Hi, I want to apologize. I was the one who did not see that you from the very beginning said you did not put much stock into the lab theory, and I basically ignored that. I didn't see it. I also did not read closely enough some other things as well. I was attacking some strawmen, some of which I have seen in the real world and others I have not.
I'm sorry, that colored a lot of my responses to you because I made unfair assumptions about what you were saying. I sent you a longer form email to your protonmail about it.
Hi you'll see elsewhere that I was very open about the fact that I, too, think an open and honest investigation from third parties is necessary. Seriously just search this page for "independent" or "investigation." I have said that several times on this post, and in the OP I linked as well. I am 100% in support of that and always have been. I just don't think the outcome will be conclusive, but I hope it will maybe prevent some of the damage this theory is causing.
I don't have time to address the rest of your comment I'm sorry, I have already sunk so much time into this post that I should have spent studying. This is the exam I have in 3 weeks: https://en.wikipedia.org/wiki/USMLE_Step_1 Pay particular attention to the section marked "effect on matching residency." I never should have responded or brought myself into this post in the first place.
Sorry, but I need to exit now. I hope you find the certainty you're looking for, either way. I hope you find the solace in "holding virologists to account" that you are looking for, although I'm not sure it will happen the way you are suggesting.
And if you actually have been playing "devil's advocate" this whole time and don't believe the interpretation of facts that you've put forth, then that is very much "arguing in bad faith." You were not up front with your beliefs or positions, you just wanted "to ask questions."
If you did not believe in good faith the statements you made, or have substance behind the questions you asked as though you believed them to be true (CGG for example), that is very much insincere.
I am not going to be dragged into an endless debate with someone who wants to play devil's advocate. There are people with actual misunderstandings and misconceptions about science that are out there that need our help to understand the world around them.
Why waste time like this if we agree on the basic points? This is not a socratic discussion, you are not Socrates, and I am not Plato. This is not a PhD defense. It is not an academic conference.
I'm here to talk about this with people who have legitimate concerns that they actually believe about the subject matter at hand.
And please, I'm sorry if I mischaracterized your position or your actions thus far, but that's what it looks like. If you had said at some point "just playing devil's advocate here!" or "I don't 100% believe this but what about this thing I saw?" then if I had seen that, I would have engaged in a completely different way, and likely disengaged much earlier.
Thanks for the interesting ideas, but I have to go study for exams, and procrastinate in ways that are better for both of our mental health.
Have a great day, and I hope this hasn't taken up as much of your mental energy as it has mine. Because it took up a lot of mine.
All of this aside, the actual point I have been making the whole time is this:
Do you think these two possibilities are equally likely?
Do you think one is more likely than the other?
Which?
You say that you find the lab possibility not very likely, so do you find the zoonotic scenario any more likely? If so, then you and I are in agreement, of a kind. You never said that above, and you definitely argued in a way that implied something else. Especially given the CGG codons.
Probabilistic thinking is the nature of the discussion in the absence of conclusive evidence. Probabilistic thinking. Heuristics. That's what I've been discussing this entire time, that's what I was talking about in my original post, and it's what your reply comments were, therefore, replying to.
I never make any claims saying either is the only possible scenario or an impossible one.
I also was not "dancing around the concrete arguments on the topic." I was directly answering arguments that had been put forth to me by random people on the internet. That's it. That's the point of the post. To answer those arguments.
I get that you've never seen it claimed that engineering made all 1200 mutations, but plenty of people claim it. You can look on my original reddit post and see people in the comments claiming it's possible because "China is so far ahead of us, they could have generated the primers 20 years ago to do something like that."
That's why it's not a strawman, I was directly answering arguments that had been made to me by people on the internet. Just because you think they are ludicrous arguments does not mean that someone has not made them. The internet is larger and more diverse in its idiocy than you have conceived of in your dreams, Horatio. etc. etc.
>2) That furin site RNA contains a non-canonical amino acid codon. To be fair, you didn't dispute this.
Hi, I have disputed the claim you've made since that the virus contains two such codons in a row. That is patently not the case in the earliest examples of the virus known. And wow, I just checked, and those three sequences from the earliest part of the pandemic I linked, they don't contain the cgg in the furin site. Literally look yourself. The earliest sequences out of China, Korea, and Iran do not have the cgg where you're talking about. It isn't there. Not that I saw, lol. Show me where it is if you find it. I just used BLOSUM similarity alignment and looked where the cleavage is supposed to be. And I don't see CGG there.
I actually address the restriction site directly in the original discussion. I don't recall you mentioning it before now. if you did, my apologies I missed it. See my comments on that copy/pasted here:
"For sticky end ligation, for example, you can examine the relative length of homologous regions around restriction enzyme cutting motifs. And sort of detect it like a photoshopped gel almost. But in sequence form. Real mutations shouldn't occur predominately around restriction enzyme motifs. But engineered mutations would. You'd have to use evolutionary comparison of similar viral species to see if there are any mutations that appear too improbable to have happened by polymerase error alone.
