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ChesterView's avatar

Apologies for this lengthy addendum, which is a summary of Nicholas Wade's excellent article on the origins of the virus. It is a long and technical piece which not everyone will have the time (or interest) to get through. But it is, in my view, essential to understanding why the lab origin hypothesis is probable, so here I provide the Cliff's Notes version.

He makes four key arguments for the lab leak hypothesis, some of which are a little abstruse to the non-scientific reader, but here they are:

1) The place of origin. If the virus had an animal origin there would be evidence of the virus in infected animals or humans outside of Wuhan, specifically in the region where these types of coronaviruses are known to come from. In a year of looking, no such evidence has materialized.

2) No evidence of gradual zoonotic mutation. In every other case of a virus making a jump from an animal host to a human host, it has gone through a process of evolutionary development which incrementally makes it more adapted to humans. This was the case for SARS and for MERS. In the case of COVID the virus emerged fully suited to human infection with no evidence of less successful antecedents.

3) The furin cleavage site. (Here we get technical.) The spike protein on the virus is composed of two separate sub-units, known as S1 and S2. Cleaving the spike protein into these two subunits is the key mechanism that allows the virus entry into a human cell. However it takes a specific enzyme on the surface of a cell to do this cleaving. There are many types of enzymes that can potentially cleave a protein, depending on the particular amino acids that comprise the protein. However only in humans is there the furin enzyme, which does its protein cutting thing in the presence of a specific amino acid sequence on the protein to be cleaved. COVID is the only coronavirus yet discovered that has this ‘furin cleavage site’ in its spike protein (between the S1 and S2 sub-units, naturally).

4) Human specific codons. (Here we get much more technical, so I will try to compress this a bit.) Proteins are simply chains of amino acids. Each amino acid is built from three units (nucleotides) of DNA, which are called codons. It turns out that there is more than one combination of the four DNA nucleotides (A, C, G, T) that produces the same amino acid. For example, the codons CGT and CGC both produce the amino acid arginine. But the key fact is that humans have a definite preference for a specific codon producing a given amino acid. It just so happens that in the furin cleavage site the codons that produce arginine are specific to humans and are very rare in the other parts of the coronavirus genome.

These are the technical arguments upon which Wade’s lab origin hypothesis rests. I find them compelling, particularly the last two points. The full paper can be found here: thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/ and I recommend it highly.

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Spartacus's avatar

Re: Item 1 - Just wrong. There are closely related viruses as far as Vietnam. I don't have the cite at my fingertips, but I saw that one. This argument is also like the old "missing link" stories that aimed to prove humans weren't evolved from lesser primates because we couldn't find all of the steps. No, you can't expect to find all the steps as suggested. That's ridiculous nonsense. RNA viruses mutate like mad. Instead you use evolutionary trees, and look at the apparent rate of mutations. There are multiple hypotheses for how SARS-CoV-2 adapted to humans. One is a set of men who got very sick for quite a while. Immune compromised might be another. It is doubtful we will find anything crystal clear. Reality isn't like that.

Re: Item 2 - Just wrong. Wade is either grossly ignorant, or deliberately falsifying here. There is plenty of evidence of natural origin. Not hard to find such studies. Here's one.

(May 2020) A close relative of SARS-CoV-2 found in bats offers more evidence it evolved naturally.

https://www.sciencedaily.com/releases/2020/05/200511142202.htm

Re: Item 3 - Just wrong. Furin is present and it's highly conserved in mammals. (May 2020) Structural and functional modelling of SARS-CoV-2 entry in animal models.

https://www.nature.com/articles/s41598-020-72528-z

"... in a panel of animal models, i.e. guinea pig, dog, cat, rat, rabbit, ferret, mouse, hamster and macaque. Here we showed that ACE2, but not TMPRSS2 or Furin, has a higher level of sequence variability in the Spike protein interaction surface, which greatly influences Spike protein binding mode.... TMPRSS2 and Furin are sufficiently similar in the considered hosts not to drive susceptibility differences.

Re: Item 4 - Just wrong. There is NO SUCH THING as a human specific codon! There are mostly mild differences in the production of tRNA for different codons. But you can use a human sequence in E. coli, and vice versa. The codon optimization just gives you somewhat higher production, that's all. So no. This is just not true.

