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Evidence on the origin of Covid leads to lab in Wuhan – Former NY Times Science Editor

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In the millions of articles, opinion pieces, and news stories written about Covid there is one topic that is more important than all the others.  It’s more important than masks, vaccines, or lockdown measures.  The origin of the virus is critical because no matter how many people die from covid, or how many businesses are wiped out, it’s critical that IF the next virus can be stopped, it mu st be.  

A science writer named Nicholas Wade has written the most thorough study on the origins of Covid to be released to the public.  Wade has worked with Nature, Science, and the New York Times, but this article was released on the public platform Medium.   In this article Wade goes through three possible scenarios and then draws the most likely conclusion.  This is a long read, but it might be the most important article yet written during this pandemic.

Here is the beginning of this extensive article from Medium. Click  here to read the full article on Medium.

Origin of Covid — Following the Clues

Did people or nature open Pandora’s box at Wuhan?

The Covid-19 pandemic has disrupted lives the world over for more than a year. Its death toll will soon reach three million people. Yet the origin of pandemic remains uncertain: the political agendas of governments and scientists have generated thick clouds of obfuscation, which the mainstream press seems helpless to dispel.

In what follows I will sort through the available scientific facts, which hold many clues as to what happened, and provide readers with the evidence to make their own judgments. I will then try to assess the complex issue of blame, which starts with, but extends far beyond, the government of China.

By the end of this article, you may have learned a lot about the molecular biology of viruses. I will try to keep this process as painless as possible. But the science cannot be avoided because for now, and probably for a long time hence, it offers the only sure thread through the maze.

The virus that caused the pandemic is known officially as SARS-CoV-2, but can be called SARS2 for short. As many people know, there are two main theories about its origin. One is that it jumped naturally from wildlife to people. The other is that the virus was under study in a lab, from which it escaped. It matters a great deal which is the case if we hope to prevent a second such occurrence.

I’ll describe the two theories, explain why each is plausible, and then ask which provides the better explanation of the available facts. It’s important to note that so far there is no direct evidence for either theory. Each depends on a set of reasonable conjectures but so far lacks proof. So I have only clues, not conclusions, to offer. But those clues point in a specific direction. And having inferred that direction, I’m going to delineate some of the strands in this tangled skein of disaster.

A Tale of Two Theories

After the pandemic first broke out in December 2019, Chinese authorities reported that many cases had occurred in the wet market — a place selling wild animals for meat — in Wuhan. This reminded experts of the SARS1 epidemic of 2002 in which a bat virus had spread first to civets, an animal sold in wet markets, and from civets to people. A similar bat virus caused a second epidemic, known as MERS, in 2012. This time the intermediary host animal was camels.

The decoding of the virus’s genome showed it belonged to a viral family known as beta-coronaviruses, to which the SARS1 and MERS viruses also belong. The relationship supported the idea that, like them, it was a natural virus that had managed to jump from bats, via another animal host, to people. The wet market connection, the only other point of similarity with the SARS1 and MERS epidemics, was soon broken: Chinese researchers found earlier cases in Wuhan with no link to the wet market. But that seemed not to matter when so much further evidence in support of natural emergence was expected shortly.

Wuhan, however, is home of the Wuhan Institute of Virology, a leading world center for research on coronaviruses. So the possibility that the SARS2 virus had escaped from the lab could not be ruled out. Two reasonable scenarios of origin were on the table.

From early on, public and media perceptions were shaped in favor of the natural emergence scenario by strong statements from two scientific groups. These statements were not at first examined as critically as they should have been.

“We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin,” a group of virologists and others wrote in the Lancet on February 19, 2020, when it was really far too soon for anyone to be sure what had happened. Scientists “overwhelmingly conclude that this coronavirus originated in wildlife,” they said, with a stirring rallying call for readers to stand with Chinese colleagues on the frontline of fighting the disease.