Is it still possible to slip one by such a method? yes, of course. Especially small insertions or deletions would be easy to hide...
[But] it literally wouldn't make sense to do it. We have established backbones that would make more sense and be easier to use. The only reason would be to "hide your work." And that's like years and years worth of genetic manipulation, several post-docs worth of work, easy. All to "hide your work." When you could just use SARS-CoV-1 and be A) more deadly, B) more "natural", and C) easier to use."
It's just really funny if we do agree about both of these being possible, but one being more likely than the other. If we both agree that the zoonotic is probably more likely, what are we arguing about? I don't disagree that it is /technically/ possible, but I also find it more likely to have occurred in nature. Restriction sites can also occur in nature, btw. This is a case of the "lottery" fallacy. There are so many goddamn restriction sites throughout any viral genome, why is this surprising?
https://pubmed.ncbi.nlm.nih.gov/16940861/ (this one says wet markets, which probably are an issue, but not as big as initially thought, and probably not the origin of CoV-2)
And you also don't have to take my word for it re: China's problem with zoonotic transmission. Here are scientific review articles that demonstrate that consensus:
https://pubmed.ncbi.nlm.nih.gov/16940861/ (this one says wet markets, which probably are an issue, but not as big as initially thought, and probably not the origin of CoV-2)
Also, I just want to reiterate here, we virologists have literally been saying this is going to happen from nature FOR YEARS.
People like Michael Osterholm and Peter Daszak and Vincent Muenster and Ralph Baric and Shi Zhengli have been saying this was going to happen /for years/. It was a matter of "when" not "if" to us virologists. We absolutely saw the writing on the wall and saw specifically SARS-1 and MERS and knew that meant there were likely other coronaviruses that could emerge.
But funding was always so low, because the viruses weren't currently infecting anybody! So the sampling efforts were always very minimal and underfunded!
And now, because of the lab leak theory, that has actually gotten worse, not better!
But these are permalinks? This is like linking to a github. It doesn't just "disappear." Unless Reddit goes under, which is just as likely as StackOverflow or HN going under.
At this point, with their market cap and increased moderation, probably less likely than the two I listed.
yeah, not in the time frame available or with the tools available. It would either have to be some hidden virus that they all lied about, or somehow an unknown contaminant in their samples that then also disappeared when they looked.
All new assumptions that make this theory less likely.
Honestly, can't find it. It was in some random facebook group about this stuff, I joined a couple dozen as the pandemic went on, so hard to find which one and my activity log search isn't turning up anything.
Sorry. :(
I don't have the time or bandwidth to re-write it at the moment. But a lot of her arguments are similar to Dr. Degerin's and also Dr. Ebright over at Rutgers. They are a small minority, like the OP says.
I tend to rely on expert consensus when it makes mechanistic sense like this one does.
Nothing, no evidence we have, makes either possibility impossible. The lab leak just requires a lot more cloak and dagger and new assumptions. Occam's razer tells me to favor the hypothesis with the least new assumptions. Hence zoonotic release is more likely in my opinion. That's truly the crux of it, the rest of it is arguing over the number of angels on the head of a pin.
>Everyone knows that mutations that increase transmissability generally hurt morbidity. Is there some reason you think this supports zoonotic hypothesis? It is public knowledge RaTG13 was collected from a mine shaft where a similar virus killed 50% of infected workers and where WIV was doing significant sampling work.
Why would this support either hypothesis? The cleavage site clearly has nothing to do with RATG-13 and it is probably one of the main drivers of SARS-CoV-2 pathogenesis. See here:
It's not super likely, because we don't have the epidemiological data (increased deaths from non-influenza pneumonia at a large scale) to support that, to my knowledge.
It's certainly possible. And it is true that our methods of detection of viruses are ill-equipped so you can assume we're almost always behind the curve a bit.
But there also isn't much more than anecdote to support this. Lots of people get influenza-based pneumonia in the winter. Could you consider the possibility that your recollection is now tainted? And that you are primed to notice those events more? It was also already a very bad flu season. See here:
Another kind of issue is that early reports of "SARS-2 positive serum!" were overblown, which colored a lot of news reports on this. They basically made the tests too "promiscuous" so they also detected antibodies against common cold coronaviruses. That was a big problem. If you're curious about how tests like this work, you can check out this other post I wrote on that! Antibody tests are actually my specialty!
Hi, you're probably right it isn't possible to know 100% the origin at this point.
All we can do is make probabilistic arguments. Inferences. Inductive reasoning.
And that sort of analysis, occam's razor based on the least new assumptions necessary to conclude the mechanism, I think the zoonotic theory is more likely.
The lab theory isn't impossible, it just requires a lot more untested and unknown assumptions.
Best epidemiological and genetic evidence suggests it originated somewhere outside Wuhan and then became a serious outbreak there as it's a major population center.