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Coronavirus Origins

I’m going to regret writing about this, but it’s not a topic to be ignored. Where did the current coronavirus come from?

If you ask that question, you get all sorts of answers from all sorts of people. Let me downgrade some of those right up front. To start at the far end of the fever scale, I do not think that this virus is some sort of deliberately engineered (and/or deliberately released) bioweapon, and I am simply not going to give that theory more time here today. But that still leaves a lot of possibilities open, and I don’t think we have enough evidence yet to sort those others out.

The other end of the scale is that this is a virus that evolved into its present form in an animal host and then made the jump into infecting humans through sheer coincidence and bad luck. That does happen, and it has happened many times throughout history, so that absolutely cannot be ruled out. But there are a lot of possibilities in between those two. As the world knows, there is a research facility in Wuhan that has been studying viruses (including coronaviruses), so we also cannot rule out the possibility of an accidental escape from such a site. And there’s also the possibility that such a virus might then be different from wild-type, depending on what sorts of work was done on it. Viruses most certainly have escaped from research facilities before, and this is not a crazy idea.

From here we get into a lot of details about the codons in the viral sequence, the presence of a furin cleavage site, similarities (and differences) between the current coronaviruse and the closest wild-type relatives. This Medium post by Nicholas Wade goes into many of these, but you should know up front that many virologists believe that he overstates the case (such as in the rarity of that furin cleavage site). I also should link to this letter that has just appeared in Science, calling for greater clarity on the whole issue, and I don’t think anyone can disagree that it’s needed:

As scientists with relevant expertise, we agree with the WHO director-general (5), the United States and 13 other countries (6), and the European Union (7) that greater clarity about the origins of this pandemic is necessary and feasible to achieve. We must take hypotheses about both natural and laboratory spillovers seriously until we have sufficient data. A proper investigation should be transparent, objective, data-driven, inclusive of broad expertise, subject to independent oversight, and responsibly managed to minimize the impact of conflicts of interest. Public health agencies and research laboratories alike need to open their records to the public. Investigators should document the veracity and provenance of data from which analyses are conducted and conclusions drawn, so that analyses are reproducible by independent experts.

From what I can see, this is pretty much exactly what hasn’t happened yet. I have to note that the actions of the Chinese government have not been characterized by the openness called for above. And as long as that is the case, suspicion will be hard to dispel. Their documented actions against Chinese physicians and scientists who spread early word of the pandemic do not inspire confidence, either. But at the same time, some politicians have also (for their own benefit) jumped at the chance to make accusations against the Chinese. This stuff has done nothing but sow fear, hatred, and confusion – what was partly the plan on the part of the people promulgating it, of course. That’s been in all directions, too, because there are many people who probably have refused to take the lab-leak idea seriously just because some demagogues and fools love it, too. This world would be a lot easier to understand if assholes were always wrong about everything, but that’s not the case. To be completely even-handed about it, there are (for example) plenty of people in both the Trump administration and in the Chinese government that I put in that category. They can’t both be right, though, can they?

So it’s all an open question, unfortunately. And I think it’s important for people to realize that it’s an open question, and that we need a lot more hard evidence before anything can be said for certain. People up and down the spectrum of opinion need to realize that this could still go in several different directions, and that no matter what the real answer turns out to be – assuming we get one – that it’s going to make some people angry. I just hope we do get one, because it’s really, really important.

 

228 comments on “Coronavirus Origins”

  1. An Old Chemist says:

    Derek, what makes you think that we should not blindly trust the words of Dr. Robert Redfield, former CDC director and an eminent virologist, when he says that:

    Former CDC Director Redfield Says He Believes Coronavirus Originated Inside a Wuhan Lab

    https://news.yahoo.com/former-cdc-director-redfield-says-130733234.html

    1. Pv=nrt says:

      You shouldn’t blindly trust the beliefs of anyone. Redfield and everyone else are welcome to cough up some data.

      1. JohnA says:

        @ Pv=nrt: “cough up some data.”

        Consider the mutations C241T, C3037T, C14408T, and A23403G.

        Over 80% of all Covid-19 viruses carry these four mutations (changes from the Wuhan variety).

        These four mutations are always found together as a group, almost never alone.

        Below the number of individual occurrences (of these mutations), in square brackets, which should be compared to the group occurrences (of these mutations), in parentheses. These numbers are derived from a collection of 14,712 viral sequences acquired in May 2020.

        C241T [10258] C3037T [10283] C14408T [10283] A23403G [10328] (10120)

        This quantifies what one means by the mutations always being found together as a group.

        Since the mutations C241T, C3037T, C14408T, and A23403G are widely distributed over the genome, they could not have all been added to the genome at the same time. However, since the number of individual occurrences of each mutation are almost the same, all four mutations had to have been added at roughly the same time. This means that these four mutations did not occur naturally.

        This proves that they are not descendant from the Wuhan variety. Which means that the British-American viruses are a separate occurrence of Covid-19. This means that both occurrences of the virus were deliberate releases, and that both are, almost certainly, engineered. Interestingly, an effort was made to derive the Group of Four from the Wuhan sequence by faking intermediate sequences. You can read about this below.

        http://preearth.net/phpBB3/viewtopic.php?f=15&t=1184

        QUESTION: Is that really proof as claimed?

        1. Fathead says:

          You say these sequences date from May, about 6 months after the first known human case. So what if just after jumping into humans a group of 4 mutations arise that are optimal for human transmission? I don’t see how this proves anything or is even surprising.

          1. JohnA says:

            It is surprising and it proves everything.

          2. Fathead says:

            Something’s wrong with either the explanation or the logic.

            “they could not have all been added to the genome at the same time” – I see no justification for this. Four changes that happened at about the same time could easily persist down all lineages, with occasional deviations. If the deviations are suboptimal I think you would see exactly what you describe.

            “since the number of individual occurrences of each mutation are almost the same, all four mutations had to have been added at roughly the same time” – I don’t think this statement is true either. The number of occurrences at the time the sequencing was done reflects the current state of infections, not the length of time since they arose.

            Since I don’t believe either of these assertions I don’t believe the conclusion follows at all. Perhaps you can provide a link to a scientific article which explains your theory better?

          3. John says:

            I have rewritten the above comment to make it clearer.

            Consider the mutations C241T, C3037T, C14408T, and A23403G.

            Over 80% of all Covid-19 viruses carry these four mutations (changes from the Wuhan variety).

            These four mutations are always found together as a group, almost never alone.

            Below are the number of individual occurrences (of these mutations) in square brackets, which should be compared to the group occurrences (of these mutations) in parentheses. These numbers are derived from a collection of 14,712 viral sequences acquired in May 2020.

            C241T [10258] C3037T [10283] C14408T [10283] A23403G [10328] (10120)

            This quantifies what one means by the mutations always being found together as a group.

            To spell it out:

            C241T occurs in 10258 sequences (out of the 14712).
            C3037T occurs in 10283 sequences.
            C14408T occurs in 10283 sequences.
            A23403G occurs in 10328 sequences.
            The group [C241T C3037T C14408T A23403G] occurs in 10120 sequences.

            Since the mutations C241T, C3037T, C14408T, and A23403G are widely distributed over the genome, they could not have all been added to the genome at the same time. However, since the number of individual occurrences of each mutation are almost the same, all four mutations had to have been added at roughly the same time. This means that these four mutations did not occur naturally.

            This proves that they are not descendant from the Wuhan variety. Which means that they are a separate occurrence of Covid-19. This means that both occurrences of the virus were deliberate releases, and that both are, almost certainly, engineered. Interestingly, an effort was made to derive these four mutations from the Wuhan sequence by faking intermediate sequences. You can read about this below.

            http://preearth.net/phpBB3/viewtopic.php?f=15&t=1184

    2. Epistaxis says:

      Before Redfield achieved all the prestige of working in the Trump administration, he was best known for being wrong about HIV. Now he shills for the dubious UV decontamination technology of Big Ass Fans. Even if we’re going to blindly trust someone for some reason, we can probably find someone better.

      But sure, I agree with Derek that this is worth investigating in excruciating detail, even if it seems obvious to most experts that there’s nothing to the lab-leak hypothesis. The first few hydroxychloroquine RCTs were worth doing too. When a lot of people care about the answer, a conclusive negative result is still constructive. And even on a grand conspiracy-theorizing level, I don’t see how the implications of the lab-leak hypothesis are any worse than the wet-market hypothesis or whatever kind of zoonotic origin anyway (nor would I expect the CCP to be any less diligent covering it up). Something happened that should have been prevented by safety measures, and it made the whole world sick, so we should find out what happened and update the safety measures to prevent the next one. Duh.

      1. theasdgamer says:

        What do we call people who put any stock in late antiviral treatment RCTs? Starts with an ‘F’.

      2. Joe Clarkson says:

        Something happened that should have been prevented by safety measures, and it made the whole world sick, so we should find out what happened and update the safety measures to prevent the next one.

        If the virus leaked out of the Wuhan lab, I suppose that lab safety measures could be improved. If the Chinese government knows that it did come from the lab (or even could have come from the lab) they are already well incentivized to correct things, because, after all, the virus caused a lot of problems in China, too. Problem solved.

        If the virus came from zoonosis, then perhaps better regulation of human/wild animal relationships ought to be developed. We’ll see how the US hunting and trapping communities react to that. But since there is unlikely to be any way to prevent ill-advised bush meat hunting or animal collecting from happening all over the world, it’s likely that new viruses will crop up from time to time.

        So, I don’t think it’s that important to find out the source of the virus. We would do better to concentrate on revising our pandemic response measures instead. Once SARS-Cov-2 appeared in humans, where it came from was not nearly as important as how we responded. It’s that response that deserves the most retrospective analysis. After a new virus makes an appearance, where it came from is irrelevant.

        1. theasdgamer says:

          So let’s continue funding gof research because it gives people jobs. So what if a few grandmothers and grandfathers die?

          1. Byrel Mitchell says:

            Gain of function research has the potential to save millions of lives too. Understanding the evolution of pathogens is important to defeating them.

            Your strawman of the argument in favor of it needs some work.

          2. jam says:

            Gain of function has bought you SARS CoV, MERS, and SARS CoV-2, and a few others.

    3. Nesprin says:

      In god we trust. All else must show data.

      1. albegadeep says:

        Amen!

      2. Lucifer says:

        I will believe in God the day he believes in me and I don’t remember him ever believing in me.

        Besides, there is no data to prove his existence!

        Faith makes you blind, because God is against knowledge, we were chased out of the Garden of Eden for eating the fruit of the Tree of Knowledge, remember that.

        1. Sheesh says:

          Another decisive victory in the crusade against aphorisms. Go Lucifer go.

          1. Lucifer says:

            Lucifer two words !
            Lux in Latin : the light.
            Cifer : the one who brings.

            The one who brings the light, the knowledge, the one who brings the knowledge, as others brought the fire to the humanity; the one who told Eve to feed on the knowledge, so the knowledge is the evil incarnated, it’s diabolic, but the blindness of the faith would be the good.

            Lucifer did not kill anyone, nor did he enslave anyone, but God knows about genocide and slavery, and yet he is the good.

        2. Lars says:

          A small (albeit important) nit to pick:

          When referring to God, it’s

          “They/Them”, not “He/Him”

          “They/Them” has the added bonus of not discriminating against polytheists.

          1. Lucifer says:

            If this is monotheism, how do they manage to be several ?
            Decidedly, it is not only Trump and the Chinese who conspire, even he and they do it !
            Deliver us from evil, bring us knowledge, I won’t eat that fruit anymore !

          2. Lars says:

            Maybe “God” is a committee, which is why their decisions are so bad.

          3. Lars says:

            …and their “intelligent” designs.

          4. Lucifer says:

            Like the Chinese Communist Party ?
            After all, if the man is in his image.