Bluntly put, Wade's article is utter garbage. Wade is not a scientist. The people pimping it (like Trish Wood) are not scientists. The whole business of "Wade's article" getting such intense press I find highly suspect. So should you. Don't be so damn gullible FFS!

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ChesterView's avatar

Thanks for the detailed reply.

I am not a scientist, just a reasonably bright guy that reads a lot, so this will have to be fought out by folks at a higher pay grade than me. Of course, the lab theory is not strictly a product of Mr. Wade. Nicholson Baker made a similar case in a New York Magazine article in January and there were folks that preceded him, going back the better part of a year (Josh Rogin, Saager Enjeti, Bret Weinstein, Matt Ridley, Crystal Ball, Steve Hilton, etc.) although they were largely met with derision from the MSM and the designated scientific establishment.

As I say, I am not a scientist and maybe you are. But now that the battle has been joined, let's hope that the experts - all of the experts - are allowed to get to the bottom of this thing.

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Spartacus's avatar

I appreciate the considered response. I am a scientist. I have publications in epidemiology, (modeling and field), biodefense, terorrism, gene therapy (patents), and policy. I do vaccine development. I've got vaccines for Ebola, COVID-19, West Nile virus, Hanta, and a few others in the freezer.

All of the parties mentioned made their cases with innuendo, pointing to Chinese governmental behavior. None of them made a case worth a worn out t-shirt. I think it is all propaganda mixed with incompetent dabbling of the Dunning Kreuger variety. (Although the real Dunning Kreuger graph is much less damning than the meme variety.)

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Spartacus's avatar

Citation date for Item 3's cite should be (sept 2020)

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DPFlorida's avatar

Trish Wood did an excellent deep-dive interview with the author of this article on her podcast, Trish Wood Is Critical.

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Blissex's avatar

«1) The place of origin. If the virus had an animal origin there would be evidence of the virus in infected animals or humans outside of Wuhan, specifically in the region where these types of coronaviruses are known to come from. In a year of looking, no such evidence has materialized.»

* If it was man-made it could have been made somewhere else and deliberately or accidentally spread in Wuhan in order to cripple a key node of the chinese economy.

* If it was of natural origin it could also have started somewhere else and collected, selected, and deliberately spread in Wuhan.

Regardless of its origin, the big deal that the smear campaigns seems design to obfuscate is what happened after the Wuhan outbreak: the test-trace-isolate approach in China resulted in less than 5,000 deaths over a year in a population over 3 times larger than the USA one where there have been over 500,000 deaths, and this without mass lock-downs, or mass vaccination.

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ChesterView's avatar

The fact that you use the phrase 'smear campaign' leads me to think that you take the current hard look at a possible lab leak to be an indictment of China. I don't see it that way - certainly not in my case at any rate. I would be far angrier with the hubris and duplicity of our medical authorities in funding this research (and then covering it up) than with the Chinese if an accidental lab leak had taken place.

You also use the phrase 'design(ed) to obfuscate' to characterize such an investigation. Again I disagree as to the motivation for finding out. If it was a lab leak then this has dramatic implications for whether this research should be done at all. Perhaps more importantly, it casts the credibility of Fauci and the medical research community more generally into question on all of the issues that it has opined on, most importantly those regarding vaccines, therapeutics, and confinement.

As to your points that speak to the virus having been hatched someplace else and then planted in Wuhan, I suppose anything is possible. This is the official Chinese position, or is at least one that they trot out periodically when they are feeling particularly defensive. More specifically, they have claimed that the virus was created in our bio lab at Ft. Detrick, MD and then deliberately released at the worldwide military games in Wuhan in the fall of '19 in order to sabotage the Chinese economy.

Godfree Roberts, who I believe lives in China and is quite sympathetic to the Chinese viewpoint, has also promoted this theory. Again, I suppose anything is possible but Occam's razor generally cuts in the right direction and with the most efficiency.

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SH's avatar

Precisely the point - whether GOF research should be done at all ...

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Citizen of Banana Republic's avatar

"resulted in less than 5,000 deaths over a year in a population over 3 times larger than the USA"

Regardless of the truth in those numbers, which is to say I doubt there's much, I've wondered why it was that China took such unprecedented steps to eradicate covid if its scientists weren't familiarized with it. Almost like its leading scientists knew exactly what it was (at the time).

