Crazy (and not-so-crazy) shit about Covid-19

[Ian C. Kuzushi]

time for a review

While there is no record of a process of early evolutionary adaptation, SARS-CoV-2′s receptor binding domain (RBD) appears to be highly optimized for binding to human ACE2 (Fig. 2) (Delgrado Blanco et al. 2020; Damas et al. 2020). In this respect, 43% of modelled mutations destabilize the binding energy of the SARS-CoV-2 spike protein RBD to human ACE2, while just 1% of the mutations stabilize it (Delgrado Blanco et al. 2020).

Overall, SARS-CoV-2 was remarkably well adapted to humans from its first appearance, yet poorly adapted to bat infection, the natural reservoirs for SARS-r-CoVs, with little evidence for gaining its human adaptation through natural recombination.

In summary, the FCS confers SARS-CoV-2 enhanced human pathogenicity and has never been identified in another Sarbecovirus. At the same time, FCSs have been routinely inserted into coronaviruses in gain-of-function experiments, and we provide a hypothesis through which the specific amino acid sequence of SARS-CoV-2′s FCS may have been generated through cell culture.

https://link.springer.com/article/10.10 ... 21-01211-0

No need to review out-of-date and largely retracted or debunked conspiracy theories that have no proof.

We’ve long known that the presence of such a site in SARS-CoV-2 increased its pathogenic power, and we also know that similar features have not been found in any other SARS-like coronavirus (though we may find them in the future). For lab-leak proponents, these facts—combined with certain details of the furin cleavage site’s structure—strongly hint at human intervention. As the science journalist Nicholas Wade argued in an influential lab-leak-theory brief last spring, this genetic insertion “lies at the heart of the puzzle of where the virus came from.” The virologist David Baltimore even told Wade that the structure of the SARS-CoV-2 furin cleavage site was “the smoking gun for the origin of the virus.” (Baltimore later walked back his claim.)

As many scientists have since pointed out, the mere presence of the furin cleavage site is not dispositive of a Frankenstein experiment gone wrong. For example, the same genetic feature has come about, quite naturally and independently, in plenty of other, more distantly related coronaviruses, including those that cause the common cold. According to a “critical review” co-authored by 21 experts on viruses and viral evolution that was posted as a preprint in July, “simple evolutionary mechanisms can readily explain” the site’s presence in SARS-CoV-2, and “there is no logical reason” why it would look the way it does if it had been engineered inside a lab. “Further,” the authors wrote, “there is no evidence of prior research at the [Wuhan Institute of Virology] involving the artificial insertion of complete furin cleavage sites into coronaviruses.”

https://www.theatlantic.com/science/arc ... er/620209/

And:

The article itself, by science writer Nicholas Wade, has become one of the most often-cited pieces in support of the lab-leak hypothesis. The quote from Baltimore is part of its argumentative bedrock.

Here’s the problem: Baltimore regrets using the phrase “smoking gun” to describe his conclusion, and doesn’t agree that it validates the lab-leak theory.

Baltimore told me by email that he made the statement to Wade, also by email, and granted him permission to use it in print. But he added that he “should have softened the phrase ‘smoking gun’ because I don’t believe that it proves the origin of the furin cleavage site but it does sound that way. I believe that the question of whether the sequence was put in naturally or by molecular manipulation is very hard to determine but I wouldn’t rule out either origin.”

Baltimore has made similar statements to others who have asked him about the quote, including Vincent Racaniello of Columbia University, a former lab colleague of Baltimore’s, and Amy Maxmen of Nature. Baltimore told Maxmen that while evolution could have produced the virus, “there are other possibilities and they need careful consideration, which is all I meant to be saying.”

https://www.latimes.com/business/story/ ... eak-theory

And finally:

While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal7 and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding7,11. Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise. This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation.

https://www.nature.com/articles/s41591-020-0820-9

[windwalker]

Even as a natural origin remains the most plausible explanation,

https://www.theatlantic.com/science/arc ... er/620209/

The two theories point to sharply different policy responses.