  2. ezra abrams says:

    Wade has made what appear to be errors in the past; for a journalist, as for a scientist, track record is important in evaluating the person
    https://election.princeton.edu/2014/07/08/race-and-mental-traits-nicholas-wades-third-error/
    https://en.wikipedia.org/wiki/Nicholas_Wade

    Of course the Chinese govt isn’t open and transparent; do you think we would be ?
    we don’t just shoot people who are whistleblowers, so there is that

    You learned in middle school that you cant prove a negative; we can’t prove that the virus isn’t man made

    recent work from WHO shows furin sites in wild virus, which under cuts, afaik, the main lab origin theory data point, that the furin site is to large a mutation, and to well designed, to be natural

    1. Owen says:

      Proof is always helps if you’re trying to get published. But we don’t need proof to make policy.

      The policy implications of this debate are: do we want to provide funding to gain-of-function research, whom should we allow to perform it, and under what conditions. These are decisions we can make now and revise as more evidence becomes apparent.

    2. AVS-600 says:

      “Can’t prove a negative” isn’t really true, and the distinction is important here. If we found evidence of a near-ancestor of SARS-Cov-2 in the wild, that would probably be sufficiently strong evidence to falsify Wade’s version of the story (i.e., that the virus was ‘created’ in a lab).

      It doesn’t of course say anything about the more mundane “lab leak” hypothesis, which is that SARS-Cov-2 was originally an animal coronavirus that escaped after being collected for study. THAT is something that likely can’t ever be truly disproven, since it requires proving a UNIVERSAL statement (“the Wuhan virology lab never collected samples of SARS-Cov-2 or its precursor”), which is indeed something that’s very difficult to do.

      1. a s says:

        In that case it also wouldn’t matter that it was a lab escape – because even if you closed the lab, people would eventually catch it from a wild bat, and now you just haven’t studied it.

        1. JD says:

          Wade’s article discusses “Gain of Function” research, which deliberately modifies the virus to be more infectious to people, in order to better understand what sorts of viruses are likely to make the jump from animals to people. He says there are US NIH grants of public record that funded this research in Wuhan, and that research was being done on bat coronaviruses related to SARS2. In his telling, such research is more likely to lead to harm than good.

          1. theasdgamer says:

            The funding went to Ecohealth and from them to WIV. Laundering the money.

    3. theasdgamer says:

      Everyone makes errors and everyone should practice due diligence to separate baby from bathwater.

      Ad hominems mean little to those who aren’t fools.

      1. Wallace Grommet says:

        Remember: it’s the baby you want to keep, not the bath water

    4. Skeptical says:

      Thanks for that Ezra. One quote from the review of “A Troublesome Inheritance” (which I will assume is an accurate paraphrase): “Wade asks why the Industrial Revolution took off in England but not in other countries. He asserts that the key difference is an inborn English tendency towards nonviolence and patience, which facilitated productive activities like standing in front of machines for many hours a day.”

      Inborn English tendency towards nonviolence? I think the Scots, the Irish, the native Americans, sub continent Indians, Kenyans, etc. might beg to differ. To say nothing of the French.

      1. Nelson says:

        @Skeptical – good points – you can add every global region to the list, courtesy of the British Royal Navy

      2. sgcox says:

        French !?
        They invaded England in 1066 an executed well documented genocide known as Harrying of the North. Then descendants of that bastard decided to pillage and plunder their native land and started 100 year war. That poisoned the nations relations forever…

        1. Skeptical says:

          Let’s be fair, it was the Normans not the French per se who invaded in 1066.

          But if you’re going to assign national tendencies based on genetics, it would be surprising if the English were gentle. After having their gene pool contaminated by pillaging Vikings, invading Anglo-Saxons, invading Romans, and invading Normans, how could there not be an English tendency toward violence?

        2. WST says:

          “the French” in 1066, interesting idea

  3. Ash says:

    I have been befuddled by how many well-meaning and smart people have vociferously denied any such possibility, even the possibility of such a possibility. Presumably they are doing this because they think that doing otherwise would encourage xenophobia. I understand this sentiment, but given the sheer scale and horror of the pandemic and China’s generally aggressive designs, it would be inexcusable for the rest of the world not to get to the bottom of this affair and hold them accountable.

    The furin site discussion in the Wade article is one of many pieces of the puzzle; even if it’s not as much of a smoking gun as he thinks, he has plenty of other political and scientific questions that collectively at least make a compelling case for entertaining the possibility of a lab release. As you said, China’s closed system hardly helps to dispel the concern. What is also very troubling for me is the connection between the Wuhan Institute and the NIH that Wade points to. There was a WaPo article the other day saying that Fauci’s claim that the NIH never funded any gain-of-function research at the Wuhan Institute is largely false.

    1. Anon says:

      Correct, it’s a sad sign of the state of both the scientific and media communities that anyone who even suggested the lab leak being a possibility was a deranged conspiracy theorist. And that’s not to mention all of the articles talking about how the lab leak had been “debunked” (Oh, how I hate that word).

      1. Patrick says:

        The problem was that it was screamed extremely loudly *by* deranged conspiracy theorists, also deliberately without clear distinction from lab leak and bioweapon leak. All that can be hard to get past, frankly. It probably *should be* – some people are evil enough (yes) that you should start with *extreme* skepticism on anything they say. It doesn’t help that, again, an enormous amount of conspiracy bullshit was used to support it. This makes it *extremely* hard to separate the sincere and reasoned arguments from the – let’s be blunt – mix of nuttiness and deliberate lying that goes broadly in the same direction.

        Basically, when people are screaming “THE EVIL YELLOW CHINESE RELEASED THE KUNG FLU TO KILL US”, it’s hard to hear the people suggesting it may have accidentally leaked from a pretty ordinary research lab in Wuhan.

        1. Jeff in Dallas says:

          Those screaming that ludicrous-sounding statement might actually be right.
          A bioweapon is in the realm of possibility. Very unlikely compared to the other possibilities, but can’t be ruled out.

      2. Anom says:

        Fully agreed. The most common media sources have progressively transitioned into a group that enforces conformity to a specific opinion-clearly derived from political interests rather than truth-and openly censors the nonconformists. For the sake of our country, this trend needs to reverse.

    2. kamil says:

      “China’s generally aggressive designs” is already xenophobia and just calling for an escalation of the cold war between the US and China. How do you measure aggressive designs? The US has waged more wars than China by a tremendous margin, is that not aggressive? The only thing that makes sense here is gross incompetence and negligence. Of course, any and all cooperation by the Chinese government is entirely out of the question if you imply malice and understandably so, as this would be an act of war and very few countries would stand for such accusations. The Chinese government may not respect civil rights, but that has little to do with foreign policy.

      1. SpinninW says:

        Well, if I was a pneumocyte and I smell some RNA floatin down the street what ain’t from around heah then I’d be paradoxed like Zeno and kinda phobic.

      2. Roland says:

        “The US has waged more wars than China by a tremendous margin”

        This is much less true than you think it is. Wars are hard to define but for example the respective Wikipedia pages list 19 wars for the PRC, and 24 for the US since the CCP came to power in 1949. (Out of interest how many of China’s could you name?) Additionally the huge disparity in their relative world power throughout most of that time has arguably (or clearly?) constrained the PRC’s ability to wage war so if we’re judging intrinsic foreign aggressiveness going forward when both are fully fledged superpowers, rather than one by necessity a turtle and the other a ‘world policeman’, their current posture is much more relevant than history.

        (Also whether or not it’s indicative of future foreign aggressiveness their rather extreme internal aggressiveness is terrible for humanity as a whole, even if not very relevant when it come to the Coronavirus.)

      3. Mycelium says:

        Such accusations could be tolerated and fairly investigated under more amicable geopolitical circumstances.

        Today? The Chinese would not cooperate. The trust isn’t there to permit what would be considered a bad-faith operation.

        I think the biggest mark against the lab leak hypothesis is the Chinese flailing around in earpy January. You don’t lock down a city of ten million in the middle of the biggest holiday of the year under circunstances other than sheer panic. If the Chinese had even an inkling that it might have been a leak, and corresponding documentation, the lockdown would have been done on Jan 18-20, before people had boarded trains and planes to visit relatives for the New Year celebrations.

        1. dearieme says:

          Could be. But my guess at the time was different. I pictured the virologists eventually confessing their safety failings to The Party , and what they had designed the virus to do. The Party cries “Good God, shut the city down.” Only later does it emerge that the virus isn’t as awful as its Frankensteins had feared.

          In other words, it’s possible that the scientists are the villains of the piece and that The Party reacted in a reasonable way, given that it forms a despotic regime.

          Was the Wuhan lab working on a bioweapon? Could be, but a bioweapon that discriminates in favour of killing old, frail people isn’t much of a success, is it?

          1. sgcox says:

            How about saving the Earth from overpopulation, climate crisis and the society stagnation due the lack of new blood ?
            Like this for example.
            https://en.wikipedia.org/wiki/Logan%27s_Run_(film)

          2. theasdgamer says:

            Perhaps the weapon was panic, not the virus. The Chinese love psy-ops as much as the British. Locking down a ten million pop city like Wuhan is nothing to a nation of 1.5 billion people, especially if the aim is to sow panic in the West. Quite possibly the Chinese had far better intel than the West did.

          3. Mycelium says:

            Wuhan Institute of Virology was under a microscope the moment the news broke on Jan 1. A major hypothesis back then was a lab leak – it was being widely speculated on from day one.

            The Central Government would not have taken two weeks to shake the truth out of WIV (you’d have had all sorts of scary people, scientists but also MSS, all over WIV by the third day). They would have gone over WIV with a fine toothed comb from the moment news of the outbreak broke.

          4. theasdgamer says:

            Yeah, and the official Chinese story was that the virus came from food. But only if you snort bat feces. Totally coincidentally, six members of WIV came down with ILIs in October 2019. It had nothing to do with covid. In fact, covid hadn’t even been invented in October 2019. So they must have had the flu.

            There, I solved it.

      4. zero says:

        “How do you measure aggressive designs?”

        In this case: Turning low-tide rocks into naval bases and claiming EEZ area around them. Overfishing in Phillipine waters. There are plenty more examples of regional bullying (or more accurately, violations of international law). More importantly, these are intentional programs by CCP that continue today in order to gain control of the area around them.

    3. Actual biologist says:

      Ash, it is true that the NIH did not find GOF research at the WIV. Alina Chan who is a strong pro-lab leak advocate says as much.

      Also, I think accidental leak is possible but the furin site is a lousy argument. It:

      – Occurs in natural CoVs
      – Those codons are highly conserved is SARS2 in human circulation, suggesting specific selection despite being disfavored at most other sites
      – Almost identical codons occur in another natural CoV at the same position
      – The furin site disappears if you culture SARS2 in most cell lines. This argues this virus didn’t likely escape from cell culture (weak evidence, but evidence)

      1. Mark Blumler says:

        First, Chan is not pro-lab leak. She is neutral. For instance, she pointed out the problems with Wade’s article that Lowe mentions above. She has, however, long called for further investigation.

        Chan also has asserted that the definition of GOF has changed over time (I have no independent knowledge about this matter), in suggesting that Rand Paul and Fauci were taking past each other in their recent, heated exchange. So I am not sure you are correctly characterizing her views. Admittedly, she tweets so often, and is so careful to not be injudicious that it can become difficult to know exactly what she does believe.

      2. Johnv2 says:

        I don’t think that is Dr. Chan’s claim. Her tweets said the research at WIV likely complied with the exceptions in the GoF ‘pause’. I think there is no universal agreement on what constitutes GoF, but whatever was happening at WIV in the study of bat virus didn’t appear to help at all in this pandemic.

        I’d also note that if one thing is clear, regardless of the origin of SARS-CoV-2, it is “don’t locate virology labs in populous cities.” These labs should be on isolated islands, at a minimum, with staff quarantining before mingling back with the population.

        1. SqueakingWheel says:

          So, if 3 lab workers unknowingly contract the Andromeda strain, they’ll return from that out in the sticks lab to their homes in multiple metropolitan areas. There ain’t no safe space in Doomsday biology.
          Fortunately, a doomsday virus is not possible. Or is it?

      3. theasdgamer says:

        The NIH laundered its funding of the Wuhan lab through the Ecohealth Alliance. Who employs the only US representative on the WHO committee investigating the origins of the Wuhan virus? Was it Ecohealth? I have read so, but others may have valuable information to the contrary.

