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So... What if China's Wuhan Institute of Virology did leak covid-19?

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abj13

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uh, we do create proteins from engineered nucleotides all the time--It's how transgenics work. The most ubiquitous tool, GFP, is used in most transgenics to induce your target to create GFP (green fluorescent protein--originally synthesized from jelly fish) at whatever active site you targeted in that animal. Surely, those semi-famous frogs with glowing eyes don't naturally have the fluorescent protein from jelly fish without human intervention, no?

We move homologous gene regions from one creature to another all of the time, in order to make new proteins in our model critter. We can even transfer little strings of mRNA into critters (from other critters), to try and get that critter to generate that protein; in the event that we have also knocked out that same protein in the same critter (common rescue experiment to confirm function and result of your gene of interest). These are decades old tools, that aren't that different from how the Moderna and Pfizer vaccines work.
No, that's not at all what I'm referring to. Creating fusion proteins or inserting known nucleotide sequences into genomes has been performed for decades now. The Moderna and Pfizer vaccines work because we know what the sequence of the spike protein is. What science can't do at this moment in time, is to consistently create a string of nucleotides that does not occur in nature to create a protein that significantly different from any other known protein. Scientists can't just type out GATCTGATGTTAGAGAGACCGAGA...x1000, put it into a computational program and it will tell you if it will be a biologically active peptide. The closest coronavirus genome to SARS-CoV-2 differs by 4%. That may seem small, but 4% difference means there are 1200 genetic variants relative to the closest neighbor. Even a single mutation can have dramatic effects on a protein and virus. For example, a single mutation causes polio to be capable of neuroinvasive, thus causing poliomyelitis. That's the difference between the oral polio vaccine and disease causing poliovirus, one freaking nucleotide. 4% currently is the difference between a bat coronavirus and a human coronavirus that has infected millions of humans.

That's why Folding@Home was big for such a long-time. Science is still without the ability to fully predict what every amino acid sequence will fold into a protein. If you are going to engineer a virus, you're going to borrow sequences that are known, hence what you described for transgenics and what has been known for decades. But to create SARS-CoV-2, with 4% differences from a viral genome that has never been cultured or extensively studied under laboratory conditions, as I said, you would need SR Hadden backing a secret cabal of scientists who would have been working for years.
 

IronWing

No Lifer
Jul 20, 2001
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Lmao, if we let ISIS establish a state, they would have launched a terrorist attack on US soil just like 9/11.
ISIS already has two established states: Saudi Arabia and Qatar; that's where ISIS was hatched. Neither instigated a violent insurrection in attempt to overthrow our republic. American fascists (Republicans) did that. It wasn't ISIS voting in the House voting to disenfranchise the voters of entire states because they didn't like the outcome, again, that was fascist Republicans.
 

Leeea

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Apr 3, 2020
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ISIS already has two established states: Saudi Arabia and Qatar; that's where ISIS was hatched. Neither instigated a violent insurrection in attempt to overthrow our republic. American fascists (Republicans) did that. It wasn't ISIS voting in the House voting to disenfranchise the voters of entire states because they didn't like the outcome, again, that was fascist Republicans.
Lies.


I get you believe that, but it is not true. The stated goal of AQ and ISIS is the overthrow of the Saudi monarchy. Qatar is more of an equal opportunity arms dealer, happily selling to all sides. Even so, Qatar is closer to the SDF then it was ever to ISIS, and even supplied armored vehicles, AT rockets, and 120mm mortars to the SDF. Qatar's deliveries to the SDF were mainly paid for by the US government and approved by the US congress as a budget line item.


Your attempting to brush over an complicated situation with a blanket statement, because it makes if feel easy to understand. But it is simply not true, and that makes it a lie that causes more harm then good.
 
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You do realize that almost every right-winger parroting right-wing extremist propaganda on this forum claims to a registered Democrat, right?
It's an troll tactic intended to make Trump-supporting right-wing extremism appear moderate. It doesn't ever work, of course, except as misdirection.
He probably doesn't because he's just the latest in a long line of morons that finally realized they're a fascist all along but they really did believe they were liberal, but due to the right winger trait of having basically zero self awareness didn't realize their actions and behavior belied the truth. Don't you understand, he was liberal but liberals made him become this!?!?

