in early April, but I don't have a ref handy.

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Yeah that's correct, although it had been promoted earlier by other GOP politicians such as Tom Cotton, and outside the government by former Trump officials like Steve Bannon. Actually I don't think Trump himself was ever too invested in this idea. There's a hilarious interview he did with Sherri Markson where it quickly becomes clear he doesn't have much more knowledge than a random person. It was more a project of Mike Pompeo, the Secretary of State and former CIA director, and a group of people working under him

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Mar 30·edited Mar 30

Proximal Origins was in review by the time of Cotton's editorial.

I think the conclusion might not have been fully exaggerated yet though.

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Ultimately the Proximal Origins controversy becomes much less interesting IMO if there was no actual inside knowledge about what happened, and even Emily Kopp of US Right to Know told me she doesn't think that's the case, although she does think scientists engaged in a "coverup" of some kind. Nothing ever prevented anyone from writing a different paper saying lab origin is plausible and many did.

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founding

Hence my specifying "Trumpist Republicans" rather than "Donald Trump". As everythingism notes, Trump himself was not really the problem, but there were plenty of people in Trump's orbit advancing the Lab Leak theory.

And advancing it well beyond what the evidence would have supported at that early date. It was absolutely reasonable for the "expert class" to push back against that, and at least understandable that they would overcorrect in the other direction.

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This is one of the situations where I don't feel any more confident trusting the expert consensus than looking at the papers and/or debates and trusting my own reasoning to evaluate the arguments.

A good example I personally like to use of this definitely being the case would be from COVID as well: during early 2020, the Finnish Institute and Wealth and Welfare (THL) officially claimed IFR of [alpha-variant, in immunonaive population, before best practices for treatment were discovered, as average within a population with a lot of elderly people] COVID to be <<.01%, purportedly repesenting the best available scientific evidence, while at the same time some .5% of entire population of Bergamo in Italy had died (and similar IFR could have been calculated from Diamond Princess data, etc). Here, rational evidence easily trumps claims made based on scientific evidence: a child could see if explained to that no matter how many unidentified cases there might be, there's no way for IFR to be lower than total excess mortality within the population. And additionally, I have a clear model where the people working in the institute with their virology doctorate doctorate degrees went wrong: they rely (indeed, might be contractually obligated to, I haven't checked) on scientific studies, but as none had been published at such an early stage, they pattern-match to the most closely analogous study, which might be about flu or something. Most people, even experts, just aren't epistemologically nuanced enough to use rational evidence, as Scott has often written about in "The Phrase "No Evidence" Is A Red Flag For Bad Science Communication".

When expert scientists are discussing statements within established science, I would trust their claims to not misrepresent the science, and since the scientific method approximates Bayes' theorem pretty well, I have a high degree of trust for the claim. This isn't such a case! Science works, but it advances one funeral at a time more or less, and there's no way this debate has gotten to a point of established science, indeed the polls lean to one direction but also specifically show the question ISN'T settled.

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Sure there can be. Not all deaths are caused by COVID, and both Diamond Princess and the population of Bergamo were heavily age-skewed. Not a representative population, that's why serosurveys were useful to determine the true number. You say the Finnish government were also making claims about the elderly but did you check that the numbers line up there?

There are other issues with early IFR estimates, for example in Italy there was mass abandonment of care home residents by the mostly foreign carers who were scared and often wanted to return home in anticipation of border closures. Deaths reported as COVID were actually in some cases caused by abandonment e.g. dehydration. Early on doctors were also way too ready to put people on ventilators, partly because they thought that would keep the virus out of the hospitals and themselves (it didn't). But ventilators are a very destructive last resort option. Once doctors stopped doing that so much the death rates went down.

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The point made in the link is classic the-social-aspect-of-opinion-formation. The world of domain experts can be analysed as a community (more-or-less closely integrated), complete with opinion leaders, followers, rebels, go-betweens, outcasts and every other (social) role related to the goings-on in any community.

The negative spin on these (social) processes in the linked post is unneccessary, though. Partly because such social processes are inevitable/unavoidable, partly because they may also be conductive in getting the joint reseach process from A to B. (The importance of all social factors on opinion formation is Janus-faced.)

(...and ACX/self-declared rationalists is also to a certain extent a community, of course.)

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I have no horse in this particular race, but I do have a lot of expertise in some of the areas rootclaims "investigates" (especially the stuff related to Syria and chemical weapons) - where their analysis is so shoddy and laughable it's indistinguishable from Youtube conspiracies - and the biggest surprise to me here is that anybody really bothers with rootclaim in the first place? The more you learn...

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Even if you do not agree with the values of the (prior) probabilities, you can choose your own, and replicate the process rootclaim uses. It is far from "shoddy" and research on Bayesian methods modelling these kinds of events is highly valuable.

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I have nothing against Bayesian reasoning. Use it all the time. But the priors, the "evidence", the weights attached were so out-there, I just assumed arguing with them was like arguing with Alex Jones who has taken a stats course. Unfortunately statistical methods don't cure brain worms (and in fact might even provide them with a rationalist veneer).

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Can we then Aumann agree that: the Rootclaim method with better priors and handling of evidence would not necessarily be shoddy, the current analysis is or might be, and the method itself remains valuable enough that it would be good if they continued to work on it (in Scott's framework, (2)).

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With good-enough priors, yes it would be good enough (by definition). But how good would those have to be? Is it possible to have priors good enough that the method isn't just laundering assumptions through some fancy statistics, as meta-analyses or financial projections or suchwhat often are? I'd answer these questions as "at least 10x better than we have" and "not really, no."

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Strange place to comment, I was aiming for agreement with Tobias.

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How so?

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You happened to laugh at an analysis where we turned out to be spot on. There is no now clear verified video evidence of the opposition carrying out the Ghouta sarin attack.

https://blog.rootclaim.com/new-evidence-2013-sarin-attack-in-ghouta-syria/

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If you are going to claim your analysis is spot on, please link to a credible independent source. Otherwise this comes across as we believe this unlikely thing and used our analysis you find shoddy to conclude we were right so you should not consider our analysis shoddy.

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Follow the link. It describes external forensic work which you can verify yourself.

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I did follow the link. My point is if you were vindicated I would expect to be able to read about it in an independent source. Otherwise I need to look at all of your sources and see both which are in support of your claim and which you are claiming support you and look at the evidence in detail. Lab leak as a plausible theory has been printed in the NYTimes since at least 2021, has any mainstream newspaper published anything about this?

