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.net in 1997. He worked as production manager for various publishing houses and as service manager for various internet companies and lives in Amsterdam. Author of “Ken Wilber: Thought as Passion” (SUNY Press, 2003), which has been translated into 7 languages, and of 150+ essays on this website.
THE CORONA CONSPIRACY
Part 1: Corona, Oxygen, 5G: The Paranoid Worldview of David Icke
Part 2: Debunking Andrew Kaufman's Virus Equals Exosome Hypothesis
Part 3: We Need to Talk about Exosomes
Part 4: Why Viruses are Not Exosomes
Part 5: The Alternative Facts of Virus Denialism
Part 6: The Subtle Science of Whole Genome Sequencing
Part 7: Stefan Lanka's Vanishing Virus Act
Part 8: Coping with Corona: The Cautious vs. The Reckless
The Corona Conspiracy
Part 6: The Subtle Science of
|VIRUS TYPE||NUMBER OF BASES|
|Bacteriophage MS2 (RNA)||3.600 or 3.6 Kb|
|Bacteriophage phiX174 (DNA)||5.400 or 5.4 Kb|
|HIV||10.000 or 10.0 Kb|
|Influenza||13.500 or 13,5 Kb|
|Measles||15.900 or 15,9 Kb|
|SARS-CoV-2||30.000 or 30.0 Kb|
|Mimivirus||1.200.000 or 1.2 Mb|
|Pandoravirus||2.500.000 or 2.5 Mb|
|OTHER ORGANISMS||NUMBER OF BASES|
|E. coli bacterium||4.600.000 or 4.6 Mb|
|Homo sapiens||3.200.000.000 or 3.2 Gb|
In sum, we have here quite distinct entities, each with its own characteristic genomes. From genomes we can go to the proteins they code for, and from there to their behavior in the cells they invade. As to the SARS-CoV-2 virus, biologists can read its genome and find areas that specifically code for the spikes or the envelop of the virus. Comparing this genome to other coronaviruses has taught us why this one is particularly harmful. And from that knowledge it becomes understandable that the new coronavirus can cause so many seemingly different types of disease.
Do we have reliable tests?
This extremely specifc and detailed nature of genomic data also translates into the specificity of virus tests. Instead of just "testing" for "general human genetic material", as the alt-medics usually claim, the tests target specific genetic sequences which are unique to a specific virus only. So let's turn to the second article.
Another landmark publication is about how to spot the virus with a so-called Real-Time RT-PCR test, published in January 2020 in Euro Surveillance by a German team. This article claims: "The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV". What made it possible to act so fast was their long-time experience with SARS-CoV, a similar virus that broke out in 2003, and the international nature of research in the present world. They "only" needed to zoom in on that which makes SARS-CoV-2 unique, a small sequences of bases (for example: GTGARATGGTCATGTGTGGCGG). This missing information was provided by Chinese researchers before the formal release of the full SARS-CoV-2 genome.
What we see here is how researchers specifically zoom in on certain small areas of the genome, which contain the genes RdPg (a RNA-dependent RNA polymerase gene), E (envelop protein gene) and N (nucleocapsid protein gene).
And here you can see where the minimal differences between SARS-CoV-2 and various other viruses could be found (dots represent identical bases, only the base changes are specified where they have been found). They had six samples of the new coronavirus (where only dots can be seen: as to these genes they were identical) and compared it to the earlier SARS-CoV virus, a bat virus from China and a more distantly related bat virus from Bulgaria (where you see more base replacements show up).
They applied their test to 22(!) respiratory and other viruses (including MERS-CoV, Influenza, Rhinovirus, Adenovirus and Legionella, to name only a few), and concluded "In total, this testing yielded no false positive outcomes"meaning, none of these related viruses were mistaken for SARS-CoV-2, which would make the test useless for detecting this virus. The test only reliably detected SARS-CoV-2. Talking about specificity!
The authors conclude: "The relative ease with which assays [tests] could be designed for this virus, in contrast to SARS-CoV in 2003, proves the huge collective value of descriptive studies of disease ecology and viral genome diversity."