        1. Aluminium says:

          Christ, what a lot of nonsense, bordering QAnon territory.

  4. sgcox says:

    Well, after a week of boring topics like C-C bond formation, protein immobilisation for biochemical assay or human evolution and mildly more amusing like psychotropics drugs, the forum really needs blood!
    Let’s see and read.

  5. Molecular biologist says:

    The idea that SARS-CoV-2 emerged from direct protein engineering of spike protein is generally seen as implausible now, unlike in the early phase of the pandemic. The idea put forward by Nicholas Wade and others that some laboratory “mishap” caused SARS-CoV-2 is exciting to a lot of people. One model that he presents seems implausible due to the lack of tell-tale marks of genomic engineering – cloning in new spike proteins. Why would the scientists use laborious methods to clone and test different spike proteins when simple cut and paste with restriction enzymes is easier?

    The more plausible model presented by Nicholas Wade is that continuous culture of bat SARS-CoV-2 resulted in mutations (erroneously called “gain-of-function”) that resulted in higher affinity for human ACE2. On its face seems to make sense, but has problems. It is true that the closest bat coronovirus spike protein does not bind human ACE2 well, and therefore poorly infects human ACE2-expressing cells. Therefore, continuous culture of bat virus in human cells (if this happened) could select for mutants in spike protein that bind human ACE2 much better. This seems possible especially since (as Nicholas Wade mentions) we still don’t see SARS-CoV-2 in any animal host so far (the most similar bat SARS-CoV-2 is only 93.7% identical to human, and we would expect much higher identity). Most importantly, the ACE2-binding domain (“RBD” or receptor-binding domain) of the bat SARS-CoV-2 does not match human SARS-CoV-2, even though much of the rest of the bat SARS2-CoV-2 more or less matches human SARS-CoV-2. The RBD is very different. So the question comes: how did the RBD sequence dramatically change to match the human virus currently in circulation? Was it continuous culture?

    The problem with these arguments is that the unique RBD of spike protein (i.e., the mutations that lead to high affinity binding of the spike to ACE2) are found in nature–in pangolins. Pangolin SARS-CoV-2 has the exact same RBD as human SARS-CoV-2. Human and Pangolin (but not bat) SARS-CoV-2 spike protein bind to human ACE2. Take a look at this interesting structural study and its binding data: https://www.nature.com/articles/s41467-021-21006-9. So, to be clear, the RBD that causes SARS-CoV-2 to be so infectious **is seen in nature**, i.e. in pangolins. The question is therefore, did it recombine with certain bat sequences to make the final human SARS-CoV-2? This is not yet known. But the disease-causing RBD of human SARS-CoV-2 is found in nature. True, continuous culture of bat coronavirus could have resulted in spontaneous mutations that resulted in the current RBD, but this is extremely unlikely. The fact that the exact same RBD sequence occurs in nature (in pangolins, possibly other animals not yet tested) makes it more likely that recombination of viral sequences (as normally occurs) resulted in the final SARS-CoV-2 that we see in humans.

    Some people say that the pangolin SARS-CoV-2 might have this remarkable similarity in its RBD to human SARS-CoV-2 since the pangolins may be been handled and then infected by humans who might also have had SARS-CoV-2. This is unlikely since the rest of pangolin SARS-CoV-2 does not match human SARS-CoV-2.

    There is still work to be done, and we still need to find the animals that harbor a more human-like SARS-CoV-2 (the closest bat SARS-CoV-2 to human is still far away from the human sequence and does not have the RBD we see in human SARS-CoV-2), but all the components of SARS-CoV-2 are found in nature, and the standard methods of viral evolution seem more likely due to evidence of RBD sequences found in the pangolin sequence.

    1. vic says:

      Can you clarify whether it is a possibility this recombination between virus strains (bat and pangolin strains) such that the resulting virus has mostly bat identity but pangolin RBD) could have been performed in a lab? Would such a splicing of sequences necessarily leave behind restriction enzyme sites if perhaps researchers were trying to engineer a “natural” chimera to study? There are some scientific details here that I am not familiar with.

      1. no problems here says:

        SARS-CoV-2 spike binds to Human-ACE2 10 times better than to Pangolin-ACE2.
        Pangolin-CoV spike binds to Human-ACE2 15 times better than to Pangolin-ACE2.

        SARS-CoV-2 spike preferentially binds to human, pangolin, and bat ACE2, in that order.

        MERS spike preferentially binds to human, horse, camel, goat, and bat DPP4, in that order.

        Everyone knows that the pre-MERS spike RBD had (much, much) less than 8,000 human cases in which to evolve its very efficient binding to the human-DPP4 receptor. Never mind, 8,000 cases is huge, humongous, totally enormous,… it is no wonder that the MERS spike RBD evolved so quickly.

        The MERS spike RBD hit the human population already completely adapted.

        No problems here.

        Everyone knows that the Pangolin-CoV spike RBD had two or three cases(?) of never-reported pre-Wuhan Covid among the Malaysian(?) population in which to evolve its very efficient binding to the human-ACE2 receptor. Pity for the Wuhanians that this impossible feat of evolution occurred.

        The SARS-CoV-2 spike RBD hit the human population already completely adapted.

        No problems here.

    2. Just a biochemist says:

      Not to argue with the rest of your post, yet the lack of “telltale marks” of restriction enzymes is outdated knowledge on your part.
      since about 2013 the use of restriction enzyme has been largely phased out by most labs that are at least moderately well funded.
      They usually use so called “Gibson cloning”, which results in scarless recombination of any DNA. If one were to employ standardized overhangs (exact sequence is utterly irrelevant), the whole process is a lot more efficient, faster and less laborious than the use of restriction enzymes!
      This might be a bit nitpicky but I just couldn’t leave that statement uncorrected.

    3. @pathogenetics says:

      There is just no such thing as a pangolin coronavirus is the main issue. These samples were all severly contaminated and cannot be used as evidence to support a natural origin.

    4. SqueakW says:

      Why need it be direct protein engineering? Why not just pass a candidate virus through humanized lab mice, +/or racks of cell cultures? The process could even be mechanized, allowing thousands of cell culture passages.

      Disclaimer: I am not remotely close to being a biologist, just putting together a snippets of what I’ve read recently.

  6. John Wayne says:

    It is a bit baffling that we aren’t going around and sequencing every coronavirus we can get our hands on. Finding the closest relatives (in the wild or in a lab) is the closest thing we are going to get to a ‘smoking gun.’ Let’s do it with the goal of fixing the problem and not the blame.

    1. AVS-600 says:

      My understanding (which may be incomplete) is that they essentially are trying to do that, and so far no clear ancestor of COVID has turned up in the wild. (That doesn’t necessarily mean the lab hypothesis is correct, only that efforts to disprove so far haven’t produced anything conclusive).

    2. Wheeling says:

      I think we should all buy the blog author a good Scotch for dealing with this subject.

    3. Mycelium says:

      That was what the Wuhan Institute was doing. Southern China gets coronavirus cases all the time, with occasional miners dying from shoveling bat poop.

    4. theasdgamer says:

      If the problem is a self-inflicted economic injury, don’t you think we should fix that? Maybe put some restrictions on panic mongering? Maybe don’t include panic mongering in pandemic wargames?

    5. Erik says:

      I had a boss who had a saying, “the first thing we must fix is the blame!” (in jest, fortunately).

  7. What do you think about the comment from David Baltimore in the “Bulletin of the Atomic Scientists” version of Nicholas Wade’s article? (linked in handle this post)

    “When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said.

    1. Mandark says:

      There’s a long Twitter thread from Kristian Andersen (named in that articile as one of the bad guys) dealing with that quote: https://twitter.com/K_G_Andersen/status/1391507230848032772

      1. sgcox says:

        I am sorry, but this guy – Kristian Andersen- tells a bit of nonsense. 12 bp insertion is always in frame (so far). Also, if you align sequences perfectly well but shift C from 3′ to 5′ no false “off-frame”. It will be simply labelled TCCTCGGCGGGC insertion. He is a bit insidious here, IMHO.
        How this _in frame_ insertion of 12 bp sequence happened – in bats, pangolins or lab – completely another question. All we know about sars2 biology and our understanding of it points overwhelmingly against lab origin, but you really should not twist stuff to fit your argument!

        1. sgcox says:

          Actually, sorry. one bp shift is still technically “of-frame” bit generate perfect ROF.
          Commenting faster than thinking carefully.

  8. debinski says:

    “This world would be a lot easier to understand if assholes were always wrong about everything, but that’s not the case.” So true, so very true.

    1. Roland says:

      Unless you were an asshole yourself, and then you’d always be wrong when it came to judging other people’s asshole status, and you wouldn’t know assholes were always wrong because you’d be wrong about whether they were always wrong. You might even think assholes were always right, but the people you thought were assholes would be non-assholes so you’d go around thinking actual non-assholes were right about everything until one of them said to you ‘assholes are always wrong’ and you’d think ‘hey that’s not right what’s going on here?’.

      It would all be very confusing. (Moral of the story: don’t be an asshole)

  9. luysii says:

    Regardless of the origin, people are still resisting vaccination, particularly minorities. Even worse, there is now evidence that one new mutant (B.1.1.7) is 50% more virulent (as well as more infectious). Nature vol. 593 pp. 270 – 274 ’21.

    Try sending the following to the antiVaxer on your Christmas list — https://luysii.wordpress.com/2021/05/19/anti-vaxers-what-is-it-that-you-know-that-we-dont/

    1. Anon says:

      I remember a year ago you didn’t care whether one goes out with or without a mask. You weren’t a big fan of lockdowns and even suggested that you’d go about your daily life if you were a teenager. What changed??

    2. theasdgamer says:

      Too soon to know if that new strain is deadlier or more virulent. Not enough data has been collected yet.

      Hey, vaccine missionary–you need to go hand out pamphlets at NIH. I hear that half of their employees are unvaccinated.

      1. luysii says:

        Nature vol. 593 pp. 270 – 274 ’21 is based on 4,945 deaths from B.1.1.7

        1. theasdgamer says:

          4,000 odd out of how many cases?

          The article was breaking news. Not something to take seriously at this point, what with all the panic mongering. Researchers will have a look at it and get back to us.

  10. Smokerr says:

    There are actually two Chinese labs in Wusan one of which was very close to the animal market (which may or may not be relevant)

    I have no oar in the water one way or the other but all I have seen says it could be either.

  11. bruce says:

    I’m no fan of the Chinese government, but I don’t blame them for resisting an investigation, even if they are innocent. They’d expect it to be conducted with all the competence and objectivity of the vote recount currently going on in Maricopa County.

  12. Zac says:

    My problem with all this finger pointing is that, in my opinion, there is about a 0% chance that China actually found patient 0 in Wuhan. Almost certainly, this virus had been slowly burning through the human population for some period of time before popping up on everyone’s radar by entering a densely populated city like Wuhan.

    1. Adrian says:

      If COVID-19 was a lab leak, the first infected person(s) would most likely have been people working at that lab.

      Early last year there were even internet rumors that a specific female scientist that had gone missing was patient 0. Take this specific rumor with a barrel of salt, but in general for a lab leak theory the number of likely candidates for patient 0 is quite small.

      1. Adrian says:

        Or for more official theories from sources of the Medium post Derek linked to:

        ‘The U.S. government has reason to believe that several researchers inside the WIV became sick in autumn 2019, before the first identified case of the outbreak, with symptoms consistent with both COVID-19 and common seasonal illnesses.’

        ‘Three people working at a BSL3 lab at the institute fell sick within a week of each other with severe symptoms that required hospitalization. This was “the first known cluster that we’re aware of, of victims of what we believe to be COVID-19.” Influenza could not completely be ruled out but seemed unlikely in the circumstances’

  13. Recovering I hope says:

    What’s the chance that Covid was circulating in the UK at the end of November 2019? We came back from holiday with viral pneumonia (visited London, Salisbury and Canterbury), showing shortness of breath, a dry cough and minimal flu symptoms. We caught it there, and ran across crowds in London and parents-of-graduates in Canterbury. I’ve read that there are blood tests from the UK before that from people who traveled to/from China, and that pneumonia cases tested positive from late Dec in France. Many people in N America complained about bad flu’s in Dec-Jan, in spite of vaccination. Hearsay? Yeah, but…

    1. Adrian says:

      No matter what the origin was, there is wide consensus to put patient 0 of COVID-19 around October 2019.

