Interesting Links for 15-01-2022

[andrewducker]

An interesting take on a simple time management tool

(tags:time )

Covid: Are Scotland and England's isolation rules different?

(tags:scotland england pandemic rules )

Operation Save Big Dog: Boris Johnson draws up plan for officials to quit over partygate so he can keep job

(tags:politics BorisJohnson Pandemic party )

Any geneticists out there able to tell me is this is paranoid nonsense or a reasonable take on COVID?

(tags:genetics Pandemic virus conspiracy )

Old stone toilet reveals Jerusalem's wealthy elite had intestinal parasites

(tags:parasites Israel archeology )

We don't know why, but being in space causes us to destroy our blood

(tags:blood space disease anaemia )

Boris Johnson's 'wine time Fridays' - No10 staff held drinks EVERY week during pandemic

(tags:BorisJohnson Pandemic Party )

How to make friends around the world

(tags:uk history food funny comic )

Some thoughts about the Sue Gray investigation into Johnson's parties

(tags:party Pandemic BorisJohnson investigation )

Countries that have managed to almost completely suppress Covid have difficult choices ahead of them

(tags:Pandemic viaDanielDWilliam )

Comments

Re: Any geneticists out there able to tell me is this is paranoid nonsense or a reasonable take on C

[toothycat]

The sequence he searches for is too short to get anything sensible, in my opinion (research scientist, genetics, but mouse and human, not viruses). And he restricts the search to viruses, claiming that " you really only want to know which virus this motif came from. You’re not really interested if the motif is found in a squid," - but we are, because viruses do pick things up from the species they infect, and they pass them on too. If you don't restrict the search (looking for TNGTKR), you end up with a whole load of different hits from bacteria, and a whole load of different proteins (transmembrane proteins, peptidases, peptide synthases, carbohydrate binding domains etc etc). I think that just points to this being a fairly common motif in a lot of proteins. It certainly isn't the smoking gun he claims. The furin cleavage site he gets so excited about is, according to Wikipedia, identical to that of the feline coronavirus, an alphacoronavirus 1 strain.
Plus, without wanting to be snobby, he makes some odd comments which I wouldn't expect from people who regularly use BLAST and other tools. BLAST is a tool (Basic Local Alignment Search Tool), not a repository. The NCBI nucleotide archive is also not the only repository - EMBL also have one (and from the point of view of a very annoyed sequence submitter, theirs is much better!). That doesn't take away from his arguments, but it does point to someone who either is unfamiliar with or doesn't care about the correct terminology, and that also makes me rather suspicious (and that's before we get onto the "manufactured influenza" thing).
Along the same lines, his comment that "The probability of a specific 5-amino acid sequence arising by random chance on the same basis jumps to 1 in 3.2million" is wrong. Amino acid sequences arise from DNA, and the codons are redundant. And 1 in 3.2million sounds like a lot, but given virus reproduction, I suspect it's not (but I am not a virus geneticist so don't take my word for that). Anwyay, again, this points to someone either not knowing or not thinking about the basics of genetics, which increases the pinch of salt I would take this with.
None of that means that SARS-CoV-2 wasn't made in a lab or leaked from a lab, but I personally don't think it was.

Re: Any geneticists out there able to tell me is this is paranoid nonsense or a reasonable take on C

[channelpenguin]

Awesome! Thanks!

Re: Any geneticists out there able to tell me is this is paranoid nonsense or a reasonable take on C

[andrewducker]

Thank you for that!

Re: Any geneticists out there able to tell me is this is paranoid nonsense or a reasonable take on C

[mtbc]

Oh, goodness, thank you, I'd thught that BLAST, MUSCLE, etc., are the tools and felt schooled for being informed it's actually a repository!

Re: Any geneticists out there able to tell me is this is paranoid nonsense or a reasonable take on C

[calimac]

My knowledge of genetics is not technical, but whenever I see anything of the "chances of random chance are 1 in 3.2 million" type, I'm suspicious.

Re: Any geneticists out there able to tell me is this is paranoid nonsense or a reasonable take on C

[hellofriendsiminthedark]

Wow, this is super interesting, thank you for sharing, andrewducker! I fall into the camp of not knowing enough about genetics and virology to be able to comment on some of the main content, but I think I was able to digest the logic and the argument, like many of the other laypeople in the comments praising the author's breakdown skills.

My understanding of the central thesis is: The SARS-CoV-2 virus has certain HIV-1-like bits that would require an insertion of 20-30 nucleotides away from any known SARS variant. Such a configuration of a SARS virus has never been seen before in the BLAST database except for one research virus which is a 100% match on certain bits to the SARS-CoV-2 virus. This is supposedly so improbable to occur naturally that it's more probably that it was artificially spliced that way in a lab.

