Michael Weissman
@mbweissman.bsky.social
I had fun. "For a general power-law prior r_0(x) proportional to x^-a with a in the range a<3 for which divergences are not problemtic P(D=2)=(4-a)(3-a)/2^(6-a). The maximum is obtained for a = (7*ln(2)-2-(4+ln(2)2)0.5/(2*ln(2)) = 0.53 which gives P(D=2) = 0.193."The other big correction is x0.182.
November 11, 2025 at 2:29 PM
I had fun. "For a general power-law prior r_0(x) proportional to x^-a with a in the range a<3 for which divergences are not problemtic P(D=2)=(4-a)(3-a)/2^(6-a). The maximum is obtained for a = (7*ln(2)-2-(4+ln(2)2)0.5/(2*ln(2)) = 0.53 which gives P(D=2) = 0.193."The other big correction is x0.182.
Wait- that's all stuff from Pekar 2022, the paper with enormous math errors that you just said was irrelevant. When those errors are fixed, its 2-spill probability becomes low, which undercuts its whole story. Tho P(other zoo stories) is unaffected by market-story errors.
November 3, 2025 at 11:30 PM
Wait- that's all stuff from Pekar 2022, the paper with enormous math errors that you just said was irrelevant. When those errors are fixed, its 2-spill probability becomes low, which undercuts its whole story. Tho P(other zoo stories) is unaffected by market-story errors.
But I see that my "before" was an overstatement. I will change it to "around the time". Thanks, these tweaks are improvements.
November 3, 2025 at 11:21 PM
But I see that my "before" was an overstatement. I will change it to "around the time". Thanks, these tweaks are improvements.
The claim some (A+another mut) variants are ruled out as possible MRCAs.
Nobody seems to think that any version of B is a candidate for MRCA, tho that doesn't rule out the possibility of a separate spill.
Nobody seems to think that any version of B is a candidate for MRCA, tho that doesn't rule out the possibility of a separate spill.
November 3, 2025 at 11:11 PM
The claim some (A+another mut) variants are ruled out as possible MRCAs.
Nobody seems to think that any version of B is a candidate for MRCA, tho that doesn't rule out the possibility of a separate spill.
Nobody seems to think that any version of B is a candidate for MRCA, tho that doesn't rule out the possibility of a separate spill.
Of course I've read that, and Bloom's response:
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree
Abstract. Several years ago, I published a paper that described the discrepancy between outgroup and date-based methods for rooting the SARS-CoV-2 phylogen
academic.oup.com
November 3, 2025 at 11:06 PM
Of course I've read that, and Bloom's response:
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
Here's my summary of the specific market-related evidence. No "A" cases were found in the market, giving a minor factor weighing against the specific market story, though not against general zoonosis.
michaelweissman.substack.com/i/142625697/...
michaelweissman.substack.com/i/142625697/...
An Inconvenient Probability v5.11
Bayesian analysis of the probable origins of Covid. Quantifying "friggin' likely"
michaelweissman.substack.com
November 3, 2025 at 10:59 PM
Here's my summary of the specific market-related evidence. No "A" cases were found in the market, giving a minor factor weighing against the specific market story, though not against general zoonosis.
michaelweissman.substack.com/i/142625697/...
michaelweissman.substack.com/i/142625697/...
That A looks more ancestral is universally agreed upon. That it was spreading widely early on is based on the Bloom paper. academic.oup.com/mbe/article/...
November 3, 2025 at 10:53 PM
That A looks more ancestral is universally agreed upon. That it was spreading widely early on is based on the Bloom paper. academic.oup.com/mbe/article/...
I have made it clear from the start that I don't know how many spillovers happened and don't think it's very relevant. A reason to think that 1 is more probable than 2 is that it is implied by the Pekar 2022 model, once its indisputable math errors are fixed.
November 3, 2025 at 10:49 PM
I have made it clear from the start that I don't know how many spillovers happened and don't think it's very relevant. A reason to think that 1 is more probable than 2 is that it is implied by the Pekar 2022 model, once its indisputable math errors are fixed.
"early" means without further downstream mutations.
November 3, 2025 at 10:47 PM
"early" means without further downstream mutations.
Why does NE Biolabs say "The advantage of using Type IIS enzymes for assembly is that the recognition sequence can be placed in the primer on either side of the cleavage site. If placed inside, 3′ to the cleaved end, it will be retained in the construct and can subsequently be reused. " ?
November 3, 2025 at 9:18 PM
Why does NE Biolabs say "The advantage of using Type IIS enzymes for assembly is that the recognition sequence can be placed in the primer on either side of the cleavage site. If placed inside, 3′ to the cleaved end, it will be retained in the construct and can subsequently be reused. " ?
The hypothesized reason for the pre-existing one would have been for convenience in repeatedly swapping in some new segments, 3-5 clones/year. Wouldn't that create different cost/benefit for RE patterns than would other uses?
November 3, 2025 at 9:02 PM
The hypothesized reason for the pre-existing one would have been for convenience in repeatedly swapping in some new segments, 3-5 clones/year. Wouldn't that create different cost/benefit for RE patterns than would other uses?
Lots of things are "empirically zero", e.g. P(FCS at S1/S2| natural sarbecovirus). Or any P(highly detailed properties| some standard hypothesis). For new situations one needs a reasonable subjective estimate of P.
November 3, 2025 at 8:55 PM
Lots of things are "empirically zero", e.g. P(FCS at S1/S2| natural sarbecovirus). Or any P(highly detailed properties| some standard hypothesis). For new situations one needs a reasonable subjective estimate of P.