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How often do mainstream newspapers publish anything about Ukrainian misdeeds in the war? Probably something like 1/1000 ratio compared to the Russian ones, whereas a reasonable prior of their prevalence would be like 1/10 at best. Similar sort of bias is probably at play with Syria.

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I'm not discussing the ratio of coverage but here is an article from le monde that is easily searchable that backs up the claim that Ukranian's committed war crimes. https://www.lemonde.fr/en/international/article/2022/04/09/ukraine-s-military-accused-of-war-crimes-against-russian-troop_5980121_4.html. If there was anything that resembled reasonable evidence, it would get some coverage the trouble is Saar has motivated reasoning that is not convincing without external collaboration. Otherwise the best you can claim is that there is some evidence that the syrian weapons were a false flag and again it's not your (Saar's) method that proves the analysis is spot on, its how strong you trust the conclusions from the grayzone/wikileaks that the appearance of impopriety means the conclusions are false.

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Sorry, I thought it was obvious. These outlets have no incentive to publish such findings. Sadly these are the kinds of things you need to verify yourself.

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How do you account for “one of the most powerful political actors in the world which has a history of controlling information flows runs the area in question and can be manipulating what evidence is available?”

I get that you have to work with the evidence you have. When the evidence you have is passing through a filter that has pretty strong incentive to hide its own wrongdoing (if that were to exist) how does that fit into your analysis?

Did they assess a probability that, ie, certain research records where the researchers tried that ~exact~ furin site were destroyed by the CCP? Wouldn’t that just be a “naked prior”?

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The CCP were trying to cover up zoonotic origin as well at first, with arresting Dr Li and cleaning up the site. Because it was seen as politically embarrassing, as China said it had fixed wet market issues after SARS. So that applies on both sides.

(The Chinese official position now is to heavily imply it came from abroad)

Also a question of whether, in the lab leak hypothesis, they'd have been able to cover up large amounts of evidence effectively, given how inept the initial covid response was. And officials at different levels acting at cross purposes to cover their asses

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This is not true. George Gao said in January 2020 that it was from the wet market. After leading sampling there and the case search, he changed his mind in summer 2020

If you look at what usually happens with research-related accidents, they are usually shrouded by obscurity for years. This is likely even more true in China. Compare e.g. the 1977 Russian flu, sverdlovsk anthrax leak, various SARS leaks. In some cases finding out that an accident occurred can take decades.

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I think you're expecting a government to act in a unified way. I'm sure if you searched you could find statements supporting every side. And I *have* encountered (reports of) official Chinese statements claiming it came from abroad. So that is one of the positions that they are (or were) taking. I've also encountered denials that COVID exists (e.g. by the mayor of Wuhan), though that was early in the epidemic.

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I was responding to the claim that the government was trying to cover up the wet market origin in early 2020. This is inconsistent with the head of the China CDC saying it came from the wet market in January 2020.

Obviously, all of their incentives are to cover up a potential lab accident.

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The problem is that everybody has incentives to cover up, whether or not they are at fault. If someone things something MIGHT be read as placing the blame on them, they'll try to suppress it. This makes things quite murky.

FWIW, I believe that if the disease originated (as a human disease) in, say, New York, but didn't get the last mutation that it needed to become pandemic until someone in Wuhan caught it, we'd see largely the same response. You can't judge things by "who's trying to cover things up".

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But you have to ask why George Gao would change his view to denying the wet market origin if it came from the lab. That's a strange thing to do if China's intention was to cover up a lab leak. What these statements from China and the various lab narratives/hypotheses have ultimately done is leave the origin unresolved within the domain of global public opinion, an outcome that may not be the worst from China's POV. They're able to avoid officially taking the blame for the pandemic and can control the narrative domestically to say the virus came from outside China.

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That would only work if the research was completed but not published before COVID happened. If someone was studying furin cleavage sites in 2018, they would want to publish a paper saying "hey, we tried cleavage sites X, Y, and Z and only X worked" and China would have no reason to think that should be kept secret because COVID hasn't happened yet.

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Even a 3 minute skim of anyones work here suggests they probably believe "math is so great you get the best answer anyway", and something something wave at criminal forensics existing

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This is discussed in the debates and in Scott's summary. It is a common theme with conspiracy theories (term used literally) to allege that the conspiracy is both capable of and motivated to make the evidence come out to whatever happens to be the case. However, just because you can imagine a hypothetical in which this might happen, doesn't mean it's remotely likely, especially when characteristics like who is involved and how competent they are change from argument to argument. China is not omnipotent and frankly probably doesn't care much about lab leak vs zoonosis. Let's consider the epidemological data pointing to the market, which is often alleged to be tainted.

1. The Chinese government first tried to cover up the existence of the pandemic at all, and failed. Also, as Peter points out, if it started much earlier, you would have many times more deaths, which is even harder to cover up.

2. They also tried to cover up (or at least, were incompetent) the wet market, by claiming animal testing showed no results, but then it turned out they hadn't actually tested live animals (roughly, I might be getting details wrong here).

3. Now they claim the virus started in the US; if they were trying to fake evidence of this, they would have had cases cluster near an airport or hotel or something, not a market that is almost exclusively visited by residents.

4. There's multiple different lines of evidence that point to the market, which makes it increasingly unlikely that China could manipulate all of them in a way that's undetectable.

5. If you don't believe the market data, why do you believe the pandemic started in Wuhan at all? Couldn't China be trying to hide, like a secret bioweapon plant in a different city? This is possible, but of course there's no evidence for it.

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Maybe you can help me understand how this would fit into a Bayesian framework, but here’s how I’d think of it:

Suppose someone did indeed to a research and create that exact strain of virus that was ostensibly “not what you’d do” if you were doing research. This would be pretty direct evidence overwhelmingly in favor of the lab, right?

Yet if that evidence existed it would be far easier to track down and destroy, precisely because someone would know “holy crap I did this” and that specific person would have a very strong incentive for that evidence not to go public.

I don’t believe that “China make the evidence go however it wants”, I just don’t see how to account for “people who knew they caused this could destroy that evidence far more easily than we could find it, and would have a very strong incentive to do so.”

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> Suppose someone did indeed to a research and create that exact strain of virus that was ostensibly “not what you’d do” if you were doing research. This would be pretty direct evidence overwhelmingly in favor of the lab, right?

