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The above quoted article by Nicholas Wade, Science writer is much quoted as offering strong indications that some scientists working on coronaviruses have been practicing bad science and therefore as a result are acting in bad faith. But the analysis here is in the form of a polemic, not a proper scientifically argued way and full of journalistic innuendos. So let us just look at some of the claims that Wade makes:
A second statement that 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
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.
What? No reference to this magic method of how to make invisible changes? Of course this is probably true but this statement without a reference is a rather popular way of throwing doubt on a paper, albeit an informed, well referenced scientific paper, by just saying, have you thought how magic could also have the same effect? Where is the evidence and where does this apply to the current discussion.
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. Andersen and his colleagues were assuring their readers of something they could not know.
But let us actually see what Anderson et al state in their opinion piece:
3. Selection during passage
Basic research involving passage of bat SARS-CoV-like coronaviruses in cell culture and/or animal models has been ongoing for many years in biosafety level 2 laboratories across the world27, and there are documented instances of laboratory escapes of SARS-CoV28. We must therefore examine the possibility of an inadvertent laboratory release of SARS-CoV-2.
In theory, it is possible that SARS-CoV-2 acquired RBD mutations (Fig. 1a) during adaptation to passage in cell culture, as has been observed in studies of SARS-CoV11. The finding of SARS-CoV-like coronaviruses from pangolins with nearly identical RBDs, however, provides a much stronger and more parsimonious explanation of how SARS-CoV-2 acquired these via recombination or mutation19.
The acquisition of both the polybasic cleavage site and predicted O-linked glycans also argues against culture-based scenarios. New polybasic cleavage sites have been observed only after prolonged passage of low-pathogenicity avian influenza virus in vitro or in vivo17. Furthermore, a hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described. Subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described. Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system18.
So the authors do not dismiss this possibility, but actually give their reason, based on actual knowledge and experience, of why this could not be the case.
The discussion part of 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.
Another typical type of conspiracy theory device, ah but wait caught in confessing in full sight.
But the mundane non-conspiratorial explanation here is simply a structural one in the way a paper is written. The passage asserting that the authors conclude that it is not a manipulated virus occurs early on in the introduction and summary and is an overall conclusion. But the other part expressing the improbability that the virus emerged through laboratory manipulation is in a paragraph where the two theories were weighed up. No smoking gun there either.
At the outset the author states:
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.
The author does not do that in any balanced way. The whole tone is skeptical, accusatory and one sided. Moreover, it has no references at all to some of the science quoted used to either prove his point, or that Anderson and Dazak is wrong. In other words, this is ahit piece, not a balanced discussion. For a balanced discussion please see this.
Be careful whom you trust, after all the New York Times is a political organ.
The issue is overpoliticised, started of by Trump and Pompeo calling it the Chinese virus, then now taken over by Biden in a new campaign against China. Remember the background. China is the new enemy and is being fought on all fronts. I will only show you this map to explain everything behind this enmity and demonization. Remember, the smoking gun of Iraq’s nuclear weapons?