It's strange that Scott has trouble comparing his factors and mine since I posted a translation as a comment on his previous "book review".
Here's a slightly simplified and improved repeat of that comment.
Net priors using Scott's grouping + Scott's "reason's WIV wouldn't do it".
Scott 2.7 MBW 12 before integration of uncertainty, 5.4 after integrating
combo of all HSM/lineage factors (Worobey/Pekar)
Scott 0.002 MBW 1
FCS-ish
Scott 25 MBW 25
cover up success
Scott 0.5 MBW: did it?
other factor: restriction enzyme pattern
Scott NA MBW 70
So really it all comes down to Worobey/Pekar, plus the surprising new FOIA find that the DEFUSERS were planning just the restriction enzyme pattern that Bruttel et al. had noticed.
Does Scott ( or anyone) really believe that there's about one chance in a thousand that the Worobey data are messed up? That there's 99.9% probability that George Gao, the official WHO summary on market linkage, Bloom, Kumar, Samsone, Lv... are all wrong? If Scott allowed any reasonable chance that they were right, then his odds would favor LL.
The "DEFUSERS" quite obviously weren't planning that since one of them published a SARS2 reverse genetics system that does not use those restriction sites because they are not actually convenient at all -- https://www.cell.com/cell/fulltext/S0092-8674(20)30675-9
Just plug the SARS2 genome in and look at the restriction map yourself. Try to find precedent for the shortest fragment. The closest you will get from papers referenced by Bruttel et al, and it's not that close, is a fragment that's only as short as it is because a longer fragment made for an unstable plasmid and it was cut in two. Then just look at where the enzymes cut and try to rationalize that with any experimental plan. And, of course, the restrictions sites (and the missing sites) are exactly what's expected based on sequences around the restriction sites and genomes of related viruses. The expectation of engineered sites is exactly the opposite.
The bit you think is relevant in the "new FOIA" has never been described accurately in the media to my knowledge. It is a sample budget sent to a lab in the USA to help prepare their budget. The same budget comes from North Carolina. It happens to include two items for a restriction enzyme to be replaced with whatever the other lab planned to buy. But... no evidence is needed that folks at WIV do reverse genetics with BsaI and BsmBI! No FOIA needed; it was published in 2017 https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006698 -- it's just simply not evidence of anything and even if it were true it would not be evidence that adds information; one of the many blips of made up evidence that reveals the lack of supporting evidence for lab leak.
The paper in PLOS is the latest one. Just look at the dates in Figure 3A -- that's where the August 2019 date that keeps getting thrown around comes from -- "estimating the divergence time of SARS-CoV-2 at around 2019.58, which corresponds to August 2019" -- what is SARS-CoV-2 diverging from in August 2019 in that picture?
"It" is the giant file of DEFUSE drafts and related communication.
The relevant text: "The genome of consensus candidates will be synthesized commercially (e.g. BioBasic), as six contiguous cDNA pieces linked by unique restriction endonuclease sites for full length genome assembly. Full length genomes will be transcribed into genome-length RNA and electroporation used to recover recombinant viruses (22,62)."
Both refs 22 and 62 use BglI which cleaves GCCNNNN↓NGGC necessarily retaining the restriction site in the assembled product. This is not necessary for BsaI or BsmBI -- no reason to add any sites ever.
Seriously just plug the sequence into https://nc3.neb.com/NEBcutter/ or similar, look at the BsaI/BsmBI digest, and wonder why you've never heard how short the shortest fragment is before.
The number of segments and that each is less than 8knt are obvious engineering constraints and show a clear pattern in synthetic viruses. Having one short segment or not doesn't fall in that category. The BsaI/BsmBI combination was used previously by WIV and by Baric.
You do understand that by pushing hard to be conservative I used only 0.2 probability that LL would show this pattern, because some other choices were possible if less likely. Also by pushing hard to be conservative I used a much higher probability under ZW than the early simulations gave, 0.002 rather than 0.0004. Then I systematically discounted for uncertainty, ending up with a ratio of 70 rather than 100. I can imagine an ultra-conservative calculation getting down to 20, but not further.
Ok it’s clear you aren’t interested in checking the length of the shortest fragment. It’s more anomalously short for engineered viruses than the longest fragment is anomalously short for natural viruses. It’s not mentioned in Bruttel et al because it’s contradictory evidence to their hypothesis and they cherry pick analysis of longest fragment length. One of the cut sites is in the middle of S2 iirc for no reason.
The odds are near 1 that a natural virus with SARS2 genome outside of these sites will have these sites or very close to it.
At this point Bruttel et al will start to say “consensus genome” but they do not know or pretend not to know what “consensus genome” means in this context. A consensus genome of genomes that differ this much is a genome that won’t cause a pandemic.
“Consensus genome” in DEFUSE means resolving differences of a handful of nucleotides in genomes sampled at about the same time and place.