I don't follow what you're saying here. It looks like "Suppose it was created in a lab, that would be evidence in favor of the lab." Can you rephrase? Is there a statement missing here?

> Yet if that evidence existed it would be far easier to track down and destroy, precisely because someone would know “holy crap I did this” and that specific person would have a very strong incentive for that evidence not to go public.

I agree that *if* some lab workers knew they had created covid, and knew how they had done it, they probably would and probably could destroy at least some evidence. It's not at all clear to me how well this would actually work (i.e. would any evidence remain? would there be evidence of this sort of cover up?) Do you have more specifics?

(Even in the case of lab leak, there might not have been any such cover up--I have seen the theory that the leak was totally accidental and came directly from samples, so they might not have even realized at first even if they were to blame, and WIV workers were behaving pretty normally through December at least. Conversely, even in the case of zoonosis, panicked workers could have engaged in some sort of cover up if they had some vague idea they might be considered responsible. So FWIW I don't think that either "there's some evidence of a cover up at the lab" or "there's no evidence of such a cover up" would be definitive evidence either way.)

> I just don’t see how to account for “people who knew they caused this could destroy that evidence far more easily than we could find it, and would have a very strong incentive to do so.”

Criminals try to hide evidence all the time, but still get convicted (or convinced to take plea deals). It's actually really hard to successfully hide, destroy, or fake all of the evidence for something this big, and also do the same for the cover-up, and for that cover-up, etc. There were whistle blowers for previous outbreaks, including lab leaks of Sars 1, as well as for Sars 2, from the hospitals, in spite of Chinese crackdown.

You can certainly put a cap on how confident you are in a theory--it's not like the judges, or Miller, or Scott, or me, or the superforecasters, are >99.9% confident in zoonosis. Seems like mostly in the 80-95% range. But it's not correct to just throw all the evidence out.

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I agree with most (all?) of what you’re saying but still don’t understand something. I couldn’t glean this from the article.

How did “people have an incentive and ability to destroy evidence” influence the computed odds here?

Yes i understand that destroying evidence would likely happen either way (due to panic, not wanting to be blamed, not knowing the true cause) and that it can be hard to totally cover something up and that people often are convincted despite trying to cover up evidence, etc.

I’m not questioning the outcome of the debate.

I’m just trying to understand how “people had an incentive to destroy evidence” influenced the computed odds. It seems like the conclusion is “that doesn’t matter because there are multiple trails of evidence that point to the zoonotic case”, but I can’t tell if this is “it shifts odds by 5%” or “we just didn’t compute that because it doesn’t seem necessary” or what.

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> How did “people have an incentive and ability to destroy evidence” influence the computed odds here?

Miller spends a fair amount of time in the debates on why the early case data is reliable enough, in ways that can't easily be faked, as well as reasons to believe that China is neither capable of nor willing to fake the data in a way that explains the evidence. So I think the conclusion is "that's theoretically true but it seems unlikely to explain anything."

I think the highest level answer is "everyone rounded the BF used for each piece of evidence down, based on how likely they thought the evidence to be wrong." If you want the specific numbers the judges used, you would have to dig into their reports, or perhaps ask them directly. As far as I can recall, I don't think Rootclaim really dove into this point, but rather just used it at a very high level ("those data could be wrong, so the evidence provided is weak") so the judges may have just taken it has most likely that the data are accurate.

Keep in mind that the data merely being limited (which is known to be the case) doesn't necessarily tell you much, because you have to explain why the cases cluster at the *market* specifically. If want to claim the pandemic started at the lab, it's not enough to say that maybe there are cases missing, because it would still be a hell of a coincidence that the cases we do know about are all at the one place in the city most likely to be the origin of a zoonotic pandemic.

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Thank you! This seems to answer my question. I appreciate your patience here, it’s a real service.

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Apr 1·edited Apr 1

A few minor niggles...

> 1. The Chinese government first tried to cover up the existence of the pandemic...

It's a bit more nuanced than that. When people started coming down with mysterious cases of a pneumonia-like disease during the first weeks of December, the local hospital MDs and administrators alerted the health authorities of Wuhan, and they in turn notified the Mayor of Wuhan and the Governor of Hubei. The mayor and the governor tried to hush it up because a big party convention was scheduled to be held in Wuhan (early in Jan IIRC). The mayor and governor of Hubei Province decided to go forward with the conference. They felt a small outbreak of some unknown pathogen would reflect poorly on their administration, and they didn't alert the national authorities to the outbreak—until people were crowding the emergency wards, and they couldn't cover up all the hospitalized patients. (This would have been around the third week of December when they couldn't cover it up anymore—although it didn't reach the Western media until the first week of January.)

Local dithering and silence wasted two critical weeks, but some of the hospital MDs notified the folks across the river at the WIV, and they were able to alert the National Health Commission of the PRC that they suspected they had a SARS-like outbreak on their hands. Not long after the MDs were beaten and arrested by local Gong An Bu, probably at the behest of the local authorities who were embarrassed about the outbreak happening on their watch (again, it's unclear who directed them to do this, but the Mayor and the Governor had the motive).

The national health authorities took the warning seriously, and they informed Chairman Xi that the situation was potentially quite serious. He immediately fired the Mayor (and then the Governor) for incompetence and he sent in a hand-picked troubleshooter to handle the situation. (I wasn't able to find out what happened to the mayor and governor. I don't know if they were allowed to fade into private life or were maximally disciplined.) Once the National-level health authorities assessed the situation (and it took them about a week), they alerted the WHO at the end of December, and the Chinese started sharing data with the WHO, the ECDC and the CDC. The local coverup wasted two critical weeks, but it was at the local level, and not at the national level.

> 2. They also tried to cover up (or at least, were incompetent) the wet market...

Due to the case cluster, the Chinese national health authorities immediately focused on the wet markets in that district. SARS1 and some Avian Flu outbreaks had started at wet markets, so the wet markets within the initial case cluster were immediately suspect. And once it was clear that they had something dangerous on their hands, public health authorities immediately shut down the wet markets in Wuhan (I believe they shut them all down all over the city). The animals were disposed of, and the market stalls were disinfected. From a public health perspective, this was a wise decision—but from a data-gathering perspective, they lost the chance to test the animals when they incinerated the carcasses. Again, I may be misremembering some of the details but they invited the WHO to visit the site in mid-January. Either the Chinese or the Chinese with the WHO collected swabs of DNA and RNA from the stalls. So the disinfection happened after they collected the DNA and RNA. The Chinese sequenced the virus and they sent the genome to the WHO, to ECDC, and the CDC on January 15th. It wasn't until March when the CIA director and Trump started accusing the Chinese of covering up a lab leak that the Chinese stopped cooperating with us. Then naturally, they blamed us for creating the virus.

