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Monday, November 15, 2021

The first review of "Viral" is out and it ain't pretty

Michael Hiltzik is first off the mark writing for the Los Angeles Times: These authors wanted to push the COVID-19 lab-leak theory. Instead they exposed its weaknesses.

Hiltzik is one of the few science writers who know what they'r talking about.1 You should read his entire review—here are some excerpts to tempt you.

... “Viral” is a laboratory-perfect example of how not to write about a scientific issue. The authors rely less on the scientists doing the painstaking work to unearth the virus’ origin than on self-described sleuths who broadcast their dubious claims, sometimes anonymously, on social media. In the end, Chan and Ridley spotlight all the shortcomings of the hypothesis they set out to defend....

“Viral” is built on vague innuendo, dressed up with assertions that may strike laypeople as plausible but have long since been debunked by experienced virologists. An entire chapter, for example, is devoted to the “furin cleavage site,” a feature of the virus’ structure through which the enzyme furin makes the spikes on its surface — which it uses to penetrate and infect healthy cells — more effective.

The furin site was originally described by lab-leak advocates as so unusual that it could have been placed there only by humans. Virologists have since determined that the feature is not all that rare in viruses similar to SARS2, and in any case, it could have emerged through natural evolutionary processes well known to experts. Chan and Ridley place a heads-I-win-tails-you-lose gloss on these findings, writing that if the site “proves to have been inserted artificially, it confirms that the virus was in a laboratory and was altered. ... If, on the other hand, the furin cleavage site proves to be natural, it still says nothing about where the virus came from.” Why write about it at all, then?

Alina Chan's reputation is already about as low as it can get and now it looks like she's dragging Matt Ridely down with her. He was already part way there so he didn't have far to go.

The book is published by HarperCollins. Should American lawmakers look seriously at regulating the publishing industry for spreading misinformation since they're already investigating Facebook for the same crime?


1. See: Is the media finally realizing that they have been duped into promoting the lab leak conspiracy theory?.

31 comments :

  1. Going after the publishers is probably not a good idea. Better to let the reviewers eviscerate the book like the one you cited.

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    1. Except the reviewer is a crackpot. Now listen, there are loads of garbage conspiracy theories. But there are documents demonstrating people were doing the kind of research that could have led to a virus with the sars cov2 properties. The key here is "could". Here are the documents: https://theintercept.com/2021/10/21/virus-mers-wuhan-experiments/

      Or you think those are garbage and not worth looking into? Sars cov might be perfectly natural, indeed.

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  2. "Should American lawmakers look seriously at regulating the publishing industry for spreading misinformation since they're already investigating Facebook for the same crime?"

    I realize (at least, I hope I'm right) that this was meant as sarcasm, meant to reflect the horrid level of ignorance our lawmakers put on parade any time representatives of "big tech" appear before them. I'd really hate to have the same level of foolishness and lack of understanding aimed at publishing, with our reps having to distinguish between "good" and "bad" science.

    We're close enough to being royally screwed here in the States. I don't want what little safety margin we have left to be eroded.

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  3. Larry, how come you don't ever mention Rick Ebright? He's been the frontman for the lab leak hypothesis and portrays himself as some sort of biosecurity expert even though his expertise is squarely on bacterial transcription. He is kinda an anti-you: You can't contemplate even a small chance that lab leak was involved and he can't imagine anything other than a lab leak.
    Both very unreasonable, IMO.

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    1. I can “contemplate” that the lab leak conspiracy theory is correct just as I can contemplate that the virus was manufactured in Fauci’s lab and released in China in order to destroy the Chinese economy. However, in the absence of evidence I dismiss both of those conspiracy theories.

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    2. https://theintercept.com/2021/10/21/virus-mers-wuhan-experiments/

      So either they make stuff up, or some virologists were experimenting on MERS cov and wild coronavirus. That's not a proof of the lab leak. But that doesn't support the idea that they were doing nothing with coronavirus or that it's "too difficult to do", as some commentors have claimed.

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  4. You do realize there are autentified documents purporting the plans of making gains of function research with coronavirus right? Or you haven't read the smbe paper? That doesn't prove anything but dismissing any lab leak theory is very odd. https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab327/6426085

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    1. Do you realize how ridiculous you sound?

      As far as we know there were no experiments done at the WIV that could have possibly led to the creation of SARS-CoV-2 and there were no experiments that qualify as gain-of-function research by any reasonable definition of the term. There's no reason to suspect that the scientists at WIV would be stupid enough to deliberately create a virus that could cause a pandemic and every reason to believe that they were trying to PREVENT a pandemic.