A lab leak tells us that the biological security of institutions doing research into live pathogens needs to be dramatically shored up.

Natural spillover warns us that contacts between human communities and wildlife harboring potentially infectious pathogens, such as bats, should be better monitored and regulated.

https://www.latimes.com/business/story/ ... eak-theory

More scientific data could swing the balance of evidence to favor one hypothesis over another.
Obtaining related viral sequences from animal sources would be the most definitive way of revealing viral origins. 
https://www.nature.com/articles/s41591-020-0820-9

"hypothesis" good word will be interesting seeing how it develops

This was surprising because both the SARS1 and MERS viruses had left copious traces in the environment. The intermediary host species of SARS1 was identified within four months of the epidemic’s outbreak, and the host of MERS within nine months.

Yet some 15 months after the SARS2 pandemic began, and after a presumably intensive search, Chinese researchers had failed to find either the original bat population, or the intermediate species to which SARS2 might have jumped, or any serological evidence that any Chinese population, including that of Wuhan, had ever been exposed to the virus prior to December 2019.

Natural emergence remained a conjecture which, however plausible to begin with, had gained not a shred of supporting evidence in over a year.

Where we are so far. Neither the natural emergence nor the lab escape hypothesis can yet be ruled out.

There is still no direct evidence for either. So no definitive conclusion can be reached.

That said, the available evidence leans more strongly in one direction than the other. Readers will form their own opinion.

But it seems to me that proponents of lab escape can explain all the available facts about SARS2 considerably more easily than can those who favor natural emergence.

https://thebulletin.org/2021/05/the-ori ... -at-wuhan/




.

[Giles]

So to summarize the current information/knowledge as to how Covid-19 got into the world at large:

Both a 'natural' route and a lab escape can reasonably seen as possibilities. Whereby evidence at the moment does not point more to a lab leak; the quoted sentence "That said, the available evidence leans more strongly in one direction than the other. Readers will form their own opinion." is tendentious.

Regarding the 'third option': At this point in time there is no well-founded evidence that credibly points to genetic manipulation of the Covid virus (intending to make it more harmful to humans).

--->
It occurs to me that the 'natural' route of transmission is actually the most frightening if you think it through. An accidental lab leak, or even a genetic manipulation (although currently not credible) would both be examples of human failing or even of reprehensible planned action. But at the same time we would then have specific 'guilty parties' to identify, to admonish or even to punish. And following on from this, as with most accidents of negligence or indeed crimes by identifiable parties, humankind can try to take specific measures (legal; oversight; sanctions etc.) to ensure that it doesn't happen again. In this way the whole disaster potentially becomes easier to grasp and deal with emotionally and, looking to the future, it becomes more 'controllable'.

But the other possibility, 'natural' transmission, the one that many scientists and academics in various fields have been pointing to all the time, is far less controllable in both emotional and practical terms. Ongoing destruction of natural habitats which brings wild animals, and the innumerable viruses they carry, into increasing contact with human environments and new potential hosts, both other animals and then humans. At the same time creating new opportunities for successful mutation - and viruses are great at mutating. Here we have no specific human guilty parties at whom we can cathartically point the finger and sanction. And far less prospect of 'making sure it doesn't happen again'. Because now the 'guilty party' is humankind at a whole, as expressed by huge parts of business/enterprise, governments and so on, which continues this process of environmental destruction. Elements of our whole economic and political system. Meaning ultimately that 'we' by our collective behaviour continue to endanger ourselves, and hence even worse new diseases and pandemics are almost inevitable if we don't make more serious changes to our own collective behaviour.
And that will have consequences. Implications that are much more uncomfortable, unwelcome and indeed disturbing (for many) than the other possibilities. I suspect (yes, in this final sentence I'm speculating) that some of the motivation to argue for a lab leak and even a genetic manipulation stems from this underlying unease about the longer-term implications.

[Quigga]

No one is going to get punished for this, lol. Nature is going to get the respect she demands one way or another. We see human life as more special than other types of life, when it couldn't be further from the truth. We're the least important on this planet - building upon everything else there is.