It's important to note that wild animal farming is a 7 billion dollar business in Hubei, and Wuhan is the second only to Guangzhou as a transshipment center for the animals and their byproducts. It's a big business, and the authorities don't want to see it shut down because it lines their own pockets. So their impulse is to cover up instead of disclose because of all of the negative attention they've garnered worldwide.

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Mar 28·edited Mar 28

What's important to realize here is that the CCP doesn't want evidence to exist for *either* of these theories. In both scenarios, the CCP would be partially responsible, which is obviously bad for their optics. Ultimately, COVID didn't hurt China relative to other countries, and so they don't really have any incentive to prevent this from happening again. Any evidence that would narrow down the truth, any truth that would implicate China, would have been destroyed already.

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I enjoyed this piece - I tried to follow this story in 2020 and have always leaned more zoonosis than lab leak (I believe I said 90-10 publicly in 2021, probably closer to 95-5 now).

Despite this, I've often been frustrated and annoyed by mainstream virologists who dismiss LL with poor reasoning, and almost always find myself defending (more reasonable) LL proponents.

I guess that this annoyance has led lots of people in rationalist-adjacent circles to lean further LL than they should have. I wonder if this is a common rationalist failure mode we need to update on.

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Without caring about which one is actually true, we can look at the costs of the beliefs of they were true or false. If LL is true, and you fight against some sort of conspiracy, that is some positive U. If LL is false and you fight against an imaginary conspiracy, that will worst case cause skepticism and more investigation. Believing that it's zoonosis means you will be enforcing a conspiracy if you are wrong, which is negative U. Otherwise slightly positive U to most people, but less than what you'd get if you were right and fighting a conspiracy. Eliezer says one should believe that which is true, but actually this sort of analysis of costs and gains of being wrong / right is very useful, because it can help to navigate the unvertainty of what you should believe in.

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If we want to go Hansonian about it, saying you think lab leak is at least plausible signals sophistication and open mindedness

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I did not take signaling that precisely into account but this is absolutely true and might have some wider implications (I did not have solid concrete examples at time of writing).

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It certainly is an important point. Every statement you make about the probability of something is at the same time a signal you send about what kind of person you want to be perceived as, and/or want to perceive yourself as.

This is unavoidable.

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You're leaving out the utility of finding another reason to blame some group you dislike. I feel this is a major driver of many human beliefs.

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Unless you go all Pascal's wager (which is obviously bullshit), your beliefs don't have immediate consequences in the world.

In the brains-as-Bayes-engines model, beliefs are probabilistic in nature.

What you do about your beliefs is then another question subject to cost/benefit analysis regarding your utility function. You might want to state your true beliefs, exaggerate them, stay quiet, pay lip service to the opposite side or even do your very best to argue against your own beliefs.

There are some corner cases where you might chose to stay strategically ignorant due to direct effects of your beliefs (e.g. infohazards, unconditionally knowing about your top 100 health abnormalities might encourage hypochondria in all the cases where you don't have serious health problems, or psychiatric disorders being at least somewhat memetically infective in populations), but for the most part the Litany of Tarski holds: if X is the case, then you want to believe X.

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I think Pascal's Wager is true. Probabilistically speaking, life is meaningful and consequential enough to treat it as such

If I had to give a number on a test I might say that our life is 60% likely to be materialistically determined. To strengthen the point, we'll go with 99%

Now multiply the likelihood by the consequences. Again, to strengthen the point, let's say it's probably not very consequential to both exist in a 'meaningful' and non- random universe and correctly believe that it is. So 99% random or probabilistic existence x 0 consequences of being correct or incorrect about that. And 1% non-random x .1 consequences of it being true. Point one units of consequence weighed against 0 seems very noticeable in an absolute sense

With my own weights of likelihood and suspicion that human beliefs and actions can be wave like, propagating and amplifying despite small discrete effects, then my take is that I am compelled to act as if my life and beliefs are potentially consequential and subject to free will

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>If LL is false and you fight against an imaginary conspiracy, that will worst case cause skepticism and more investigation.

The worst case of convincing people that someone is out to get them is that they decide to preemptively attack those people.

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It's a little weird to cite Eliezer as the person who says one should believe that which is true! This really seems like something that should be much more fundamental than one guy who's famous for an unrelated issue (AI safety).

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He wrote less wrong and also a screed on what "the simple truth" is, as well as "Harry Potter and the Methods of Rationality", not "Harry Potter and the sealing of horcruxes" or similar.

I don't think you can say he has *no* claim on being the truth guy, or he isn't famous for wanting to believe true things.

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Thank goodness he came along in the early 21st century and upended thousands of years of philosophic practice by inventing the idea that people should believe true things to be true!

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I mean, that might not be a novel idea, but it's not really universal either. You'll find plenty of people insisting that sometimes believing or teaching false things -- even tricking yourself into believing things you don't know to be true -- is a good idea. (Plato and Pascal being two famous examples.)

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To be the Truth Guy, he doesn't have to say it, he has to be the first or the best in some way. A lot of the problem is that EY's fans tend to be naive about the history of thought, so it all seems new to them. It's not even the first iteration of out-of-the-mainsteam philosophy that claims to answer everything.

The thing called "rationalism" has little to do with rationalism as the term is understood in mainstream philosophy. It is better understood as part of a pattern where a succession of small, insular groups engage in a very self confident style of amateur philosophy. Unlike other cult-like groups, they claim to have a strong orientation to science, logic and reason(and to be able to implement them much better everyone else).

Examples include Yudkowsky's "rationalism", Critical Rationalism (Karl Popper's philosophy, articularly David Deutsch's version), Ayn Rand's Objectivixm and Korzybski's General Semantics. There are often several such movements overlapping each other, some are reactions to others, and some borrow ideas from others.

In more detail, This kind of Thing is characterised by:-

• Being science-orientated , but having much more specific claims than "science good"

* Being strongly to stridently irreligious and anti religious. Also opposed to New Age thinking and continental pilosophy.