      Several athletes participating at the World Military Games in Wuhan in the second half of October claimed that they and many other athletes had COVID-19 there, and some that they infected people after returning home.

      Some people have also looked at this in a more scientific way:
      https://link.springer.com/article/10.1007/s11845-020-02484-0

      Taiwan did not participate in the World Military Games for obvious political reasons, and having the World Military Games as major source for non-Wuhan spread would help explain how Taiwan managed to have so low initial numbers despite no less than 4 different airlines offering direct flights between Wuhan and Taipei.

      Such an early superspreader event for international spread might also help explain why the D614G mutation was common outside China from the beginning, but rare in Wuhan.

      The weak point of such an explanation is that the UK did not participate in the World Military Games, but London being the largest hub for air transport in Europe still makes it plausible that COVID-19 might have spread there early if it was anywhere in Europe.

      I would consider it possible that it was COVID-19 you had in the UK at the end of November 2019, but I would not rule out that it was some other virus you had.

      1. ezra abrams says:

        widespread consensus is not correct
        see page 82 ff here
        https://www.who.int/health-topics/coronavirus/origins-of-the-virus

        thank you

    2. ezra abrams says:

      The updated WHO report discusses this at length
      there is data for Covid 19 in Italy and other countries as early as Nov 2019, but the data is not really conclusive

      see the page numbered 82 in the pdf here
      https://www.who.int/health-topics/coronavirus/origins-of-the-virus

      At the current time, the Dec/Jan in Wuhan makes sense as the start of the outbreak; certainly, if virus was present before that, it doesn’t seem to have led to widespread disease

      1. J says:

        I posted this link on a previous article and repeat it here as it is relevant to the time line.
        “Unexpected detection of SARS-CoV-2 antibodies in the prepandemic period in Italy”.
        This would seem to imply that the virus was around in, say, late August 2019 into September 2019.

        https://journals.sagepub.com/doi/10.1177/0300891620974755

        Thank your Derek for this article and for all the serious and informative postings which are appearing.

        1. J says:

          Below is a link to a publication of the paper produced by the University of Barcelona on waste product samples done in March 2019 and at other intervals.
          “Sentinel surveillance of SARS-CoV-2 in wastewater anticipates the occurrence of COVID-19 cases”

          https://www.medrxiv.org/content/10.1101/2020.06.13.20129627v1

        2. Ron says:

          A copy from the SAGE article about Italy–“SARS-CoV-2 RBD-specific antibodies were detected in 111 of 959 (11.6%) individuals, starting from September 2019 (14%),” This implies those who had antibodies detected in Sept 2019 could had been exposed to SARS2 MONTHS before. Could SARS2 have started in Northern Italy in early 2019 and spread to China?

          1. J says:

            Ron – I posted a reply to you on this but it appears to be in the blog responses not where I expected it to be – it will be somewhere at the end of the entries. The Italian / China link is likely to be the Fashion Industry and outsourcing to China, notably to Wuhan. I found a newspaper link for reference.

    3. Siddharth Dasgupta says:

      Very close friends – a couple – went from Los Angeles to India and back, via China in February 2020. They came back and were sick as dogs – like never before. They had weakness for several weeks.
      We went to New Zealand in during the Christmas break in 2019 – till early January 2020. In Auckland we were staying at the Chinese owned Skytower hotel. The adjacent casino was mainly Chinese. Now we wonder what a bullet we must have dodged that we came back with no illness.

      1. Adrian says:

        You dodged a huge bullet if you have been in the US in 2020 without catching COVID-19, being worried about contact with people from China is either uninformed or racist.

        You are overestimating the spread of COVID-19 in China, and your friends likely caught something in India.

        The Hubei lockdown that brought the number of daily new infections in China back to 0 affected only 4% of the population of China.

        Beijing with a population of 21 million people had less than 1000 infections and 9 deaths.
        Nine deaths. During the whole pandemic.

        The US had more COVID-19 deaths in a single day than China during the whole pandemic.
        Even today the US still has more new infections every week than China had during the whole pandemic.

        1. Twitchly says:

          Kinda hard to believe those numbers, dontcha think? China hasn’t been exactly transparent during this pandemic.

          1. Adrian says:

            It can be hard to believe when the facts contradict your perception.

            Exact numbers one might dispute, but on the order of magnitude the Chinese numbers sound correct.

            There is no indication that China ever had a widespread outbreak of COVID-19 among the 96% of their population outside the affected province. And in that province they got it under control with a 2 month strict lockdown.

            China quickly puts millions of people under very strict lockdown when a two digit number of infections are found somewhere, and they are not doing murderous mistakes like reopening schools in regions with a non-zero number of cases.

            One really has to remember that from a quantitative point of view COVID-19 in China affected only one province with 4% of the population for 2 months, and after that they only had very small outbreaks due to imported cases.

  14. Anon says:

    “The U.S. government has reason to believe that several researchers inside the WIV became sick in autumn 2019, before the first identified case of the outbreak, with symptoms consistent with both COVID-19 and common seasonal illnesses.”

    If the US government has reason to believe, i think it is over. It’s pretty clear where it originated from.

  15. Sok Puppette says:

    I am suspicious of people’s reasons for caring. What would anyone *legitimately* do differently depending on the answer?

    1. Adrian says:

      Reinstate the moratorium on funding gain-of-function research.

      Increase lab safety requirements (no gain-of-function research outside BSL4) and safety monitoring.

      1. Sok Puppette says:

        So you believe that whether this particular event was a lab event decisive with respect to the advisability of doing those things? Would you, personally, advocate doing those things if this were a lab escape, and advocate against doing them if this were not a lab escape? Would it matter if the research going on at the time had in fact been gain-of-function research?

        1. Adrian says:

          Chernobyl was helpful for raising awareness for the risks of nuclear energy.

          If COVID-19 would be proven to be caused by NIH-funded gain-of-function research, this would raise the awareness for the risks of doing such research.

          1. Squeak says:

            Chernobyl showed the risks of using a 1940s research reactor which was design scaled up 1000 times with designed in instability in order to use a cheaper great of uranium. Then Management ordered the operators to violate red letter safety procedures. They refused, so Management brought in a different crew which would flip off the rules. The result was inevitable.

            This was not a result of using nuclear power, it was the result of radioactive recklessness.

          2. Adrian says:

            The US narrowly avoided disaster in Three Mile Island.

            11 years ago it would have been inevitable that you would have cited Japan as an example for safe usage of nuclear energy.

            Then came Fukushima.

          3. James Millar says:

            Probably the greatest lasting harm from Chernobyl is the damage done to the nuclear industry. Same with TMI and Fukushima. It is remarkable that such a massive series of mistakes in design and operation in those three accidents led to such minimal consequences, and it should serve as evidence (if any more is needed!) that a well-designed, well-run plant has minimal risk.

    2. Grahame Grieve says:

      +1 it doesn’t matter how it originated – gain-of-function should be super-highly regulated if it’s justified at all, and we should be watching for new virii from natural sources as a top priority and as soon as there’s any evidence of one, everything stops while we throw the kitchen sink at it

      Where it came from is interesting from a scientific viewpoint, but irrelevent from a public policy perspective

      1. Adrian says:

        From a public policy perspective it would matter a lot if risky research that was justified with helping against future pandemics would turn out to be the root cause of COVID-19 – in the upcoming years such gain-of-function research will become either swamped with taxpayer money or heavily restricted.

        1. Grahame Grieve says:

          Gain of function/release from the lab can’t be ruled out except by finding it happened a different way. So It *could* be the source. How does it matter whether it was? Gain-of-Function needs such regulation irrespective of whether it was the source, but it could have been

          1. AVS-600 says:

            I think the point he is making is that regardless of how you personally feel about the issue, restricting gain-of-function research becomes a lot easier and more pressing *politically* if this is proven to be a lab escape.

  16. Ed says:

    Until somebody proves and shows how the virus spread from animal to human, the theory that the virus may have escaped from the research lab, will keep gaining traction.

  17. steve says:

    Two months before the pandemic started in China, Trump decimated the CDC in Beijing and withdrew support for the USAID PREDICT project, whose entire purpose was surveillance and early warning for pandemics. That project identified 1,200 different viruses that had the potential to erupt into pandemics, including more than 160 novel coronaviruses. That initiative, also trained and supported staff in 60 foreign laboratories — including the Wuhan lab that now everyone is trying to blame for SARS-CoV-2. Yell about China all you want but it was Trump’s anti-science campaign that destroyed our ability to track the outbreak of this pandemic.

    1. cliveb says:

      Timeline seems to be:

      – 2014 Oct: Pause certain GoF research by Obama
      – 2017 Jan: P3CO framework put in place
      – 2017 Dec: Removal of Pause by Fauci
      – 2020 Apr: EHA WIV grant terminated by Trump
      – 2020 July: EHA must provide Wuhan sample to resume funding
      – 2020 Aug: NIH awards EHA new grant
      – 2021 April: NIAID bypassed NIH P3C0 review of EHA grant

      Source links on wiki website

      1. steve says:

        Not sure what Fauci has to do with Trump decimating CDC and the PREDICT project but whatever.

  18. theasdgamer says:

    Very ironic, Derek, that you refuse to consider the biological warfare theory. Maybe this is just some jingoism, but just yesterday, Ping claimed victory over the US. Ping is a senior member of a CCP think tank–the China Institute at Fudan University. This might get backtracked in the future and is likely just testing the water.

    “Admitted! Chen Ping, Senior Researcher at #FudanUniversity, professor at #PekingUniversity, says the #CCP won the trade war, science & technology war, and especially the biological war in 2020. “The achievement is unprecedented. This is an epoch-making historical record.””

    https://twitter.com/jenniferatntd/status/1394691764741627907?ref_src=twsrc%5Etfw%7Ctwcamp%5Etweetembed%7Ctwterm%5E1394691764741627907%7Ctwgr%5E%7Ctwcon%5Es1_&ref_url=https%3A%2F%2Fwww.thegatewaypundit.com%2F2021%2F05%2Fsenior-member-ccp-think-tank-claims-china-won-unprecedented-biological-war-us-2020-put-us-back-place-video%2F

    1. steves says:

      Ridiculous. No one on earth could have planned SARS-CoV-2; it involves mechanisms we’re still trying to figure out. And no one on earth would design it as a “bioweapon” given how easily it would spread throughout the world. Bioweapons are things like anthrax that have local effects, not highly transmissible viruses that inevitably will attack the country that released them. You’re reading way too many right wing fantasy websites.

      1. theasdgamer says:

        Lol, the attack was via the lockdown. Self-inflicted injury. Covid was possibly an economic attack more than anything.

        You are correct that any useful bioweapon would attack the working population rather than nursing home residents and would be of short duration.

        From my commentary, you should infer that I have my doubts about whether covid was used as a biowarfare weapon. I saw it more as an opportunity for corrupt govt. officials and pharma to profit from vaccines. Lockdowns helped to cement the panic in people’s minds. Maybe the CCP were able to predict the western response from the pandemic wargaming that had been done.

        1. steve says:

          From your commentary I should infer that you’re out to lunch.

          1. John says:

            This guy has a history of posting severely ridiculous posts on this blog. Derek has asked him more than once to take this shit back to facebook where it belongs. He refuses to budge. The fact that he understands extremely little about the subject and that he barely reads these blog posts by Derek is obvious in his retoric. I think the best thing to do with this guy is to ignore him at this point.

        2. theasdgamer says:

          I don’t reply to members of the peanut gallery.

          1. John says:

            This post says otherwise

    2. Surfactrant says:

      Could he mean the response to the pandemic?
      China’s response, hands down, beat the US and Europe.

