Private channel session 1716
19 messages over 39m, 2022-01-27 – 2022-01-27.
A “conversation” here is an activity session — a run of messages with under 60 minutes of silence inside it. The channel had no native conversation boundaries.
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SLACK_001292 Hi all. Just been looking at some snippets of DQ's book. Looks good - my only quibble (other than calling the sequence file format a 'fasterfile') is with the timeline of the pangolin genome with the RBD in it. DQ says: > "What the email shows," Andersen said later, on Twitter, in response to criticisms, "is a clear example of the scientific process.[i] They were considering possibilities, lab leak included, engineered virus included, natural spillover included, and they hungered for more data that might support or negate one or another. "It's just science.Boring, I know," Andersen wrote, "but it's quite a helpful thing to have in times of uncertainty."[ii] Three weeks passed, without resolution, carrying the effort into late February. Then came the pangolins.We had the first pangolin sequence very early Feb (it was posted on virological on 31st Jan) and then Tommy's one very shortly after. So the pango RBD was in our very early drafts. And of course we posted the thing to Virologicalon the 17th Feb. Worth correcting him?
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nope not responding Nerozzi, Timothy Le &<: Thu 1/27/2022 9:38 PM To: * Garry, Robert F External Sender. Be aware of links, attachments and requests. Dr. Garry, My name is Timothy Nerozzi, and I am a writer for Fox News Digital. I am writing to ask you about a conference ofvirologists convened by Dr. Anthony Fauci in the early days of the pandemic, and subsequent information releasedby the White House.To my understanding, early into the pandemic, numerous experts stated that a man-made virus, somehow leaked from a virology lab, was the simplest and most rational explanation for the begins of the pandemic. Notes from the meeting in question show that a lab leak hypothesis was criticized as a danger to "international harmony."Flashing forward, we are only now reaching a point where suggestions of man-made viruses are no longer beingtreated as conspiratorial.Do you believe that the Biden administration, NIH, CDC, or any other national or international organizationintentionally obscured or suppressed facts relating to the coronavirus pandemic from the public? Any comment or insight you can give me would be very much appreciated.Regards.Timothy H.J. Nerozzi, FRSAWriter, Fox News DigitalThis message and its attachments may contain legally privileged or confidential information. It is intended solely for the named addressee(s). If you are not an addressee indicated in this message (or responsible for delivery of the message to an addressee), you may not copy or deliver this message or its attachments to anyone. Rather, you should permanently delete this message and its attachments and kindly notify the sender by reply e-mail. Any content of this message and its attachments that does not relate to the official business of Fox Corporation, or itssubsidiaries must be taken not to have been sent or endorsed by any of them. No representation is made that this email or its attachments are without defect.
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Bob, might be worth a simple response. "No, I do not believe that origin theories were obscured or suppressed. I can categorically say that for the work I have been involved with - including the conference call you refer to - such suggestions are false".
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Just received the same email...
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@Andrew Rambaut - yes, worth pointing out the Pangolin "evolution". Here's what I said to DQ in an email: Definitely looking forward to reading the whole book!! Once I'm out of grant hell (two more weeks), I'd be delighted toread through it if that's helpful. It's actually interesting reading through the old version of the version of Proximal (via the wayback machine - the current version on Virological is the most recent) to compare it to the final version in Nature Medicine. It's pretty clear that we still considered the "passage" (hypothesis 3) quite plausible at the time - and we had failed to realize the real importance of the pangolin RBD. Fascinating seeing the process of science through this document - even if it's myown :wink:.
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"we had failed to realize the real importance of the pangolin RBD" That bit is pretty key.
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Yes - the 7th Feb version on google docs (basically the 'report') doesn't have pangolins in the alignment.
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No - we didn't use the pangolin genomes initially because they were so fragmented.
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OK. Good. More evidence of science being done
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From the 8th Feb version on GoogleDocs: > Although RaTG13 remains the closest relative to 2019-nCoV across the genome as a whole, the Malayan pangolin CoVs are identical to 2019-nCoV at all six key RBD residues. Analyses of these pangolin viruses are ongoing, although they do not carry the furin cleavage site insertion.
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I think the key for me was when one of us pointed out that "if the RBD was natural, then the whole thing is natural." Also we were arguing all sides of this from the get go - the whole o-linked glycan thing which was discussed on theconf call was pointing to natural although I do agree with K that it's as likely as not that that's a common regulatory mechanism for FCS rather than immune evasive - still think that it could possibly have some role there though too -the FCS is a major epitope in other class I fusion proteins in SARS-CoV-2 it isn't AFAIK which is strange.
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And if it is used as a regulatory system there is no way a human designer would know how to do that
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Yeah, but notice our discussion of "passage". The Pangolin RBD _disproves_ that, but we didn't catch that until later- we use the RBD to say "not engineering" but we didn't yet use it to say "not passage". That only came after peer review
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And by disproving - I mean, it disproves that the specific RBD mutations seen in SC2 arose via culture passage, but,of course, it doesn't directly disprove passage itself.
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Thinking of sending this to Fox - because somebody's gotta at least get it on the record... Thoughts? ```Dear Timothy, No, I do not believe that origin theories were obscured or suppressed, although the question has become heavily politicized by lab leak proponents. I can categorically say that for the research I have been involved with, such allegations, including those recently made in a Fox New Special Report, are false. Our scientific investigations -published in scientific journals - have only been driven by scientific enquiry. Any suggestions to the contrary are false. The events you describe date back to the Trump White House, and it is public knowledge that the question of origin was taken up by the White House Office and Science Technology Policy, immediately following early discussions:https://www.nationalacademies.org/news/2020/02/national-academies-provide-rapid-response-to-white-house-on-coronavirus-data-needs#As was the case in early 2020, available evidence point strongly towards a natural emergence of SARS-CoV-2, ashas been the case for other pandemics. Best, Kristian```
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Fauci and Collins made zero edits to out papers - the CREID Grant was written, reviewed and scored prior to the Feb 1 conf call.
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No harm in doing so but it will have zero impact I think.
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@Kristian Andersen Yeah - I agree with that. Will leave DQ's timeline as it is.
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A few edits. I agree - unlikely to have impact, but need it on the record - and I can't see how it would cause additional harm (which would be the reason to _not_ email them back). ```Dear Timothy,No, I do not believe that origin theories were obscured or suppressed, although the question has become heavilypoliticized by lab leak proponents. I can categorically say that for the research I have been involved with, such allegations, including those recently made in a Fox New Special Report, are false. E.g., your report suggested that Drs. Collins and Fauci made edits to our paper - that is false. Your report also suggested we received a grant as a"quid pro quo" - that is also false (and shows a complete lack of understanding of how NIH grants are funded). Further, the grant in question was written, scored, reviewed, and ranked for funding in 2019 - prior to the pandemic. Our scientific investigations - published in peer-reviewed scientific journals - have only been driven by scientificenquiry. Any suggestions to the contrary are false. The events you describe date back to the Trump (not Biden) White House, and it is public knowledge that the question of origin was taken up by the White House Office and Science Technology Policy, immediately following early discussions:https://www.nationalacademies.org/news/2020/02/national-academies-provide-rapid-response-to-white-house-on-coronavirus-data-needs#As was the case in early 2020, available evidence point strongly towards a natural emergence of SARS-CoV-2, ashas been the case for other pandemics. We are continuing our research and have several additional scientific studies forthcoming.Best, Kristian```