[FRIAM] whackadoodles go mainstream!

[Roger Critchlow]

I found the assertion weak that the simple presence of these previously
unreported sequence features (the binding domain ACE2 specificity, the (I
think) detaching spike adaptation of the glycan collar) in wild type
populations is evidence against purposeful engineering.  Maybe the glimmer
of a natural evolutionary path does absolutely beat any protein engineering
budget that anyone has ever seen, I think that's the gist of the
argument, and if I state it that way I start to believe the argument more.
I found the absence of any protein/gene engineering scaffolding a fairly
persuasive argument, too.  These sorts of manipulations leave lots of
pencil marks in the sequences, marks which you would not waste time erasing
until you were sure you had what you wanted, so if you accidentally
released something that was under development, it would almost certainly
look like something a bunch of monkeys had been hacking at with machetes.

It's funny that the core of conspiracy theory is an unbounded faith in
human ingenuity, and the core of anti-conspiracy theory is experience of
large budgets and clever, motivated people never getting anywhere close to
their goal.

-- rec --

On Mon, Apr 20, 2020 at 7:36 PM uǝlƃ ☣ <gepropella at gmail.com> wrote:

> It's unclear to me whether we'd expect the virus to evolve faster or
> slower, depending on where it "originated". It seems to me that if it first
> appeared in a species that was dissimilar, then when it finally landed in a
> more optimal host type, it would evolve quickly (at least in non-critical
> regions) to thrive in that host type. On the other hand, if it lands in an
> almost already optimal host type, then it shouldn't evolve much at all. And
> only if it's under some sort of pressure to evolve (e.g. the immune system)
> would it do so quickly.
>
> What *would* you people who can read all this stuff *expect* to happen?
>
> On 4/20/20 3:57 PM, Marcus Daniels wrote:
> > As a ballpark the receptor binding domain is 211 residues, so 20^211,
> however only a small part of it seems to be actively evolving. [1]  (see
> Table 1)
> >
> > https://www.biorxiv.org/content/10.1101/2020.03.10.986398v1
> >
> > *From: *Friam <friam-bounces at redfish.com> on behalf of David Eric Smith
> <desmith at santafe.edu>
> > *Reply-To: *The Friday Morning Applied Complexity Coffee Group <
> friam at redfish.com>
> > *Date: *Monday, April 20, 2020 at 3:49 PM
> > *To: *The Friday Morning Applied Complexity Coffee Group <
> friam at redfish.com>
> > *Subject: *Re: [FRIAM] whackadoodles go mainstream!
> >
> >
> https://www.nature.com/articles/s41591-020-0820-9?fbclid=IwAR1vyx1SqreXoeVgFVKBIayEWGOgZn5IbXmx3-V4nsrWiIlrYvYHQW2TuLA
>
> >
> > There is discussion in here about the kind of mosaic it is, and the
> nearest identified variants for different parts.  I find this interesting
> as a question in evolutionary dynamics of either convergence or
> recombination.  The question of how “hard” an engineering problem it is to
> find non-local optimizers for various biding problems if you happen not to
> have templates in the same basin of attraction is an interesting question
> to me in methods of protein biochemistry.  The question of what level of
> sophistication we currently imagine is in use around the world is a
> potentially interesting question of sophistication versus availability of
> method, also practical if one works in threat defenses.
>
> --
> ☣ uǝlƃ
>
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