As to my source for what I wrote regarding Covid outbreak - I'll have to do some digging to find the article, sorry.

[Ian C. Kuzushi]

No one is going to get punished for this, lol. Nature is going to get the respect she demands one way or another. We see human life as more special than other types of life, when it couldn't be further from the truth. We're the least important on this planet - building upon everything else there is.

I think there is something to this. The only pushback I would give is that humans, as irrelevant as we are from a planetary perspective, have actually become a primary geologic agent who are collectively changing the biosphere, atmosphere, hydrosphere, cryosphere, and lithosphere (ie: the earth system). But, I agree about nature and the lack of respect as well as the response from Gaia.

[Ian C. Kuzushi]

So to summarize the current information/knowledge as to how Covid-19 got into the world at large:

Both a 'natural' route and a lab escape can reasonably seen as possibilities. Whereby evidence at the moment does not point more to a lab leak; the quoted sentence "That said, the available evidence leans more strongly in one direction than the other. Readers will form their own opinion." is tendentious.

Regarding the 'third option': At this point in time there is no well-founded evidence that credibly points to genetic manipulation of the Covid virus (intending to make it more harmful to humans).

--->
It occurs to me that the 'natural' route of transmission is actually the most frightening if you think it through. An accidental lab leak, or even a genetic manipulation (although currently not credible) would both be examples of human failing or even of reprehensible planned action. But at the same time we would then have specific 'guilty parties' to identify, to admonish or even to punish. And following on from this, as with most accidents of negligence or indeed crimes by identifiable parties, humankind can try to take specific measures (legal; oversight; sanctions etc.) to ensure that it doesn't happen again. In this way the whole disaster potentially becomes easier to grasp and deal with emotionally and, looking to the future, it becomes more 'controllable'.

But the other possibility, 'natural' transmission, the one that many scientists and academics in various fields have been pointing to all the time, is far less controllable in both emotional and practical terms. Ongoing destruction of natural habitats which brings wild animals, and the innumerable viruses they carry, into increasing contact with human environments and new potential hosts, both other animals and then humans. At the same time creating new opportunities for successful mutation - and viruses are great at mutating. Here we have no specific human guilty parties at whom we can cathartically point the finger and sanction. And far less prospect of 'making sure it doesn't happen again'. Because now the 'guilty party' is humankind at a whole, as expressed by huge parts of business/enterprise, governments and so on, which continues this process of environmental destruction. Elements of our whole economic and political system. Meaning ultimately that 'we' by our collective behaviour continue to endanger ourselves, and hence even worse new diseases and pandemics are almost inevitable if we don't make more serious changes to our own collective behaviour.
And that will have consequences. Implications that are much more uncomfortable, unwelcome and indeed disturbing (for many) than the other possibilities. I suspect (yes, in this final sentence I'm speculating) that some of the motivation to argue for a lab leak and even a genetic manipulation stems from this underlying unease about the longer-term implications.

Yes, a lab leak is possible. But, it should be made clear that it is pure speculation and is a theory usually fueled by political motivations.

As humans continue to encroach on novel environments and change familiar ones, we will likely see more pandemics. The "age of pandemics" has long been predicted and we could be in the begining stages of it now.

[windwalker]

In 2012, researchers in the Netherlands and the United States shocked the establishment by publishing studies on making avian influenza contagious through the air among mammals. The work of professors Ron Fouchier and Yoshihiro Kawaoka renewed the debate over whether potential pandemic virus research is too dangerous to conduct.

The most prudent course of action is to impose a moratorium on this mammalian airborne transmissible avian influenza research.

This moratorium is not meant to apply to other gain-of-function research,
as every proposal must be evaluated on its merits and risks.

https://thebulletin.org/2021/09/the-gra ... pathogens/

gain of function research..



mmm what could happen.

