The Effectiveness of Ineffective Vaccines

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242 thoughts on “The Effectiveness of Ineffective Vaccines

  1. Flint:
    Just out of curiosity, are there beneficial viruses, to us or to bacteria or whatever?
    I wonder, given the opportunity and rate of virus mutation, if there haven’t been a great many “strains” that failed utterly, lasting at most only a few generations. My intuition is that the large majority of mutations are, as with everything else, either neutral or harmful to the virus. Fire enough billions of times, though, and now and then you hit the bullseye.

    Oceans can’t survive without viruses… but you knew that, right?

  2. J-Mac:
    The “vaccines” are very effective that ‘s why you need a booster every 3-6 months…
    Who could argue with that shittific argument?

    Eating is very effective. That’s why you need to keep eating fairly often. What a terrible argument for eating!

  3. Flint: Eating is very effective. That’s why you need to keep eating fairly often. What a terrible argument for eating!

    Time will tell, but I’m not aware that T-cell immunity declines quickly with time. Or that variants are eluding immunity at this level.

    There are, of course many people with immune system deficiencies, but many treatment options are coming online.

  4. Flint,

    I’m giving up on haircuts for the same reason. Or I would if it weren’t for Jimmy Savile (UK-centric joke).

  5. So, we have two competing theories for the origin of variants. The one I’m critiquing in the piece is the specific role of vaccines in variant selection. Jmac is also opposed to that hypothesis. So, we’re on the same side in that regard, bizarrely.

  6. Allan Miller: Jmac is also opposed to that hypothesis. So, we’re on the same side in that regard, bizarrely.

    Why do you believe that J-Mac is opposed to that hypothesis? Did he ever explicitly state that? If not, I wouldn’t assume things. It wouldn’t surprise me in the least if J-Mac is just collecting contrary opinions, regardless of whether they are mutually exclusive.

  7. I find it interesting that while there is no shortage of conjectures on the origin of covid and the origin of omicron, we have no actual evidence.

    We confirm that a direct proximal ancestor to SARS-CoV-2 has not yet been sampled, since the closest known relatives collected in Yunnan shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for dramatically more wildlife sampling to (i) pinpoint the exact origins of SARS-CoV-2’s animal progenitor, (ii) the intermediate species that facilitated transmission from bats to humans (if there is one), and (iii) survey the extent of the diversity in the related sarbecoviruses’ phylogeny that present high risk for future spillovers.

    https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac018/6524630?login=false

  8. J-Mac: I agree that the mutations that SARS CoV2 has “acquired’ leads to only one conclusion: another lab leak, unless, of course you are ready to abandon your evolutionary faith???
    It will come to that. I guarantee it. Are you ready??? lol

    I’m ready to abandon my evolutionary faith. What have you got for me that might push me over the edge? I’m ready!

    What’s the best you’ve got J-Mac?

  9. Corneel: Why do you believe that J-Mac is opposed to that hypothesis? Did he ever explicitly state that? If not, I wouldn’t assume things. It wouldn’t surprise me in the least if J-Mac is just collecting contrary opinions, regardless of whether they are mutually exclusive.

    Of course I don’t expect jmac to realise it. But he supports ‘repeat lab-leak’ and considers evolutionary scenarios impossible, so it can’t be both.

    Antivaxxers simultaneously believing that vaccines are ineffective and have selective power is a similar cognitive dissonance. See also: PCR doesn’t work, yet PCR-determined endpoints support ivermectin and the supposed superiority of ‘natural’ immunity.

  10. Allan Miller: Of course I don’t expect jmac to realise it. But he supports ‘repeat lab-leak’ and considers evolutionary scenarios impossible, so it can’t be both.

    If for once he bothered to defend his position instead of delivering the usual bluff, somebody might get something out of it.

    Mainly amusement, I’d wager. But at least it’s something.

  11. “When I told Eliza about the suspicions over the origins of the new coronavirus, she advised that everyone involved in the delicate conversations should raise our guard, security-wise. We should use different phones; avoid putting things in emails; and ditch our normal email addresses and phone contacts.