• Being largely outside of mainstream academia etc

• Being an insular group that mostly talk to each other

• Having difficulty in communicating with outsiders , in any case, because their own theories are expressed in a novel jargon.

• Centering on a charismatic leader, with a set of mandatory writings

• Having an immodest epistemology..which claims to be able to solve just about any problem..

• ..which is based on a small number of Weird Tricks. Nothing requires the same level of deep study as mainstream academia, and the key ideas are often brief slogans.

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> To be the Truth Guy, he doesn't have to say it, he has to be the first or the best in some way.

I used lower case truth guy, clearly in reference to him becoming well known in some respect for this. I use it in the same way that I would call a somewhat competent local mechanic the "car guy" or I can call Bill Nye "the science guy" without claiming he's the best person in the world at science, or that he invented science.

Or that I was replying to the statement

> It's a little weird to cite Eliezer as the person who says one should believe that which is true!

Which, like, do you believe that you should only cite the things from the best formulation or inventor? Maybe start auditing Kenny about what other dastardly crimes against citation he has committed would be better.

I feel it's not a coincidence that this type of misreading is common to, as one would say, "haters",whom all seem to share the following traits, excuse me they are Characterized by:

> Perceive any group seeking improvement to be automatically suspect

>Incapable of reading even slightly positive sentiments about their target and stay silent

>seem to predictably misread incredibly common use of language, seeing "good vibes" and assuming it means GOAT or inventor being a common example

>Incapable of putting forth or discussing any object level example, preferring instead to talk in innuendos about how there's a large population of informed disagreement, yet fails to link or write something. If an example is provided, it is full of guilt by association and sneering arrogance and little else, and they converge on it like little flies, congratulating each other about how many good points have been made.

> does not seem to be aware of their own constant isolated demand of rigors, or that many of their objections can be answered with less than five minutes of thought

> become obnoxiously self congratulatory about how they used middling to low wit to dunk on their targets

You see, listing a bunch of negative traits is a great way to be truth seeking. If someone tries to engage, it's because they are insecure and you, yes you, personally are correct, no matter how obviously derailing or irrelevant that list is. If you can play to an audience, that's all that matters. :-)

Well, you know, one can choose the quality of their friends, but not their enemies. There are ways to choose the quality of your enemies, but the world is not ready to hear them.

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I am puzzled that you include Karl Popper here, his view on the demarcation criterion between science and non-science (i.e. that a hypothesis should at least in principle be falsifiable) is very mainstream among scientists. (I do not know Deutsch' interpretation, though.)

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If you believe in malicious plots that aren't real you reduce social trust which is one of the main predictors of sociatal succes. Messing with that has huge potential negative U.

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I think this is definitely a common failure mode in general, and I observe it way more often in rationalist circles.

Personally, I experienced the exact same thing with the mask and airborne debates. I still get an emotional reaction every time I see someone wearing a cloth mask.

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FWIW, cloth masks are a major help in many environments. They slow down the speed of the air ejected by someone who is infected, so it tends to remain near them. They also absorb moisture, so any wet globules ejected are likely to be absorbed.

Note: Almost all masks are more effective at preventing an infected person from spreading the disease than they are at preventing someone from catching it.

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I fully agree with you, but the standard response is that (1) wearing masks is "dehumanizing", (2) we will all catch the diseases anyway, sooner or later, and (3) many people wear the masks incorrectly anyway. Therefore, the proper way to signal sophisticated thinking is to refuse wearing the masks. Especially when the cost of doing so will mostly be paid by the others.

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Yeah, I think. There's a common failure mode of overcorrection from "don't blindly follow the mainstream" to believing the most popular contrarian option by default.

You see a similar thing in the left with people over correcting from "America is always right" to supporting genocidal dictators as long as they oppose the USA.

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As Scott described in the article, Lab Leak is the "mainstream" view among the general public, even if it's contrarian in academia and prestige / elite / media / whatever you want to call it circles.

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JFK conspiracies are also the "mainstream" view. I think it's possible for "mainstream" to be a slight "term of art" even if the raw survey data says otherwise.

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Well, there is a big Oscar-winning Hollywood movie heavily implying that the official JFK narrative isn't the whole story, so calling that view mainstream seems reasonable in any sense.

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Jun 21·edited Jun 21

> You see a similar thing in the left with people over correcting from "America is always right" to supporting genocidal dictators as long as they oppose the USA.

Ironically, nowadays the right tends to do the same thing, due to associating the US with Evil Wokeists. It really is a trip, seeing politics flip to basically the exact opposite of 20 years ago.

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Well there's the question of how far this was an overcorrection. It may very well be that it was correct to put (as a random number) 80% on it given your state of information & willingness to investigate & priors, while 90% was too much.

(I think it is easy for social-posts, like notable blogposts, pointing out that some belief of the community was likely wrong to end up having the same problem of overcorrecting to "don't disagree" rather than "what degree did we do worse than we should have")

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I think that there's almost no difference between 80% and 90%. Even if one believes in objectively correct priors, someone who was off by this much is basically as right as possible.

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I was using them as random example numbers, the same logic holds for 5% vs 30%.

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True.

And there is a danger if offering more precise probability estimates, in particular when offering predictions about the future (and even if you offer them only to yourself): The danger that you may convince yourself that you have more precise knowledge that you actually have, or can possibly ever have.

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> I wonder if this is a common rationalist failure mode we need to update on.

Absolutely. I sometimes feel like a very large fraction of comments on any topic on this blog are reaction formation by rationalists who are annoyed at something that MSNBC watchers are saying and have talked themselves into the diametric opposite to rationalize their annoyance.

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It's often worse than that--it's rationalists who are annoyed at a caricature of what MSNBC watchers are saying, and have talked themselves into the diametric opposite of that caricature.

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True!

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Jun 21·edited Jun 21

Nate Silver justifies his belief in lab leak pretty much entirely with frustration with the mainstream media's attempts at narrative control in 2020 (nevermind that the mainstream media has been breathlessly *promoting* lab leak ever since). It really is sad to see this from someone who should know better.

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I don't think this grapples with the problems the Mr Chen case poses for the zoonosis argument. Both sides in the debate agree that Mr Chen contracted symptoms on 16th Dec. This suggests he was exposed around 10th Dec. He thinks he was exposed on the train or in hospital on 8th Dec.