      1. Squeak says:

        China immediately locked down Wuhan, and then prohibited the entire population of food by province from traveling anywhere else in China. The military was brought in, and restrictions went to the level of welding the exits closed on apartment blocks. There was one exception however; the Wuhan international airport remained open for outbound flights. Not long after, Xi ordered a review and increase of safety measures at all of Chinese biological research laboratories.

        Perhaps these were simply the canned responses from a bureaucratic plan. Perhaps China immediately knew something other countries did not.

        1. Mycelium says:

          The day before Chinese New Year’s Eve is a bit late to orchestrate a lockdown. If it were a script or a known lab leak, you’d lock down on Jan 18-20, before people take those trains and planes to see family worldwide.

          Lab leak was the first thing on a lot of minds in early Jan 2020, including mine. The Chinese, paranoid as they are about underlings lying to cover up mistakes, would have gone over the lab with a fine toothed comb immediately. It would not have taken three weeks to shake the truth out of WIV. It is unlikely to have been a leak.

        2. Passerby says:

          Squeak: My thoughts exactly. It’s as if they knew exactly what plan they had to put into action for lockdown in case there was a leak and were fully prepared.

          1. Daniel Barkalow says:

            They did have the original SARS epidemic in 2002, and were researching coronaviruses due to the high probability that something similar would happen again. They’re obviously going to have a plan for what to do if it does, but those plans are going to be based on the properties of SARS-CoV-1 (in particular, cases pretty much all being symptomatic and proceeding rapidly), which explains the delayed response and failure to successfully contain the outbreak. If you look at the SARS diagnostic criteria, it’s entirely plausible that they determined that WIV didn’t have a chain of people with high fevers and casual contact within 10 days and didn’t look for what we now know to be relevant for COVID-19 contact tracing, but eventually did the SARS plan anyway because the outbreak seemed sufficiently similar.

        3. Squeak says:

          *Hubai Province

          As always, not proofreading my posts bounces back.

  19. HA2HA2 says:

    So is a pandemic virus “escaping from a lab” something that’s ever happened before? Or would this be the first?

    I’ve been assuming this would be a historic first (mostly because otherwise, people would be citing “Just like [previous incident] all the time), but that seems like it would make it super improbable.

    Why is this being considered as a serious theory in the first place, besides a political desire to blame the Chinese government?

    1. sgcox says:

      old, not a newly created pathogen and not proven but still.
      https://en.wikipedia.org/wiki/Sverdlovsk_anthrax_leak

    2. Adrian says:

      Quoting the Medium post linked by Derek:
      ‘The smallpox virus escaped three times from labs in England in the 1960’s and 1970’s, causing 80 cases and 3 deaths. Dangerous viruses have leaked out of labs almost every year since. Coming to more recent times, the SARS1 virus has proved a true escape artist, leaking from laboratories in Singapore, Taiwan, and no less than four times from the Chinese National Institute of Virology in Beijing.’

  20. eff says:

    cue “Danger Zone” by Kenny Loggins. 😀

  21. Bash says:

    I was very much on the Natural Origin side of the debate, until I wasn’t.

    I have listened to the GoF debates. It seems to boil down to parsing words as to what exactly is the definition of GoF, which seems a little silly because the outcome is a modified virus which has enhanced infectivity i.e. GoF. Weird to see very smart people mince words like that. Its also nothing new – GoF isn’t something that virologists haven’t been doing

    I would have expected by now that after 1.5 years of scouring the countryside and farming bats and pangolins and every conceivable creature that could have been the reservoir for the virus, that we would have found something. SARS-1 and MERS took a matter of months and a very clear lineage was established

    I do find it odd that SARS-2 was so particularly suited to human infection from the word Go. I do find it odd that in animal experimentation, SARS-2 seems to bind most readily to human ACE2 receptors, with more affinity than any other species

    I do find it odd that while governors and mayors and leaders of Western nations were telling people that they should still live normally, probably based on the traditional belief that viruses take quite a bit of time to evolve human-to-human infectivity after jumping species, that the Chinese government seemed to know exactly what they were dealing with and locked down a country of 1,5bn overnight.

    The Natural Origin theory is plausible. So is the Studied In A Lab, Allowed to Culture in Genetically Engineered Mice, and Accidentally Escaped + We Might Have Added Specific Genes to See What Happens theory. Why is this so impossible? Especially with new methods that don’t really leave a trace.

    It wouldn’t change anything regarding the pandemic. It is an accident in the end. But I would sure like to know that we are changing how we run virology labs!

    1. theasdgamer says:

      Bio-economic warfare drill:

      Step 1. Create some infectious, mildly dangerous virus suited to large indoor spaces. Ensure that you have antivirals to treat and own the patent on the virus.

      Step 2. “Leak” the virus. Institute panic attack. Weld your own people into their homes. Institute a national travel ban from Wuhan. Make sure that these stories make it to the media. Refuse to cooperate with public health authorities from other nations except to warn them that the virus is _extremely_ deadly…3.4% mortality. Those PHAs will then coordinate with the media to monger panic and institute lockdowns based on previous pandemic wargames.

      1. Chris Phillips says:

        Loony drill:

        Find a website to ruin.

        Think of some nonsensical gibberish to post there.

        Post it there 50 times a day.

  22. Some Dude says:

    To someone who has worked in many different labs and has witnessed how many things accidentally go wrong all the time, it is indeed strange that the laboratory escape hypothesis was so strongly rejected in the beginning. To every practicing scientist, it should be obvious that the possibility at least exists.

  23. johnnyboy says:

    I think the virus escaped the lab because they didn’t add zinc.

  24. A Nonny Mouse says:

    Introduction of the furin cleavage site in the original SARS virus

    https://www.pnas.org/content/106/14/5871

  25. Charles H says:

    Why is this important?

    Accidents happen, and requiring adherence better protocols around labs doesn’t need proof. So that’s not a reason.

    To me this seems largely motivated by looking for someone to blame, and that’s a worthless activity. It’s reasonable to judge China by the degree of openness and honesty in their responses, but unless you’re going to think this is an “act of war”, I don’t see any worth in playing the blame game. (Even then it’s dubious.)

    So *why* is it important to know the origin of the particular corona virus that caused the plague? Yes, better precautions are needed. That’s true anyway. Yes, better preparations are needed. That’s true anyway. Etc.

    1. NPs says:

      “Accidents happen, and requiring adherence better protocols around labs doesn’t need proof. So that’s not a reason.”

      I see your point but I don’t think it’s consistent with human behavior. Proof forces positive change. As a hypothetical let’s say the origin is determined as accidental lab leak from WIV. I’ve got to assume that prior to the leak, WIV officials would’ve argued with the utmost confidence that their experimental procedures and security measures were fully sufficient to eliminate the possibility of escape. Establishing the origin would provide clear evidence that the current protocols were insufficient. This would in theory increase the level of scrutiny and expectation for virology labs that want to receive funding for this type of study in the future (globally and not just in China).

  26. Jonathan B says:

    What do we actually know about the origin of SARS-CoV-2? We know that it was first identified in Wuhan, China, in December 2019 and all cases around the rest of the world can be traced back to that first outbreak. So it most likely arose in that locality, or at least within travelling distance. The phylogenetics of virus sequences suggests that the putative common ancestor arose only a few months before the disease was described, sometime around September 2019. (Reports of evidence of the virus’s presence elsewhere in 2019 are not well enough documented to suggest an earlier or geographically different origin).

    The other thing we know that the closest related coronavirus is one that has been identified in bats. Since bats carry a large range of coronaviruses and others have jumped species before, the most plausible explanation is that the same happened with SARS-CoV-2. However the known bat equivalent has large enough sequence differences to suggest either that there is another as yet undescribed bat virus as the origin, or that it underwent substantial changes along the way. So what are the reasonable hypotheses of how that occurred?

    1. Direct jump from bat to human. That is feasible as a rare event, there are reports of humans working in close proximity to bats (e.g. miners) getting infected with bat coronaviruses. However such infections inevitably have very poor human-to-human transmission since the human ACE2 receptor targeted by the virus is significantly different from the bat version. You would have to hypothesise as the starting point a putative bat virus much closer to SARS-CoV-2 than any known, plus a mechanism for it to evolve to something much better at infecting humans. There is at least one documented case (in Boston) of SARS-CoV-2 undergoing multiple mutations within an immunocompromised individual, so you could think of a story where such a person either caught it directly from a bat or at least from a primary infectee they lived in close proximity with and then the virus gained the mutations which allowed it much better to bind the human receptor and become readily transmissible between humans. An early recipient of this altered form must then have been responsible for seeding the outbreak in Wuhan.
    2. Indirect move from bat to human via an animal intermediary. This has been believed to happen for other infections, and the focus has been on pangolins since their ACE2 receptors are closer than bat ones to the human version. In this case the necessary intermediate mutations to become easily infective to humans could have occurred out of medical sight in wild pangolin communities. Alternatively a viral recombination event could have occurred putting a better ACE2 receptor binding domain from some other endemic pangolin virus into the bat precursor due to an individual suffering a double infection. Most people would be convinced of this explanation if a coronavirus resembling ancestral SARS-CoV-2 were identified in another animal – quite likely pangolins but the human virus is also known to be transmissible to other animals including cats and mink.
    3. Indirect move from bat to human via a laboratory stage. While this idea is excellent to feed conspiracy theorists, for it to be scientifically credible there has to be a proposed mechanism. One would be deliberate bio-engineering, but that would imply the sequence was constructed using known elements of other viruses – and that has not been found to be the case. Another mechanism would be the one Wade refers to in his blog post of getting an initial virus to infect human cells in lab culture, and rely on variants emerging which could be selected for over multiple infection rounds to optimise its clinical infectiousness. Although feasible as an experiment that would be incredibly unlikely to generate a virus so successful as to cause a pandemic, not least because infection of cultured cells will only mimic a fraction of the features which are required to infect people. For example, they might allow optimisation of receptor binding but would not select for the ability to evade innate immunity in the whole human or for that matter the weak acquired immunity that most of us probably have from prior infection with other coronaviruses.

    My take on this is that any serious discussion of the origin of SARS-CoV-2 has to acknowledge all possibilities. On the face of it the lab idea seems the least likely, but assessing likelihood is difficult when all possibilities involve unlikely events. If a virus circulating in bats was found that would only have needed a small number of consequent mutations to become infective, then a jump direct to humans would suddenly become the favourite hypothesis. Similarly, if a virus in pangolins (or other potential intermediate) was found in circulation that had changed from a bat origin to one with more potential to jump to humans then the animal intermediate would be favoured. And if some lab somewhere turned out to have a database of sequences unshared with the wider world, and segments of SARS-CoV-2 contained copies from those, then there would be a definite smoking gun.

    1. J says:

      Jonathan B – many thanks for the several posts you have made which are most helpful. As Derek’s blog is such a rich source of information and responses, I decided to post the link below to help complete some of the history of this pandemic for those who may not have seen it.

      “Covid: Wuhan scientist would ‘welcome’ visit probing lab leak theory”
      21 December 2020
      https://www.bbc.co.uk/news/world-asia-china-55364445

  27. wim says:

    Interesting how recently quite a few authors have started to more strongly defend the idea of a lab origin in concert. As far as I’m concerned it’s relatively unlikely (perhaps 10%) but not impossible.
    A few interesting things:
    -the Science letter was signed by Ralph Baric, who is well known for GoF work on coronaviruses. I would like to read Baric’ view in detail, because if there is anyone who could make a real informed estimation it’s him and and coworkers. It would also be interesting to hear what safety precautions they are taking in their own research – not that I’m trying to accuse his group of anything.
    -I did not like Wade’s piece, in my opinion it is clear he is convinced of the lab theory and not just “asking questions with an open mind”, his presentation is cherry-picked between proof of multiple lab theories that are incompatible with each other. For example, the “smoking gun” about the furin cleavage site codons(which would point to precise genetic engineering) with other arguments for “serial passage”. Conveniently, the pangolin coronavirus S protein RBD which is much closer to sars cov 2 one, perhaps via convergent evolution, which was discussed in the WHO report (which by the way is a very interesting read ) and other potential ancestors than RaTG13, including some related viruses that also have some of the peculiar features that puzzle some of the lab theory curious, are not mentioned.