What stands out to me is that none of the probabilities given in the blog post exceed an order of magnitude higher than 1 in 1 billion. But fallacies of probabilistic scale tell us that given sufficiently large pool, even extremely rare outcomes will happen. Given the difference in magnitude between 1 billion and [the number of living cells on the globe from any type of life], I find it hard to believe that this is really as improbable as the author says it is. And without that critical piece of reasoning, the entire conjecture comes crumbling down.

There's also the fact that entries in the database have to be sequenced and subsequently uploaded, right? So by nature, if some weird viral mutation happens in nature by sheer chance while also not infecting humans, how likely is it for that virus to be identified, located, sequenced, and added? Databases are only as pieces they contain, and considering how there are whole macroorganisms that science fails to formally "discover" every day, I feel like it would make sense that not only are quite a lot of viral mutations are passing researchers by all the time, but also that those mutations are compounding constantly to create more and more statistically improbably deviances from existing human knowledge.

One commenter does manage to ask about this. In my opinion, the author's response is a lot of bunk (derailing to be conspiratorial about incomplete data from Wuhan's viral database), so I don't feel the need to give i the time of day, but another party did attempt to explain it:

Isn't this assuming the BLAST database is complete? There must be less than 1% of all wild viruses on there and the rest haven't been discovered yet. Doesn't this whole hypothesis about it not being wild rely on this?

I could be wrong, but yes, it does depend on all relevant viruses being in the database, but those other viruses would also require certain nt / protein sequences, that all appear in certain other virus / patented (ie synthesized) sequences, with the same probability of random mutation matching 100% at each segment as outlined here.

All you are doing is kicking the impossible probability can down the road, it's still impossible or at the very least highly, highly improbable.

It would power the Heart of Gold easily.

The idea that lab are synthesizing new nucleotide sequences at the same probability as nature seems... unlikely to be correct, in my opinion. It's such a weird claim to make.

In my opinion, it also dodges the question. If the answer is that yes, the BLAST database's inherent incompleteness creates doubt about the likelihood of a certain sequence happening, then... that's a meaningful critique of the very logic that the conjecture is founded upon. "Kicking the impossible probability can down the road" sounds to me like handwave-y conspiracy theorist "eh, trust me, it makes sense somehow."

But there's also the fact that... yes? If the logic is that we should already know about possible viral configurations in advance of them appearing in the wild, then wouldn't that explain why the listed HIV-1 virus in the database predates SARS-CoV-2? Wouldn't that explain the whole Moderna patent quite reasonably, without the need for extra conjecture about Moderna infecting the globe and trying to cash in on a novel vaccine?

It's not unusual that the HIV-1 virus the author identifies matches SARS-CoV-2 100% along one segment--the whole point of the database is that it shows how different viruses match each other. Is it unusual for that HIV-1 virus to match along four segments? Well... I don't know, that's waaay too far outside of my scope. The author even poses this as a rhetorical question and then, critically, fails to answer it. (Bolding is original to the blog post.)

What are the odds that HIV-1 would pop up in all 3 searches?

So, there we have 4 matches to HIV sequences with no other viruses* appearing in all 4 match lists (*barring synthetic ones created after the event). What are the odds of that - close to zero.

The final flimsy point that I see to the "improbability" argument is this part, written by the author within the main text:

In other words, no virus in existence has this genetic sequence. Well this is strange, because in order for a virus to acquire a large sequence like this it has to get it from another organism. It has no lab to manipulate gene sequences, neither do the bats (hence Jikky the lab mouse’s little joke)…

As far as I'm aware, That's Not How That Works. I don't think viruses need labs in order to manipulate their gene sequences. I don't think animals need labs in order to carry novel viral strains. I'm also pretty sure that the whole "we got it from bats" things has been debunked on-and-off some number of times by now, and I think that even if first contact to humans happened through bats, that the virus's genetic manipulations didn't necessarily have to happen in bats. Without going into some of the wild tin foil hat stuff that the author get into in the comments, this strikes me as an very "conspiracy theory" element of the main argument, which is simply not a good look for somebody trying to make a scientifically-founded case.

That and the Moderna conspiracy leg. Which makes no sense to me for the simple reason that an mRNA vaccine is so cutting-edge to begin with that if Moderna wanted credit for it, they could have simply said "we made this virus in a lab and made a vaccine for it" and it would have been a huge sensation, even without the need to infect the global population. Or they could have skipped the novel virus entirely and worked on HIV. I get that vaccines=money, but surely there are much less convoluted outlets for obtaining profit.