    Use different phones? These are not things that normal people do and I had no idea where to start. I contacted the communications tech manager at Wellcome: 27 Jan 2020, at 11: 59: Special request! Can I get a second phone today? Separate number, need to have one separate to my existing Wellcome one, I hope just for 3–6 months–can explain when we meet He found me a blank phone in the Wellcome cupboard and left it charging on my desk while I was in a meeting. I didn’t know the term then but I now had a burner phone, which I would use only for this purpose and then get rid of.

    When I got home, Christiane insisted I rang people close to us, so they would understand what was going on in case anything happened to me.”

    — Spike: The Virus vs. The People – the Inside Story by Jeremy Farrar, Anjana Ahuja
    https://a.co/4z21nMY

    Without judging the merits of origins theories, I think it is a fact that opposition to the lab leak possibility is an argument from consequences.

    Failure to find precursors in wild populations is strange, since few populations have been collected and studied as much as Chinese bats.

  12. petrushka: Without judging the merits of origins theories, I think it is a fact that opposition to the lab leak possibility is an argument from consequences.

    A fascinating sentence, here. Petrushka is noting that there are various “origins” theories but, rather than attempting to judge them based on their merits, he jumps to the conclusion (a ‘fact’, even) that people who oppose the “lab leak” theory must do so because they are indulging in the {argument from consequences} fallacy.
    Why does petrushka prefer the “lab leak” theory? Well, not based on the merits, as he freely admits. Rather, he prefers the “lab leak” theory because he finds the Sinophobic consequences appealing.
    It’s the fastest self-pwn ever.
    Which makes it all the more impressive that petrushka should cite Jeremy Farrar. Sir Jeremy has been outspoken in his searing criticism of the Chinese and British governments and their handling of COVID-19. Now, the slightly paranoid passage that petrushka quotes here has an element of “I’ve got a book to sell” sensationalism to it, and the colleague “Eliza” from whom he gets the burner phone advice is in fact Eliza Manningham-Buller, the former head of the UK counter-intelligence agency: a certain amount of paranoia comes with a career in spying. But Farrar is one of the top experts in the world and the whistle-blower who originally raised the concern that SARS-2-CoV might have originated in a lab. Does he still think that it did? No he does not, writing.

    We believe the strongest clue from new, credible, and peer-reviewed evidence in the scientific literature is that the virus evolved in nature, while suggestions of a laboratory-leak source of the pandemic remain without scientifically validated evidence…

    Of course, to the tin-foil hat crowd, this merely proves that he’s been “got at”. Data be damned.

  13. You neglect to mention that no theory of the oiigin of covid has any scientific evidence.

    Unless you believe that 40 years of molecular evolution can occur without leaving a trace in any extant population. I leave that as a possibility, but deny that any supporting evidence has yet been published.

    The alternative conjecture, which does not require intention or malice, does require one to believe the Chinese government could lie to cover up responsibility for millions of deaths.

    So which is more plausible? That molecular evolution can leap tall buildings in a single bound, without a population, or that the Chinese government fibs a bit, and arrests people who step outside the party line?

    If you read the entire chapters on the first months of the pandemic, you cannot miss the undercurrent of fear. Not so much personal fear, but fear of contributing to a world war, or at least to serious unpleasantness.

    Not, I would assert, the conditions under which one can be a disinterested weigher of probabilities.

  14. One other thing. The politics surrounding this is so thick, that anyone wishing to have a rational discussion on the origin if covid is immediately branded a conspiracy theorist. Any request for a discussion is immediately met with the accusation that one has already prejudged the issue.

    There are, of course, nut cases jumping to conclusions, but simply not trusting the Chinese government is not sufficient to make one a nut case.

    Cats have covid.
    Ferrets have covid.
    Hamsters have covid.
    Rats are suspected of having covid.
    Where I live, the wild deer that wander through my yard have covid. Or, at least a significant percentage do.

    But no one finds it interesting that bats have not been found to have covid. As in SARS-Cov-19.

    If only someone had taken the trouble to study bat viruses and compile and preserve a database of virus genomes.

  15. I don’t suppose it matters to anyone here, but I agree that people who have positions of authority in science should not make serious “criminal” accusations without proof.

    However, I find this reticence rather rare when it come to accusing entities less powerful and belligerent than China. But what’s the market value of integrity these days?

    I still find it odd that accepted rules of thumb — such as evolution occurring one bit at a time and occurring in populations rather than in individuals — can be cast aside. Not just ignored, but deemed dangerous.