  28. Twitchly says:

    I’m a complete neophyte, so forgive me if this is an idiotic question: could having been exposed to SARS1 provide any immunity against SARS2? I have wondered if this could be a factor in lower rates of SARS2 among some populations but have seen no research about this.

    1. Adrian says:

      SARS had around 8000 infections with a fatality rate around 10%.

      There are around 7000 survivors of SARS still alive, this number is far too small for having any effect.

  29. J says:

    The potential Italian / China link? Suggest the Fashion industry.
    “COVID-19: Did you know about Italy’s China connection”

    https://timesofindia.indiatimes.com/videos/international/covid-19-did-you-know-about-italys-china-connection/videoshow/74694266.cms

    “The northern part of Italy has been a traditionally prosperous region due to the flourishing fashion and garment industry. ”
    “A large number of these Italian fashion and garment houses had outsourced their manufacturing to Chinese labour, specifically in Wuhan.”

  30. James Cross says:

    I read a paper that speculated that COVID-19 might actually be a mutation of SARS that had remained endemic in China since early 2000’s.

    1. Adrian says:

      Please provide a link to that paper.

      It sounds quite improbable, considering the fact that the virus causing COVID-19 is a lot closer related to many known bat viruses than to the virus causing SARS.

    2. J says:

      “Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic”
      Published 28th July 2020

      https://www.nature.com/articles/s41564-020-0771-4

      A comprehensive paper.

      1. Adrian says:

        This paper estimates that the last common ancestor of SARS‑CoV‑1 and SARS‑CoV‑2 was around 800 years ago.

  31. TallDave says:

    ugh

    like driving, politics lowers everyone’s IQ

    at any rate, lab leaks are surprisingly common, so whatever you think of various CCP or American officials, and wherever COVID really came from, we should all agree viral gain-of-function research needs to be banned yesterday

    1. theasdgamer says:

      Banned in the US already. But the NIH should not finance gof in other countries. We should tell Fauci and Ecohealth gfy.

  32. Craken says:

    So, when vulgar, unserious, non-experts like Trump lie to the American people–this makes him an “asshole.” But, when polite, very serious, experts like Fauci lie to the American people–this does not make him an “asshole.” The lesson, I suppose, is that when officials lie, we want to ensure that the liars are facially the most credible people available. Because we want to make sure their lies stick? For some reason, I think it’s entirely the other way around. Not only that, but people like Fauci and institutions like the CDC/FDA/NYT are permanent. Permanently positioned liars are far more significant “assholes” than impermanent ones. Trump was removed; our abysmal ruling class not only remains, but remains as incompetent/mendacious as ever–and utterly beyond any accountability for its crimes (just like the CCP).
    Anyone without a great backlog of agnostic responses to complex questions is a liar.

  33. shion arita says:

    Of course, as a scientist one must not jump to premature conclusions but I would bet at pretty heavy odds on this being an unintentional leak from WIV. All of the natural origin hypotheses have failed to produce any evidence for them whatsoever (contrary to the popular adage, absence of evidence is in fact evidence of absence, albeit weak evidence), and the leak has tremendous amounts of indirect evidence, such as the strange behavior of the WIV, the fact that not many other places have such facilities researching these exact things and the virus just happens to appear at the same location.

    To put it more simply if there were a leak from WIV, there would be nothing that happened that would be unexplained or seemingly inexplicable about the virus itself, the nature of the outbreak, and the behavior of everyone in response to it. But if there were a ‘natural’ origin, there are quite a few things about all of those that come along with big question marks.

    What bothers me most about this whole business is not even the fact that if it were a leak, WIV/China covered it up. Nay, the most infuriating and insane part of it is the concerted effort of all facets of the establishment to forbid this hypothesis from being considered for more than a year. We’re finally now coming around to talking about it seriously, but people have been suggesting this since last February, and there was a concerted, directed, and intense effort to suppress their ideas, and discredit and smear their names. It is a reasonable hypothesis and the fact that it was shouted down so thoroughly makes me have no faith in anything the establishment is saying about this matter. We go from “this virus is not dangerous, and people are panicking needlessly and are only acting because they are racist against Chinese people” to “masks don’t work and no one should buy them, and if anyone does they’re a harmful idiot” to “there’s no way this thing came from anywhere other than the Wuhan meat market and anyone who says otherwise is an idiot and also is racist against Chinese people” to “There’s no way that Ivermectin is helpful because we haven’t run large scale trials of it and won’t bother to and if you think it does you’re an idiot and like the Trump supporters that were ingesting bleach and fishtank cleaner”. And we talk about vaccine hesitancy, about people not believing “of course these vaccines are completely safe and if anyone says otherwise they’re an idiot and a Trump supporter conspiracy theorest etc.” well, even if they are correct about the safety, it’s like the boy who cried wolf. The WHO/CDC/Fauci et al. have given people good reason not to trust them, and are surprised when they don’t. This should be an all hands on deck moment but what we’ve seen instead is a complete and utter failure to act reasonably and logically about this matter.

    I’m sorry for the rant, but this whole thing is making me despair for the future of humanity.

    1. Jonathan B says:

      Absence of evidence isn’t quite evidence of absence, it is evidence of unlikeliness. And the weight you put on it depends on how extensive the search was for evidence.

      From what I have read China have resisted anyone from other countries getting involved in attempts to track down the origin of the virus. They would anyway prefer to believe the virus was an import from elsewhere. I am not sure we know that evidence has been looked for sufficiently carefully for us to believe it is absent. (The WHO team were not engaged in field research).

      If the human form of SARS-CoV-2 arose from a bat origin via another species, it would at least imply that an intermediate ancestor is circulating in animal populations so there might be something to look for. However it isn’t even clear what animal to investigate (pangolins have been thought plausible, but not proven) or where to look. It would need a massive study to rule out the idea for wild populations.

      If the virus arose from a lab escape and there was a cover up, all easily identifiable evidence would have been destroyed or well hidden. An expert forensic team might still turn something up, but unless there has been such a search (which itself would need good justification) absence of evidence doesn’t mean a lot.

      I pointed out above that another conceivable origin could be in a single immunocompromised patient in whom the virus could have persisted long enough to go through a series of adaptive mutations (since such an event has been observed for SARS-CoV-2). In this case there might be evidence but only if you were able to identify the single individual to investigate.

      My conclusion is that in this case, absence of evidence means we simply don’t know and no reasonable hypothesis can be rejected.

  34. Gus says:

    Conspiricy theories , when they have any validity, seem to serve two purposes. One is to midirect people away from the truth with nonsense (eg the CIA deliberately seeding UFO conspirices around Area 51 to deflect attention from their experimental aircraft program) and secondly to cover up for incompetance.
    I suspect that if it leaked from a lab – someone cocked up rather than a deliberate leak and the Chinese govt is desperately trying to cover up to prevent any kind of liability. Either that or it didn’t leak for a lab. I don’t think it was a deliberate leak – whats the economic advantage ? If china destroys the world economy who will buy their shit ? So at the end of the day – does it really matter other to ensure better lab protocols in future ?

  35. Lucifer says:

    China is a dictatorship, everything is said !

  36. Lars says:

    Our gracious host Derek Lowe says “As the world knows, there is a research facility in Wuhan that has been studying viruses (including coronaviruses), so we also cannot rule out the possibility of an accidental escape from such a site. And there’s also the possibility that such a virus might then be different from wild-type, depending on what sorts of work was done on it. Viruses most certainly have escaped from research facilities before, and this is not a crazy idea.”

    Thank you, thank you, thank you , Derek Lowe for acting like a scientist in recognizing the significant uncertainty surrounding the origin of SARSCov2.

    For over a year now, many in the media and even some scientists have been acting in a decidedly UNscientific manner by making a pronouncement that was and still is UNjustified by the available evidence: that the SARSCov2 virus definitely had a totally natural origin and that the lab origin hypothesis — in all of its manifestations, including the leak of the virus from a lab with the purest motives could therefore be ruled out ( as if the mere fact that the virus came from a lab would necessarily mean that it was manipulated as part of some sort of bioweapons program).

    Worst of all, some of these people (including a few who call themselves “scientists” and include “Dr” before their name) have been painting anyone who asks the question “did the virus have a lab origin?” as a “conspiracy theorist” and in some cases, even “racist”.

    Rather than acting as scientists, the latter folks are acting as politicians to effectively dismiss the lab origin (and in particular, accidental lab leak) hypothesis out of hand without regard for the possible evidence and arguments behind it.

    The latter is a gross politicization of the scientific process which is damaging not only to the public but to science and scientists because, even though it’s a relatively small number of scientists doing it, it has the potential to undermine public trust in scientists and science in general.

    1. Lars says:

      Not incidentally, the fact that Derek prefaced his post with

      “I’m going to regret writing about this…” pretty much says it all.

      When scientists feel that they can’t freely air their honest views on scientific matters without “regrets” (presumably over a backlash),we are in very deep trouble.

    2. BRetty says:

      @Lars

      Thank you for stating the problem, as I see it, directly,

      The immediate attacks on anybody who suggested the origin of this virus MIGHT BE the adjacent laboratory that collects and studies these viruses, the ad hominem attacks screaming racism or political manipulation, that is the huge failure of our scientific establishments. That is the true outrage.

      We will never know if this virus escaped from a laboratory, but the “scientists” who put themselves forward to announce that they knew the Truth, should be remembered.

      BR

      1. Lars says:

        It certainly doesn’t help things that we have actual scientists leveling the “conspiracy theory/theorist” charge against anyone who dares to posit any form of the lab leak hypothesis (including the accidental version).

        I hate to single out astrophysicist Ethan Siegel , but he has a platform that allows him to reach a lot of people (he writes a column for Forbes) and he has been especially loud and arrogant (some might say downright obnoxious) in this regard.

        https://www.forbes.com/sites/startswithabang/2021/06/03/the-wuhan-lab-leak-hypothesis-is-a-conspiracy-theory-not-science/?sh=6738c601dd8c

        Thank goodness we have at least a few scientists who don’t believe they know everything there is to know about the origins of sarscov2 and, even at the risk of being branded conspiracy nuts, are courageous enough to admit a modicum of open-mindedness until direct evidence for the zoonotic hypothesis (the intermediate virus host animal between bats and humans,) is forthcoming.

    1. Adrian says:

      This Forbes article says:
      ‘None of the staff at the Wuhan Institute were infected with SARS-CoV-2; they were PCR/antibody negative, which should be disqualifying for the lab leak hypothesis.’

      The US State Department has stated publicly:
      ‘The U.S. government has reason to believe that several researchers inside the WIV became sick in autumn 2019, before the first identified case of the outbreak, with symptoms consistent with both COVID-19 and common seasonal illnesses. This raises questions about the credibility of WIV senior researcher Shi Zhengli’s public claim that there was “zero infection” among the WIV’s staff and students of SARS-CoV-2 or SARS-related viruses.’

      This Forbes Senior Contributor gives no rationale why he trusts Shi Zhengli more than the US government, or any discussion at all that what is presented as facts and proof is actually disputed.

      1. Bored says:

        Who owns Forbes?
        The Forbes family sold it years ago.

    2. Lars says:

      No, Ethan Siegel clearly shows that he does not understand that science is NOT (ever) about certainty, when he claims

      “Science Clearly Shows That COVID-19 Wasn’t Leaked From A Wuhan . It occurred naturally, and scientists know this for certain. ”

      Since neither Siegel nor “scientists” can know this (or anything else) for certain from science (even in principle), We must assume that their certainty derives from something else.

      Perhaps from looking to the the stars?(Siegel IS an astrophysicist by trade)

      Or maybe from consulting their Magic Covid Ball (Siegel looks the part of a mystic in his photo)

      Ethan Siegel:” Magic Covid Ball, did SARSCov2 occur naturally?”
      Magic Covid Ball: “It is certain.”

      Ethan Siegel, an astrophysicist, and his apocryphal “scientists” must be consulting the stars (or maybe the Magic Eight Ball) when they claim to know for certain that SARSCov2 was not leaked from a Wuhan lab.

      1. theasdgamer says:

        Actually, there are a few things you can know for certain.