"The odds are near 1 that a natural virus with SARS2 genome outside of these sites will have these sites or very close to it." That's just flat wrong, by orders of magnitude. I go through 4 distinct ways of estimating this chance and none give any number near one. One unused variant urged by a zoonatus gave zero/64k.
An LL advocate has confidently explained that the one very short segment between the last BsaI site and the first BsmBI site is a needed engineering feature due to issues with double digestions, important for re-use. You say that no one would use it for some unspecified reason. At that level of ultra-detail Texas sharpshooters can draw targets around the data and reverse Texas sharpshooters can draw targets away from the data forever. I try to stick to the basics where you know the data and the model well enough to not have to argue whether the likelihood ratio is 100/1 or 1/100 depending on which motivated argument you're listening to.
For the record, I messaged you and asked you to summarize your factors, before Scott's first blog post, so that your work could be part of the discussion.
You refused to make a summary and said that I needed to instead read every blog post that you've written and find any relevant numbers.
As such, you ended up a footnote to Scott's posts. That was entirely your choice.
No, not really. Scott wrote a blog post and sent it to Saar and I before posting, for feedback and comments.
In the draft post, Scott had already made a table comparing the odds everyone gave, as well as his own numbers. I had already made my own table comparing the odds everyone gave in the debate:
The way Scott and I set up the priors was different, though -- Scott wanted to start with a global prior on lab leaks, the same way that Rootclaim did in the week 1 debate. I objected to this for various reasons, one of the main ones being that neither of the judges used a global prior on lab leaks, so you would basically just have to make up a number for them.
After some arguing, Scott did change his table so the priors were set up somewhere between what I did and what he did (without making any other changes).
The part about Michael was kinda separate. Since Scott chose to include one debate viewer's analysis, I thought it could be interesting to include some other pro-lab leak bayesian analyses like Michael's. I would have either added his to my spreadsheet or sent it to Scott and maybe he would include it. But I didn't get a helpful response from Michael so I scrapped that idea.
Sounds like Scott wasn't that interested in reading all of Michael's blog posts and figuring out his latest theories either.
It's strange that Scott has trouble comparing his factors and mine since I posted a translation as a comment on his previous "book review".
Here's a slightly simplified and improved repeat of that comment.
Net priors using Scott's grouping + Scott's "reason's WIV wouldn't do it".
Scott 2.7 MBW 12 before integration of uncertainty, 5.4 after integrating
combo of all HSM/lineage factors (Worobey/Pekar)
Scott 0.002 MBW 1
FCS-ish
Scott 25 MBW 25
cover up success
Scott 0.5 MBW: did it?
other factor: restriction enzyme pattern
Scott NA MBW 70
So really it all comes down to Worobey/Pekar, plus the surprising new FOIA find that the DEFUSERS were planning just the restriction enzyme pattern that Bruttel et al. had noticed.
Does Scott ( or anyone) really believe that there's about one chance in a thousand that the Worobey data are messed up? That there's 99.9% probability that George Gao, the official WHO summary on market linkage, Bloom, Kumar, Samsone, Lv... are all wrong? If Scott allowed any reasonable chance that they were right, then his odds would favor LL.
The "DEFUSERS" quite obviously weren't planning that since one of them published a SARS2 reverse genetics system that does not use those restriction sites because they are not actually convenient at all -- https://www.cell.com/cell/fulltext/S0092-8674(20)30675-9
Just plug the SARS2 genome in and look at the restriction map yourself. Try to find precedent for the shortest fragment. The closest you will get from papers referenced by Bruttel et al, and it's not that close, is a fragment that's only as short as it is because a longer fragment made for an unstable plasmid and it was cut in two. Then just look at where the enzymes cut and try to rationalize that with any experimental plan. And, of course, the restrictions sites (and the missing sites) are exactly what's expected based on sequences around the restriction sites and genomes of related viruses. The expectation of engineered sites is exactly the opposite.
The bit you think is relevant in the "new FOIA" has never been described accurately in the media to my knowledge. It is a sample budget sent to a lab in the USA to help prepare their budget. The same budget comes from North Carolina. It happens to include two items for a restriction enzyme to be replaced with whatever the other lab planned to buy. But... no evidence is needed that folks at WIV do reverse genetics with BsaI and BsmBI! No FOIA needed; it was published in 2017 https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006698 -- it's just simply not evidence of anything and even if it were true it would not be evidence that adds information; one of the many blips of made up evidence that reveals the lack of supporting evidence for lab leak.
The paper in PLOS is the latest one. Just look at the dates in Figure 3A -- that's where the August 2019 date that keeps getting thrown around comes from -- "estimating the divergence time of SARS-CoV-2 at around 2019.58, which corresponds to August 2019" -- what is SARS-CoV-2 diverging from in August 2019 in that picture?