  16. petrushka: You neglect to mention that no theory of the oiigin of covid has any scientific evidence.

    Likewise, I neglected to mention that the square root of 64 is 19, and a million other things that are factually incorrect.
    To be serious though, have you reviewed

    Latinne et al 2020 “Origin and cross-species transmission of bat coronaviruses in China”

    and

    Garry, 2021 “Early appearance of two distinct genomic lineages of SARS-CoV-2 in different Wuhan wildlife markets suggests SARS-CoV-2 has a natural origin.”

    and

    Zhou et al 2021 “Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses.”

    and

    Wacharapluesadee et al 2021 “Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in southeast Asia.”

    ?
    Because if you have not read, understood, and found fatal flaws in all of these, you cannot claim that no such evidence exists.

    petrushka: One other thing. The politics surrounding this is so thick, that anyone wishing to have a rational discussion on the origin if covid is immediately branded a conspiracy theorist. Any request for a discussion is immediately met with the accusation that one has already prejudged the issue.

    There are, of course, nut cases jumping to conclusions, but simply not trusting the Chinese government is not sufficient to make one a nut case.

    There are plenty of people having perfectly good rational discussions about the origins of SARS-CoV2. I was originally about 50:50 on the lab leak theory; but there’s a lot more data now, and (after a fair dose of rational discussion) I am more like 95:5. And not because I trust the Chinese Government: in fact, I don’t trust them at all. Did you read the section in Farrar’s Spike book where he lays out the Chinese government’s blatant dishonesty regarding SARS-CoV1?
    However, if you show up spouting Republican talking points that have been repeatedly debunked, as you have on this site, then the pushback you receive is entirely justified.

    petrushka: But no one finds it interesting that bats have not been found to have covid. As in SARS-Cov-19.

    Well, that really is not interesting at all. Firstly, seeing as COVID-19 is a human diagnosis, bats cannot get COVID-19, by definition. They do have viral infections closely related to SARS-CoV-2, the virus that causes COVID-19. No idea what the hell SARS-Cov-19 might be…

    If only someone had taken the trouble to study bat viruses and compile and preserve a database of virus genomes.

    Sarcasm, you are doing it wrong.

    petrushka: I don’t suppose it matters to anyone here, but I agree that people who have positions of authority in science should not make serious “criminal” accusations without proof.

    I agree. This applies even more so to people in positions of authority in politics.

    However, I find this reticence rather rare when it come to accusing entities less powerful and belligerent than China. But what’s the market value of integrity these days?

    Ooh, goody. An vague, unsubstantiated accusation of dishonesty. Weren’t you just complaining about well-poisoning? Are you really so unaware?

    I still find it odd that accepted rules of thumb — such as evolution occurring one bit at a time and occurring in populations rather than in individuals — can be cast aside. Not just ignored, but deemed dangerous.

    No idea what you are getting at here. The only thing I can think of is the suggestion that Omicron may have arisen as the result of a long-lasting, chronic infection in a South African individual. You do realize that it is the virus that is evolving, and not the infected individual?
    Here’s the thing: you have been lied to.
    Also, I find your comment re integrity disgusting.
    E2fixlink

  17. How could it have been a lab leak when none of the lab workers nor their relatives tested positive for SARS-Cov-2 antibodies?

  18. “ Garry, 2021 “Early appearance of two distinct genomic lineages of SARS-CoV-2 in different Wuhan wildlife markets suggests SARS-CoV-2 has a natural origin.”

    “The multi-market aspect of the early outbreak can be explained by distribution of SARS-CoV-2 infected animals to more than one market”
    This seems unlikely to me, as it implies multiple independent animal-human outbreaks, from multiple infected animals, when we have yet to detect evidence of any animal infected with early SARS-CoV-2. This explanation requires multiple near simultaneous sources of infection, or a single source that went to multiple markets, only in Wuhan, but the infection was missed by the search for infected animals of farms in the Hubei province.
    ….
    In my view, I haven’t seen anything in the association between early confirmed cases and the markets that suggests anything about the origin of SARS-CoV-2, other than that the time of the origin had to be prior to December 2.

  19. “ Because if you have not read, understood, and found fatal flaws in all of these, you cannot claim that no such evidence exists.”

