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CIA now favors lab leak theory to explain Covid's origins

nytimes.com

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Re: CIA now favors lab leak theory to explain Covid's origins

#281

Post by throwawaymaths »

ndr42 wrote: post #192
throwawaymaths wrote: post #176

Earlier quoted context omitted.

FTA: The absence of CTCCTCGGCGGGCACGTAG from any mammalian or viral genome in the BLAST database makes recombination in an intermediate host an unlikely explanation for its presence in SARS-CoV-2. You can verify for yourself that there are no other sequences with an exact match. The subsequent comment about statistics of blast searching is irrelevant.

So the conclusion of the comment-article cited in the parent of your comment is false? "According to the current phylogeny, FCS appeared independently six times in the Betacoronavirus lineages, demonstrating that FCS insertion is compatible with natural evolution (2, 7, 8). [...] 7. Wu Y, Zhao S. Furin cleavage sites naturally occur in coronaviruses. Stem Cell Res (2021) 50:102115. doi: 10.1016/j.scr.2020.102115"

it's incompatible. Why is there COVID speculation in Stem Cell Res?

Re: CIA now favors lab leak theory to explain Covid's origins

#282

Post by throwawaymaths »

nickburns wrote: post #138
throwawaymaths wrote: post #101

Earlier quoted context omitted.

there's a 23? bp sequence that is directly lifted from the moderna hiv vaccine patent (which preceded covid-19 by a decade). now an exact match of that length isn't impossible, but which is more likely? that this managed to be exactly correct on accident? or some grad student was told to just copypasta every furin cleavage site in the database into a GOF library and surprise surprise the most virulent form that becam…

> there's a 23? bp sequence that is directly lifted from the moderna hiv vaccine patent (which preceded covid-19 by a decade). could you cite this? not because i'm questioning the statement's credibility, but because i'm curious (and you could save me a lot of time from even knowing where to begin to look for credible information for myself—full disclosure, lol).

sorry. it was 19bp

Here. you can do it yourself. databases are public.

CTCCTCGGCGGGCACGTAG

Re: CIA now favors lab leak theory to explain Covid's origins

#283

Post by TylerE »

ironyman wrote: post #7
mmooss wrote: post #4

Earlier quoted context omitted.

Yes, but we can assume - Trump and his people have openly communicated, planned, and followed through on it - that the actions of executive branch agencies are politicized. Here we are told that the "C.I.A.’s new director, John Ratcliffe, ... wants the agency to get “off the sidelines” in the debate."; that he's long favored the lab-leak theory (which is a politicized issue); and of all the things a brand new new CIA…

Senator Tom Cotton (R-Arkansas), Chairman of the Senate Intelligence Committee, released the following statement about the CIA’s findings on the origins of the Coronavirus: “I’ve said from the beginning that Covid likely originated in the Wuhan labs. Communist China covered it up and the liberal media covered for them. I’m pleased the CIA concluded in the final days of the Biden administration that the lab-leak theor…

Tom Cotton is one the lowest integrity people I washington. Watch him in Cspan sometime. Just a buffoon.

Re: CIA now favors lab leak theory to explain Covid's origins

#284

Post by giantg2 »

therealpygon wrote: post #246
giantg2 wrote: post #149

Earlier quoted context omitted.

I have family that have worked on developing NBC equipment for the military. The first thing they said when covid was spreading was that it was most likely from a lab. That was before anyone in the news was saying that. So an independent first-look assessment by someone with experience, followed by later finding out that there was in fact a lab there, has me heavily leaning towards it being true. But it doesn't reall…

You should realize experience in a tangentially related field and there being a lab somewhere in the area is not the same as insight and evidence. That’s like saying that if a new flu came out of Atlanta, the fact the CDC is there proves it came from a lab, and must be true because someone’s janitor cousin who worked there one summer said it was true. “Low confidence” means that there is a lack of evidence and the st…

Actually, it's more difficult to prove a wild origin than a lab origin, because labs have papertrails and witnesses.

I never said I was right. I said it makes a lot of sense and I believe it's probably true.

This is the sort of thing that neither of us can prove to the other at this point. You seem awfully aggressive to prove something though.

Re: CIA now favors lab leak theory to explain Covid's origins

#285

Post by [deleted] »

wk_end wrote: post #241
Retric wrote: post #114

Earlier quoted context omitted.

Carful when assuming how a lab leak must have unfolded, there’s many possibilities. A single worker gets infected/accidentally releases multiple variants, sloppy worker messing up twice doesn’t seem that crazy. A lab leak is also consistent with an infection person visiting a location that experienced a separate variant. And that’s just a few options there’s also things like an intentional leak followed by another in…

> I’ve read that the lab was intentionally set near that wet market... That seems unlikely, given that - per Wikipedia - the WIV opened in 1956 and the wet market opened in 2002.

