Last weekend there was a video presentation by Drs. Kaufman and Cowen, which can be located here. It is very long, and the technology they use, called Webinarjam, is clunky. Even though it is now in replay mode, you cannot fast forward or go back. There is on the right hand side a comment thread, but they roll by so fast you cannot read them, nor can you stop them. Neither can you search the comments for keywords. I think the creators of the software deserve a hat tip nonetheless, so here is to you Mrs. Olsen’s fourth grade class.
There is at a point far into the video (it cannot be time stamped) a Q&A, and very shortly into that session a Dr. Wilson called and did quite a monologue on how Kaufman and Cowen are misrepresenting the virus isolation process. Kaufman asked him if he had a paper on the matter, and yes, said Wilson, he had linked to it twice in the comments. Good luck on finding those links using Webinarjam. In the end, Wilson promised to send the paper to both Kaufman and Cowen, who would read and report back.
I had a problem with that. There are leaders and there is controlled opposition, and we can never be sure of anyone’s true status. As much as I have learned from K and C, I want to keep them at arm’s length. Therefore I realized that I needed to get a hold of that paper and read and judge it for myself. Oregon Matt found it, and I found the link to a printable version here.
It is short, but has in it very dense wording and lots of inside baseball talk. I suppose that is OK if it is a scientific paper, as scientists talk to other scientists like that, all of them being familiar with the terminology. But for me, the non-scientist, it leaves me out of the loop. Consequently, as I knew that Steve, Matt and Stephers would be reading the paper as well, I volunteered to take all of the jargon contained therein and find working definitions. I include my work at the very end of this blog post for any of you who want to immerse yourself. You will find definitions the the same sequence as they appear in the paper itself.
But something bothered me right at the outset. The paper, called In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges, describes work done on the SARS-CoV-2 virus. Where did it come from? Kaufman asked Wilson about that, did it come from a patient? No, said Wilson, it was generated elsewhere in other isolations, as with each iteration of an isolation of a virus, all of the toxins used in the initial isolation are shed, and in the end, you wind up with a pure virus.
That’s nonsense. Even today, May 20, 2021, Jon Rappoport writes about The Pandemic Virus That Doesn’t Exist. If you’ve not reviewed the widely available literature on the process that virologists mislable “isolation,” JR’s article will give you the quick rundown.
So the paper in question, whose lead author is Beata Turonová, is about angels on the head of a pin. The authors do this for a living, and are so soaked in the fraud of their profession that they imagine they are doing real work. The object of the paper is probably to produce a vaccine, as when that happens, truckloads of money back up to your garage.
In an exchange I had with Oregon Matt, we each suggested that Turonová et al had nothing with which to work, and so ASSERTED the virus. It reminded me of a talk I once heard by a man named Fr. Stanley, who taught philosophy. The talk was lighthearted and funny, called something like Counting From One to Ten – Philosophically Speaking. I only remember the opening, as it has been decades. Stanley said that from a rational standpoint, there is no way to count to 10 unless you first go from 0 to 1. But that cannot be done. But there is a way around it, he said, and that is simply to ASSERT that 1 exists.
This, he said, is called existentialism. And that is the nature of the paper in question, existentialist. (This reminds me of a joke: Jean-Paul Sartre was sitting in a coffee shop in Paris, and asked the waitress for coffee, without cream. A few minutes later, the waitress came back and said to him, “I am sorry, monsieur, but we are all out of cream. Would you instead like your coffee without milk?”
Below are my notes from the Turonová et al paper. I’m still waiting on Kaufman and Cowen, but don’t think I need any help from them. I think we handled this on our own, without consultation with experts.
Some of the terminology used, and definitions, as best I could do:
Angiotensin-converting enzyme 2, or ACE2 “receptor”: the protein provides the entry point for the coronavirus to hook into and infect a wide range of human cells. Note, entry into a cell by a virus has never been documented.
Virion: the complete, infective form of a virus outside a host cell, with a core of RNA or DNA and a capsid.
Glycosylation site: Glycans (carbohydrates, sugars, monosaccharides, oligosaccharides and polysaccharides) are widely distributed in nature, in all living life forms. Glycosylation is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule. In biology, glycosylation mainly refers in particular to the enzymatic process that attaches glycans to proteins, or other organic molecules, but actually this chemical reaction can also be non-enzymatic.
Tropism: the turning of all or part of an organism in a particular direction in response to an external stimulus.
S: The spike protein surface.
Trimeric: A chemical compound or molecule consisting of three identical simpler molecules.
Ectodomain: The domain of a membrane protein that extends into the extracellular space (the space outside a cell). Ectodomains are usually the parts of proteins that initiate contact with surfaces, which leads to signal transduction.
Receptor Binding Domain (RBD): The S protein mediates viral entry into host cells by first binding to a host receptor through the RBD.
N-terminal domains: In the molecule of a peptide, the amino acid residue on one end has an amine group on the alpha carbon. This amino acid residue is called the N-terminal of the peptide.
Epitope: the part of an antigen molecule to which an antibody attaches itself.
Supernatant: denoting the liquid lying above a solid residue after crystallization, precipitation, centrifugation, or other process.
Tomography: a technique for displaying a representation of a cross section through a human body or other solid object using X-rays or ultrasound.
Trimer: A macromolecular complex formed by three, usually non-covalently bound, macromolecules like proteins or nucleic acids.
Vero E6: Vero E6 cells show some contact inhibition, so are suitable for propagating viruses that replicate slowly.
Sanger sequencing: A method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Frederick Sanger and colleagues in 1977, it became the most widely used sequencing method for approximately 40 years.
Asp614 > Gly (D614G) allele: refers to mutation at 614th position of the Spike protein (D614G) rapidly.
NovaSTA and STOPGAP: Might possibly refer to brand names.
Cryo-electron microscopy (Cryo-EM): A type of transmission electron microscopy that allows for the specimen of interest to be viewed at cryogenic temperatures, i.e., very cold.
11-residue Leu repeat sequence: “Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different.” (From paper: Leucine rich repeat, http://www.ebi.ac.uk/interpro/entry/InterPro/IPR001611/
Single particle electron Microscopy (EM): In a single-particle cryo-EM experiment, macromolecular assemblies are frozen in a thin layer of ice and imaged with an electron microscope. Thousands to millions of images of individual assemblies must be computationally aligned and merged to arrive at a three-dimensional structure.
Micelle(s): an aggregate of molecules in a colloidal solution, such as those formed by detergents.
Serine protease TMPRSS2: Having to do with prostate cancers.
Furin cleavage site: The furin cleavage site consists of four amino acids PRRA, which are encoded by 12 inserted nucleotides in the S gene.