NOW ON KINDLE: The Corona Conspiracy: Combatting Disinformation about the Coronavirus
INTEGRAL WORLD: EXPLORING THEORIES OF EVERYTHING
An independent forum for a critical discussion of the integral philosophy of Ken Wilber
Publication dates of essays (month/year) can be found under "Essays".
Frank Visser, graduated as a psychologist of culture and religion, founded IntegralWorld in 1997. He worked as production manager for various publishing houses and as service manager for various internet companies and lives in Amsterdam. Books: Ken Wilber: Thought as Passion (SUNY, 2003), and The Corona Conspiracy: Combatting Disinformation about the Coronavirus (Kindle, 2020).
Frank Visser brings light and sanity to the miasmal confusion of suspicions and misinformation. (David Quammen, November 23, 2020)
Andrew Kaufman and the "Fake Delta Variant"
The Corona Conspiracy, Part 31
I have never seen a more conceited, misinformed and misleading speaker on the current pandemic, hankering for attention of the gullible.
I could not resist. I just could not resist.
Virus denialist Andrew Kaufman recently released a new video, which can be found on several Bitchute accounts, but not (yet) on his own media channels, called "DR. ANDREW KAUFMAN ON THE FAKE DELTA VARIANT." He tells his audience that he was asked about his opinion about the so-called Delta variant, and he took the opportunity to create a video giving some background and especially explaining "how sequencing is done in the first place". After all, he reminds us, all variant are the result of "what they call genome sequencing."
Now, as we have seen abundantly in previous Parts of this series (see Part 26), Andrew Kaufman is not exactly your go-to source when it comes to genome sequencing. Instead, he hasn't scratched the surface of that topic, and spreads multiple wrong ideas about it, all with a single aim: to cast doubt on the reliability of these modern techniques of identifying pathogens.
He cautions his audience that these variants "have not been studied actually with clinical correlations", and are "based on computer similations and are purely theoretical". Now it is true that no clinical research has been set up to compare these variants in different groups of patients, but that is not to say that no empirical data about this particular variant is available, even of a preliminary nature. For one thing, symptoms seem to be milder than earlier variants, but vaccines seem to be slightly less effective. This is ongoing research, but nothing warrants the conveniently dismissive qualification "purely theoretical".
The "In Silico" Genome
After some introductory remarksabout genetics, DNA and RNA, the spiral helix, complementary bases, transcription and translation, and so onwhich are largely correct, Kaufman talks about the difference between a human genome and a viral genome. In his understanding, a human genome is actually based on genetic material taken from a human being, whereas a viral genomes are taking place "entirely in the mechanics and circuitry of a computer" and are therefore "IMAGINARY" (capitals used by Kaufman in his presentation).
This is the definition he works with:
In silico (adjective)
This is, however, a rather odd comparison. Deciphering the human genome took a huge amount of computer power, and has taken place over many decades, and viral genomes are based on samples taken from real patients (however you might think about the reliability of this method, see below). And in both cases genomes are digital reconstructions of actual molecular phenomena recorded by highly sensitive equipment. But because it is so much easier to work with A, C, T, G bases compared to intricate molecules, once the DNA or RNA extraction and digitization has been accomplished, all further work happens digitally.
Kaufman seems confused between computer simulations that are in a sense "purely theoretical" because they are fed with variables we put into the computer (think: climate change research, or epidemiological predictions) on the one hand, and digital recordings or reconstructions, that are based on real physical data (think: digital recording of music, or genome sequencing) on the other. A rather crucial distinction.
Then Kaufman moves on to Next Generation Sequencing, which is a highly sophisticated process of sample centrifugation, purification, amplification, library preparation, sequencing and analysis, used for human genome sequencing. He claims that in the case of viral sequencing, the centrifugation and purification steps are skipped, so the genetic material that is consequently analyzed is of unknown origin. Therefore, the resulting alignment can only be a "theoretical virus", in his opinion.