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Blissex's avatar

«Regardless of the truth in those numbers, which is to say I doubt there's much»

Similar sickness and death rates have been reported by China-Taiwan, Korea-south, Kerala, New Zealand, Vietnam and Japan. It is shocking to imagine that they are all complicit with Chinese Communist Party. :-)

«I've wondered why it was that China took such unprecedented steps to eradicate covid if its scientists weren't familiarized with it. Almost like its leading scientists knew exactly what it was (at the time).»

The same approach with the same results was taken by China-Taiwan, Korea-south, Kerala, New Zealand, Vietnam and Japan. It is shocking to imagine that the leading scientists in those countries “knew exactly what it was”.

Or perhaps your comment is made entirely of handwaving smears.

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Citizen of Banana Republic's avatar

You're ignoring how China led with its unprecedented steps and many other countries followed, including us, because, well, they were unprecedented.

But haven't you ever wondered why China locked down - and I mean *locked down*, China style - many of its major cities if covid wasn't killing its people? Or that China was deathly afraid of what it released. Or both?

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Blissex's avatar

«You're ignoring how China led with its unprecedented steps and many other countries followed, including us, because, well, they were unprecedented.»

That the steps were "unprecedented" seems to me pure hallucinatory smears, here is appropriately for this post some "fact checking", for example in strongly "anti-communist" China-Taiwan similar steps were not at all unprecedented, they were part of a plan:

https://edition.cnn.com/2020/10/29/asia/taiwan-covid-19-intl-hnk/

“Authorities activated the island's Central Epidemic Command Center, which was set up in the wake of SARS, to coordinate between different ministries. The government also ramped up face mask and protective equipment production to make sure there would be a steady supply of PPE. The government also invested in mass testing and quick and effective contact tracing. Former Taiwanese Vice President Chen Chien-jen, who is an epidemiologist by training, said lockdowns are not ideal. Chen also said that the type of mass-testing schemes undertaken in mainland China, where millions of people are screened when a handful of cases are detected, are also unnecessary. "Very careful contact tracing, and very stringent quarantines of close contacts are the best way to contain Covid-19," he said.”

The "anti-communist" governments of China-Taiwan and Singapore accordingly took "unprecedented" measures that had been carried out in previous epidemics at the end of December 2020:

https://taiwantoday.tw/news.php?unit=2,6,10,15,18&post=168773

“Publication Date: January 02, 2020

Taiwan has implemented more stringent inspection measures for inbound flights from Wuhan, China, following an outbreak of pneumonia in the city, according to the Centers for Disease Control under the Ministry of Health and Welfare Dec. 31, 2019.”

https://www.straitstimes.com/singapore/ministry-of-health-issues-advisory-on-viral-pneumonia-outbreak-in-chinas-wuhan

“Travellers arriving at Changi Airport from Wuhan to undergo temperature screening after pneumonia outbreak

Published Jan 2, 2020, 9:01 pm SGT”

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Citizen of Banana Republic's avatar

CCP welded shut doors of repeat offenders of its lockdowns. Entire cities were shut down. No biz, no mingling, no food except what the local govt had to offer. UNPRECEDENTED.

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Blissex's avatar

“Entire cities were shut down. No biz, no mingling, no food except what the local govt had to offer. UNPRECEDENTED.”

Further fact checking of this moronic handwaving hallucination with a simple web search returns for example:

https://www.nationalgeographic.com/history/article/how-cities-flattened-curve-1918-spanish-flu-pandemic-coronavirus/

“In 1918, a San Francisco health officer shot three people when one refused to wear a mandatory face mask. In Arizona, police handed out $10 fines for those caught without the protective gear. But eventually, the most drastic and sweeping measures paid off. After implementing a multitude of strict closures and controls on public gatherings, St. Louis, San Francisco, Milwaukee, and Kansas City responded fastest and most effectively: Interventions there were credited with cutting transmission rates by 30 to 50 percent. New York City, which reacted earliest to the crisis with mandatory quarantines and staggered business hours, experienced the lowest death rate on the Eastern seaboard. [...]