That or he really does believe that clown routine works on anyone but himself.
 

Jhhnn

No Lifer
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No, that's not at all what I'm referring to. Creating fusion proteins or inserting known nucleotide sequences into genomes has been performed for decades now. The Moderna and Pfizer vaccines work because we know what the sequence of the spike protein is. What science can't do at this moment in time, is to consistently create a string of nucleotides that does not occur in nature to create a protein that significantly different from any other known protein. Scientists can't just type out GATCTGATGTTAGAGAGACCGAGA...x1000, put it into a computational program and it will tell you if it will be a biologically active peptide. The closest coronavirus genome to SARS-CoV-2 differs by 4%. That may seem small, but 4% difference means there are 1200 genetic variants relative to the closest neighbor. Even a single mutation can have dramatic effects on a protein and virus. For example, a single mutation causes polio to be capable of neuroinvasive, thus causing poliomyelitis. That's the difference between the oral polio vaccine and disease causing poliovirus, one freaking nucleotide. 4% currently is the difference between a bat coronavirus and a human coronavirus that has infected millions of humans.

That's why Folding@Home was big for such a long-time. Science is still without the ability to fully predict what every amino acid sequence will fold into a protein. If you are going to engineer a virus, you're going to borrow sequences that are known, hence what you described for transgenics and what has been known for decades. But to create SARS-CoV-2, with 4% differences from a viral genome that has never been cultured or extensively studied under laboratory conditions, as I said, you would need SR Hadden backing a secret cabal of scientists who would have been working for years.
Well, yeh, but you can't bash the Chinese or excuse the ineptitude of our own leadership with an attitude like that. Get with the program, you Commie loving freak. I'll bet you don't believe in Birtherism or the stolen election, either.
 

Muse

Lifer
Jul 11, 2001
30,169
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Let's say it was from a lab. That means the MAGAts were knowingly and proudly spreading the 'Chinavirus' and killing their fellow Americans because it's too much of a hastle to wash their hands, socially distance, wear a mask and get a vaccine. China send their thanks.
China also bought up most of our N95 masks.
 

cytg111

Lifer
Mar 17, 2008
16,035
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I don't have time to go into more details for the rest of the comments, but this statement highlights misunderstanding of the author regarding the biology of SARS-CoV-2. A furin cleavage site has been identified in other coronaviruses including MERS and HKU1. Both of those are within the beta coronavirus clade that includes SARS-CoV-2. The finding of a furin cleavage site in other naturally occurring and related coronaviruses that infect humans is not a surprising finding. To suggest it isn't naturally found in other related coronaviruses is false, and to suggest any furin cleavage site is evidence of genetic engineering is not based on any facts.



Science hasn't reached a point in which scientists can string together engineered sequences of nucleotides or amino acids to fully create a new protein. Such a process would take currently years of failed attempts to engineer a protein. If a lab was going to engineer a virus, you would find long regions of the virus that match 100% with other viruses. That doesn't occur with SARS-CoV-2. CoV-2 even has unique sequences, within the receptor binding domain that make it different from the pangolin coronavirus.

Even a 1% difference in nucleotides between coronaviruses is a significant difference. For coronaviruses that means 300 nucleotides are divergent.
uh, we do create proteins from engineered nucleotides all the time--It's how transgenics work. The most ubiquitous tool, GFP, is used in most transgenics to induce your target to create GFP (green fluorescent protein--originally synthesized from jelly fish) at whatever active site you targeted in that animal. Surely, those semi-famous frogs with glowing eyes don't naturally have the fluorescent protein from jelly fish without human intervention, no?