Zach- It specified using 6 segments in a way that would allow repeated swaps, i.e. leaving the sites in. Be honest.
"It" is the giant file of DEFUSE drafts and related communication.
The relevant text: "The genome of consensus candidates will be synthesized commercially (e.g. BioBasic), as six contiguous cDNA pieces linked by unique restriction endonuclease sites for full length genome assembly. Full length genomes will be transcribed into genome-length RNA and electroporation used to recover recombinant viruses (22,62)."
Both refs 22 and 62 use BglI which cleaves GCCNNNN↓NGGC necessarily retaining the restriction site in the assembled product. This is not necessary for BsaI or BsmBI -- no reason to add any sites ever.
Seriously just plug the sequence into https://nc3.neb.com/NEBcutter/ or similar, look at the BsaI/BsmBI digest, and wonder why you've never heard how short the shortest fragment is before.
The number of segments and that each is less than 8knt are obvious engineering constraints and show a clear pattern in synthetic viruses. Having one short segment or not doesn't fall in that category. The BsaI/BsmBI combination was used previously by WIV and by Baric.
You do understand that by pushing hard to be conservative I used only 0.2 probability that LL would show this pattern, because some other choices were possible if less likely. Also by pushing hard to be conservative I used a much higher probability under ZW than the early simulations gave, 0.002 rather than 0.0004. Then I systematically discounted for uncertainty, ending up with a ratio of 70 rather than 100. I can imagine an ultra-conservative calculation getting down to 20, but not further.
Ok it’s clear you aren’t interested in checking the length of the shortest fragment. It’s more anomalously short for engineered viruses than the longest fragment is anomalously short for natural viruses. It’s not mentioned in Bruttel et al because it’s contradictory evidence to their hypothesis and they cherry pick analysis of longest fragment length. One of the cut sites is in the middle of S2 iirc for no reason.
The odds are near 1 that a natural virus with SARS2 genome outside of these sites will have these sites or very close to it.
At this point Bruttel et al will start to say “consensus genome” but they do not know or pretend not to know what “consensus genome” means in this context. A consensus genome of genomes that differ this much is a genome that won’t cause a pandemic.
“Consensus genome” in DEFUSE means resolving differences of a handful of nucleotides in genomes sampled at about the same time and place.
"The odds are near 1 that a natural virus with SARS2 genome outside of these sites will have these sites or very close to it." That's just flat wrong, by orders of magnitude. I go through 4 distinct ways of estimating this chance and none give any number near one. One unused variant urged by a zoonatus gave zero/64k.
An LL advocate has confidently explained that the one very short segment between the last BsaI site and the first BsmBI site is a needed engineering feature due to issues with double digestions, important for re-use. You say that no one would use it for some unspecified reason. At that level of ultra-detail Texas sharpshooters can draw targets around the data and reverse Texas sharpshooters can draw targets away from the data forever. I try to stick to the basics where you know the data and the model well enough to not have to argue whether the likelihood ratio is 100/1 or 1/100 depending on which motivated argument you're listening to.
For the record, I messaged you and asked you to summarize your factors, before Scott's first blog post, so that your work could be part of the discussion.
You refused to make a summary and said that I needed to instead read every blog post that you've written and find any relevant numbers.
As such, you ended up a footnote to Scott's posts. That was entirely your choice.
Bullshit. I said just scan down the latest version for the logits that were all in bold face as stand-alone lines.
Scanning through the text from start to the first Appendix is fast with a track pad. The slow way, with a down arrow, took 80 seconds.
Peter, the way you phrase this suggests that Scott delegated this part of the research to you. Is that right?
No, not really. Scott wrote a blog post and sent it to Saar and I before posting, for feedback and comments.
In the draft post, Scott had already made a table comparing the odds everyone gave, as well as his own numbers. I had already made my own table comparing the odds everyone gave in the debate:
https://docs.google.com/spreadsheets/d/1LG2-Ir5Bl2sU0_USYV-IlfafrrQMWbNr/edit?usp=drive_link&ouid=107312989181202525546&rtpof=true&sd=true
The way Scott and I set up the priors was different, though -- Scott wanted to start with a global prior on lab leaks, the same way that Rootclaim did in the week 1 debate. I objected to this for various reasons, one of the main ones being that neither of the judges used a global prior on lab leaks, so you would basically just have to make up a number for them.
After some arguing, Scott did change his table so the priors were set up somewhere between what I did and what he did (without making any other changes).
The part about Michael was kinda separate. Since Scott chose to include one debate viewer's analysis, I thought it could be interesting to include some other pro-lab leak bayesian analyses like Michael's. I would have either added his to my spreadsheet or sent it to Scott and maybe he would include it. But I didn't get a helpful response from Michael so I scrapped that idea.
Sounds like Scott wasn't that interested in reading all of Michael's blog posts and figuring out his latest theories either.
That makes more sense, thanks.