This raises two problems:

1. Mr Chen lived 30km away from the Huanan market on the south of the river, and never went anywhere near it in December, according to his interviews. His case was only recorded because he happened to be transferred to the top tier Wuhan Central Hospital, which is a sentinel hospital for respiratory outbreaks in Wuhan. It is in the north of the river from his local hospital because his relative happened to work there. This is evidence of a geographical bias in he case search. How many other cases were missed on the south of the river because they happened not to visit top tier hospitals, which were largely near the market.

Geographic bias in the case search is also confirmed by:

- Literal statements to the effect that 'we focused too much on the market' by the man in charge of the case search https://www.bbc.co.uk/sounds/play/m001ng7c

- A mountain of evidence in official Chinese documents of a market-bias in the case search. https://journals.asm.org/doi/full/10.1128/mbio.00313-23

- This short statistical argument -https://academic.oup.com/jrsssa/advance-article-abstract/doi/10.1093/jrsssa/qnae021/7632556?redirectedFrom=fulltext&login=false Cases with no links to the market were closer to the market than linked cases. This is evidence FOR ascertainment bias in the case search.

2. Given that there was a confirmed case 30km from the market around 10th of December, this suggests widespread community transmission across Wuhan in early December and late November. i.e. not that there was a zoonosis in early Dec. The first confirmed case was on 10th/11th Dec (even for that case, it is unclear whether the first case was market linked). There was no published retrospective case search. The first case was initially thought to be 1st Dec. Usually if you do contact tracing and a case search, the first official case goes backward in time. In this case, it went *forward* in time to 10th Dec.

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As I wrote in an earlier post, I think it was circulating in rural China long before it was officially detected. Catching it on the train fits in with this quite well. My main hypothesis is that a "merchant" carrying produce (of some sort) to the wet market was the source of that epicenter. (That could actually be widened a bit, as all that is required is that someone infected in a rural village for some reason visited the wet market area for awhile.)

Remember that prior to special tests being developed, COVID was being diagnosed as "atypical pneumonia", at least in a Washington (I presume state rather than DC) hospital.

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>Remember that prior to special tests being developed, COVID was being diagnosed as "atypical pneumonia", at least in a Washington (I presume state rather than DC) hospital.

Good point!

Personally, I'm somewhat skeptical about the "geographic focus" evidence because there so very many asymptomatic cases. Even if there had been consistent diagnosis from patient 0 onwards, we would have only been seeing the tip of the iceberg.

( I have to admit, I haven't been following LL vs. Z terribly closely. )

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It's common for COVID to have an incubation period of only a day or two, so the fact that he developed symptoms on December 16th doesn't exclude that he was exposed on December 14 or 15th.

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Rai et al (2022), a meta-analysis of the covid incubation period for patients infected by early variants from January to March 2020, found that the average time from exposure to symptom onset is around 5.7 days, with a 95% confidence interval of 5.2 to 6.3 days. This suggests he was likely infected around the 10th December.

https://link.springer.com/article/10.1007/s10389-021-01478-1

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I think you're misreading the paper. The 95% confidence interval means that there's a 95% chance that the mean incubation period is between 5.2 and 6.3 days. It doesn't say anything about how likely a 1-2 day incubation period is in an individual.

I haven't read the paper (I only read the abstract), so perhaps there's information there about how common a 1-2 day incubation period is.

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Ah yes, I think you're right. In either case, in expectation, he was exposed around 10th Dec, and thinks he was exposed on the 8th

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Does when he thinks he was exposed matter at all? Why should we assign any weight to his speculation? He had symptoms in the hospital on Dec 16th which seems very consistent with contracting COVID in the hospital a few days before that.

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I agree it is consistent with that, I am just saying that the average time to symptom onset is 6 days. he could also have been exposed ten days earlier, per this logic, which is a further update from zoonosis and these two effects cancel out, no?

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Mar 29·edited Mar 29Author

Not sure why this is mysterious.

The first officially confirmed case, the shrimp vendor, got sick December 11. So she was probably infected December 5. She probably wasn't the first human case, because she didn't interact with the raccoon-dogs; more likely a raccoon-dog vendor got (quietly) sick first and spread it to some other vendors. It's not even clear she was in the second batch of cases - only 5-10% of COVID gets detected, probably less when it was first starting, so she could be anywhere from one to four transmissions away from human Patient Zero. So human Patient Zero probably got sick in late November or early December.

Let's say Patient Zero got COVID November 27 (with high error bars). He infects other people at his workplace (the market), and some of those people infect still other people at the market, or other people elsewhere (for example when they're on the train home from work). COVID case numbers double every 3.5 days, so by 12/11 when the shrimp vendor starts feeling sick, there are somewhere around 16 cases (with high error bars - and maybe more if there was a second spillover for Lineage A, but ignore that for now). Any of those people could have passed it to Mr. Chen on the train on the 8th/10th/11th/whenever.

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See above comment re this illustrating bias in the case search.

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My final comment. It is important to consider how different SARS-CoV-2 is to other zoonoses. I have a challenge for zoonosis proponents to find me a zoonosis with all of the following features

- Spillover occurred after 2000 when sequencing became much cheaper

- There were more than a hundred human cases

- There are zero infected animals.

This characterises SARS-CoV-2, but no other zoonosis meets these criteria. Why?

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What evidence do you have that there are zero infected animals? I only see evidence that none of the animals that have been tested were infected with an essentially-genetically-identical pathogen, but there are many animals that were not tested. (I assume the claim you're making is about essentially-genetically-identical pathogens, since there are plenty of samples from animals of coronaviruses closely related to SARS-CoV-2.)

I think there are also some viral hemorrhagic fevers that haven't had their animal reservoir identified yet, though I'm not very familiar with this, and I don't know if any of them have had over 100 human cases.

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Yes I am saying that they haven't found an infected animal in their testing efforts, which were very extensive, and included testing of species sold at the market in Hubei and across China. Usually, for a zoonosis with more than 100 human cases, they find numerous infected animals and the first people infected mostly interacted with those animals. This did not happen for SARS-CoV-2.

This is true for: SARS-1, MERS, H7N9 avian flu, 2018-2021 Langya Henipavirus outbreak in China, NIPAH, and all other zoonotic coronavirus spillovers with more than 100 human cases.

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I guess you mean at the initial detection? Since obviously many (many) infected animals have been found subsequently.

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yep i mean infected with a progenitor

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Some important context here is that according to the WHO, China also claims to have found zero infected animals total, during the course of the entire pandemic, even after COVID swept across the country infecting (most likely) hundreds of millions of people.