By comparing fatality rates, timing, and public health interventions, they found death rates were around 50 percent lower in cities that implemented preventative measures early on, versus those that did so late or not at all. The most effective efforts had simultaneously closed schools, churches, and theaters, and banned public gatherings. This would allow time for vaccine development (though a flu vaccine was not used until the 1940s) and lessened the strain on health care systems.”

Is the National Geographic a "communist" mouthpiece that is out to lie about the “UNPRECENTED” idiocy of your hallucinations?

Here is another source:

https://history.com/news/spanish-flu-pandemic-response-cities

“When a flu outbreak at a nearby military barracks first spread into the St. Louis civilian population, Starkloff wasted no time closing the schools, shuttering movie theaters and pool halls, and banning all public gatherings. There was pushback from business owners, but Starkloff and the mayor held their ground. When infections swelled as expected, thousands of sick residents were treated at home by a network of volunteer nurses. Dehner says that because of these precautions, St. Louis public health officials were able to “flatten the curve” and keep the flu epidemic from exploding overnight as it did in Philadelphia.”

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Citizen of Banana Republic's avatar

I don't think your comparing today's CCP to America 100 years ago is the win you think it is.

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Blissex's avatar

«I don't think»

I have been fact checking that! :-) Here is one more fact check:

«comparing today's CCP to America 100 years ago»

What about Singapore, with a hard-right anti-communist government, a little over 15 years ago?

https://mothership.sg/2020/02/sars-wuhan-outbreak-explained/

“From then on, Singapore's SARS death toll started rising with another four deaths reported by Mar. 31, 2003, according to MICA.

With deaths inducing panic among parents, and the virus spreading rapidly, the government announced the closure of schools on Mar. 27, 2003 — which happened to be during the March school holidays that year. From preschools to junior colleges, schools would remained closed till Apr. 6, 2003, though the period of closure was subsequently extended.

Following incidents of quarantined individuals breaking the requirement to stay at home, MOH announced on Apr. 10 that surveillance cameras would be placed in homes of those quarantined. The next day, Apr. 11, mobile thermal scanners were installed at Changi Airport. On Apr. 12, it was decided that those who flouted home quarantines would be required to wear electronic tags. Later that month, on Apr. 24, the penalties for breaking quarantine were stiffened — this included possible jail sentences for quarantine breakers and higher fines. On May 2, a 50-year-old was arrested and later jailed for breaking his quarantine order twice. [...] According to the WHO, dozens of police officers wearing surgical masks cleared the Pasir Panjang wholesale market of people on Apr. 19.

They also built barricades and prohibited people from entering.

It would later be announced that the vegetable market, Singapore's largest, would be closed for 10 days, though this was later extended to 15 days. And all this was because in the month of April, a vegetable seller who worked at the market had fallen ill.”

https://www.straitstimes.com/singapore/sars-in-singapore-timeline

“March 24: The Infectious Diseases Act is invoked. About 740 people are home-quarantined for 10 days. [...] March 27: All schools are shut till April 6. Those who die of Sars must be cremated within 24 hours. [...] March 29: Temperature checks are introduced for all passengers entering Singapore through Changi Airport.”

That was all "UNPRESIDENTED"! :-)

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SH's avatar

Huh? Initially the entire Hubei province was shut down ...

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Blissex's avatar

Not quite, and anyhow other places occasionally: it takes time to prepare for mass testing and trace-isolate. The boast by the ex vice-president of China-Taiwan that no lock-down is ever needed is quite excessive. But there is a big difference between a mass lock-down of an entire country for a year and a some weeks in some place or another, that said the Wuhan metropolitan area has 10-11 million people, so it has more people than many countries.

For an idea of the approach taken:

https://www.bbc.com/news/world-asia-54504785

“The Chinese city of Qingdao is testing its entire population of nine million people for Covid-19 over a period of five days. The mass testing comes after the discovery of a dozen cases linked to a hospital treating coronavirus patients arriving from abroad. In May, China tested the entire city of Wuhan - home to 11 million people and the epicentre of the global pandemic. The country has largely brought the virus under control. That is in stark contrast to other parts of the world, where there are still high case numbers and lockdown restrictions of varying severity. In a statement posted to Chinese social media site Weibo, Qingdao's Municipal Health Commission said six new cases and six asymptomatic cases had been discovered.”