    I really don’t need to find flaws in your sources, because none of them say anything contrary to what I said.

    No obvious progenitor to covid has been found in the wild. The molecular distance between covid and the closest known wild viruses is estimated at 40 years.

  20. Do we have a source for the claim that no lab worker tested positive?

    Would that include the three that were hospitalized in November?

    The pre-December history of covid is full of unsubstantiated claims. But it’s undisputed that the Chinese lied to WHO about human transmission in January, delaying the Western response.

  21. Response on the Origin of SARS-CoV-2

    Those who know of the longtime proximity and collaboration between Bob Garry and myself will not find it surprising that I concur with the above post. Indeed, I publicly endorsed the “natural origin” hypothesis for SARS-CoV-2 at midnight Feb 6, 2020, two weeks before the Andersen et al. analysis appeared.

    The reader will be surprised that, given the long collaborative history of Bob and myself, I will now publicly correct him.

    Just prior to the Discussion in the foregoing post, Garry states that : “The Guangdong (GD) strain of pangolin coronavirus carries a receptor binding domain (RBD) that is highly similar to the RBD of SARS-CoV-2 .“ He cites references that deal only with the amino acid sequences of the pangolin and SARS-CoV-2 isolates. At the amino acid level, this statement is true.

    However, as Boni et al (1) alluded to in passing, and I detailed later (2), this is far from true at the RNA level. Over a relevant span of 268 nucleotides, the GD pangolin and SARS-CoV-2 RNA sequences differ by 10.4%, virtually all of that difference in an accumulation of synonymous wobble-base substitutions. This degree of difference indicates several decades of evolution, and is completely incompatible with the sequence found in pangolins being the proximal source of the sequence found in the RBD of SARS-CoV-2.

    SARS-CoV-2 is a mosaic derived from distinct bat coronavirus lineages. The proximal sources of these mosaic segments are far from identical to any known viral isolates, but rather to inferred second or third cousin divergent RNA sequences with common ancestors dating back decades.

    In addition to the RBD just discussed, I also detailed (3) the dissimilar region in orf1A that follows the acidic region of nsp3. From nt 3059 to nt3335, the RNA sequences of SARS-CoV-2 and BatRaTG13 differ by 9.3% and the corresponding amino acid sequence by 18.1%. The sequence in SARS-CoV-2 bears no significant resemblance to any known sampled source.

    One can create suspicion by talking about amino acids, but the proof must account for the divergence of RNA that takes a very long time. After sixteen months of evolution in humans, isolates from April 2021 differ by about 0.1% from the December 2019 Hu-1 reference strain, roughly 30 out of 30,000 nucleotides.

    My second correction relates to the ongoing speculation about animal intermediates. There are zero data that any animal but a bat served as a host to SARS-CoV-2 prior to its introduction into humans. The 2012 Tongguan mine outbreak in six miners in Yunnan province, of a COVID like pneumonia with thromboembolism, that killed three of the miners, is ample precedent for direct infection of humans from bats (3). The closest known relative to SARS-CoV-2, Bat RaTG13, was isolated from that same mineshaft the following year. That mine is now closed, and referred to by locals as the “mine of death”. That sounds like a “hot zone” to me.

    My final correction to my good friend concerns hypothesis vs. theory. In common parlance the “hypothetical” and “theoretical” tend to be used interchangeably. However, in science there is a very clear distinction. A “Theory” arises to that status only when there is a substantial body of evidence that supports what was previously regarded as a hypothesis. As in, Theory of Evolution, Germ Theory of Disease, or Tectonic Plate Theory. Even the Fusion Peptide is still only a hypothesis. So, we should not be throwing around the designation of Theory for hypotheses with zero to little supportive factual information to support them.

    https://virological.org/t/early-appearance-of-two-distinct-genomic-lineages-of-sars-cov-2-in-different-wuhan-wildlife-markets-suggests-sars-cov-2-has-a-natural-origin/691

  22. I’m aware that my quotes are from responses to Garry, and not from Garry.

    Doesn’t affect their validity in either direction.

  23. Upon rereading, a small quibble.

    The distinction made between hypothesis and theory is not the one currently in favor.