We move homologous gene regions from one creature to another all of the time, in order to make new proteins in our model critter. We can even transfer little strings of mRNA into critters (from other critters), to try and get that critter to generate that protein; in the event that we have also knocked out that same protein in the same critter (common rescue experiment to confirm function and result of your gene of interest). These are decades old tools, that aren't that different from how the Moderna and Pfizer vaccines work.
No, that's not at all what I'm referring to. Creating fusion proteins or inserting known nucleotide sequences into genomes has been performed for decades now. The Moderna and Pfizer vaccines work because we know what the sequence of the spike protein is. What science can't do at this moment in time, is to consistently create a string of nucleotides that does not occur in nature to create a protein that significantly different from any other known protein. Scientists can't just type out GATCTGATGTTAGAGAGACCGAGA...x1000, put it into a computational program and it will tell you if it will be a biologically active peptide. The closest coronavirus genome to SARS-CoV-2 differs by 4%. That may seem small, but 4% difference means there are 1200 genetic variants relative to the closest neighbor. Even a single mutation can have dramatic effects on a protein and virus. For example, a single mutation causes polio to be capable of neuroinvasive, thus causing poliomyelitis. That's the difference between the oral polio vaccine and disease causing poliovirus, one freaking nucleotide. 4% currently is the difference between a bat coronavirus and a human coronavirus that has infected millions of humans.

That's why Folding@Home was big for such a long-time. Science is still without the ability to fully predict what every amino acid sequence will fold into a protein. If you are going to engineer a virus, you're going to borrow sequences that are known, hence what you described for transgenics and what has been known for decades. But to create SARS-CoV-2, with 4% differences from a viral genome that has never been cultured or extensively studied under laboratory conditions, as I said, you would need SR Hadden backing a secret cabal of scientists who would have been working for years.
See? This is why you discuss politics on a tech site, odds are that there are people around that *knows* something!
Getting into the details, you guys mind giving us an idea about your credentials? You obviously have insight into the domain.
So the deduction actually arrives at the redundant logical conclusion : Rand Paul is an idiot. I am thinking of the case(s) where he tears into Fauci for the research into "gain function" at the Wuhan lab alluding that the virus was actually something they engineered at the site. According to abj13, this is not possible. Its actually right out.
So the question is reduced to the core of it. Did it *leak* from the lab? (did they ever realize what they had? when did they pick it up? can we go back and find prior break outs in China that they managed to contain?).
 

abj13

Senior member
Jan 27, 2005
927
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See? This is why you discuss politics on a tech site, odds are that there are people around that *knows* something!
Getting into the details, you guys mind giving us an idea about your credentials? You obviously have insight into the domain.
So the deduction actually arrives at the redundant logical conclusion : Rand Paul is an idiot. I am thinking of the case(s) where he tears into Fauci for the research into "gain function" at the Wuhan lab alluding that the virus was actually something they engineered at the site. According to abj13, this is not possible. Its actually right out.
So the question is reduced to the core of it. Did it *leak* from the lab? (did they ever realize what they had? when did they pick it up? can we go back and find prior break outs in China that they managed to contain?).
As I've mentioned, the data behind the virus being engineered by man in the lab is very weak, conflicts with the current status of virological techniques, and doesn't make logical sense. But let's assume it is for a moment, how was it made? There would be three ways I could invision it being theoretically possible

1) The virus was built from the ground up, meaning the creator(s) built the virus nucleotide by nucleotide. As I've already described in previous posts, this is not compatible with current genomic techniques. Science does not have the capacity to choose random nucleotide and therefore amino acid sequences, building proteins from the ground-up. Science has to rely on borrowing ideas from nature, and can modify those sequences. If the virus was built from the ground up, it would have taken years, used scientific techniques that don't exist, and an incredible amount of resources. SARS-CoV-2 is too different from any other known virus at this point in time. And logically, it doesn't make sense either. If you want to build the next SARS virus, you would build something close to SARS-CoV-1 and modify it. Building something completely new and different would take too long, used so many researchers and resources, and like I said, you would have to invent techniques that don't currently exist in the public scientific world. On top of it, you have no idea whether your virus will be more effective than SARS-CoV-1. To make this possibility a reality, you have to invoke a secret cabal of scientists working in secret for years funded by someone like SR Hadden.

