From the section:
There are other explanations. Maybe the FCS was acquired by recombination with an animal (e.g. a pangolin) that also had a human-like CGG preference for arginine.
The wet market hypothesis involves a zoonotic path involving just those sorts of intermediate. There may well have been multiple back and forth human-animal transmissions.
Checking the Genscript codon usage tables, here are the fractional “usages” of CGG in different organisms:
| Organism | fraction |
|---|---|
| E. coli | 0.11 |
| Yeast | 0.04 |
| Human | 0.21 |
| Mouse | 0.19 |
| Pig | 0.20 |
| C. elegans | 0.09 |
| Drosophila | 0.15 |
| Arabidopsis | 0.09 |
| Streptomyces | 0.38 |
| Corn | 0.15 |
| Tobacco | 0.08 |
So, @Giltil, what do you make of the fact that, contrary to Washburne’s claim, the CGG preference in the SARS-Cov2 furin cleavage site is actually optimized for streptomyces and not humans (or other animals)? Indeed, it seems to be streptomyces-specific.
It’s irrelevant to the actual origin of the virus.
Focusing on claimed censorship is not consistent with scientific dialogue. What matters is the evidence.
I could not agree more. Did I say something to suggest it was?
Claimed censorship?
Is that your tactic to avoid a reality you can’t for some unknown reason acknowledge?
Focusing?
The censorship prevented the scientific dialogue. Scientific dialogue.was prevented from happening by the censorship.
Are you applauding the censorship?
Scientists don’t get their data from social media. Removing stuff from Facebook and Twitter doesn’t put a dent in any scientific dialogue. Preventing the spread of a foundationless conspiracy theory on social media does not prevent scientific dialogue.
Social media platforms can do whatever they want with their servers. I could care less.
Are you interested in actual scientific dialogue, or are you just here to whine about completely irrelevant topics?
CGG being the most frequent of the 6 arginine codons in human, it is legitimate to say that the 2 argine codons of the furin cleavage site are optimal for expression in human cells. This is what Washburne’s means by « human optimized » arginine codons.
Is sarcasm your chosen weapon to hide your obfuscation?
You’ve already proven my general confusion by pointing to my computer incompetence and that people are laughing at me. Good on you! You are a champion at making your case about my general confusion.
But as to your specific claim,
Do comments such as,
To which you enlightened me with,
You’ve shown squat. Up your game. Or as you stated,
What a surprise.
Science isn’t done through social media, in case you have forgotten.
You complain that there isn’t scientific dialogue, and yet here you are discussing stuff that is irrelevant to the scientific dialogue. The one thing that is preventing scientific dialogue is the continual red herrings we have to deal with, such as what Facebook or Twitter allows on their sites.
On the off chance that anyone is actually interested in why I believe @Sam is confused about the video I posted, here is the video in question, the pertinent section of which starts at about 50 mins:
And this is Sam’s comment to which it was intended as a response:
That should suffice.
Let me see if I can do this now more successfully than you seem to have been able.
The usages of four of the six arginine codons (CGC, CGG, AGA, and AGG) in humans are virtually indistinguishable. There are many, many plausible ways by which the two codons Washburne fixates on could have ended up in the SARS-Cov2 genome, including random chance. Deliberate engineering is way, way down the list of likely explanations. (Actually it does not belong at all on that list. It goes on the list of unlikely explanations.)
The thing is that probably none of the numerous surprising facts (under the zoonotic theory) that are advanced to support the lab leak theory represents by itself strong evidence. But collectively, they do.
Exactly, here’s the frequency of arginine codons in the human genome according to this paper:
AGA: 21.50%
AGG: 20.81%
CGG: 20.40%
CGC: 18.41%
CGA: 10.94%
CGU: 7.93%
Since 4 out of the 6 codons have a frequency around 20%, any of those 4 would apparently be sufficient to be called “human-specific”.
In other words, there’s around a ~67% chance that a random arginine codon would apparently be called “human specific”, so how is this supposed to be the least bit notable?
Even collectively the evidence is extremely thin and borders on just conspiracy theory. Even the few US agencies that have shown some support of the lab leak theory don’t think the virus is the product of genetic manipulation by humans. That ship has sailed, and it isn’t coming back to port.
It is still possible that a naturally occurring virus that was held in the lab leaked out. However, all of the evidence demonstrating an outbreak in the Wuhan market has pretty much closed down this lab leak theory.
The way I look at it, 0+0+0+0=0. Adding more 0’s to the equation doesn’t change the outcome.
Where was this, again? The scientific dialogue happened in the peer reviewed literature. What was at least partially prevented from happening was the riling up of facebook Karens with speculations and conspiracies.
That also seems to suggest the AGA codon is optimal as that’s the most frequent in humans, with CGG coming third.
Interestingly the most used arginine codon(AGA) in SARS-Cov2 is also most used in humans. The CGG codons from the furin cleavage site seems better suited to Pig and Cattle. See table 1 in this paper:
Amino acids Codon SARS CoV-2 Human Dog Cat Pig Horse Cattle Bat Arginine CGU 1.44 0.48 1.17 0.41 0.40 0.55 0.49 0.49 CGC 0.6 1.1 0.92 1.09 0.89 1.15 1.17 0.94 CGA 0.31 0.65 0.71 0.55 0.79 0.61 0.68 0.74 CGG 0.2 1.21 0.48 1.19 1.94 1.08 1.32 1.18 AGA 2.64 1.29 1.29 1.33 1.08 1.3 1.14 1.26 AGG 0.82 1.27 1.42 1.41 0.90 1.32 1.2 1.36
The way you look at it is wrong
You left out an explanation as to why it is wrong.