      You are just imagining that these experiments were being done. But let's consider, for the sake of argument, that the scientists are WIV could have been doing experiments that would lead to creation of a pandemic virus. What evidence do you have that they were actually doing those experiments and what evidence do you have that they were actually working with SARS-C0V-2 before the pandemic started? What evidence do you have that dozens of people were secretly creating SARS-CoV-2 in 2019 and hiding that work from all of their friends and colleagues? Why would they do that? What are the chances that this secret work wouldn't be exposed?

      The answer is that you have no evidence whatsoever to support your suspicions. That's the same amount of "evidence" you have that American labs were doing that kind of research and created SARS-CoV-2.

      Do you often continue to support conspiracy theories that aren't supported by any evidence and are denied by the people you are accusing?

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    2. BTW, the paper by Alina Chan that you reference in your comment is about the furin cleavage site. No experts in the field of coronavirus evolution agree with the slant taken by Chan and Zhan in that paper.

      Here's the abstract of a paper published last month that illustrates the scientific consensus.

      "Knowledge about coronaviruses (CoVs) with furin cleavage sites is extremely limited, although these sites mediate the hydrolysis of glycoproteins in plasma membranes required for MERS-CoV or SARS-CoV-2 to enter cells and infect humans. Thus, we have examined the global epidemiology and evolutionary history of SARS-CoV-2 and 248 other CoVs with 86 diversified furin cleavage sites that have been detected in 24 animal hosts in 28 countries since 1954. Besides MERS-CoV and SARS-CoV-2, two of five other CoVs known to infect humans (HCoV-OC43 and HCoV-HKU1) also have furin cleavage sites. In addition, human enteric coronavirus (HECV-4408) has a furin cleavage site and has been detected in humans (first in Germany in 1988), probably via spillover events from bovine sources. In conclusion, the presence of furin cleavage sites might explain the polytropic nature of SARS-CoV-2- and SARS-CoV-2-like CoVs, which would be helpful for ending the COVID-19 pandemic and preventing outbreaks of novel CoVs."

      https://www.frontiersin.org/articles/10.3389/fmicb.2021.649314/full

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  5. "We constructed the full-length infectious clone of MERS-CoV, and replaced the RBD of MERS-CoV with the RBDs of various strains of HKU4-related coronaviruses previously identified in bats from different provinces in southern China,”
    https://theintercept.com/2021/10/21/virus-mers-wuhan-experiments/


    This comes from the NIH report. I don't know what more you want. It's written they funded research to create new coronavirus that had increased infectivity. So yes those experiments were being done, they have admitted it themselves. I never said they did it on purpose to create a pandemics. But saying no experience was made creating more infectious coronavirus, is blatant fake news

    What else do you want? I have not been accusing you of having caused the pandemics btw wtf?

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    1. From the rather abbreviated description of the paper causing much comment from the 'lab-leak' proponents that you reference second hand in your above link I get this simplified layman's description.

      They took a known human infective CoV (MERS) and produced a copy missing its RBD (making it incapable of infection) then adding the RBD from various bat CoVs and testing if they restored the MERS infectivity. This sounds like a good way to find bat CoVs of interest that might eventually be able to infect humans and so we should keep an eyer on the3m. Apparently one of them made a MERs that was more infective than usual. I would think that the bat Cov involved should be especially watched.

      Is that at least close to what was happening?

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    2. Yes that's simply my point and the point of Chan, at least from her paper (no idea about her book): they WERE doing dangerous experiments with highly infectious virus. To the point the NIH itself freaked out, literally. Now, SARS-CoV-2 might very well be natural. But as the Chinese bleached the Wuhan market so, we might in fact never know. But even if the sars cov2 is natural, should we not at least discuss if playing with coronavirus is a good idea? Such talks have been ongoing for at 10 years, at least, for Influenza virus.

      So why dismiss it now? Chan is calling for more sampling of natural covid to keep doing spike proteins alignments. I believe this is actually consensual among virologists. But we might never know because Chine doesn't seem so cooperative, let's remember journalists taking pics of the situation are now in jail. So I don't know why Larry insinuates we should a priori trust the Chinese authorities. Especially since they bleached the Wuhan market and destroyed all the wild animal farms. Finding the virus os natural and coming from one of their farm would be equally bad for China. The virus either comes from management error in a lab, or from massive illegal wildlife smuggling. In both scenario someone fucked up badly.

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    3. Someone is going to have to explain to me why this experiment is supposed to be dangerous. they seem to me to be a reasonable, nay prudent, means to discover possible future human infective viruses. Since there were no experiments on the bat Covs, what possible connection is there to CoV 19?

      Why are those to only two scenarios you consider? And what a surprise, a government stops cooperating when they are accused of lying and they vigorously decontaminate possible sources of a dangerous pathogen.

      The charges and counter charges are at this point sounding highly political and far from scientific.

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    4. You quoted yourself they used bat coronavirus, though I suppose you meant not as a backbone. That's a fair point.

