However, despite not fully understanding your article due to lack of some knowledge, I would like to say that likely, Ba.1 specifically was directly edited, and did NOT appear as a result of lab passage.
The reason is an extreme lack of synonymous mutations. Any kind of genuine evolution would produce synonymous mutations on top of non-synonymous mutations because evolution is driven by random mutations.
Also trying to put "dates" on directly edited virus genomes makes little sense.
I agree with you on Ethical Skeptic.
What do you think?
(I am not saying that Ba.2 is different, I just did not look at it).
It depends to some extent on how extreme the selection pressure is. Now that we have BA.2 to provide a "snapshot" halfway through the evolution of both, we can see that both show signs of extreme pressure in three different directions (one shared for the first half, than one for BA.1 and one for BA.2 separately for the second half). I really need to add illustrations for the mutation skew because it is very stark. I should have those up by tomorrow.
But otherwise, yes, for BA.1 especially it seems like passage wasn't the whole story.
But BA.2 actually brings a load of unique synonymous mutations (7/16 Syn/Total) in Orf1 (again illustrations would look really impressive here). So for my "fictional" story, I gave BA.2 a somewhat substantial passage period as a co-infector with pressure for random changes in Orf1, and BA.1 an accidental recombination make-over (BA.2 does not have BA.1's crazy NTD deletions and inserts). It's just one way of many to imagine things played out.
I'll probably have a revised origin theory after I finish my "why the BA.1 spike can't use fusion" theory.
Seems likely. Or, again, it could have had something to do with a deadline-rushed recombination, maybe an attempted insertion of a "cleaner" Orf1 while keeping the mutated spike, who knows.
Very much appreciated the "story hour version" i.e not smarter than a pre pandemic fifth grader. I am trying. Could you try a kindergarten version next time...big words and a cute drawing on every page. :)
Feb 23, 2022·edited Feb 23, 2022Liked by Brian Mowrey
For the layman just start at 'What Could Go Wrong'. Wicked description! Loved it. Feedback loops are hard, EVOLUTIONARY feedback loops now good luck debugging that one X)
That paragraph created enough intrigue to try to understand the technical details. Should that not be first ??
Perhaps. I wrote that part first, thought I would post it as that followed by remarks on the alternate ways a lab loss / recovery theory could play out, and then thought "oh let me just put a little bit in the beginning about X, so it's clear why a lab origin should be considered." I didn't realize how much X there was...
Your theory is somewhat lacking in parsimony, though it does offer a way in which multiple variants of the same lineage but with apparently several years' worth of mutations separating them might emerge in the same geographic region at the same time. At this point I'm content with the idea that it probably involved mice, and given the unusual rate of mutation and the fact that mice are our lab animal of choice for this virus, there's a decent chance that at least some of those were lab mice. Beyond that, you may have solved the mystery, or there may have been a few other twists and turns along the way.
Parsimony, naturally, can be retroactively added. As mentioned the goal was to totally drive away the current implausibility factors, and replace them with a new set, haha.
Hi, just like you I started thinking about Ba.1 specifically being a lab product. I even wrote an article stating that on December 2.
https://igorchudov.substack.com/p/urgent-omicron-variant-likely-to
However, despite not fully understanding your article due to lack of some knowledge, I would like to say that likely, Ba.1 specifically was directly edited, and did NOT appear as a result of lab passage.
The reason is an extreme lack of synonymous mutations. Any kind of genuine evolution would produce synonymous mutations on top of non-synonymous mutations because evolution is driven by random mutations.
Also trying to put "dates" on directly edited virus genomes makes little sense.
I agree with you on Ethical Skeptic.
What do you think?
(I am not saying that Ba.2 is different, I just did not look at it).
It depends to some extent on how extreme the selection pressure is. Now that we have BA.2 to provide a "snapshot" halfway through the evolution of both, we can see that both show signs of extreme pressure in three different directions (one shared for the first half, than one for BA.1 and one for BA.2 separately for the second half). I really need to add illustrations for the mutation skew because it is very stark. I should have those up by tomorrow.
But otherwise, yes, for BA.1 especially it seems like passage wasn't the whole story.
But BA.2 actually brings a load of unique synonymous mutations (7/16 Syn/Total) in Orf1 (again illustrations would look really impressive here). So for my "fictional" story, I gave BA.2 a somewhat substantial passage period as a co-infector with pressure for random changes in Orf1, and BA.1 an accidental recombination make-over (BA.2 does not have BA.1's crazy NTD deletions and inserts). It's just one way of many to imagine things played out.
I'll probably have a revised origin theory after I finish my "why the BA.1 spike can't use fusion" theory.
Awesome, I will follow it.
Mind you, it is easy to add synonymous mutations, right?
So whoever designed Ba.1, having done so via direct genetic editing, purposely wanted to send a signal to us that Omicron was lab created,
Seems likely. Or, again, it could have had something to do with a deadline-rushed recombination, maybe an attempted insertion of a "cleaner" Orf1 while keeping the mutated spike, who knows.
It is also possible that ba1 was purposely designed, but NOT intended to be released, and got released accidentally.
VAXSCAM
https://peterwebster.substack.com/p/vaxscam?utm_source=url
Big oopsie. How do you know there's an elephant in your refrigerator? Answer: footprints in the butter. Lab leak theory gaining traction. https://www.dailymail.co.uk/news/article-10542309/Fresh-lab-leak-fears-study-finds-genetic-code-Covids-spike-protein-linked-Moderna-patent.html
Very much appreciated the "story hour version" i.e not smarter than a pre pandemic fifth grader. I am trying. Could you try a kindergarten version next time...big words and a cute drawing on every page. :)
I will be trying to incorporate more illustrations, but despite having a display drawing tablet I am no DrBeen yet...
For the layman just start at 'What Could Go Wrong'. Wicked description! Loved it. Feedback loops are hard, EVOLUTIONARY feedback loops now good luck debugging that one X)
That paragraph created enough intrigue to try to understand the technical details. Should that not be first ??
Perhaps. I wrote that part first, thought I would post it as that followed by remarks on the alternate ways a lab loss / recovery theory could play out, and then thought "oh let me just put a little bit in the beginning about X, so it's clear why a lab origin should be considered." I didn't realize how much X there was...
Your theory is somewhat lacking in parsimony, though it does offer a way in which multiple variants of the same lineage but with apparently several years' worth of mutations separating them might emerge in the same geographic region at the same time. At this point I'm content with the idea that it probably involved mice, and given the unusual rate of mutation and the fact that mice are our lab animal of choice for this virus, there's a decent chance that at least some of those were lab mice. Beyond that, you may have solved the mystery, or there may have been a few other twists and turns along the way.
Parsimony, naturally, can be retroactively added. As mentioned the goal was to totally drive away the current implausibility factors, and replace them with a new set, haha.