This too, is an over-simplification of the processes followed in these two sequencing tracks. What Kaufman doesn't seem to get is that most of the purification can be done digitally, because during sequencing all host (human) RNA will be discarded and all viral RNA will be retained, whereas in the past this had to be done with physical substances. Stefan Lanka more or less makes the same argument: we can never know the source of the genetic material that has been sequenced, hence the genome is a fiction.
The "Wu-Holmes-Zhang" paper
Moving on to deeper waters, Kaufman mentions one of the first scientific papers describing the full SARS-CoV-2 genome, which was published in Nature very early on in the pandemic: submitted January 7, 2020 and published February 3, 2020. Kaufman can barely hide his astonishment when he reads that genetic material was extracted from only one individual. Indeed, the paper reads: "A patient presenting with acute onset of fever (temperature over 37.5 °C), cough and chest tightness, who was admitted to the Central Hospital of Wuhan, in Wuhan, China, was considered to be a suspected case." However, the first human genome was also based on one individual only, the genome researcher Craig Venter.
No less is his astonishment about the fact that in this genetic material, about 56,565,928 reads were gathered, which formed the foundation on which the viral genome had to be built. Verily a gigantic task, only heavy computers can accomplish. From this immense number of reads, the non-human reads (23,712,657 reads) were filtered out and the human reads were discarded, cutting the number of reads by half. Then, these reads were combined into larger "contigs" (384,096 and 1,329,960 in number respectively, using two different sequencing systems: Megahit and Trinity).
Long story short, these contigs were assembled into a full genome of an apparent new virus. The researchers noted a high similarity with a known bat virus SL-CoVZC45 (which we have encountered in Part 17). Recombination analysis was executed, to see if parts of the virus were perhaps of different viral origin. Phylogenetic analyses were performed, which showed it to be a SARS-related bat virus, which was named WH-Human 1 coronavirus (WHCV) and of which the size was determined to be close to 30.000 base or nucleotides (to be precise: 29,903).
Now, presented with this level of sophistication, someone not armed with this expertise will most likely feel overwhelmed. How can we trust the end result of so many operations with so many different systems? Is the resulting genome really the genome of a new and dangerous virus? It might indeed seem incredible that modern scientists can assemble a 30.000 base viral SARS-CoV-2 genome from millions of short reads coming from various types of organisms, this is exactly what is feasible.
Questioning this is a typical case of freshman skepticism.
Freshman skepticism arises in that magical place where a lack of general knowledge, critical thinking, and scientific understanding, collides with paranoid speculation, fallacious reasoning, and glib over-generalization.
Does this book exist?
Kaufman then elaborates on the familiar metaphor of comparing the human genome to a book, with words, sentences and paragraphs. The analogy goes like this: genomes are compiled from millions of reads (words), tiny RNA fragments. These reads are combined into contigs (sentences, paragraphs), and these in turn are combined into a hypothetical whole book. His question: how do we know this book exists?
In his understanding, contrary to human genomes, viral genomes are completely computer generated, arbitrary and artificially constructed. Millions of words are put together to form sentences and paragraphs, though, without any example we don't know if that makes any sense.
He gives the example of the very short phrase "writing in", which can be culled from many different books (The War of the Worlds, 1984, Fahrenheit 451 and so on), and can be used in many, even nonsensical sentences. How do we know which book it really came from, he asks us.
Now this is all very disingenious. Stefan Lanka often uses the same sleight of hand. This only works with very short fragments - in this example "writing in" makes up 10 characters only, including the space. Taken out of context, it is impossible to determine their true source. But guess what, when we take slightly longer strings of characters, such as "start teaching reading and writing in", "writing in a foolish facetious tone" or "he began writing in my study and", the situation changes dramatically. These phrases are identifiably unique to a particular book or source:
The analogy both Kaufman and Lanka continuously use to confuse their audience spectacularly backfires, because in whole genome sequencing even the smallest reads or words are much, much longer than that. What is more, multiple copies overlap, which gives us even more confidence in establishing the full genome (see Part 6). In the "Wu-Holmes-Zhang" paper, for example, the RNA fragments that were assembled were 150 base pairs long. This is a sentence of 150 characters:
In the "Wu-Holmes-Zhang" paper, for example, the RNA fragments that were assembled were 150 base pairs long. This is a sentence of 150 characters:
This string of characters is highly unique, and even leaves room for overlap with other equally long fragments on both ends. That's "how sequencing is done in the first place", dr. Kaufman, not in any of the imaginary ways you present it to your audience.
