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Libertarian_Virologist Profile picture
Libertarian_Virologist
@ban_epp_gofroc
Nov 29 • 11 tweets • 4 min read
Just in time for Thanksgiving, Anthony Fauci and @greg_folkers are out with a new paper on the HIV and COVID pandemics—they claim that SARS-CoV-2 is very likely to have a natural origin, citing the deeply flawed work of the Proximal Origins and Friends author group. 🧵 Image Fauci neglects to mention that Worobey et al 2022 (citation 35) has two published rebuttals in the Journal of the Royal Statistical Society Series A that detail its use of flawed statistical methods and data suffering from ascertainment bias. 2/
Oct 12 • 7 tweets • 3 min read
At around minute 46 of the origins panel, Simon Wain-Hobson mentions the Sutton et al 2014 study, which serially passaged H7N1 10 times so that it was capable of airborne spread among ferrets—and found it retained high lethality. 🧵 Image Just when you think they’re done with serial passage, there’s another! And another! And another! 2/
Oct 6 • 13 tweets • 4 min read
The abstract of Pekar et al 2022 says it is likely that lineage A spilled to humans after lineage B. Their simulation results are nowhere close to being statistically significant. The 95% HPD covers -30 to +44 days, the Bayesian equivalent of spotlighting a p-value of 0.7. 🧵 Image The paper says the 95% highest posterior density (HPD) for lineage B is 23-Oct to 8-Dec and for lineage A is 29-Oct to 14-Dec. When the 95% credible intervals overlap to that extent (11 out of 17 days), it would be shocking if a 95% HPD on the difference didn’t contain zero. 2/ Image
Sep 21 • 6 tweets • 3 min read
Most phylogenetic analyses of SARS-CoV-2 found that lineage A with 1 or more ancestral mutations were likeliest candidates for MRCA. Pekar et al 2022 summarily dismisses those results in a single paragraph. Given Pekar’s documented errors, why trust they are correct on this? 🧵 Image MRCA = most recent common ancestor. Here are citations 19-21 in Pekar et al 2022. 2/
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Aug 15 • 5 tweets • 2 min read
Why People Don’t Trust Legacy Media: A 🧵
CNN engages in a moral panic about @elonmusk rolling out largely unconstrained image generating AI, but pretends not to notice when researchers order synthetic DNA that could recreate the 1918 pandemic flu virus.
amp.cnn.com/cnn/2024/08/15… Recreating the 1918 flu virus is a way bigger threat to humanity than creating silly AI images mocking politicians and celebrities. CNN’s reaction to the threat posed by recreating the 1918 flu? 😴 2/ thebulletin.org/2024/06/mit-re…
Jul 7 • 6 tweets • 2 min read
Where did China get key components used in reverse genetics systems (BsmBI, BsaI, pBeloBAC11) and training in how to properly use them? Who gave them hACE2 mice? Who suggested to them lines of research that would result in viruses with all the distinguishing features of SARS2? Metzl deserves a lot of credit for discussing evidence for a lab origin of COVID when few would touch the subject. But he’s clearly got a foot in the political game here and this is pushing him toward an origin story of COVID that is geopolitically convenient.
Jun 26 • 12 tweets • 3 min read
The authors of the raccoon dog preprint and their supporters don’t understand how a correlation coefficient works. A correlation coefficient between reads of animal DNA and SARS2 RNA will not change over time even if both degrade at different rates. A 🧵 Image A hypothesis must generate predictions that can be tested, otherwise it is non-falsifiable. Authors of the raccoon dog preprint claimed that no positive correlation could be found between SARS2 RNA and raccoon dog DNA because environmental testing was done too late… 2/
Jun 7 • 14 tweets • 6 min read
Fauci lied to Congress: A 🧵
- NIH staff reasonably anticipated in advance that EcoHealth’s virus experiments in Wuhan would enhance the pathogenicity or transmissibility of a SARS or MERS-like virus.