2) The virus was built from a related virus but changed. I've talked about this too. SARS-CoV-2 is simply too different from any known virus. Even the possible ways it could have been created that people have suggested (taking the virus and growing it for months to years and letting it spontaneously mutate) conflicts with previous published science. This approach would have required years if not a decade's worth of waiting for the virus to be grown. But that's just growing the virus. If you are going to modify it, you have to develop essential techniques to handle the virus. Which cells do you grow it in? What are the cell culture conditions? How do you measure the virus quantity? PCR? Viral plaque assays? Then you have to sequence the virus. And if you want to further modify the virus, you have to build the reverse genetics system. So you have to take the sequences, build plasmids or an bacterial artificial chromosome, and then modify the sequences. And how do you know it works? This isn't trivial techniques, someone's entire career could be based off of what I just described. This is years to decades worth of science. Like with possibility 1, if you want to make some badass coronavirus, you're not going to dick around with some bat coronavirus, hope it develops mutations in cell culture over years, and build techniques that don't exist. If you wanted to make a nasty coronavirus, then use SARS-CoV-1 as your starting point and make small changes to create an even more deadly virus.

3) SARS-CoV-2 was identified from a sample, and purposely mutated for gain of function research. Even this doesn't make much sense. In order to study gains of function, you would have to know what the baseline capacity of a virus is, modify it, and determine if it is a more effective virus. So if someone is going to study gain of functions for coronaviruses, why the heck would you choose some unknown virus with unknown functions, and take years to study how it infects to understand how it works? Then you would have to build the techniques to modify the virus through reverse genetics, create the mutations, and it is likely your first attempt isn't very effective, so you have to go through several iterations of mutating the virus to create enhancements. Or you could use a virus that has been studied for 15 years, SARS-CoV-1, and insert gain of functions like this furin cleavage site that has been described. So which makes more sense? Spending years building a system to study a virus that nobody else has studied, building all these necessary techniques and skills, and then mutating it... or starting with SARS-CoV-1, not needing to build anything since it already exists, and mutate SARS-CoV-1? If one really wanted to examine the furin cleavage site, it would have taken only a few months to a year to do this for SARS-CoV-1. Again, one would have to invoke SR Hadden with a hidden cabal of scientists working for years on this possibility. Even from a scientific perspective, if you discovered a novel coronavirus that had some potential capacity to infect humans, this would be a major scientific finding. Altruistic scientists would want to get this information out, not only for public knowledge, but this would be a major paper (career advancement) and would get lots of scientific attention. You would have to invoke that somehow a government or SR Hadden was smart enough to recognize the potential, and squashed any reporting of the virus until years of required scientific effort to modify it was completed. So not only was there a secret cabal of scientists and enormous funds spent, but it was systematically covered up. Damn Pizzagate people, once again hiding the truth!

Now could have the virus leaked from the lab? Sure. They could have had some bat, pangolin, or other animal sample, and a researcher was contaminated and the virus got out. But that's harder to prove. But that is entirely different from someone purposely modifying/engineering a virus, which is what the a proportion of people want to invoke.
 

[DHT]Osiris

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Dec 15, 2015
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2) The virus was built from a related virus but changed. I've talked about this too. SARS-CoV-2 is simply too different from any known virus. Even the possible ways it could have been created that people have suggested (taking the virus and growing it for months to years and letting it spontaneously mutate) conflicts with previous published science. This approach would have required years if not a decade's worth of waiting for the virus to be grown. But that's just growing the virus. If you are going to modify it, you have to develop essential techniques to handle the virus. Which cells do you grow it in? What are the cell culture conditions? How do you measure the virus quantity? PCR? Viral plaque assays? Then you have to sequence the virus. And if you want to further modify the virus, you have to build the reverse genetics system. So you have to take the sequences, build plasmids or an bacterial artificial chromosome, and then modify the sequences. And how do you know it works? This isn't trivial techniques, someone's entire career could be based off of what I just described. This is years to decades worth of science. Like with possibility 1, if you want to make some badass coronavirus, you're not going to dick around with some bat coronavirus, hope it develops mutations in cell culture over years, and build techniques that don't exist. If you wanted to make a nasty coronavirus, then use SARS-CoV-1 as your starting point and make small changes to create an even more deadly virus.
What?
On February 3, 2020, with the COVID-19 outbreak already spreading beyond China, Shi Zhengli and several colleagues published a paper noting that the SARS-CoV-2 virus’s genetic code was almost 80% identical to that of SARS-CoV, which caused the 2002 outbreak. But they also reported that it was 96.2% identical to a coronavirus sequence in their possession called RaTG13, which was previously detected in “Yunnan province.” They concluded that RaTG13 was the closest known relative to SARS-CoV-2.
Maybe your definition of 'too different from any known virus' is different from mine, but I'd say 96.2% is pretty close to identical. 3.8% could easily be wiggle room for adapting the virus to infect humans.