    Regarding the rate of evolution: the possibility that omicron evolved quickly in a single person still does not shed much light on how decades of molecular evolution occurred in the covid precursor, without leaving some cousins in wild populations, or in populations of animals being farmed.

  24. petrushka:
    However, as Boni et al (1) alluded to in passing, and I detailed later (2), this is far from true at the RNA level. Over a relevant span of 268 nucleotides, the GD pangolin and SARS-CoV-2 RNA sequences differ by 10.4%, virtually all of that difference in an accumulation of synonymous wobble-base substitutions. This degree of difference indicates several decades of evolution, and is completely incompatible with the sequence found in pangolins being the proximal source of the sequence found in the RBD of SARS-CoV-2.

    Prof. Gallaher, whom you quote here, is arguing in favor of the natural origin explanation. He and Garry are debating the potential role of the pangolin in different natural origin scenarios.
    Here’s a fun fact: the data that Gallaher is citing here — all those synonymous substitutions — can actually be used as a powerful test of the man-made virus hypothesis. Duly motivated, I went to his paper [ref 2 in your quote] and reviewed the pattern of synonymous substitutions. Those wobble substitutions in SARS-CoV2 cannot be the result of any rational design, thus the ‘engineered’ explanation is pretty much dead in the water. As a result, my confidence in the natural origin explanation has increased from 95% to 99.9%. So I thank you for that.
    You find it implausible that the progenitor of SARS-CoV2 was evolving away in bats and/or another wild animal for years, undetected.
    I don’t: it’s par for the course.

    petrushka: I really don’t need to find flaws in your sources, because none of them say anything contrary to what I said.

    Yes. I understand that you believe this. Hence your maintaining that there is no evidence supporting a natural origin. Pasting blocks of text written by others is not the awesome rejoinder that you suppose: they may be wrong (like random netizen “ebom”) or not saying what you think they are saying (like Gallaher).

  25. petrushka: Regarding the rate of evolution: the possibility that omicron evolved quickly in a single person still does not shed much light on how decades of molecular evolution occurred in the covid precursor, without leaving some cousins in wild populations, or in populations of animals being farmed.

    Huh? I must admit, I had not made that connection, but you are absolutely wrong: chronic infections in a handful of pangolins and people would be sufficient to explain the mutational distance covered. And they could all be dead and buried (or eaten) before anyone started getting ill. Also, what makes you so certain that there are not any “cousins” out there — have we checked every bat in Asia?
    Finally, a lot of people seem to be assuming, when they do their rate-of-evolution calculations, that synonymous mutations are under zero selective pressure; it’s a pretty standard assumption to make. With HIV and SARS-CoV, it just so happens to be WRONG.

  26. I don’t recall ever promoting a “man made” hypothesis. At least not in the sense of designed. The concept of lab accident could include mishandling of collected specimens.

    The bottom line is, the evidence for “natural” origin is zero, none. It boils down to not violating any laws of physics.

    Reasons to suspect lab involvement include all the behaviors of the Chinese government.

    Taking their papers and databases offline.
    Arresting whistleblowers.
    Destroying virus samples
    Lying about the timeline of the outbreak
    Lying to WHO about human to human transmission
    After isolating Wuhan from internal travel, allowing the international airport to continue functioning, spreading the virus all over the world, before informing WHO of the outbreak. (This was AFTER they had sequenced the virus, so they were not ignorant of its existence.)
    Lying about the geographical origins of the virus. Accusing other nations. This is part and parcel of taking steps that ensured worldwide outbreaks before admitting it was in Wuhan.

  27. “ Serendipitously, prior to the COVID-19 outbreak, over the period May 2017–Nov 2019, we were conducting unrelated routine monthly surveys of all 17 wet market shops selling live wild animals for food and pets across Wuhan City …”

    https://www.nature.com/articles/s41598-021-91470-2/tables/1

    Strangely missing from this chart are bats and pangolins.

    Is Nature a politically incorrect source?

  28. I’m curious.

    I admit the lab accident conjecture is a conjecture with no proof, and will possibly remain so.

    What would it take for you to revise your probability estimate? I really can’t see anything that would move it from 50-50 to 95-5.

    An I really can’t see any justification at all for asserting a consensus in favor of a hypothesis having no positive evidence.