        E.g., when SARS-COV-2 RNA is cycled at 37 and influenza virus is cycled at 27, ceteris paribus, there is 1,000 times more likelihood of a covid misdiagnosis than an influenza misdiagnosis.

        You can know that PCR is better suited to nucleic acid research than to clinical diagnosis. You can know that viral culturing should be done in clinical research that involves viral transmission.

        You can know that SARS-COV-2 can be cultured in Vero cells.

        You can know that SARS-COV-2 has a higher mortality rate for comorbidities and older ages.

        You can know that there was tremendous panic mongering around Jan.-Feb. 2020 concerning covid by China. And that the panic mongering was pushed by SPI-B (as they admit in online documents). And that the media mongered panic.

        As a physicist, you might not know about RCTs, and you might laugh at RCT fundamentalists’ silliness about RCTs being the ‘gold standard.’ (Rigor in experimental physics is unsurpassed, in silico excluded.)

        A biophysicist might know about masks culturing bacteria in a humid environment and about masks causing _more_ net infection by viruses in a dry environment. Which is not necessarily a bad thing, as it might help to build strong immune systems.

        As a physicist, you might understand statistics and systematic error better than physicians. (Chemists also should know this, but some might need a refresher.)

        Physicists should know that what works in the lab might not work in the field–a fact to which numerous engineers will attest.

        You might reasonably be uncertain about covid mortality, the origin of SARS-COV-2, whether certain antivirals are effective (to a degree), whether vaccines are effective, whether the US achieved herd immunity before vaccines were rolled out, and many other things surrounding covid.

        1. Lars says:

          Actually, every scientific hypothesis, every scientific theory, every measurement, every experimental result and every conclusion drawn from statistics done on measurements is UNcertain to some degree. The very purpose of doing statistics is to characterize the uncertainty.

          This is precisely why experimental results published in scientific journals ALWAYS include uncertainty estimates.

          Without the attached uncertainty estimate, it’s not science. Indeed it’s meaningless.

          1. theasdgamer says:

            You’ve obviously never opened the pages of a physics journal.

        2. Lars says:

          Think about it.

          Your claim that

          “You can know that SARS-COV-2 has a higher mortality rate for comorbidities and older ages” is a conclusion drawn from statistics based on a particular sample.

          One can use statistics to estimate the uncertainty attached to the claim and it may be low, but It is NOT a certain conclusion. The result could depend on the particular sample.

          Your example
          .g., when SARS-COV-2 RNA is cycled at 37 and influenza virus is cycled at 27, ceteris paribus, there is 1,000 times more likelihood of a covid misdiagnosis than an influenza misdiagnosis.”

          Is also based on statistics and hence also uncertain to some degree.

          That is not to say that the uncertainty is necessarily large, just that it exists. ALWAYS.

          1. theasdgamer says:

            Degree matters. If the p-value is very small, uncertainty is very low and we assume that we know something.

            It’s always possible to imagine that the sun rises in the west and sets in the east or that chairs are able to think and feel. Empirical data triumphs over imagination, doesn’t it?

            It’s always possible that a black swan exists somewhere, but it’s not very useful to base your decisions on the remote possibility of a black swan if you have been diligent to search for one to disprove your hypothesis.

          2. Lars says:

            Of course degree matters.

            But saying that the degree of uncertainty is small or even very small is quite different from saying there is NO uncertainty — is, that one is certain.

            The very reason for specifying the uncertainty of a scientific result of conclusion is to provide an indication of how confident one can be in that result of conclusion.

            Without such an uncertainty estimate, one can have no idea how reliable a result of conclusion is.

            My point from the very beginning (my comment that you questioned) was that there is no “certainty” in science.

            But I would suggest reading Richard Feynmans book because he explains very clearly why that is the case.

          3. theasdgamer says:

            I’ve read Feynman and I’ve read Feyerabend. Both wright about philosophy of science. Feyerabend is better.

        3. Lars says:

          Nobel physicist Richard Feynman wrote an interesting little book called “The Meaning of It All” in which he talked about the uncertainty of science. In fact, that was the title of one of the very first chapter.

          Here are some of the things he said:
          “Every scientific law, every scientific principle, every statement of the results of an observation is done kind of a summary which leaves out details, because nothing can be stated precisely.”

          “It is necessary and true that all of the things we say in science , all of the conclusions , are uncertain, because they are only conclusions. They are guesses as to what is going to happen, and you cannot know what will happen because you have not made the most complete experiments.”

          “Scientists are used to dealing with doubt and uncertainty. All scientific knowledge is uncertain. This experience with doubt and uncertainty is important. I believe it is of very great value , and one that extends beyond the sciences. I believe that to solve any problem that has never been solved before, you have to leave the door to the unknown what. You have to permit the possibility that you do not have it exactly right. Otherwise, if you have made up your mind already, you might not solve it”
          “If we were not able or didn’t desire to look in any new direction, if we did not have doubt or recognize ignorance, we would not get any new ideas. There would be nothing worth checking because we would know what is true. So what we call scientific knowledge today is a body of statements of varying degrees of uncertainty. Some of them are most unsure; some of them are nearly sure; but none is absolutely certain.”
          // End of quotes

          1. Lars says:

            Sorry about any typos.

            I copied it manually from a hard copy of the book.

          2. Lars says:

            Feynman’s statement about the importance of doubt to solving problems is highly relevant to the topic of this post.

            “To solve any problem that has never been solved before, you have to leave the door to the unknown **what**. You have to permit the possibility that you do not have it exactly right. Otherwise, if you have made up your mind already*, you might not solve it”

            //End quote

            *As folks like Kristian Andersen, Peter Daszak and Ethan Siegel have done when it comes to solving the mystery of the origin of SARSCov2.

          3. Lars says:

            Leave the door to the unknown “ajar”

            Autocorrect keeps changing it to “what”

          4. theasdgamer says:

            Feynman is especially talking about the Laws of Physics here. Nancy Cartwright did it better in “How the Laws of Physics Lie.” It’s very technical and impossible to understand without a physics background. Basically, the stated Laws of Physics only apply to the lab environment with tight controls. Once you leave the lab, those laws are only approximations to the non-lab environment.

            Don’t try to apply Feynman’s statements too broadly, except that it helps to keep an open mind. We really don’t know much about what “science” is, except that it seems to be a high-value brand. Everyone and his brother seem to want to get in on it. Economists, sociologists, psychologist, mathematicians.

            How much uncertainty is there in mathematics? Some things are uncertain, but some are very certain.

            It helps to understand which statements are less certain and which are more certain. It also helps to understand where you have a lot of ignorance and uncertainty. For example, there is a great deal of uncertainty about whether covid was natural or artificial. And if artificial, was the release accidental or deliberate. So I’m agnostic on all those questions.

            It also helps to be able to recognize systematic error and reduce your uncertainty.

          5. Lars says:

            Feynman was actually not just talking about the laws of physics but about science in general. Read his book The Meaning if it All, which is what the quotes were taken from.

            But even if he had been talking specifically about the laws of physics, those are at the heart of every natural science, including biology.

            Because the laws of physics are uncertain, so is EVERY natural process.

            It’s clear that you and I are never going to agree on this, but I think we can agree that Ethan Siegel was certainly not justified in saying with certainty that SARSCov2 did not come from the Wuhan lab.

          6. Lars says:

            Here’s Feynmans statement that I quoted above that indicates quite clearly that he was NOT just talking about the laws of physics but science in general:

            “Every scientific law, every scientific principle, every statement of the results of an observation is some kind of a summary which leaves out details, because nothing can be stated precisely.”

            But as i indicated, it’s not even worth discussing this further.

  37. kontoller says:

    to day The Wall Street Journal

    Intelligence on Sick Staff at Wuhan Lab Fuels Debate on Covid-19 Origin:
    WASHINGTON—Three researchers from China’s Wuhan Institute of Virology became sick enough in November 2019 that they sought hospital care, according to a previously undisclosed U.S. intelligence report that could add weight to growing calls for a fuller probe of whether the Covid-19 virus may have escaped from the laboratory.

  38. Lucifer says:

    Isn’t there a big basic problem, both in the comments and in the press articles ?
    The scientists also say enormities !

    1° – it is not the coronavirus; but they are: the coronaviruses. There are several of them!

    2° – a virus triggers, or not, a disease. It is not a disease!

    3° – the virus, here, is the Sars-cov-2. It is the second of its subgroup.

    4° – there is a Sars-cov-1; which explains why some people have sprays of 2018 on which it is mentioned Sars-cov, appeared in 2002 in China.

    5° – the Sars-cov-2 virus can trigger the disease: Covid-19.

    6° – the origin of the Covid-19 disease is the Sars-cov-2 virus.

    7° – what we are looking for is the origin of the Sars-cov-2 virus.

    Thank you !

    1. Lars says:

      Good point and I think when people make such mistakes it is actually very telling.

      Folks like Ethan Siegel (an astrophysicist and Forbian ( from the Planet Forbes), who (among other things) conflated the disease with the virus when he claimed “No, Science Clearly Shows That COVID-19 Wasn’t Leaked From A Wuhan Lab” , lack the necessary background and are wandering very far from their field of expertise when they draw definitive conclusions on this subject.

      Physicists seem to be particularly susceptible to “know-it-all” disease.

  39. A Concerned American says:

    Why does the Asshole who writes this column always attack the excellent Trump Administration which successfully enabled, facilitated and expedited two highly effective messenger RNA vaccines?

    Is Derek the Asshole Lowe a Socialist, Communist or Marxist?This Asshole should shut his fat yap for once and leave our great former President alone. This Asshole should keep his nose stuck in an organic chemistry textbook, since that seems to be the only thing this big mouth is any good at.

    1. Skeptical says:

      It’s truly a pity that you can’t tell satire from the sincere opinions of horrible people when it comes to politics anymore.

  40. JohnA says:

    UPDATE OF VAERS DATA:

    As of 14 May 2021 the number of deaths associated with the three vaccines given to Americans are:

    PFIZER 1731
    MODERNA 1979
    JANSSEN 319
    TOTAL 4201

    As to thrombocytopenia we have:

    PFIZER 153
    MODERNA 136
    JANSSEN 100

    Readable VAERS (Vaccine Adverse Event Reporting System) data can be downloaded from

    http://preearth.net/phpBB3/viewtopic.php?f=15&t=1184

    The VAERS people are throttling the data. For example, data from December last year is still being released. It is becoming more and more noticeable. I wonder what is really happening?

    1. theasdgamer says:

      Maybe doing some preliminary investigation?

      When bureaucrats and snails race, snails usually win.

      1. John says:

        Or maybe they are just spreading out the bad news (to make it more palatable).

        You know,…. flattening the curve.

  41. An Old Chemist says:

    Intelligence on Sick Staff at Wuhan Lab Fuels Debate On Covid-19 Origin (05-23-21):

    https://www.msn.com/en-us/news/world/intelligence-on-sick-staff-at-wuhan-lab-fuels-debate-on-covid-19-origin/ar-AAKiwGD?ocid=msedgntp

    1. Lucifer says:

      The origin of the Covid-19 disease is known !
      It is the Sars-cov-2 virus !

      Avoid the metonymy; you are not drinking a glass, but the contents of the glass.

      What we are looking for is the origin of the virus: Sars-cov-2.

    2. Lars says:

      Thanks for the metonymies!

  42. tally ho says:

    Given the political stakes and current US-China political climate, it will be nearly impossible to get a clear answer on the Wuhan Lab hypothesis. Which means all bets are off. But unfortunately, humans have a keen appetite for conspiracy theories, especially when it comes to black swan events. Human stupidity is much like artificial intelligence when it’s trained on faulty and sparse data.

    1. Lars says:

      Is the current pandemic a Black swan event?

    2. Ewe Anchor says:

      It’s true that _some_ people have an appetite for conspiracy theories, 5G nonsense, magnetized vaccine nonsense.

      On the other extreme, some people have an aversion to any sort of conspiracy theory, even when the evidence of a conspiracy is overwhelming.

      Forming conspiracies is part of human nature.