It seems wildly implausible that there are really zero animal infections (including those passed on by humans) in a region as large as the entire continent of Europe, that also has millions of susceptible species being raised on farms. More likely China is either failing to identify infected animals or failing to report this information to the world.

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2013-16 West African Ebola outbreak; almost 30k cases, no animal intermediate. This is probably the most notable zoonotic episode of the last 20 years apart from SARS-2, I'm surprised you missed it. There are also 7 other Ebola outbreaks that match your criteria. We've been studying Ebola for over 40 years and have yet to determine the animal reservoir. It took 20 years to identify the reservoir for HIV-1's progenitor. Sometimes finding the reservoir is easy, sometimes it's hard. Typically it is easy when you have lots of cases and the virus is not very efficient at human-to-human transmission, because that necessitates lots of separate zoonotic events, which necessitates lots of infected animals. For something that spreads fast (i.e., the kind of virus likely to start a pandemic), you don't need a big reservoir, so you have a smaller target. For example, we *did* find the reservoir for the 2009 flu pandemic, but it took 7 years: https://elifesciences.org/articles/16777

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I hadn't actually looked into ebola yet, so I take it back

I thought the ebola host was known to be bats?

also hadn't looked at the swine flu one, I was overconfident there.

I agree re HIV, but that was before 2000 and sequencing was much more expensive.

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There is strongly suggestive evidence for bats -Marburg virus has been isolated from bats, we've been able to identify antibodies in various bat species that react to Ebola, and in one case we were able to isolate a short bit of RNA that was similar in sequence to Ebola, but nobody's been able to isolate the virus, nor is it clear how it might get to humans from bats.

HIV reservoir was confirmed to be chimps in the mid-2000s, well after sequencing technology was cheap enough to do it. Main limiting factor was just that many chimp populations don't have it, plus having to go into the jungle and track chimp troops and isolate fragile RNA from their poop...not at all trivial to do.

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Doesn't SARS1 meet these criteria?

Wikipedia says they found "SARS-like" viruses in civets, which made them think civets were the natural reservoir, but I don't think they ever caught SARS itself in the wild.

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There's different types of evidence for infected civets, some of which comes from higher seroprevalence among civet traders.

In May 2003, Guan et al (2003) identified SARS-CoV-like virus in animals in a live-animal market in Shenzhen, Guangdong Province, China. Guan et al (2003) also tested for antibodies among workers in the market. They note that “8 out of 20 (40%) of the wild-animal traders and 3 of 15 (20%) of those who slaughter these animals had evidence of antibody, only 1 (5%) of 20 vegetable traders was seropositive.” This suggests that the majority of the infections of the 11 people with close contact with animals were zoonotic.

Among 508 animal traders, 66 (13%) tested positive for IgG antibody to SARS associated coronavirus by ELISA, while the control groups including hospital workers, Guangdong CDC workers, and healthy adults at clinic had an antibody prevalence of 1–3%. Among animal traders, the highest prevalence of antibody was found among those who traded primarily masked palm civets (72.7%), wild boars (57.1%), muntjac deer (56.3%), hares (46.2%), and pheasant (33.3%). Those for cat, other fowl, and snake were 18.6%, 12%, and 9.2%, respectively.

We have no such evidence for covid. As I have noted, none of the cases in the market worked at the animal stalls; there is no evidence that they had close contact with animals.

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That's an interesting result and something similar was later found for wildlife workers in Myanmar and Laos -- antibodies to SARS viruses but the workers themselves having no memory of being sick. However one reason we have no such evidence for COVID is because this kind of testing for workers at the Huanan Market was never released by China. There also is an article stating that one of the first to get sick at the market interacted with animals, although it's unclear to me whether this person was included in the WHO report or not. The first known case at the market, the shrimp vendor, has said she thinks she may have been infected by sharing a toilet with the wild game traders.

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Thanks for your deep and well-reasoned dive into a truly important topic. For me, your most important take-home messages were a) Bayesian reasoning has serious practical limits; b) we need to take the potential dangers of viral lab leaks seriously; and c) we need to take the potential dangers of natural zoonotic spread very seriously. One point I haven't seen mentioned is that the Earth harbors roughly 10**27 virus particles.

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Mar 28·edited Mar 28

I'd guess that most of them are bacteriophages...

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Probably, and most are marine. But it's a big number even if you cut it x 1,000. It's a big number even if you cut it x 1,000,000. It's a big number even if you...

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Well, you _could_ think of it as "just" about one kilomole or so... :-)

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It's also interesting how b and c support somewhat opposite reactions to gain-of-function research. If zoonosis is the bigger threat, we'd want to learn more about how this happens.

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good point. I'd say that on the one hand there probably *should* be more gain-of-function research, but it needs to be performed far more cautiously. ALL such work on virus should be performed in BSL-3 conditions, using only virions that have been genetically crippled to be intrinsically non-virulent. I guess the question is whether the scientific "community" can ensure that some jerk somewhere doesn't do something really stupid. Unfortunately, we tend to underrate the raw power of Stupid.

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a) is particularly important. What this blog post has shown beyond reasonable doubt is that "real" Bayesianism is not for amateurs.

A little knowledge is a dangerous thing. Better to only teach students who will be tasked to make difficult decisions in their professional lives (such as medical doctors, psychologists, investigators, judges and child protection officers) awareness of cognitive biases & where heuristics may go wrong, and NOT to also teach them formal Bayesian analysis - as they are unlikely to have the time & information & sufficiently advanced methodological skills to do it properly (plus be aware of all the pitfalls).

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My rule of thumb for something like this is 'whose evidence stands up to scrutiny'. I am not smart enough to understand any of this stuff, but I vaguely knew about the evidence beforehand from podcasts and social media. And then Peter just explained it all away effectively without significant pushback. This never happens in UFO debates. Or political conspiracies. Someone spends a billion hours researching sounds smart makes 30000 claims and then you pick 5 at random and 4 are nonsense and 1 is true or misleading or misinterpreted. I notice that my plausible theories of lab leak after hearing Peters argument about the implausability are *not* those advanced by rootclaim and so I assume they are obviously wrong I just don't know why but I'm confident Peter could convince me instantly. Rootclaim's inputs fell apart under scrutiny', which makes me doubt his statistical analysis. Garbage in garbage out. Note my real confidence about who is right is super low because I am dumb. But the debate definitely moved me away from lab leak 70-30

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You are conflating the spoken debate part, where Peter had far superior memorized knowledge, to the written parts, where there is basically no zoonosis evidence that survived scrutiny. We'll elaborate in a post soon.