How do you know we haven't also been performing gain-of-function research on SARS-CoV-1?
 

abj13

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Jan 27, 2005
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What?

Maybe your definition of 'too different from any known virus' is different from mine, but I'd say 96.2% is pretty close to identical. 3.8% could easily be wiggle room for adapting the virus to infect humans.

How do you know we haven't also been performing gain-of-function research on SARS-CoV-1?
Your definition is very different. As I mentioned above, a single mutation in the poliovirus vaccine is the difference between a virus that cannot cause polio vs one that can. 3.8% difference is 1200 genetic variants between SARS-CoV-2 and a bat coronavirus.

Just think about human diseases. One mutation (on both alleles) resulting in deletion of a single amino acid is the difference between a child being completely healthy or having Cystic Fibrosis. Genetics is fincky. Being "close" enough by 96.2% may work in other fields but not virology and not genetics.

Where did I say we haven't been doing gain of function on SARS-CoV-1?
 
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zinfamous

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Jul 12, 2006
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No, that's not at all what I'm referring to. Creating fusion proteins or inserting known nucleotide sequences into genomes has been performed for decades now. The Moderna and Pfizer vaccines work because we know what the sequence of the spike protein is. What science can't do at this moment in time, is to consistently create a string of nucleotides that does not occur in nature to create a protein that significantly different from any other known protein. Scientists can't just type out GATCTGATGTTAGAGAGACCGAGA...x1000, put it into a computational program and it will tell you if it will be a biologically active peptide. The closest coronavirus genome to SARS-CoV-2 differs by 4%. That may seem small, but 4% difference means there are 1200 genetic variants relative to the closest neighbor. Even a single mutation can have dramatic effects on a protein and virus. For example, a single mutation causes polio to be capable of neuroinvasive, thus causing poliomyelitis. That's the difference between the oral polio vaccine and disease causing poliovirus, one freaking nucleotide. 4% currently is the difference between a bat coronavirus and a human coronavirus that has infected millions of humans.

That's why Folding@Home was big for such a long-time. Science is still without the ability to fully predict what every amino acid sequence will fold into a protein. If you are going to engineer a virus, you're going to borrow sequences that are known, hence what you described for transgenics and what has been known for decades. But to create SARS-CoV-2, with 4% differences from a viral genome that has never been cultured or extensively studied under laboratory conditions, as I said, you would need SR Hadden backing a secret cabal of scientists who would have been working for years.
ah fair enough, synthetic biology, basically. But it is a thing, with, I think, very moderate success to this point.

Craig Venter, among others, has been focusing on this for some time now. I think his synthetic bacteria, with the initial intent to generate anti-malarial drugs, is still the main achievement here--but I haven't been following this. I last saw him give a lecture on this c. 2013 or so.

 

Jhhnn

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Nov 11, 1999
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What?


Maybe your definition of 'too different from any known virus' is different from mine, but I'd say 96.2% is pretty close to identical. 3.8% could easily be wiggle room for adapting the virus to infect humans.

How do you know we haven't also been performing gain-of-function research on SARS-CoV-1?
It's not close to identical at all, considering that the genomes of chimps & humans are 98.8% the same.
 
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abj13

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ah fair enough, synthetic biology, basically. But it is a thing, with, I think, very moderate success to this point.