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SH's avatar

So we fu...d up there, too ...

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Blissex's avatar

«So we fu...d up there, too ...»

BTW not everywhere, Bloomberg BusinessWeek has also reported that "communist" Minnesota has done a mass testing plan, even if not quite on such a large scale and speed as in other countries:

https://www.bloomberg.com/news/features/2021-01-14/covid-testing-minnesota-is-the-best-state-for-checking-for-coronavirus

“The U.S. Needs More Covid Testing, and Minnesota Has Found a Way Get everybody in an entire state to spit into a tube? You betcha.”

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SH's avatar

So if only Minn. could figure out a way to get everyone to properly mask up ...

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Blissex's avatar

«So we fu...d up there, too ...»

And that is the real story, not vaccinations, not lock-down, not masks, which are all distractions from the stark comparison between neoliberal countries and civilized countries. In the USA, UK, etc. the priority has been whichever policy impacted least the upper-middle and upper classes, and made the best marketing copy for "big pharma". It is not as if test-trace-isolate was unknown to "atlantic" epidemiologists, here are articles written early in 2020 be the UK Chief Medical Officer and Chief Science Officer:

https://www.theguardian.com/world/2020/apr/14/england-coronavirus-testing-has-not-risen-fast-enough-science-chief

“Sir Patrick Vallance says testing needs to be done at scale to find outbreaks and isolate people [...] Sir Patrick Vallance’s comments echo those of Chris Whitty, England’s chief medical officer, who said a week ago that Germany “got ahead” in testing people for Covid-19 and that the UK needed to learn from that.”

Eventually, even Bloomberg BusinessWeek broke with the neoliberal ideology that not getting infected and not infecting others is a matter of individual choice:

https://www.bloomberg.com/news/features/2020-10-01/coronavirus-pandemic-how-the-u-s-can-implement-rapid-covid-testing

“Better, Faster Testing Is the Path to an American Comeback

Imagine going safely to a bar, or a wedding, or parent-teacher night, without a vaccine. It’s still possible, if the U.S. can get its act together.”

On this the Democratic politicians and press have not at all criticized the Trump policies, have respected that neoliberal ideology, just arguing distractingly about how hard lock-downs should be and how fabulous "big pharma saviours of humanity" have been.

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SH's avatar

Yup, we are fuc..ing up there, too, and have been for decades - "reaching across the 'bipartisan' aisle" to achieve "bipartisan" consensus in the endeavor ...

What I think you may be missing that lockdowns are not uniformally bad in any circumstance, but that folks in lockdown should be provided with the means to satisfy their basic needs during those lockdowns. Sorry, a couple of $2000 checks ain't gonna cut it ...

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DarkSkyBest's avatar

When was the Wuhan outbreak?

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Blissex's avatar

That is a rather vague and difficult questions, because "outbreak" is not well defined: in China and elsewhere there are "outbreaks" of something almost every year, and SARS-2 symptoms, at least initially, can easily be mistake for something else, and many people infected with SARS-2 have no symptoms or trivial symptoms, so the SARS-2 outbreak in Wuhan could have started well before it got noticed and recognized as a new thing.

As to noticed and as a new thing, that was sometimes in December 2019. The official UK government timeline for example gives "end of December":

https://www.gov.uk/government/publications/wuhan-novel-coronavirus-background-information/wuhan-novel-coronavirus-epidemiology-virology-and-clinical-features

«On 31 December 2019, the World Health Organization (WHO) was informed of a cluster of cases of pneumonia of unknown cause detected in Wuhan City, Hubei Province, China.»

The WHO statement has these details:

«Symptom onset of the 41 confirmed nCoV cases ranges from 8 December 2019 to 2 January 2020. No additional cases have been detected since 3 January 2020. The clinical signs and symptoms reported are mainly fever, with a few cases having difficulty in breathing, and chest radiographs showing invasive pneumonic infiltrates in both lungs.»