    And I think news media are, at best, disingenuous for continuing to report demonstrably untrue things about the wet markets. I can’t prove they were not involved, but there is no supporting evidence, and pretty good disconfirming evidence.

  29. petrushka: I don’t recall ever promoting a “man made” hypothesis. At least not in the sense of designed. The concept of lab accident could include mishandling of collected specimens.

    But that would still leave us with a natural origin.

    The bottom line is, the evidence for “natural” origin is zero, none.

    And that seems inconsistent with the above.

    As for the behavior of the Chinese, I have been taking that as a reaction to Donald Trump. It was clear that Trump wanted to make the Chinese a scapegoat, so they did what they could to make that difficult.

  30. petrushka: I don’t recall ever promoting a “man made” hypothesis. At least not in the sense of designed. The concept of lab accident could include mishandling of collected specimens.

    My apologies. So, when (in the thread where you uncritically posted the GOP’s crock of shit with its whole chapter on “Evidence of Genetic Modification”) you chose to post a link to the discussion of Gain of Function Research and its potential role in the 1977 flu outbreak, what you were actually doing was arguing AGAINST the Trumpian claim that the Chinese were conducting GoF research, and the COVID-19 was the result? Wow! I really misjudged you there. So you are in fact arguing that the Chinese never had any malicious intent, and — at worst– they are guilty of accidentally releasing a naturally occurring virus?
    Good for you.
    You learn something new every day.

  31. petrushka: I don’t recall ever promoting a “man made” hypothesis. At least not in the sense of designed. The concept of lab accident could include mishandling of collected specimens.

    Now you have lost me as well. So you are claiming that the missing 40 years of molecular evolution occurred in a freezer of some Chinese lab? This you deem more plausible than that the precursor virus lives in some as yet undiscovered animal reservoir?

  32. petrushka:
    “ Serendipitously, prior to the COVID-19 outbreak, over the period May 2017–Nov 2019, we were conducting unrelated routine monthly surveys of all 17 wet market shops selling live wild animals for food and pets across Wuhan City …”

    https://www.nature.com/articles/s41598-021-91470-2/tables/1

    Strangely missing from this chart are bats and pangolins.

    Is Nature a politically incorrect source?

    If they were conducting tests with animals in the vicinity of the lab, and that’s the origin of the leak, shouldn’t it be trivial to find a proximal strain in those same animals now? Wouldn’t the fact that they can’t find it actually debunk that hypothesis?

  33. I have no idea how covid originated.

    But I see no evidence that bats were sold in Wuhan wet markets.
    Nor pangolins.
    And yet there is a consensus that covid originated in bats and pangolins in the wet markets.

    The consensus is insane. Unsound. That’s not to say it is wrong. I can’t prove it wrong, but the reasoning is unsound, and the conclusion unwarranted.

    “ Now you have lost me as well. So you are claiming that the missing 40 years of molecular evolution occurred in a freezer of some Chinese lab? This you deem more plausible than that the precursor virus lives in some as yet undiscovered animal reservoir?”

    I never implied any such thing. The stored viruses presumably constituted a record of what was collected and what variants occurred in the course of research.

    How is it more likely that the evolution occurred in nonexistent wet market animals? And why is everyone scapegoating the wet market, when the best available evidence says that scenario is impossible?

    You are welcome to argue that I am wrong because I have bad motives, or because I cited evil politicians, but it’s a pretty weak line of reasoning.

    I have never thought the deliberate release was likely, for the simple reason that virus warfare is Dr Strangelove doomsday stuff, and I have a high opinion of the intelligence of the Chinese.

    I do believe the Chinese violated international agreements regarding disclosure of the outbreak, and I think it possible they hoped it would spring up in other countries before it was identified. If they did not deliberately work toward that result, they certainly stumbled into it.

  34. dazz: If they were conducting tests with animals in the vicinity of the lab, and that’s the origin of the leak, shouldn’t it be trivial to find a proximal strain in those same animals now? Wouldn’t the fact that they can’t find it actually debunk that hypothesis?

    I’m genuinely confused by this question. Who is “they” and what tests on what animals? Are you suggesting there were, in early 2020, lab animals that could have been tested?

    Who would have tested them and reported the results? Seems to me that a number of people were arrested and re-educated just for mentioning the existence a new strain of pneumonia in an e-mail. That’s a pretty strong disincentive.