The Nature of Variants
How does Kaufman interpret the many viral variants that science has identified? In his (mis)understanding, variants are failed attempts at reproducing the original SARS-CoV-2 genome, which is no surprise to him, because there is no index virus in the first place. What is more, he just can't accept variants of something that isn't really there!
So while Kaufman acknowledges the reality of human genomes - they are based on actual organisms and can reliably be reproduced -- he questions the reality of viral genomes, because they are based on a mixture of sources, cannot be reproduced and are entirely theoretical. In reality BOTH human and viral genomes are based on real organisms, are highly reproducible (within margins) and are theoretical reconstructions of actual, natural realities. It is unfathomable how Kaufman can frame these results as proof for the non-existence of viruses.
So if the Delta variant, which has become dominant now in many Western countries, is just another “failure to reproduce the original index genome”, how come all these thousands of Delta “failures” miraculously all point in the same direction and display the same characteristic mutations - if it is not a real variant? Indeed, one would expect a huge amount of meaningless noise in the sequencing data without a clear signal. Yet, what we consistently get to see is a real new variant that shows up again and again, and has almost completely replaced earlier SARS-CoV-2 variants.
What is more, this new Delta variant has a specific set of mutations that predictably changes its behavior: its infectiousness or how efficiently it can bind to the various human cells that share the same receptor. Weird, huh? As much as we still have to learn about these details, dismissing all this as "purely theoretical" is a rather unfruitful approach, to say the least. Instead of listening to Kaufman's clueless conjectures, get educated by this great recent article from Nature. The animation shown above is from this article and is titled "A computer simulation of the structure of the coronavirus SARS-CoV-2. (Credit: Janet Iwasa, University of Utah)".
Kaufman & company will predictably scorn: "Oh, that's just an animation, that doesn't count." Well, it is a superb animation, and more importantly, one that is grounded in data. There is a 1-on-1 relationship of the viral genomic sequence to the lock-and-key enabling structure of the proteins built by it. To the extent that, when the researchers simulated mutations in that area, the spike protein collapsed.
Since the start of the COVID-19 pandemic, scientists have been developing a detailed understanding of how SARS-CoV-2 infects cells. By picking apart the infection process, they hope to find better ways to interrupt it through improved treatments and vaccines, and learn why the latest strains, such as the Delta variant, are more transmissible.
What has emerged from 19 months of work, backed by decades of coronavirus research, is a blow-by-blow account of how SARS-CoV-2 invades human cells.... Scientists have discovered key adaptations that help the virus to grab on to human cells with surprising strength and then hide itself once inside. Later, as it leaves cells, SARS-CoV-2 executes a crucial processing step to prepare its particles for infecting even more human cells. These are some of the tools that have enabled the virus to spread so quickly and claim millions of lives.
And there is always more to learn:
It is not easy to keep pace with the quickly mutating virus. Most mutations so far are associated with how effectively the virus spreads, not with how much the virus damages the host, experts agree. This month, a study reported that the Delta variant grew more rapidly and at higher levels inside people's lungs and throats than did earlier versions of the virus. But it is not yet certain how Delta's mutations have supercharged the variant in this way, says Stern-Ginossar.
But Andrew Kaufman knows no better than come up with this priceless gem:
Variants are simply the inability to reproduce or validate the original results. (Andrew Kaufman)
Another "Bombshell" Interview
It looks like only a massive data blindness can cause virus denialists like Andrew Kaufman to deny these data. Yet this “medical authority” now reaches an audience of millions through his appearance this week on the Info Wars show of Alex Jones. He is a long-time distributor of misinformation, who has been banned from almost all mainstream social media, even before the pandemic started.