The First Plague Pandemic was the first Old World pandemic of plague, the contagious disease caused by the bacterium Yersinia pestis. Also called the Early Medieval Pandemic, it began with the Plague of Justinian in 541 and continued until 750 or 767; at least fifteen or eighteen major waves of plague following the Justinianic plague have been identified from historical records.[1][2] The pandemic affected the Mediterranean Basin most severely and most frequently, but also infected the Near East and Northern Europe.[3] The Roman emperor Justinian I's name is sometimes applied to the whole series of plague epidemics in late Antiquity, as well as to the Plague of Justinian which struck the Eastern Roman Empire in the early 540s.

Pandemics are understood, having a long historical record by which to understand them by.

This virus seems to be quite different not following the pattern of past pandemics as understood by their origins.

[origami_itto]

gain of function research..

mmm what could happen.

Do you have any evidence that COVID-19 is the product of gain of function research or that any gain of function research was being performed at Wuhan or is this just more conjecture? (you don't have to answer)

So far the smoking gun has been somebody applied for a grant in 2018 that was not funded.

But imagination fills in the blanks with whatever supports the desired conclusion.

[Giles]

a primary geologic agent who are collectively changing the biosphere, atmosphere, hydrosphere, cryosphere, and lithosphere (ie: the earth system).

Yes, the Anthropocene era.
From our own perspective we may view ourselves as 'more special' in some respects, and in some situations I think that's acceptable. Every time we build a house or a road, we destroy many other forms of life at that local spot. That doesn't mean we should simply stop building houses or roads. But that is something else than eradicating other forms of life in general. Then again, parasites, harmful bacteria and viruses are also other forms of life (okay, viruses are borderline), and we talk about 'eradicting' some of these without seeing ourselves as monsters. Just about any kind of animal survives and flourishes by consuming/destroying/overcoming other living things. Arguably that's a tragedy of existence, but it's how it is. At least so far.

We are certainly not 'least important', that's just the flip-side of the coin proclaiming we are the pinnacle of God's creation. We have our place, and due to our unique level of intelligence and (self)awareness among creatures on this planet, we also bear a responsibility of curatorship. Which collectively we are currently screwing up badly.
Well, back to Covid-19 ??

[Giles]

But imagination fills in the blanks with whatever supports the desired conclusion.

And once again, the clear consensus on the Novel Coronavirus among scientists/researchers who are actually able to understand what they are looking at - at the molecular level - is that its aquired ability to rock'n'roll with humans seems very much NOT to be the result of human tweaks in the lab, which would have a different kind of signature, but instead is far more consistent with a naturally occuring mutation.
Some might now say: "Yes, but that this mutation makes it infect humans can't be a coincidence." Which would be fallacious, because there will have been innumerable previous mutations which didn't make the grade. It's only the player with the winning lottery ticket who gets rich - all the other lottery losers never appear in the headlines. ---> Or shall we run the headline...?:

MAJOR SHOCK: 137 SOUTH DAKOTA HOUSEWIVES BUY LOTTERY TICKET FOR 2 DOLLARS BUT ALL FAIL TO HIT THE JACKPOT !!

[windwalker]

gain of function research..

mmm what could happen.

Do you have any evidence that COVID-19 is the product of gain of function research or that any gain of function research was being performed at Wuhan or is this just more conjecture? (you don't have to answer)

So far the smoking gun has been somebody applied for a grant in 2018 that was not funded.

But imagination fills in the blanks with whatever supports the desired conclusion.

Innuendo does not lend validity to an argument

Do you have an "evidence" GOF was not conducted there

What is known

"It is clear that the Wuhan Institute of Virology was systematically constructing novel chimeric coronaviruses and was assessing their ability to infect human cells and human-ACE2-expressing mice," says Richard H. Ebright, a molecular biologist at Rutgers University and leading expert on biosafety.

https://www.nationalheraldindia.com/sci ... ore-easily

What this means, in non-technical language, is that Shi set out to create novel coronaviruses with the highest possible infectivity for human cells. Her plan was to take genes that coded for spike proteins possessing a variety of measured affinities for human cells, ranging from high to low.