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I look forward to reading it, and I have in anticipation 'rolled back' my change in beliefs until I do!

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“Okay we got our asses kicked in the mutually agreed format *that we ourselves proposed*, but now after the fact we want to re-litigate in a format that plays more to our advantages” *really* feels like shifting the goalposts in an unfair way.

If you take that route I think it would only be fair to give Peter access to the same resources you have in doubling down on the research and time to refute your refutations.

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i was referring to the written parts of the debate. anything that didn't require real time responses.

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I agree it should reflect poorly on Saar that he didn't realize that sophisticated debaters are in fact a huge problem (see: https://web.archive.org/web/20190129225836/http://commonsenseatheism.com/?p=1437 and to be clear I don't begrudge him for not knowing about a link rotted post from 2018 by a niche atheism blogger).

But I feel you should be engaging in the object level too, and realize that a spoken debate in fact is not the best at eliciting truth, for usual status reasons as well as the reasons Saar cited:

1.Debate importance is rated via time spent on a topic, not its actual importance, see Scott's point about the UFO detail debater.

2. It mostly explores how many layers of point-refutation each person has at the moment of debate, rather than what the reflectively endorsed endpoint would be. I would rather people take the time to decide how much each point matters to their main point, be explicit about this ahead of time and then decide if hashing it out is a good use of time. This is difficult to do in real time format.

3. If it is indeed true that Saar has found the ~one epistemology~, it seems much better to agree upon that frame (but not its conclusions) beforehand. This is not just to advantage it, but if it turns out to be as dismal as debate afterwards, well, that should give us a pretty good idea how well it generalizes.

That said, you are correct that retooling the die is a social faux pas, and that we should downrate the second round result.

I think if you are as confident on lab leak as Peter is, you should be rubbing your hands together, salivating that Saar is going to eat crow in HD this time.. Maybe not by Peter in particular, because Peter sick of this and won.

I think Saar should state up front that he commits to doing only this one round of welching / sore losering, and have it framed for everyone to see after, if he wants to dodge the "after wit who keeps coming up with reasons why he is right 3 weeks after losing the argument" accusations.

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Seems more like he was fine with the format when he thought he was the more sophisticated interlocutor, and changed his mind afterwards when he lost.

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Yes, this was included in my initial assessment of "penalty for not understanding that debates suck". I don't know why people keep thinking it's good to debate! Judges predictably flop the other way they started at the beginning, we know about the existence of truth independent debaters! This is an opinion I've had before I even heard it was a debate, and to my eye this mostly looks like every other case where an amateur debater loses, but had a better case (not that I think rootclaim had a better case, but rootclaim at least pattern matches to non sour grape, honest dismay at debates sucking).

I don't think sophistication is a good way of tracking truth, because sophistication is often displaying that you understand deep nuances and details, regardless of how it connects to the bigger picture. So anything that tracks sophistication tracks more of your ability to fight on specific sub topics, rather than subtopic weighted by centrality to claim.

I think I can be convinced away from this position if Saar goes on to repeat this similar behavior, or if he reflects and decides he was wrong after all. Or if Saar wasn't willing to additionally show his reasoning, or welches on the actual bet.

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This is not a niche atheism blogger and the post is not from 2018.

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founding

This post has actually left me with a deep curiosity on Rootclaim itself. To be honest, rather than the Nth post on the topic of lableak I'd very much rather read a primer on how to use the method.

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I read your reply and found it quite persuasive, and am tentatively back in the lab leak camp

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A lesson Scott draws is that Bayes is effectively impossible to apply in complex real-world situations, and that ultimately we are forced to rely on our intuitive reasoning. We’ll just throw a little math in at the end to make sure we aren’t making some clear and obvious blunder. I suggest this means the true epigraph for ACX should not be “P(A|B) = [P(A)*P(B|A)]/P(B), all the rest is commentary,” but rather “commentary, and all the rest is P(A|B) = [P(A)*P(B|A)]/P(B).”

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Well, I would argue that Hillel's standing-on-one-foot summary of the Torah was similarly too simple to apply in reality and largely just ends up being a rationalization for our intuitive aesthetic judgements, so I'd say that just makes the epigraph all the more fitting.

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My main take-home point also.

Like cost-benefit analysis that is not done by a very skilled and aware-of-own-biases practitioner, hard/real Bayesianism seems to create a danger that uncertainties are hidden in the priors & underlying assumptions & the empirical material used for the calculations, rather than appearing openly for all to see.

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> When psychoanalysts claim their therapies work, they don’t mean that someone who just read a two page “What Is Psychoanalysis?” pamphlet can do good therapy. They mean that someone who spent ten years training under someone who spent ten years training and so on in a lineage back to Freud can do good therapy.

And Robyn Dawes in House of Cards showed the evidence doesn't support the idea that training makes them any better.

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I had forgotten that over a decade ago I'd written about Dawes vs the concept of "metis" among professionals here:

https://entitledtoanopinion.wordpress.com/2010/11/28/robyn-dawes-robin-hanson-as-antidotes-to-james-scott/

And a follow-up here:

https://entitledtoanopinion.wordpress.com/2011/01/26/bogus-expertise-as-weapon-not-of-the-weak/

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Jeremy Howick (The philosophy of evidence-based medicine) cites the derogatory acronym GOBSAT related to the problems with "Metis": Good Old Boys Sat Around A Table (and agreed on diagnosis & treatment).

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“One read out of 200,000,000 is completely statistically insignificant,” said Pond. “It really had no SARS-CoV-2. There is no evidence based on genetic analysis there was SARS-CoV-2 in that sample. One read out of 200,000,000 — it could have been a low level of trace contamination.”

What’s more, as Bloom’s preprint reports, Q61 was the only swab above a certain threshold for raccoon dog genetic material that contained any SARS-CoV-2 RNA at all: “13 of the 14 samples with at least 20% of their chordate mitochondrial material from raccoon dogs contain no SARS-CoV-2 reads, and the other sample [swab Q61] contains just 1 of ~200,000,000 million reads mapping to SARS-CoV-2.” When Bloom plotted the quantity of animal genetic material found in the swabs with their SARS-CoV-2 RNA content, he determined that there was in fact a negative correlation