      Otherwise, I agree it's political. But with the two scenarios it's inescapable. The last solid paper on the natural origin, suggests the Wuhan market, hence wildlife kept there, which was ALREADY the cause of the first sars. That rises some political questions too, no?

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    5. The Chinese government has other reason not to want to cooperate, like the violent racist trolling of Trump's administration, the Ouighurs question, Taiwan, etc ... It's not like the Chinese have a track record of openness and cooperation with the US (and vice-versa). It's true it's making the investigation much more difficult. But should we pretend we can trust Chinese authorities? That's a real question I have. Science operates on the basis of your partners behaving in good faith. I believe there are reasons to think it's not the case with China. Note that China likely believes the US is not to be trusted (of course many Chinese scientists are willing to help, that's not the question, but since disagreeing with the government tends to make you disappear). So what do we do? I have no answer to offer.

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    6. They were investigating bat Covs by *using* the MERS virus. Is there *any* evidence in those papers you quote that indicate was any, or contemplation of any, 'gain of function' experiments or any changes made to the bat CoVs? I don't see any.

      So the only 'evidence' you have for the 'lab leak' theory is your (justified) dislike and distrust of the Chinese government. Does any *scientific* data support the theory?

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    7. Oh, and you still haven't told me why the quoted experiment should be considered 'dangerous'.

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    8. https://theintercept.com/2021/09/06/new-details-emerge-about-coronavirus-research-at-chinese-lab/
      Here they mention the collecting and testing of the infectivity of many bat coronavirus. I am not sure what proof of dangerousity you need. Putting at the same place, in a big city, dozens (?) potential pathogens sounds risky to me. Also making a Mers 1000 times more infectious. I have never understood why people keep putting such labs in big city centers (it's the same in France, I don't blame the Chinese).

      A very good thing would simply be to have access to the logs of the lab. But it seems that's gonna be impossible. To make things clear, I am not sure there was a lab leak. It is consensual that there was (and probably still is) a risk of spillover from bat coronavirus from the wild in Asia. And that might well be what happened. There is a very good recent paper about that in Science, I think, provided we can trust the data about the first cases. But can we?
      Honestly, if you were in charge, wouldn't you have the idea to start by asking the institute "hey guys, what kind of things were you doing, can we check the logs"? And then "okay, I want to make sure you handled in everything"? And then "who were the first patients? What did the doctors that were arrested by the police had to say"? The thing is, whatever the source of the pandemics is, China isn't going to let people come and check. They just don't allow that. And that creates a very unhealthy climate of paranoia, I grant you that. I feel it's almost impossible to do good science on the first cases. If you prefer it framed this way, okay. I am also open to confess sympathy for Chan, because attacking the Chinese state is not an easy or safe thing to do. That's of course not a free pass to tell anything you want. But I find her smbe paper reasonable. I like the sequence alignment she provides and the question she has about it. And I feel Larry could discuss it rather than discussing the review of a book he hasn't read. One other important point on which I would like an answer "why, contrary to other coronavirus spilloves, was this one so efficient at spreading among humans and why did it take much longer than in previous cases for more infectious variants to emerge, which suggests that maybe it was difficult for them to emerge"? This could totally be by chance, and an effect of poor sampling/understanding of spillovers. I am genuinely curious about that and it's not a sarcasm.

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    9. Or to make it very brief: authoritarian states are paranoiac, so they act to cover up, even when there is nothing to cover up. Which makes "truth" almost an impossible concept there. That's what I am afraid of the most. That's probably my bias. I stand by Chan, though, in that I don't believe she deserves to be treated like a Qanon or intelligent design supporter.

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  6. If you are trying to make me say "they engineered a spike protein from nowhere to create a pandemics and have Bill Gates take over with vaccines", I am sorry but it's a straw man argument.

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  7. Sorry for the third message in a row, but have you actually read worked done by Chen? She IS acknowledging the existence of the natural occuring spike protein. I don't even know why you bring this up. If I recall well, it's David Baltimore who first said he found the codon bias of the furin site suspicious, but then said he realized it could indeed be natural. You act as if dealing with creationist nutjobs. Disclaimer: I haven't read Chan book but her paper and preprints, which make interesting observations.

    But don't worry I am not gonna start to tout support from Trump or anything, or that the Jew engineered the virus. I am well aware of the danger of seeing lab leak hypothesis being used by Qanon and other mad men. I understand you probably deal with a lot of such stupidity but I am not one of them. And yes the whole idea of scientists doing virology in secret cave in Wuhan to promote bitcoin usage is ridiculous.

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  8. I see that the Canadian journalist and author, Elaine Dewar, has a new book, On the Origin of the Deadliest Pandemic in 100 Years: An Investigation out on the Wuhan lab leak hypothesis. text

    From an interview on CBC Radio 1's Ontario Morning program 2021/11/24, it sounds a bit "interesting?". Any opinions or references?