Craig Venter, among others, has been focusing on this for some time now. I think his synthetic bacteria, with the initial intent to generate anti-malarial drugs, is still the main achievement here--but I haven't been following this. I last saw him give a lecture on this c. 2013 or so.

And Daniel Gibson of Gibson Assembly fame!

IIRC, their synthetic bacteria involved them using preexisting sequences, but stitching it together to make the smallest replicating genome. So while it was synthetic (made in the laboratory setting), the sequences were not created by man, rather they were "borrowed" sequences that already existed in nature. Its really cool and a first step in synthetic biology.
 
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Paratus

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And Daniel Gibson of Gibson Assembly fame!

IIRC, their synthetic bacteria involved them using preexisting sequences, but stitching it together to make the smallest replicating genome. So while it was synthetic (made in the laboratory setting), the sequences were not created by man, rather they were "borrowed" sequences that already existed in nature. Its really cool and a first step in synthetic biology.
So I’m trying to come up with a metaphor here.

A genome could be considered a text document and our genetic tools are mostly like cut and paste. Nature makes a bunch of genomes and we can go in there and cut certain sequences from one and paste them into a new sequence, like cutting text from one document and pasting to another another.

Because we are cutting from naturally produced genomes we have a good idea what the sequences we cut actually do. They make “sense”. Just like if we cut a word from a document in a language we don’t understand we still have a good idea it’s actually a word and not gibberish.

It also seems like you are saying we don’t have the ability to create our own novel genomic sequences. We could conceivably put together our own genomic sequences but without spending 1000’s of man hours we’d have no idea if what we created did anything like what we wanted or was just gibberish. Sort of like banging a on keyboard will most likely create gibberish.
 
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abj13

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So I’m trying to come up with a metaphor here.

A genome could be considered a text document and our genetic tools are mostly like cut and paste. Nature makes a bunch of genomes and we can go in there and cut certain sequences from one and paste them into a new sequence, like cutting text from one document and pasting to another another.

Because we are cutting from naturally produced genomes we have a good idea what the sequences we cut actually do. They make “sense”. Just like if we cut a word from a document in a language we don’t understand we still have a good idea it’s actually a word and not gibberish.

It also seems like you are saying we don’t have the ability to create our own novel genomic sequences. We could conceivably put together our own genomic sequences but without spending 1000’s of man hours we’d have no idea if what we created did anything like what we wanted or was just gibberish. Sort of like banging a on keyboard will most likely create gibberish.
Yeah! That's a great analogy to describe the current status. We've advanced far enough that we can open a document, recognize there are letters on the page, recognize that there are words that have meaning, and we now have genetics tools that we can cut and paste words from documents. We can even sometimes substitute a letter or two, but the meaning remains the same (like writing color vs colour). Some of the most recent advances have been creating new documents filled with cut and pasted words.

We also have the ability to type into documents, but the only words we know is what exists in nature. We could assemble letters to write out new words that don't currently exist, but most would not have meaning, and it would take years to figure out what are and are not words.

With SARS-CoV-2, there are enough new assortments of letters that in some areas of the document that the words don't look like words we've seen in the past. Somebody either had to have years worth of training and resources to type out these new words (engineered virus), or it nature is telling us that new combinations are possible.
 

Bitek

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Aug 2, 2001
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So I’m trying to come up with a metaphor here.

A genome could be considered a text document and our genetic tools are mostly like cut and paste. Nature makes a bunch of genomes and we can go in there and cut certain sequences from one and paste them into a new sequence, like cutting text from one document and pasting to another another.

Because we are cutting from naturally produced genomes we have a good idea what the sequences we cut actually do. They make “sense”. Just like if we cut a word from a document in a language we don’t understand we still have a good idea it’s actually a word and not gibberish.

It also seems like you are saying we don’t have the ability to create our own novel genomic sequences. We could conceivably put together our own genomic sequences but without spending 1000’s of man hours we’d have no idea if what we created did anything like what we wanted or was just gibberish. Sort of like banging a on keyboard will most likely create gibberish.
To add, proteins are simply too large and far too complex to predict shape and function with our current level of technology.