  35. petrushka: I never implied any such thing. The stored viruses presumably constituted a record of what was collected and what variants occurred in the course of research.

    Well, it sorta is what you are implying: Most labs just freeze the samples which stops evolution of the stocks. Without modifying or actively introducing variants, 40 years worth of molecular evolution requires 40 years of cultivating viruses. Those must have been zealous researchers.

    petrushka: How is it more likely that the evolution occurred in nonexistent wet market animals? And why is everyone scapegoating the wet market, when the best available evidence says that scenario is impossible?

    The way I understand it, the original host was bats and the immediate precursor virus made its way to the wet market via several unknown intermediate hosts, possibly even humans that got infected someplace else. We just don’t know.

    petrushka: I do believe the Chinese violated international agreements regarding disclosure of the outbreak, and I think it possible they hoped it would spring up in other countries before it was identified. If they did not deliberately work toward that result, they certainly stumbled into it.

    The main concern of the Chinese government is its reputation, which often harms the safety of its citizens. Few people here will argue against that. That still doesn’t establish why a Chinese wet market can’t be the first known source of a new zoonotic pandemic.

  36. petrushka: I’m genuinely confused by this question.Who is “they” and what tests on what animals? Are you suggesting there were, in early 2020, lab animals that could have been tested?

    Who would have tested them and reported the results? Seems to me that a number of people were arrested and re-educated just for mentioning the existence a new strain of pneumonia in an e-mail. That’s a pretty strong disincentive.

    I may have misunderstood. Weren’t you saying, based on that Nature article, that chinese scientists from the Wuhan lab were collecting and testing animals at the time of the outbreak, and that supports the leak hypothesis?

  37. dazz: I may have misunderstood. Weren’t you saying, based on that Nature article, that chinese scientists from the Wuhan lab were collecting and testing animals at the time of the outbreak, and that supports the leak hypothesis?

    I still don’t understand the question.

    The Chinese definitely collected bats prior to the outbreak, but I don’t know any details.

    I have no evidence for a lab outbreak. I have evidence that the Chinese behavior looks like destruction of evidence. See Enron and the destruction of emails. Intimidating lab workers by arresting whistleblowers also looks like obstruction of investigation. This doesn’t prove anything, but it’s really bad PR.

    My primary gripe is the claim that there is a consensus for the bat—pangolin—>human scenario. Or something like it.

    A few days ago I posted an article on the recombination conjecture. My understanding is that recombination is the presumed way that a pangolin virus feature wound up in a bat virus and became covid.

    There are two problems with this. One is that recombination doesn’t account for the missing decades of molecular evolution.

    The other problem is more serious, and that is, an exhaustive survey of the wet markets, conducted in the years just prior to the outbreak, found zero bats or pangolins in the wet markets. This survey had no axes to grind, because there was no virus to politicize.

    Also, there is no reason to suspect some secret back channel trade in bats, because the survey article notes that MOST of the trade was illegal. Bats and pangolins were not double secret super illegal. Chinese simple don’t eat bats, as a rule.

    So why does the wet market conjecture persist as the consensus conjecture?

    We have reason to believe bats were brought to the lab and studied. We have reason to believe this is the only population of relevant bats in Wuhan. Other than that, we have no positive evidence at all, for the origin of covid.

  38. Corneel… That still doesn’t establish why a Chinese wet market can’t be the first known source of a new zoonotic pandemic.

    Two unrelated issues. Nothing about the lab activities, or possible coverup, says anything about the wet market.

    Direct study of the wet market is the source of my doubt. According to the best evidence — and it Is pretty solid— there were no relevant animals in the wet market.

    The continuing claim to the contrary is mystifying.