Contrary to the letter writers’ assertion, the idea that the virus might have escaped from a lab invoked accident, not conspiracy. It surely needed to be explored, not rejected out of hand. A defining mark of good scientists is that they go to great pains to distinguish between what they know and what they don’t know. By this criterion, the signatories of the Lancet letter were behaving as poor scientists: they were assuring the public of facts they could not know for sure were true.

It later turned out that the Lancet letter had been organized and drafted by Peter Daszak, president of the EcoHealth Alliance of New York. Dr. Daszak’s organization funded coronavirus research at the Wuhan Institute of Virology. If the SARS2 virus had indeed escaped from research he funded, Dr. Daszak would be potentially culpable. This acute conflict of interest was not declared to the Lancet’s readers. To the contrary, the letter concluded, “We declare no competing interests.”

Virologists like Dr. Daszak had much at stake in the assigning of blame for the pandemic. For 20 years, mostly beneath the public’s attention, they had been playing a dangerous game. In their laboratories they routinely created viruses more dangerous than those that exist in nature. They argued they could do so safely, and that by getting ahead of nature they could predict and prevent natural “spillovers,” the cross-over of viruses from an animal host to people. If SARS2 had indeed escaped from such a laboratory experiment, a savage blowback could be expected, and the storm of public indignation would affect virologists everywhere, not just in China. “It would shatter the scientific edifice top to bottom,” an MIT Technology Review editor, Antonio Regalado, said in March 2020.

A second statement which had enormous influence in shaping public attitudes was a letter (in other words an opinion piece, not a scientific article) published on 17 March 2020 in the journal Nature Medicine. Its authors were a group of virologists led by Kristian G. Andersen of the Scripps Research Institute. “Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus,” the five virologists declared in the second paragraph of their letter.

Unfortunately this was another case of poor science, in the sense defined above. True, some older methods of cutting and pasting viral genomes retain tell-tale signs of manipulation. But newer methods, called “no-see-um” or “seamless” approaches, leave no defining marks. Nor do other methods for manipulating viruses such as serial passage, the repeated transfer of viruses from one culture of cells to another. If a virus has been manipulated, whether with a seamless method or by serial passage, there is no way of knowing that this is the case. Dr. Andersen and his colleagues were assuring their readers of something they could not know.

The discussion part their letter begins, “It is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus”. But wait, didn’t the lead say the virus had clearly not been manipulated? The authors’ degree of certainty seemed to slip several notches when it came to laying out their reasoning.

The reason for the slippage is clear once the technical language has been penetrated. The two reasons the authors give for supposing manipulation to be improbable are decidedly inconclusive.

First, they say that the spike protein of SARS2 binds very well to its target, the human ACE2 receptor, but does so in a different way from that which physical calculations suggest would be the best fit. Therefore the virus must have arisen by natural selection, not manipulation.

If this argument seems hard to grasp, it’s because it’s so strained. The authors’ basic assumption, not spelt out, is that anyone trying to make a bat virus bind to human cells could do so in only one way. First they would calculate the strongest possible fit between the human ACE2 receptor and the spike protein with which the virus latches onto it. They would then design the spike protein accordingly (by selecting the right string of amino acid units that compose it). But since the SARS2 spike protein is not of this calculated best design, the Andersen paper says, therefore it can’t have been manipulated.

But this ignores the way that virologists do in fact get spike proteins to bind to chosen targets, which is not by calculation but by splicing in spike protein genes from other viruses or by serial passage. With serial passage, each time the virus’s progeny are transferred to new cell cultures or animals, the more successful are selected until one emerges that makes a really tight bind to human cells. Natural selection has done all the heavy lifting. The Andersen paper’s speculation about designing a viral spike protein through calculation has no bearing on whether or not the virus was manipulated by one of the other two methods.

The authors’ second argument against manipulation is even more contrived. Although most living things use DNA as their hereditary material, a number of viruses use RNA, DNA’s close chemical cousin. But RNA is difficult to manipulate, so researchers working on coronaviruses, which are RNA-based, will first convert the RNA genome to DNA. They manipulate the DNA version, whether by adding or altering genes, and then arrange for the manipulated DNA genome to be converted back into infectious RNA.