Jones is the publisher and director of the InfoWars website. The InfoWars website receives approximately 10 million monthly visits, making its reach more extensive than mainstream news websites such as The Economist and Newsweek. (Wikipedia)
“MIT Scientist Exposes Covid-19 Hoax in Bombshell Interview - MUST SEE!” is the screaming headline. Alex Jones, looking quite lost before a table with dozens of copies of news articles and scientific papers, looks up to Andrew Kaufman, “author of many books” [not], as his final mentor on virology. He seems desperate to know the "real truth" about the SARS-CoV-2 virus, and now hears that... it doesn't even exist.
Listen to Jones introducing Kaufman:
Right now we are going to dr. Andrew Kaufman, he is a psychiatrist, he has a BS from MIT, and an MD from Medical University of South Carolina. We are going [to skip] his whole background, the books he has written and all things... From the very start he has been criticizing this whole roll-out and what has been unfolding.
I don't think Kaufman has written any book we should know of, least of all in the field of virology. Nevertheless, he claims that, having a medical background, he is able to read and interpret the scientific literature. We have seen that his understanding of the relevant papers leaves much to be desired. He repeats his views on the Wu paper and in the same breath discounts the PCR test, which supposedly was developed before the new virus was even available and completely based on the genome of 2003 SARS-CoV. (For a full report on this so-called PCR-Gate see Part 20 and Part 24).
Kaufman bluffs in this Info Wars interview that Stefan Lanka has already given proof of the total arbitrariness of viral genomes by being able to produce the same results even in the complete absence of a virus - but that revolutionary paper still awaits the light of day, as far as I can tell (see Part 26 and Part 28). Or perhaps he refers to the few pictures Lanka put up on Bitchute? Seriously? As proof of what exactly?
If Andrew Kaufman is your hope of winning the Info Wars, then you are really lost. Or perhaps, it is only typical of info war heroes that they have so much lost touch with reality that they have started to believe their own illusions. I have never seen a more conceited, misinformed and misleading speaker on the current pandemic, hankering for attention of the gullible, but hiding from confrontations with real scientists.
SARS-CoV-2 Delta variant
It has mutations in the gene encoding the SARS-CoV-2 spike protein causing the substitutions T478K, P681R and L452R, which are known to affect transmissibility of the virus as well as whether it can be neutralised by antibodies for previously circulating variants of the COVID-19 virus. (Wikipedia)
 Andrew Kaufman, "DR. ANDREW KAUFMAN ON THE FAKE DELTA VARIANT", www.bitchute, July 23rd, 2021.
 Lara Herrero, "The symptoms of the Delta variant appear to differ from traditional COVID symptoms. Here's what to look out for", www.theconversation.com, July 1, 2021.
 Carl Zimmer, "Scientists Finish the Human Genome at Last", www.nytimes.com, July 23, 2021.
 Fan Wu et al., "A new coronavirus associated with human respiratory disease in China", www.nature.com, 3 February 2020.
 Susan Mayor, "Genome sequence of one individual is published for first time", BMJ. 2007 Sep 15.
 Megan Scudellari, "How the coronavirus infects cellsand why Delta is so dangerous", www.nature.com, 28 July 2021.
 Special Report, "MIT Scientist Exposes Covid-19 Hoax in Bombshell Interview - MUST SEE!", www.infowars.com, July 23rd 2021, 10:10 am
83 Vaccine Myths from docbastard.net
To all those who claim SARS-CoV-2or any virusdoes not exist: the virosphere consists of 4 realms, 9 kingdoms, 16 phyla, 2 subphyla, 36 classes, 55 orders, 8 suborders, 168 families, 103 subfamilies, 1421 genera, 68 subgenera, 6590 species. Take that. https://talk.ictvonline.org/taxonomy/
A summary of early parts of this series has appeared in the Dutch magazine Skepter 33(3), September 2020, as "Viruses don't exist" (covering Parts 1-5). German: Skeptiker (December 2020); English: Skeptic.org.uk (January 2021)
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