      1. Lucifer says:

        So let’s invent a conspiracy with suppositories, it’s much funnier ; after all, aliens travel across the universe just to stick their noses in.

      2. Flat Wheel says:

        No conspiracy is required for an unintended event, which is what the lab leak hypothesis is based on.

        1. Lars says:

          But there may be a conspiracy to cover it up.😀

    3. Adrian says:

      Note that your “impossible to get a clear answer” and “conspiracy theories” are mutually exclusive.

      When both natural origin and lab leak are possible explanations that cannot be ruled out, then calling either a “conspiracy theory” is fake news.

      When this Forbes propaganda piece says “Science Clearly Shows That COVID-19 Wasn’t Leaked From A Wuhan Lab”, we can all agree that this is provably wrong.

      Both origin theories have their merits, and the rational approach is to form an own opinion based on the arguments of both sides.

      1. Lars says:

        We should definitely look into the oranges of the pandemic.

        And maybe the apples too.

  43. An Old Chemist says:

    WHO coronavirus investigators pinpoint overlooked Chinese data for further study, source says (05-24-21):

    https://www.cnn.com/2021/05/25/china/covid-china-who-probe-intl-hnk/index.html

    1. Lucifer says:

      “Chinese data ?! ”
      On the genocide of the Uyghurs or that of the Tibetans ?

      “Chinese data”, no but, credibility ?!
      China is a dictatorship, it’s the central committee of the Chinese Communist Party that runs everything ; it’s like saying that data on child protection provided by a pedophile would be credible ; come on, be serious.

      If a KKK moron provides you with data on Jewish and black people, I’m going to have my doubts.

      1. Lars says:

        If SARSCov2 actually originated from a Wuhan lab , even if people like WIV researcher Shi Zhengli wanted to tell the truth, they and their families would be under enormous pressure (facing jail or even possibly “disappearance”) not to do so.

        Any Chinese researcher would have to have balls and/or ovaries of titanium to come forward with such information.

      2. Lars says:

        China is a “dicdataship”

  44. An Old Chemist says:

    5 Questions: David Relman on investigating origin of coronavirus (Stanford Medicine)

    https://med.stanford.edu/news/all-news/2021/05/david-relman-on-investigating-origin-of-coronavirus.html

  45. bacillus says:

    Not sure at what biosafety levels various bat coronaviruses were handled at Wuhan. Undoubtedly SARS-CoV-1 would have been handled at BSL3. However, given that SARS-CoV-2, unlike the former, is not very virulent in various animal models including NHP, and unlikely to infect lab staff wearing full BSL3 PPE, it could have been downgraded to a BSL2 pathogen leading to lesser levels of PPE and covert infection of healthy lab staff who took it out into the community. However, even if this was the route to the pandemic, the Chinese authorities are never going to fess up to this, and any Wuhan staff who might be in the know are unlikely to put their lives in danger by speaking out. Without the co-operation of these groups, you’ll never get a definitive answer about whether this started off as a laboratory acquired infection.

    1. Lars says:

      If the photos and videos of Chinese researchers collecting bats and bat dung samples and handling said bats and samples with minimal to no PPE are any indication, I’d say they were (and perhaps still are) operating at no higher than “Level -1”

      “Video shows Wuhan lab scientists admit to being bitten by bats
      Chinese scientists shown using little to no PPE while handling bats in wild, samples in lab”
      https://www.taiwannews.com.tw/en/news/4102619

      “A video released two years before the start of the Wuhan coronavirus pandemic shows Wuhan Insitute of Virology (WIV) scientists being cavalier toward protective equipment and being bitten by bats that carry deadly viruses such as SARS, demonstrating a lax safety culture in the lab.”

      On Dec. 29, 2017, Chinese state-run TV released a video designed to showcase Shi Zhengli, (石正麗), also known as “Bat Woman,” and her team of scientists at the WIV in their quest to find the origin of SARS. Despite the fact that the scientists work in a biosafety level 4 lab, they show a shocking disregard for safety when handling potentially infectious bats both in the wild and in the lab.”

      1. Lars says:

        Even Robin expressed concern about the wanton disregard for safety in the Batcave when he said

        “Holey PPE , Batman!”

  46. Lars says:

    The words of Robert Frost come to mind here “We dance round the internet and suppose. But the Secret sits in China* and knows.”

    *In the wilds of China (as an intermediary between bats and humans) or in a Chinese lab.

  47. Big Fool says:

    This investigation (ordered today by Biden) seems to be a fool’s errand.

    The ending can be reasonably predicted:

    – Either an intermediate host will be identified

    … or it won’t be.

    The chance that there will ever be proof that it was a leak from the Wuhan lab are approximately zero. The Chinese government will see to that.

    Spending resources investigating this when people are dying worldwide seems like a waste of time.

    Better to spend time ensuring that gain of function research is banned worldwide. And continuing to try to find an intermediate animal host.

    And to put effort into ensuring that vaccines are manufactured and distributed worldwide while better vaccines are developed and treatments are developed.

    When the back of the building continues to collapse as we work at repairing the front of the building, it is not time to demand knowing how the building started collapsing in the first place, when we really know that we aren’t going to be able to get a definitive answer anyway.

    1. Siddharth Dasgupta says:

      It is not clear: Will President Biden putting his weight behind this publicly cause the Chinese to give more information (if not full transparency) – IF they have nothing to hide, that would be the rational thought.
      Perhaps nothing will come out of it – except increase suspicions that there is something hidden!

      1. jam says:

        The Chinese probably feel they are being completely setup.

        Which, of course, they are.

  48. "Pissing Up the Wrong Stick" By Golden Showers says:

    A fantastic conspiracy theory with which to continue the trade war with the PRC. An enquiry disproving a negative, wonderful. We can search for decades! Every motor-mouthed muttonhead in the US Senate can proclaim the most absurd drivel from their bully pulpit and the commission will be tasked to look for evidence for or against it, endlessly chasing its tail. Tax dollars wasted in the billions, research proposals stretched ad absurdum to suck grants from the commissions teats, endless misleading copy for the less discriminating elements of the gutter press. And every misleading headline an excuse for another pointless and useless defence programme. A circus for all occasions.

  49. J says:

    Suggest it would be good if we could hear more about how the risk of a pandemic is to be recognised, and the measures to be taken to stop/minimise viruses travelling around the world. There appears to be a failure of systems currently in place perhaps? Hopefully this will be part of any investigation.

  50. Whenbowl says:

    Derek, why regret about writing this? I love your attitude about this issue.

  51. An Old Chemist says:

    Daily Mail (UK):
    By JOSH BOSWELL FOR DAILYMAIL.COM
    PUBLISHED: 17:50 EDT, 28 May 2021 | UPDATED: 03:04 EDT, 30 May 2021

    EXCLUSIVE: COVID-19 ‘has NO credible natural ancestor’ and WAS created by Chinese scientists who then tried to cover their tracks with ‘retro-engineering’ to make it seem like it naturally arose from bats, explosive new study claims

    https://www.dailymail.co.uk/news/article-9629563/Chinese-scientists-created-COVID-19-lab-tried-cover-tracks-new-study-claims.html

  52. kontoller says:

    continuation of the “banquet”
    whoever read the original article:
    Much of the work was centered around controversial ‘Gain of Function’ research – temporarily outlawed in the US under the Obama administration.

    Gain of Function involves tweaking naturally occurring viruses to make them more infectious, so that they can replicate in human cells in a lab, allowing the virus’s potential effect on humans to be studied and better understood.

    Dalgleish and Sørensen claim that scientists working on Gain of Function projects took a natural coronavirus ‘backbone’ found in Chinese cave bats and spliced onto it a new ‘spike’, turning it into the deadly and highly transmissible SARS-Cov-2.

    One tell-tale sign of alleged manipulation the two men highlighted was a row of four amino acids they found on the SARS-Cov-2 spike.

    In an exclusive interview with DailyMail.com, Sørensen said the amino acids all have a positive charge, which cause the virus to tightly cling to the negatively charged parts of human cells like a magnet, and so become more infectious.

    But because, like magnets, the positively charged amino acids repel each other, it is rare to find even three in a row in naturally occurring organisms, while four in a row is ‘extremely unlikely,’ the scientist said.

    ‘The laws of physics mean that you cannot have four positively charged amino acids in a row. The only way you can get this is if you artificially manufacture it,’ Dalgleish told DailyMail.com.
    the question is where did pfaizer or moderna so quickly understand that it was possible to use spike as a drug for training human immunity ?? did they have access to information about the structure and production of the spike used for the production of a chimeric virus ?? it is known that the first vaccines based on the spike were produced by a crush with a pfaizer at the beginning of 2000 … they did not want to think about the bad .. there are a lot of coincidences and I think that not only me … I hope that the cia investigates this … but there is little hope

    1. drsnowboard says:

      If you want your science from a National Enquirer style ‘newspaper’ , by all means quote The Daily Fail as a credible source.

  53. Dalgleish who? says:

    ‘The laws of physics mean that you cannot have four positively charged amino acids in a row. The only way you can get this is if you artificially manufacture it,’ Dalgleish told DailyMail.com

    I found 79 hits for 4 positive amino acids in a row from a search of human sequences. The human PP2A protein has 4 positively charged amino acids in a row (KRKK 402-405). So does ABCA3 (RRRR 1340-1343) and 5HT2C has six (RRRKKK, position 287-292).

    I guess this proves humans must have been artificially manufactured too. Wow, this is massive! Hold the front page…

    1. WST says:

      Their logic seems flawed to me, the mutations happen in the mRNA that doesn’t know if the resultant expressed sequence “makes sense”.
      And quite often it does not and results in a non-replicating virus.

  54. sgcox says:

    Michael Bulgakov wrote “Heart of a Dog” in 125. Not sure how it was published in Soviet Union but then it was before Stalin came to power… Dialogue of a Professor and his assistant during the dinner:
    – If you care about your digestion, my advice is – don’t talk about bolshevism or medicine at table. And, God forbid – never read Soviet newspapers before dinner.
    – M ’mm . . . But there are no other newspapers.
    – In that case don’t read any at all.
    I believe Professor Preobrazhensky advice should be equally applied to “Daily Mail” and similar.
    https://en.wikipedia.org/wiki/Heart_of_a_Dog

  55. kontoller says:

    gentlemen
    I wrote that I turned to the article itself not to the newspaper, do not be too lazy to read it, do not indiscriminately find fault with the authors, write your objections to the authors of the article, gentlemen, let’s see what they answer you, and publish here … that I don’t believe in protein soup from which living things appeared on earth .. your principle, what I don’t know doesn’t exist speaks at best about naivety and at worst about interest in confusion .. very quickly answered

  56. kontoller says:

    22-page paper which is set to be published in the scientific journal Quarterly Review of Biophysics Discovery, Dalgleish and Sorensen
    gentlemen
    I understand that this magazine is for you the yellow press
    about Heart of a Dog read the whole very interesting things there, especially about head transplant with brains

  57. kontoller says:

    gentlemen, I especially liked that you were able to see the valence of amino acids in the genetic code in 5 minutes after I wrote a review

    1. Dalgleish who? says:

      Thanks, but it wasn’t difficult. Anyone who knows a little bioinformatics could run this search on a public server and prove this claim to be nonsense in a few minutes. What this tells me is that the author is so sure of his own theory that he can’t be bothered to carry out a simple reality check, also that any more of my time spent on this paper would be time flushed down the drain.

      1. sgcox says:

        What service did you use, BTW ?
        I tried UniProt but it sort oh hang-up on me and never finished.
        PepBank returns pubmed link or something but not protein name.
        Expasy Prosite just gives no hits 🙁

  58. Skeptical says:

    See https://www.ncbi.nlm.nih.gov/protein/NP_001001.2
    188-112: hkrrr
    230-233: krrr

  59. Sergei says:

    This post is about a very important and serious issue and can be viewed by anyone regardless of their education. When I read it for the first time, it sounded like it was sarcastic (I’m not at all a biologist), but at the second reading, it became much less clear. Could you please clarify the author’s position on the issue and whether this post is serious?

  60. sareh says:

    This Virus Vanish 2 Years Old

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