[deleted]

Re: CIA now favors lab leak theory to explain Covid's origins

#287

Post by throwawaymaths »

giantg2 wrote: post #149
drewbug01 wrote: post #17

> The agency made its new assessment with “low confidence,” which means the intelligence behind it is fragmentary and incomplete. I do believe that's all one really needs to know about this shift in their thinking. In other words: it's really far from certain. --- One thing that is, however, quite certain: there are very real political reasons to favor one theory or another. For example, Sen. Tom Cotton is quoted as…

I have family that have worked on developing NBC equipment for the military. The first thing they said when covid was spreading was that it was most likely from a lab. That was before anyone in the news was saying that. So an independent first-look assessment by someone with experience, followed by later finding out that there was in fact a lab there, has me heavily leaning towards it being true. But it doesn't reall…

there's a 19 bp sequence CTCCTCGGCGGGCACGTAG that is directly lifted from the moderna hiv vaccine patent (which preceded covid-19 by a decade). now an exact match of that length isn't impossible, but which is more likely? that this managed to be exactly correct on accident? or some grad student was told to just copypasta every furin cleavage site in the database into a GOF library and surprise surprise the most virulent form that became a pandemic came from the sequence that is engineered to be efficient.

any scientist that has any molecular biology wet experience will tell you this is exactly what they would have done (though us researchers would probably not have pulled from the patented BLAST sequences, since that selector is turned off by default by the NCBI)

Re: CIA now favors lab leak theory to explain Covid's origins

#288

Post by Enginerrrd »

therealpygon wrote: post #246
giantg2 wrote: post #149

Earlier quoted context omitted.

I have family that have worked on developing NBC equipment for the military. The first thing they said when covid was spreading was that it was most likely from a lab. That was before anyone in the news was saying that. So an independent first-look assessment by someone with experience, followed by later finding out that there was in fact a lab there, has me heavily leaning towards it being true. But it doesn't reall…

You should realize experience in a tangentially related field and there being a lab somewhere in the area is not the same as insight and evidence. That’s like saying that if a new flu came out of Atlanta, the fact the CDC is there proves it came from a lab, and must be true because someone’s janitor cousin who worked there one summer said it was true. “Low confidence” means that there is a lack of evidence and the st…

There's a paper from 2014 that tried to estimate the annual chance of a pandemic from a lab leak. They estimated it at 2%.

I assumed they overestimated a bit for effect and put it at around 1%.

Pandemics have historically happened somewhere around ever 100 years. What's that annual probability? 1%.

So if you knew NOTHING else, from a bayesian standpoint, if you have to differentiate a once in a 100 year spillover or a lab leak, you would put it at 50/50.

Now add in the fact that the outbreak occurred right next to a BSL lab. Now add in the fact that this lab specialized in the exact type of virus that caused the pandemic. Now add in the fact that lab workers at that lab got hospitalized with respiratory symtpoms in November. Now add in the fact that China responded with tons of secrecy, pulled down their genomic database of known viruses in their Wuhan lab, Xi issued a proclamation in February that they were revamping safety at BSL labs to prevent leaks, and that the virus in question is remarkably similar to one they found in 2013 thousands of miles away, and add the fact that there was a proposal to modify cornaviruses to have a furan cleavage site to perform gain of function research and that the COVID virus has just such a furan cleavage site, and this virus emerged remarkably well adapted to humans very very quickly. Now how about the fact that China pushed the wet market theory even after they'd figured out that probably wasn't the case? Now add in the fact that China let SARS escape from the lab TWICE in the previous decade.

How does that affect your truth value? All the facts above push the probalistic truth value toward a lab leak. There are a few facts that push it back a little the other way, but there aren't very many that I've found.

Re: CIA now favors lab leak theory to explain Covid's origins

#289

Post by mrcsharp »

philjohn wrote: post #253
nxm wrote: post #122

Earlier quoted context omitted.

Back then anyone who suggested the lab leak theory was immediately labeled a conspiracy theorist by main stream media.

Were they? Or were those who claimed it was the only possible answer, without the evidence to back that up?

That's not a good enough reason to censor.

Re: CIA now favors lab leak theory to explain Covid's origins

#290

Post by throwawaymaths »

cakealert wrote: post #130
throwawaymaths wrote: post #101

Earlier quoted context omitted.

there's a 23? bp sequence that is directly lifted from the moderna hiv vaccine patent (which preceded covid-19 by a decade). now an exact match of that length isn't impossible, but which is more likely? that this managed to be exactly correct on accident? or some grad student was told to just copypasta every furin cleavage site in the database into a GOF library and surprise surprise the most virulent form that becam…

Can you estimate the entropy of the sequence? Maybe by walking to it from other known sequences?

rough estimate worse than 1 in 3^7 (based on # of wobble codons) but its even lower likelihood if you also allow AA variation in the universe of all furin cleavage sites
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