She would insert these spike genes one by one into the backbone of a number of viral genomes (“reverse genetics” and “infectious clone technology”), creating a series of chimeric viruses. These chimeric viruses would then be tested for their ability to attack human cell cultures (“in vitro”) and humanized mice (“in vivo”). And this information would help
https://republicans-energycommerce.hous ... Letter.pdf

for review


https://www.youtube.com/watch?v=Gdd7dtDaYmM&t=29s

[origami_itto]

But imagination fills in the blanks with whatever supports the desired conclusion.

And once again, the clear consensus on the Novel Coronavirus among scientists/researchers who are actually able to understand what they are looking at - at the molecular level - is that its aquired ability to rock'n'roll with humans seems very much NOT to be the result of human tweaks in the lab, which would have a different kind of signature, but instead is far more consistent with a naturally occuring mutation.
Some might now say: "Yes, but that this mutation makes it infect humans can't be a coincidence." Which would be fallacious, because there will have been innumerable previous mutations which didn't make the grade. It's only the player with the winning lottery ticket who gets rich - all the other lottery losers never appear in the headlines. ---> Or shall we run the headline...?:

MAJOR SHOCK: 137 SOUTH DAKOTA HOUSEWIVES BUY LOTTERY TICKET FOR 2 DOLLARS BUT ALL FAIL TO HIT THE JACKPOT !!

I'm fully in the much scarier "natural evolution" side of this debate. Life, uh, finds a way.

Remember when the board was really into Derren Brown and his film "The System"? His foolproof method for picking 8 straight horse race winners is similar to the coronavirus evolution.

https://youtu.be/9R5OWh7luL4

[windwalker]

And once again, the clear consensus on the Novel Coronavirus among scientists/researchers who are actually able to understand what they are looking at - at the molecular level - is that its aquired ability to rock'n'roll with humans seems very much NOT to be the result of human tweaks in the lab, which would have a different kind of signature, but instead is far more consistent with a naturally occuring mutation.

Might want to check out some of the ways its done, that would not necessarily leave a signature.

Recent incidents involving smallpox, anthrax and bird flu in some of the top US laboratories remind us of the fallibility of even the most secure laboratories, reinforcing the urgent need for a thorough reassessment of biosafety. Such incidents have been accelerating and have been occurring on average over twice a week with regulated pathogens in academic and government labs across the country

http://www.cambridgeworkinggroup.org/

Happened before,
the difference in this case seems to be access to the lab and lab notes to either confirm or not what happened.

There is a lot of circumstantial evidence yet to be proven,
that many have questions about.

[Ian C. Kuzushi]

a primary geologic agent who are collectively changing the biosphere, atmosphere, hydrosphere, cryosphere, and lithosphere (ie: the earth system).

Yes, the Anthropocene era.
From our own perspective we may view ourselves as 'more special' in some respects, and in some situations I think that's acceptable. Every time we build a house or a road, we destroy many other forms of life at that local spot. That doesn't mean we should simply stop building houses or roads. But that is something else than eradicating other forms of life in general. Then again, parasites, harmful bacteria and viruses are also other forms of life (okay, viruses are borderline), and we talk about 'eradicting' some of these without seeing ourselves as monsters. Just about any kind of animal survives and flourishes by consuming/destroying/overcoming other living things. Arguably that's a tragedy of existence, but it's how it is. At least so far.

We are certainly not 'least important', that's just the flip-side of the coin proclaiming we are the pinnacle of God's creation. We have our place, and due to our unique level of intelligence and (self)awareness among creatures on this planet, we also bear a responsibility of curatorship. Which collectively we are currently screwing up badly.
Well, back to Covid-19 ??

If Covid came from a zoonotic jump, it is a result and part of the Anthropocene.

[windwalker]

would be interested in reading


Any evidence that supports the

"natural evolution" side of this debate. Life, uh, finds a way."

That would point to this virus being the product of "natural evolution"

For example

he Yaravirus, which was named after Yara, a mythological Brazilian water goddess, was found in Lake Pampulha, an artificial lagoon in the city of Belo Horizonte, according to a new research paper on BioRxiv.

https://nypost.com/2020/02/12/new-myste ... in-brazil/

Very clear, expected

Or are there virus's who's origins were never found ?

would be interesting reading...