But that wasn't the recCA you claimed, which already treated its most likely version as 100% probable.
November 3, 2025 at 8:24 PM
But that wasn't the recCA you claimed, which already treated its most likely version as 100% probable.
Not a guess. Gadboit did the sims and the current P(pattern) fits them almost perfectly.
November 3, 2025 at 8:21 PM
Not a guess. Gadboit did the sims and the current P(pattern) fits them almost perfectly.
The theory was that the number was planned. The number was 6 and the plan found later was for 6. The prior wanderings of others are not relevant to my analysis, but the subjective P(leave in|DEFUSE) is. In effect I use ~0.4 for it, but that could get revised downward after more checking.
November 3, 2025 at 8:20 PM
The theory was that the number was planned. The number was 6 and the plan found later was for 6. The prior wanderings of others are not relevant to my analysis, but the subjective P(leave in|DEFUSE) is. In effect I use ~0.4 for it, but that could get revised downward after more checking.
Assuming that hypothetical ancestor also differed by ~400 nt, I'd say P(pattern|ancestor)=~0.43. That would beat or about tie engineering estimates.
If...
If...
November 3, 2025 at 8:01 PM
Assuming that hypothetical ancestor also differed by ~400 nt, I'd say P(pattern|ancestor)=~0.43. That would beat or about tie engineering estimates.
If...
If...
No. Even your recCA is off at one site, and the ~400 syn muts needed to get from it to SC2 have ~2.8% chance of getting it to the (6, <8k) criterion. Not negligible but still kind of low, depending on the competing hypothesis.
November 3, 2025 at 7:55 PM
No. Even your recCA is off at one site, and the ~400 syn muts needed to get from it to SC2 have ~2.8% chance of getting it to the (6, <8k) criterion. Not negligible but still kind of low, depending on the competing hypothesis.
Prophetic cherry picking: called the multiple clones plan, 6 segments, BsmBI. Not ex post facto.
November 3, 2025 at 7:42 PM
Prophetic cherry picking: called the multiple clones plan, 6 segments, BsmBI. Not ex post facto.
probability for actual existing "dogs":
RpYN06: 3/32000 0.009375%
BtSY2: 58/32000 0.1812%
BANAL-20-236: 69/32000 0.2156%
BANAL-20-52: 52/32000 0.1625%
BANAL-20-103: 386/32000 1.206%
RaTG13: 94/32000 0.2938%
and ChimericAncestor: 210/32000 0.6562%
your possible ancestor 888/32000 2.775%
RpYN06: 3/32000 0.009375%
BtSY2: 58/32000 0.1812%
BANAL-20-236: 69/32000 0.2156%
BANAL-20-52: 52/32000 0.1625%
BANAL-20-103: 386/32000 1.206%
RaTG13: 94/32000 0.2938%
and ChimericAncestor: 210/32000 0.6562%
your possible ancestor 888/32000 2.775%
November 3, 2025 at 7:37 PM
probability for actual existing "dogs":
RpYN06: 3/32000 0.009375%
BtSY2: 58/32000 0.1812%
BANAL-20-236: 69/32000 0.2156%
BANAL-20-52: 52/32000 0.1625%
BANAL-20-103: 386/32000 1.206%
RaTG13: 94/32000 0.2938%
and ChimericAncestor: 210/32000 0.6562%
your possible ancestor 888/32000 2.775%
RpYN06: 3/32000 0.009375%
BtSY2: 58/32000 0.1812%
BANAL-20-236: 69/32000 0.2156%
BANAL-20-52: 52/32000 0.1625%
BANAL-20-103: 386/32000 1.206%
RaTG13: 94/32000 0.2938%
and ChimericAncestor: 210/32000 0.6562%
your possible ancestor 888/32000 2.775%
This trait is transparent to selection, unlike e.g. FCS.
November 3, 2025 at 7:34 PM
This trait is transparent to selection, unlike e.g. FCS.
They corrected 3 coding errors under pressure. They have not corrected the main two remaining errors, which would reverse their conclusion. These are not subjective errors but straight math.
November 3, 2025 at 7:12 PM
They corrected 3 coding errors under pressure. They have not corrected the main two remaining errors, which would reverse their conclusion. These are not subjective errors but straight math.
Unlike the more subjective P(pattern|DEFUSE) it's easier to use stats for P(pattern|Z). Overall for coronaviruses it's 0.15%. With your generous assumptions re recCA, it could go up to 2.8%.
November 3, 2025 at 7:07 PM
Unlike the more subjective P(pattern|DEFUSE) it's easier to use stats for P(pattern|Z). Overall for coronaviruses it's 0.15%. With your generous assumptions re recCA, it could go up to 2.8%.
If I understand, those sites were added but then removed by the cuts, different from the leave-sites-in procedure. That's relevant but doesn't tell us whether for many serial partial replacements leaving sites in would be convenient. Hard to get an unbiased answer ex post facto.
November 3, 2025 at 7:01 PM
If I understand, those sites were added but then removed by the cuts, different from the leave-sites-in procedure. That's relevant but doesn't tell us whether for many serial partial replacements leaving sites in would be convenient. Hard to get an unbiased answer ex post facto.
By that token anything by anyone who cites anything by any of the 29 authors of Pekar et al. 2022 would have to be presumed false. Let's stick to the specific points. Here the only relevant one is whether leaving RE sites in eases making a series of partial new clones.
November 3, 2025 at 6:48 PM
By that token anything by anyone who cites anything by any of the 29 authors of Pekar et al. 2022 would have to be presumed false. Let's stick to the specific points. Here the only relevant one is whether leaving RE sites in eases making a series of partial new clones.