At best, we are just acquiring the ability to predict the shapes of small molecules that could interact with a protein (eg enzyme or receptor) that's already been very well characterized in shape and function.

This is the future direction of pharmacological drug development. Instead of brute force "try everything and see what happens, maybe we get lucky" approach of the last 100+ yrs, we can use computer modeling to predict a shape and chemical compound that could be close to doing what we want.

Still requires lots of testing and optimization in the lab, but at least starting at a closer point.

For reference, a classic small molecule drug could have a molecular weight of 500.
Covid's spike has a molecular weight of 200,000.

Not only that, it has a very specific 3D shape that's created from a single continuous chain of 1270+ amino acids that must be precisely folded up like origami (in ways we don't fully understand) to get the intended shape and function. Even small deviations can have significant impacts.

That's just amino acids then. We still need to consider the DNA/RNA sequence, understanding that each amino acid is encoded by three letters (nucleotides) and that next step adds and additional layer of variation and potential side effects.

We are a long way off from being able to custom engineer complex functional proteins from the ground up.
 
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desy

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So if they were tinkering, its what labs do, over here too. the problem is the accountability and why China is a country I often find lacking credibility in most respects on the world stage
End of Story
 

Bitek

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What?


Maybe your definition of 'too different from any known virus' is different from mine, but I'd say 96.2% is pretty close to identical. 3.8% could easily be wiggle room for adapting the virus to infect humans.

How do you know we haven't also been performing gain-of-function research on SARS-CoV-1?
What's more important is where that 4% is coming from. According to the sources in OP:

The cov2 virus and WIV's bat coronavirus RaTG13 is 96% similar, but there is a greater divergence centered around the Spike.
Not as much as other CVs, but consequential.

Recall that Spike is critical for species targeting and infectivity. By itself it's not suspicious, especially if RaTG13 shows affinity to human ACE2. Minimally it means it likely a close relative. RaTG13 did infect and kill 3 guano miners years ago who were literally mucking in the shit, but never really spread after that.



In this graph, covid19 is the 100 other sequences are being compared to.
Where it gets interesting is looking at the Spike region, and comparing it to other strains on file. Most important are the receptor binding regions of the Spike.

This is where the WTF moment comes in.


The author focused on these RBM regions, and identified nearly a 100% match to the pangolin sample. The rest of the pangolin virus is very divergent, so it's would not be considered to be closely related.



Understand also when variants that get discussed, some of the most consequential mutations are in this region.

The most consequential mutation identified has been at the 484 amino acid position of the chain, where a single amino acid is changed to from an acid to a base (E484K mutation). This is a feature of the Brazil, South African and a New York variant, amongst others. It's evolved separately multiple times.
Another mutation is at the 452 position. That's in another NY variant, a California variant, as well as the India variant.

In fact, the variants we now see circulating seem more diverged from the original (wild type) Wuhan cov2 in this particular spike region than the wt Wuhan is from the pangolin receptor binding domain.

Wt Wuhan and pangolin RBM being an almost exact match at a key region at Time=Zero is really odd.

Could be some lucky natural recombination between two viruses naturally found 1000 miles away from each other, could be some yet to be identified convergent evolutionary pathway (we are missing the virus "fossils" in between linking them) OR maybe some lab worker was perhaps doing copy/paste of the pangolin RBM into a close cousin of WIVs published RaTG13 for research, (plus don't forget that weird furin site insertion), creates a real baddie they aren't careful with, then three WIV lab workers get infected from it, then go out spreading it around town.

It's not a perfect theory, but it's odd enough it warrants further investigation.
 
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abj13

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Wt Wuhan and pangolin RBM being an almost exact match at a key region at Time=Zero is really odd.
It is not really odd at all. This finding is also consistent with the zoonotic jump of SARS-CoV-2 from an unknown host to humans. If SARS-CoV-2 was already optimized for infecting and circulating in humans, mutations like E484K would have been present in the first place. The fact the virus is evolving to be more pathogenic in humans is also consistent with the virus infecting organism X and being adapted to organism X. Now that it has infected million of humans, there's such evolutionary pressure on the virus strains that E484K were selected for and now are common in the entire pool of SARS-CoV-2 genomes. SARS-CoV-2 is adapting before our eyes. So this finding isn't odd at all. It is a prediction that would be very much consistent with the virus jumping from one host to humans, and only now is it able to pick up these "beneficial" mutations for human infection.