The WHO a few days later called it “Pneumonia of unknown cause – China”. Wikipedia has a 2019 timeline that says:

https://en.wikipedia.org/wiki/Timeline_of_the_COVID-19_pandemic_in_2019

«Phylogenetics estimates that SARS-CoV-2 arose in October or November 2019. It is not known whether the virus itself evolved in wildlife populations or if its distinctive spike proteins were selected for after zoonotic transfer to humans. A September 2020 review noted "The possibility that the COVID-19 infection had already spread to Europe at the end of last year is now indicated by abundant, even if partially circumstantial, evidence", including pneumonia case numbers and radiology in France and Italy in November and December. RT-PCR (Reverse transcription polymerase chain reaction) testing of untreated wastewater samples from Brazil and Italy have suggested detection of SARS-CoV-2 as early as November and December 2019, respectively, but the methods of such sewage studies have not been optimised, many have not been peer reviewed, details are often missing, and there is a risk of false positives due to contamination or if only one gene target is detected. Antibodies to SARS-CoV-2 receptor-binding domain were reported in 111 (11.6%) of 959 asymptomatic participants in a lung cancer screening trial in Italy from September 2019, which the authors claim may indicate an earlier start to the COVID-19 pandemic. The World Health Organization stated it was reviewing the results, seeking verification of the neutralization results, and that "the possibility that the virus may have silently circulated elsewhere cannot be ruled out"»

In any case the timeline is an interesting detail for amusement, the real story is that the government of China-Taiwan and other thoroughly capitalist countries as well as as "communist" ones have had negligible sickness and deaths rates thanks to state funded and organized test-trace-isolate, with nearly no lockdowns and nearly no business or jobs losses, and are in no hurry to be guinea pigs for vaccines.

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DarkSkyBest's avatar

But you have done so well, you don't need the vaccine! Cheers!

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Godfree Roberts's avatar

Yet every expert rubbished the lab leak hypothesis when it was first proposed. And all 17 of the WHO inspectors plus their 17 Chinese counterparts ranked it least likely.

It also requires the virus to be able to time travel, since it was circulating in the USA 3-5 years ago. https://johnmenadue.com/who-had-covid-first/

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Adam's avatar

Okay, so what are you proposing then? That the virus began naturally somewhere years ago; has been circulating but somehow not causing a detectable outbreak; somehow made its way to Wuhan in late 2019; and then started an outbreak there?

Is that your hypothesis? How many of those 17 WHO inspectors have ranked your hypothesis as likely? If you think it's significant that they ranked the lab leak hypothesis least likely, then surely you have to accept that it's significant if they didn't rank your hypothesis higher? Or is their opinion only relevent for hypotheses you don't like, but doesn't count when it's yours?

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Spartacus's avatar

The Wade article is innuendo with zero scientific content

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ChesterView's avatar

What specific points do you object to and what is your background?

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Skutch's avatar

He's MarkS from last week under a new sock puppet name but still pretending to be a scientist.

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Spartacus's avatar

See above. I responded to you. Wade's article is drivel.

PhD microbiology. Vaccine research and development. Epidemiology papers. Chapters in West Point sponsored books on biodefense and terrorism.

And you? What is yours?

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Skutch's avatar

Okay, then show them to me.

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Matthew's avatar

I admittedly haven’t read much on the lab origin stuff, as Wade’s article got just a *bit* too technical for me and my eyes glazed over, but has anybody reconciled the lab leak theory with claims based on analyzing sewage (I think?) and finding reason to believe the virus has been in USA/Europe for many months longer than initially believed? Can the two theories even coexist or are they in competition? I really haven’t looked much into either one but it seems like they both have their own set of implications that kind of compete with each other.

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RAH's avatar

All valid hypotheses compete with one another to some extent. In the case of the Wuhan story, if you put the two major hypotheses respectively on a scale, the evidence is tipping in favor of a lab release. Give Wade's article another go; it's worth the effort.

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Madjack's avatar

It was a great article. Gain of function is reminiscent of Frankenstein. Just smaller

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ChesterView's avatar

Or much larger, if total damage is taken into consideration. :)

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Madjack's avatar

True. I meant the organism, not the end results. I would gladly join a mob to hunt down Fauci though!!

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ChesterView's avatar

I knew what you meant. Hence the smiley. :)

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Matthew's avatar

Gotcha, I’ll give it another look, thanks. Sorry my question was vague and I probably shouldn’t have asked if they “compete” per se when I was really asking if they’re mutually exclusive. I’ll give Wade’s article that second look though and I imagine that will give me a different perspective regardless.

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