Only a certain number of these DNA backbones have been described in the scientific literature. Anyone manipulating the SARS2 virus “would probably” have used one of these known backbones, the Andersen group writes, and since SARS2 is not derived from any of them, therefore it was not manipulated. But the argument is conspicuously inconclusive. DNA backbones are quite easy to make, so it’s obviously possible that SARS2 was manipulated using an unpublished DNA backbone.

And that’s it. These are the two arguments made by the Andersen group in support of their declaration that the SARS2 virus was clearly not manipulated. And this conclusion, grounded in nothing but two inconclusive speculations, convinced the world’s press that SARS2 could not have escaped from a lab. A technical critique of the Andersen letter takes it down in harsher words.

Science is supposedly a self-correcting community of experts who constantly check each other’s work. So why didn’t other virologists point out that the Andersen group’s argument was full of absurdly large holes? Perhaps because in today’s universities speech can be very costly. Careers can be destroyed for stepping out of line. Any virologist who challenges the community’s declared view risks having his next grant application turned down by the panel of fellow virologists that advises the government grant distribution agency.

The Daszak and Andersen letters were really political, not scientific statements, yet were amazingly effective. Articles in the mainstream press repeatedly stated that a consensus of experts had ruled lab escape out of the question or extremely unlikely. Their authors relied for the most part on the Daszak and Andersen letters, failing to understand the yawning gaps in their arguments. Mainstream newspapers all have science journalists on their staff, as do the major networks, and these specialist reporters are supposed to be able to question scientists and check their assertions. But the Daszak and Andersen assertions went largely unchallenged.

Doubts about natural emergence

Natural emergence was the media’s preferred theory until around February 2021 and the visit by a World Health Organization commission to China. The commission’s composition and access were heavily controlled by the Chinese authorities. Its members, who included the ubiquitous Dr. Daszak, kept asserting before, during and after their visit that lab escape was extremely unlikely. But this was not quite the propaganda victory the Chinese authorities may have been hoping for. What became clear was that the Chinese had no evidence to offer the commission in support of the natural emergence theory.

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 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.

And as long as that remains the case, it’s logical to pay serious attention to the alternative conjecture, that SARS2 escaped from a lab.

Why would anyone want to create a novel virus capable of causing a pandemic?

To read the rest of this article on Medium click here

Nicholas Wade

I’m a science writer and have worked on the staff of Nature, Science and, for many years, on the New York Times. [email protected]

 

By the way.. Medium is a fascinating place.  If you haven’t checked it out yet here’s a link to medium.com.

From About Medium:

We’re an open platform where 170 million readers come to find insightful and dynamic thinking. Here, expert and undiscovered voices alike dive into the heart of any topic and bring new ideas to the surface. Our purpose is to spread these ideas and deepen understanding of the world.

After 15 years as a TV reporter with Global and CBC and as news director of RDTV in Red Deer, Duane set out on his own 2008 as a visual storyteller. During this period, he became fascinated with a burgeoning online world and how it could better serve local communities. This fascination led to Todayville, launched in 2016.

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COVID-19

Poilievre among those marching with soldier charged for criticizing vaccine mandates

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By Lee Berthiaume in Ottawa

Conservative leadership candidate Pierre Poilievre joined the final leg of a march led by a Canadian soldier charged for speaking out against COVID-19 vaccine requirements that has sparked promises⁠ — and fears — of a new wave of protests in the capital.

James Topp was charged in February with two counts of conduct to the prejudice of good order and discipline for comments made while wearing his uniform, and has since been leading a four-month march to the capital from Vancouver.

His march has been supported by many of the same figures involved in the “Freedom Convoy” that snarled downtown Ottawa for weeks until police used force to end what they and the government described as an illegal occupation.