Could be some lucky natural recombination between two viruses naturally found 1000 miles away from each other,
Recombination of coronaviruses is a well known phenomenon. It has been clearly described at least seven recombination events helped generate SARS-CoV-1. Recombination of coronaviruses have been described going back as far as 1985. So it is not surprising or blind luck to find a recombination event in SARS-CoV-2.
 
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Bitek

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Aug 2, 2001
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It is not really odd at all. This finding is also consistent with the zoonotic jump of SARS-CoV-2 from an unknown host to humans. If SARS-CoV-2 was already optimized for infecting and circulating in humans, mutations like E484K would have been present in the first place. The fact the virus is evolving to be more pathogenic in humans is also consistent with the virus infecting organism X and being adapted to organism X. Now that it has infected million of humans, there's such evolutionary pressure on the virus strains that E484K were selected for and now are common in the entire pool of SARS-CoV-2 genomes. SARS-CoV-2 is adapting before our eyes. So this finding isn't odd at all. It is a prediction that would be very much consistent with the virus jumping from one host to humans, and only now is it able to pick up these "beneficial" mutations for human infection.


Recombination of coronaviruses is a well known phenomenon. It has been clearly described at least seven recombination events helped generate SARS-CoV-1. Recombination of coronaviruses have been described going back as far as 1985. So it is not surprising or blind luck to find a recombination event in SARS-CoV-2.
Well, that's the challenge the natural origin theory is going to have to explain and better full in information gaps.

A lucky recombination between strains spacially and species distanced from each other, and 1000 miles away from the sole outbreak in Wuhan. Another odd but lucky furin site insertion outta the blue, lack of known sequences establishing a pedigree, lack of known animal reservoirs, a lack of previously circulating virus, and a lab who holds a lot of the data locking down and not sharing what they working on nor large sections of their databases or unpublished virus samples.

Hanging hats that the wt Wuhan isn't fully optimized by a base pair (and hand waiving away the rest) in what's very visibly a multimodal environment won't be sufficiently convincing.

Beyond the science, the politics will certainly demand a much stronger explanation
 

[DHT]Osiris

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Dec 15, 2015
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It is not really odd at all. This finding is also consistent with the zoonotic jump of SARS-CoV-2 from an unknown host to humans. If SARS-CoV-2 was already optimized for infecting and circulating in humans, mutations like E484K would have been present in the first place. The fact the virus is evolving to be more pathogenic in humans is also consistent with the virus infecting organism X and being adapted to organism X. Now that it has infected million of humans, there's such evolutionary pressure on the virus strains that E484K were selected for and now are common in the entire pool of SARS-CoV-2 genomes. SARS-CoV-2 is adapting before our eyes. So this finding isn't odd at all. It is a prediction that would be very much consistent with the virus jumping from one host to humans, and only now is it able to pick up these "beneficial" mutations for human infection.


Recombination of coronaviruses is a well known phenomenon. It has been clearly described at least seven recombination events helped generate SARS-CoV-1. Recombination of coronaviruses have been described going back as far as 1985. So it is not surprising or blind luck to find a recombination event in SARS-CoV-2.
You have to admit, it's still awfully suspicious that yes, a possible natural mutation happened, but it happened within countable steps of one of three viral labs that works with bat viruses on the planet, shortly after a group of bat virologists died from a mysterious, unidentified covid-like disease. Occam's razor man, occam's razor.
 

cytg111

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Mar 17, 2008
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You have to admit, it's still awfully suspicious that yes, a possible natural mutation happened, but it happened within countable steps of one of three viral labs that works with bat viruses on the planet, shortly after a group of bat virologists died from a mysterious, unidentified covid-like disease. Occam's razor man, occam's razor.
OR they had the virus in lab, collected on the moon (or somewhere else), experimented on it, and dropped the ball. <~ that is your razor.
 

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