    Thanks

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    1. The deadliest pandemic in the last 100 years was HIV/AIDS.

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    2. Are you sure it's not tuberculosis?

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    3. I don't think TB counts as a pandemic, because it had spread around the world before the 100 years began. Likewise measles.

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  9. Another review of Alina Chan book
    https://forbetterscience.com/2021/11/24/viral-by-alina-chan-matt-ridley-book-review/

    Much more positive and where we learn at the lab they even kept live bats, making the lab effectively similar to the Wuhan market. It also interestingly point out how the most blatant opponent of lab leaks are the people who were doing the experiments. This is called a conflict of interest. And before you say it's conspiracy, I remind you that scientific journals ask you to disclose potential conflict of interests. Interesting how when the book is reviewed by a big media it's a conspiracy trash but when it's reviewed by a scientist it is informative. At least, it's now clear that the idea that the Wuhan lab had no bat, no bat coronavirus, or was not doing experiment with them, was fake news. How much was honest mistake due to the Chinese lack of transparency or coverup we don't know.

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    1. For the benefit of those who don't bother to follow that link, here are some quotes from that "review."

      "Lacking even a shred of evidence for that elusive animal transmission, including a total zilch for the entire Huanan seafood market which is still being pushed as the epicentre of the pandemic, all we have is bad science of wishful thinking in badly peer-reviewed papers in elite journals on a political mission to “defend science” and to please the Chinese Communist Party (CCP), each time religiously hailed by journalists as the breakthrough we all prayed for."

      "It is very likely that all those top virologists, epidemiologists and other experts who publicly reject a lab leak as unlikely or even as a conspiracy theory know very well that this theory is in fact at least as probable as a zoonotic origin. They are surely themselves shocked by the massive cover-up in China. Some of them are protecting their friends and close collaborators in Wuhan. Others are afraid of a moratorium and of losing funding for gain-of-function research, a worst-case nightmare scenario in academic ivory tower, much worse than a theoretical danger of yet another lab-generated pandemic."

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    2. You are still not commenting for the now proven coverup of the Ecohealth alliance experiment by the NIH. Unless you believe those documents are fake?
      https://www.newsweek.com/how-dr-fauci-other-officials-withheld-information-chinas-coronavirus-experiments-1652002

      Here is a science interview of Daszal where he admits that he didn't even know that the Wuhan lab had live bats. https://www.science.org/content/article/we-ve-done-nothing-wrong-ecohealth-leader-fights-charges-his-research-helped-spark-covid-19 of course that's not a proof of anything, just that no one knew what was happening. Perfectly normal handling of potential pandemics virus. Not worth investigating further.

      By the way, congrats for trashing Leonid Schneider, one of the few with Elizabeth Bik to denounce the frauds in Academia. All that on the basis of papers you haven't read yourself but believe competent to comment about. I am sure you didn't know either that a virtually identical strain to the original SARS-CoV-2 one was discovered recently, the only difference? No furin cleavage site. https://www.researchsquare.com/article/rs-871965/v1

      So they were sending to the Wuhan institute strains virtually identical to the ones having caused the pandemics but it's a conspiracy theory to request for more investigation.

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    3. By "virtually identical strain" you must mean less similar across the genome as a whol0e than the other closest known relative to SARS-Cov2, RaTG13. It only appears to be more similar specifically in the receptor binding domain of the spike protein, with only one or two residues difference there.

      So that's definitely NOT the only difference in the genomes. Heck, even the actual receptor binding domain of the spike protein has 1 or 2 amino acids different.

      Did you even read that paper? They also show nicely in figure 2 that all the closest known relatives of SARS-Cov2, are genomic mosaics produced by a lot of recombination events. Furin cleavage sites are evolvable amino acid sequences, and the spike protein of SARS-Cov2 is already known to basically be a recombination hotspot. You're bound to get insertions and deletions there. Sorry buddy but there's just no need for this hypothesis that the virus had to be engineered to explain any of it's attributes.
      As usual the only evidence you have is to try to connect disparate dots (someone X didn't know Y) with some handwaving.

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  10. Actually this book doesn't conclude there was a lab leak, just that it is more possible than what has been said. Maybe next time it would be better for Larry to comment books he has actually read.

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  11. Here is a review of the book from a scientist who has actually read the source material: https://forbetterscience.com/2021/11/24/viral-by-alina-chan-matt-ridley-book-review/

    Interesting how it turns out very different from what Los Angeles Times reports. Among the very "amusing" facts are that the so called experts Larry is so proud of committeed many breaches of scientific ethic, such as publishing several times the SAME virus genome, forget to mention that virus was responsible for lethal pneumonia, etc ... So we have actual and verifiable evidence of data manipulation. Anyone can recheck by itself by investigating gene banks. But that's conspiracy theory, it's perfectly normal for a scientist to publish several times the same genome, you can forget.

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