  39. We hypothesized that the increase in virus virulence and circulation in human populations results from a general replicative fitness gain that could be monitored in a simpler system such as cell culture. To examine the possibility of establishing a link between real-life evolution of viral sequences and this simple experimental paradigm, we serially passaged OPV2 strain in HeLa S3 cells for 14 replication cycles, at either 33°C or 39.5°C (Figure 1B). High temperature was used in order to create strong selection pressure that could accelerate gain of fitness (Manor et al., 1999), whereas 33°C, the vaccine manufacturing temperature, was designed as a control. Importantly, we used large viral population sizes for our experiments: during each passage, we ensured an input of 106 particle forming units (PFUs) with a burst size of ∼108 particles. Based on population genetics theory, these large population sizes are expected to accelerate adaptation (Rouzine et al., 2001), especially as compared to real-life setting, where transmission bottlenecks severely slow down the rate at which a population can adapt due to the effects of genetic drift.

    https://www.cell.com/fulltext/S0092-8674(17)30292-1

    This touches on the rationale for the conspiracy theory currently in vogue. I can’t judge it, but I note the lack of discussion in the press. For whatever reason, there is no public discussion.

  40. Those wobble substitutions in SARS-CoV2 cannot be the result of any rational design, thus the ‘engineered’ explanation is pretty much dead in the water.

    I confess to the crime of posting excerpts from people who promoted the engineered theory. It was my intention to start a discussion of origins, and not to argue for any particular theory.

    You are 99.9 percent certain that covid was not deliberately engineered, but that say nothing about the possibility of mishandling collected specimens. Or the possibility of collecting specimens much closer to covid than any publicly known.

    I am 99.9 percent certain that there is no known link between the wet markets and the origin of covid.

    So it’s a mystery. Could be solved by new evidence or new witnesses.

    In the world of investigating the causes of accidents and calamities, intimidation of witnesses and destruction of evidence is suspicious and in some cases, criminal. The Chinese did both. And the western world continues to engage in name calling toward anyone who questions the wet market conjecture. That’s a form of intimidation.

  41. petrushka: My primary gripe is the claim that there is a consensus for the bat—pangolin—>human scenario. Or something like it.

    “Or something like it” might cover a multitude of sins… The pangolin has been off the hook since October 2020, so you are misinformed. The consensus is for bat -> {another animal} -> human.

    petrushka: The other problem is more serious, and that is, an exhaustive survey of the wet markets, conducted in the years just prior to the outbreak, found zero bats or pangolins in the wet markets.

    Well, given that you were wrong about the pangolin consensus, do you now see that your ‘more serious’ problem is no such thing? You are misinformed.
    Lastly, what the hell does an in vitro study on polio in Cell have to with zoonoses?
    Again, pasting random chunks of text, whose context you do not understand, is not the killer argument that you suppose.

  42. petrushka: I am 99.9 percent certain that there is no known link between the wet markets and the origin of covid.

    Apart from the epidemiology, that is. You have been lied to.

  43. Regarding the Cell article, I have to ask questions for which I don’t know the answer.

    The article leads me to believe synonymous mutations can accumulate more rapidly in a lab culture than in the wild, because it takes time for them to be fixed in the wild population.

    Is this a correct reading, and could it be relevant?

  44. https://www.science.org/doi/10.1126/science.abf8003

    “ Our estimates for the timing of the Hubei index case further distance this individual from the outbreak at the Huanan Seafood Wholesale Market. Finding the animal reservoir or hypothetical intermediate host will help to further narrow down the date, location, and circumstances of the original SARS-CoV-2 infection in humans.”

    I might point out that I have been discussing the origin of the virus in relation to the wet market. And the widespread reporting that the wet market sold the bats and pangolins presumed to have contributed to the recombination events.

    This is distinct from tracing the earliest cases.

  45. petrushka: We have reason to believe bats were brought to the lab and studied. We have reason to believe this is the only population of relevant bats in Wuhan. Other than that, we have no positive evidence at all, for the origin of covid.

    My point is, if those bats that were brought into the lab were infected with SARS-Cov-2 and that’s where the leak came from, it should be trivial to find other bats in the area infected with very close relatives to the virus, right? And even if they found them, how could they determine if the zoonotic event happened in the lab vs in the wild?

  46. petrushka: Is this a correct reading, and could it be relevant?

    No, for the reasons given above.

    petrushka: DNA_Jock: Apart from the epidemiology, that is. You have been lied to.

    Evidence?

    Again, information that I provided on your previous muck-raking thread.

    petrushka: And the widespread reporting that the wet market sold the bats and pangolins presumed to have contributed to the recombination events.

    Say what? This is as epic as your “Just a little milestone you won’t read about in any newspaper.” fiasco.
    What a strange state of mind.

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