His arrival in the capital and promises of a new round of protests starting Canada Day have set residents on edge. Ottawa Mayor Jim Watson and the city’s interim police chief, Steve Bell, have promised to crack down on any illegal activity.

Poilievre walked alongside Topp for about half an hour after the two met in the parking lot of a strip mall west of downtown Ottawa shortly before noon, where hundreds of people had gathered to see the army reservist.

Video of the meeting shows Poilievre citing to Topp a famous quote by then-prime minister John Diefenbaker about being a “free Canadian” when the latter signed the Canadian Bill of Rights in 1960, before expressing his opposition to vaccine mandates.

When Topp says he wants the reinstatement and reparations for anyone who lost their job because of vaccine mandates, Poilievre said: “Everybody who lost their job simply because of a COVID mandate should be restored to their job, no question about it.”

The two also spoke about the divisions within Canada, with Poilievre saying: “People are desperate for hope … I think it’s time to put this country back together, and heal the wounds and reunite our country.”

The two were then followed by about 200 supporters, many of them carrying Canadian flags and some sporting camouflaged backpacks and other gear, as they walked down the sidewalk of a major street for about half an hour before Poilievre left.

Poilievre’s appearance with Topp comes as the presumed Conservative leadership front-runner has been accused of unabashedly cozying up to anti-vaccine protesters and other groups associated with the “Freedom Convoy.”

Topp has said he has no plans to lead an occupation of the capital, and invited Ottawa police to work with him to facilitate his march through the city to the National War Memorial.

However, an organizer for a group calling itself Veterans 4 Freedom said in a recent video posted to YouTube that it plans to set up a semi-permanent camp east of Ottawa called “Camp Eagle” and hold events in the city all summer.

While police have since managed to prevent similar protests from taking over the city, stopping planned demonstrations from getting out of hand during Canada Day is likely to be complicated by the presence of thousands of people celebrating the holiday.

The charges against Topp relate to two videos posted online in the winter in which the army reservist appears in uniform criticizing vaccine requirements for military personnel and other federal employees.

Canadian Armed Forces members are severely restricted in the comments they can make while in uniform, particularly when it comes to criticizing government policies, in large part to protect the military from any perception of politicization.

His lawyer has argued such restrictions should not apply to policies that affect Armed Forces members personally.

Prime Minister Justin Trudeau on Thursday said police are taking their responsibility to keep people safe during Canada Day celebrations “very seriously,” while Ontario Premier Doug Ford called on those intending to protest in Ottawa to respect the law.

“Folks, be considerate this weekend, you’re going to Ottawa, be considerate. It’s Canada Day, we’re Canadians, just everyone have a good time, a safe time, stay healthy and safe and spend time with your families,” Ford said.

Ford said he is disappointed to see such protests return to the capital.

“I’m all for peaceful protests and you can demonstrate, but no shenanigans this weekend, just be peaceful and let the people of Ottawa enjoy their weekend,” he said.

“Honestly, we shouldn’t even be going through this. It’s disappointing, but it is what it is.”

More than two dozen Conservative MPs hosted Topp and other leading figures in the Freedom Convoy on Parliament Hill last week, posing for pictures, promising their support and listening to a lecture on the purported dangers of COVID-19 vaccines.

Health Canada says only vaccines that meet strict safety, efficacy and quality standards are approved for use in the country, and the benefits of COVID-19 vaccines continue to outweigh the risks of the disease. About 85 per cent of Canadians have received at least one dose.

Topp told the MPs that he was marching in part to get all vaccine mandates repealed, as well as to demand the reinstatement of anyone who lost their job because of such a requirement and compensation for wages lost.

At the same time, he and the others raised the spectre of civil war in describing the state of the country.

“We won’t be intimidated by any group that plans to disrupt the celebrations,” Mayor Jim Watson said during a briefing earlier this week. “We’re prepared and we will not tolerate any illegal activity by anyone.”

Bell said police are prepared for a number of different scenarios, and will respond quickly to any illegal activity, including efforts to set up structures such as stages.