- Their experiments then did enhance the pathogenicity of a SARS-like virus. Image NIH staffers Jenny Greer and Erik Stemmy flagged EcoHealth’s proposed research as being subject to the 2014 gain of function moratorium, yet it was quickly allowed to go ahead under bespoke guidelines determined by EcoHealth. 2/
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May 22 • 13 tweets • 5 min read
In 2012, Anthony Fauci anticipated almost the exact situation that very likely led to the COVID pandemic: gain of function research on potential pandemic pathogens done under low biosafety conditions. Fauci knew the risks, knew that the research had no benefits, and proceeded. 🧵 Image Fauci claimed pandemics were more likely to occur in nature and doing gain of function with potential pandemic pathogens could help to prepare for natural pandemics. But even after it was very clear the research didn’t help to prepare for pandemics, Fauci charged ahead. 2/ Image
May 9 • 11 tweets • 4 min read
In his testimony, Ralph Baric claimed that the Wuhan Institute of Virology never developed a working infectious clone of MERS-CoV. The delayed 2019 EcoHealth grant report shows that WIV *DID* generate infectious clones of MERS and chimeras with the MERS backbone. A 🧵 Image Baric probably just didn’t know, given it was not his work. Putting this information together, it seems that WIV attempted to make a reverse genetics system around 2016, failed, sought Baric’s help, and succeeded around mid 2018-19 but did not inform Baric of their success. 2/ Image
Apr 25 • 16 tweets • 4 min read
17 of 19 potential restriction sites in SARS2 that were identified by @gadboit as being removed are exact nucleotide matches to BANAL-52 in those areas. These sites already silently mutated out of SARS2’s closest relatives, so their absence in SARS2 means nothing. A 🧵 Restriction enzyme recognition sequences are irrelevant to natural selection for human and animal viruses. They can appear and disappear as a result of silent mutations, with basically no effect on viral fitness. Closely related viruses may share naturally occurring sites… 2/
Apr 16 • 8 tweets • 2 min read
As @NateSilver538 said, this is why free speech is in trouble. Left and right grow increasingly hostile to any institutions that could challenge their political orthodoxies. Wherever you are politically, you will not enjoy living in a country without free speech. Academia cannot function as a worthwhile societal institution without free thought, free expression, and even the freedom to be wrong. Left and right insist now that the role of universities is ideological indoctrination, combined with punishment and ostracism for wrong ideas.
Mar 18 • 16 tweets • 4 min read
A bootstrap permutation test shows that HSM-linked cases have a different distribution than unlinked cases (using Dec 2019 data from Worobey et al). Worobey et al grants differences in distribution but @gtuckerkellogg suggested they might be (near) identically distributed. A 🧵 Image First, I want to thank @gtuckerkellogg for productively raising this point, which is important to consider. Given that there are more cases unlinked to HSM than linked (120 vs 35) might the seeming difference in distributions be a function of different group sizes? 2/
Feb 12 • 6 tweets • 2 min read
Reference checking request: Peter Miller claims that SARS2 could not have been passaged through hACE2 transgenic mice, claiming that studies that did this showed these mice acquired an N501Y mutation (not seen in original SARS2). Mini 🧵… 1/ Image What’s the source of this claim? Closest I found was Gu et al 2020, which passaged SARS2 through BALB/c mice, which are of course not hACE2 transgenic mice. Fig 3D shows that after 3 passages, over 90% have acquired the N501Y mutation (from A23063T). 2/ncbi.nlm.nih.gov/pmc/articles/P…
Feb 8 • 12 tweets • 2 min read
More Fun with Restriction Sites: another statistic shows that the spacing of BsmBI/BsaI sites in SARS2 is highly uniform and very unlikely to arise by chance. Here we consider the mean absolute difference from uniform. A 🧵 1/ As before, we will normalize the nucleotide locations of restriction sites so that they run from 0 to 1. If we have a genome with 5 restriction sites, a perfectly uniform distribution would be to locate them at 1/6, 2/6, 3/6, 4/6, and 5/6. 2/
Feb 6 • 16 tweets • 4 min read
A Curious Omission: Two independent groups that included LeDuc and Baric designed reverse genetics systems with seamless ligation for SARS2 using BsmBI/BsaI. But neither discussed how these systems needed to be designed around already occurring BsmBI/BsaI sites. A 🧵1/ Both papers read like textbook examples of seamless assembly: a novel CoV is divided up into 7 fragments with BsmBI and BsaI recognition sites with unique overhangs and seamlessly ligated to produce infectious clones. But there’s an interesting detail… 2/