In late April, the Ottawa Police Services Board approved a request from Bell to appoint up to 831 RCMP officers to help with the Rolling Thunder motorcycle events, and made those appointments valid until July 4.

The city is warning that vehicles will be ticketed and towed if they’re found violating no-stopping zones, although the full extent of the areas that will be off limits has not been determined.

Many Ottawa residents remain angry at how the city and police handled the “Freedom Convoy” protests, with several community groups banding together to launch a citizens’ inquiry into how that protest was handled.

This report by The Canadian Press was first published June 30, 2022.

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COVID-19

Soldier charged for criticizing vaccine mandates arrives in Ottawa amid protest fears

Published on

By Lee Berthiaume in Ottawa

A Canadian soldier charged for speaking out against COVID-19 vaccine requirements will march through Ottawa on Thursday, kicking off what organizers are promising — and residents fear — will be a new wave of protests throughout the summer.

Army reservist James Topp was charged in February with two counts of conduct to the prejudice of good order and discipline for comments made while wearing his uniform, and has since been leading a four-month march to the capital from Vancouver.

His march has been supported by many of the same figures involved in the “Freedom Convoy” that snarled downtown Ottawa for weeks until police used force to end what they and the government described as an illegal occupation.

His arrival in the capital and promises of a new round of protests starting Canada Day have set residents on edge. Ottawa Mayor Jim Watson and the city’s interim police chief, Steve Bell, have promised to crack down on any illegal activity.

More than two dozen Conservative MPs hosted Topp and other leading figures in the Freedom Convoy on Parliament Hill last week, posing for pictures, promising their support and listening to a lecture on the purported dangers of COVID-19 vaccines.

Health Canada says only vaccines that meet strict safety, efficacy and quality standards are approved for use in the country, and the benefits of COVID-19 vaccines continue to outweigh the risks of the disease. About 85 per cent of Canadians have received at least one dose.

Topp told the MPs that he was marching in part to get all vaccine mandates repealed, as well as to demand the reinstatement of anyone who lost their job because of such a requirement and compensation for wages lost.

At the same time, he and the others raised the spectre of civil war in describing the state of the country.

The charges against Topp relate to two videos posted online in the winter in which the army reservist appears in uniform criticizing vaccine requirements for military personnel and other federal employees.

Canadian Armed Forces members are severely restricted in the comments they can make while in uniform, particularly when it comes to criticizing government policies, in large part to protect the military from any perception of politicization.

His lawyer has argued such restrictions should not apply to policies that affect Armed Forces members personally.

Topp has said he has no plans to lead an occupation of the capital, and invited Ottawa police to work with him to facilitate his planned march through the city to the National War Memorial.

However, an organizer for a group calling itself Veterans 4 Freedom said in a recent video posted to YouTube that it plans to set up a semi-permanent camp east of Ottawa called “Camp Eagle” and hold events in the city all summer.

While police have since managed to prevent similar protests from taking over the city, stopping planned demonstrations from getting out of hand during Canada Day is likely to be complicated by the presence of thousands of people celebrating the holiday.

“We won’t be intimidated by any group that plans to disrupt the celebrations,” Mayor Jim Watson said during a briefing earlier this week. “We’re prepared and we will not tolerate any illegal activity by anyone.”

Bell said police are prepared for a number of different scenarios, and will respond quickly to any illegal activity, including efforts to set up structures such as stages.

In late April, the Ottawa Police Services Board approved a request from Bell to appoint up to 831 RCMP officers to help with the Rolling Thunder motorcycle events, and made those appointments valid until July 4.

The city is warning that vehicles will be ticketed and towed if they’re found violating no-stopping zones, although the full extent of the areas that will be off limits has not been determined.

Many Ottawa residents remain angry at how the city and police handled the “Freedom Convoy” protests, with several community groups banding together to launch a citizens’ inquiry into how that protest was handled.

This report by The Canadian Press was first published June 30, 2022.

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