Great insight into how virological science-in-action works is given by "Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands", which is currently (2020/6/27) only available as preprint on bioRxiv, and is published by a Rotterdam based research group. On February 27th the first COVID-19 case was found in the Netherlands, and two days later(!) the first complete SARS-CoV-2 genome sequences of the first two patients were generated, analyzed and shared.
By March 15th, 189(!) full genome sequences were generated and released on GISAID, a worldwide database that contains 55.000 genomic sequences of SARS-CoV-2 submitted from all over the world. This Whole Genome Sequencing (WGS) was accomplished by so-called multiplex PCR for Nanopore sequencing, in which 86 overlapping sequences of 500 base pairs, with 75bp overlap, were used to span the full 30.000bp genomeon a device that can be held in the palm of your hand. This is a stunning scientific and technological accomplishment.
The interesting thing is that these relatively cheap and fast devices can directly be put to use in health policy decisions. The tiniest mutations anywhere in the complete viral genome can be detected as it is assembled from patient's samples, and it becomes possible to trace the complex spread of infections across national borders.
Assembling the viral genome
Alt-medics such as Kaufman and Lanka often suggest these whole genomes are useless artefacts, because they are based on snippets of RNA that first get multiplied and then arbitrarily "stitched together" with the help of advanced computers to form a digital whole genome sequence, which might as well be related to normal human cell material. This shows a complete lack of understanding of how digital genome assembly works.
In the most simple of terms:
- a virus test works by targeting specific viral material in a sample (say sputum or lung fluid), and multiplying that material so it can be made visible by phosphorisation. This doesn't mean that everybody will test positive if enough multiplications are done; if you don't have the viral material present, no multiplication will help you. You will never get a false positive.
- Building the whole viral genome is done by producing and detecting small segments of the genome in huge quantities (so not only the segments that are unique to that virus, but all of them, the whole string of bases), and then "assembling" these again on a computer, which can be done because these snippets show overlaps on both sides.
A good explanation of how genome assembly works in practice can be found in this video from Bioinformatics DotCa a Canadian Open Source bio-informatics educational institute:
A more homely example would be: putting multiple copies of a book through a shredder and re-assembling all the pages and sentences in a single, complete book again by comparing the various fragments. Of course, this is a Herculean task no human being would be able to accomplish, but computers can do this ever faster and faster, especially today.
With long snippets or "reads" the genome assembly would be easier, but these are very difficult to make. Hence genome sequencing works with relatively small sequences, which can be assembled into a full genome. But the smaller these snippets are, the more challenging the task becomes. Hence the need for high performance computers.
Here's a final example, of my own making. Say we have several copies of a long sentence, which get cut up in smaller fragments. If the fragments are too small, of the size of individual letters, no sentence assembly will be possible. But if the fragments contain a string of letters, even if the fragments themselves make no sense to us, a computer can assemble the full sentence if it has multiple versions of this fragmented sentence at hand for comparison (in this case there are seven):
So we end up here, not with a random string of meaningless fragments "stitched together", but with a meaningful sentence that has a unique structural order.
I leave it to you to further explore and read these scientific articles and training videos, to get a feel for the complexity and usefulness of modern genomics. This is how science goes about in knowing viruses to the very base of their genomes. If you want to follow the real-time mutations happening now in the various strands of SARS-CoV-2 that are freely roaming around in the world, do regularly check out the fabulous Nextstrain.org website.
Personally I think that dismissing these research data out of hand borders on the insane. Instead of babbling about bubbles in cell photos, Lanka and Kaufman should familiarize themselves with the fields of bioinformatics and genomics. Dismissing these data as nothing more than the observation of exosomes under a microscope (Kaufman), or as the sequencing of mere "dead cell material" caused by the way viruses are cultured during sequencing procedures (Lanka), is without any reasonable scientific ground. You simply don't get this precise and specific knowledge about viruses and their evolutionary relationships based on dead human cell material.
Viral biology is an entirely different ball game these days.
 Jeong-Min Kim et.al., "Identification of Coronavirus Isolated from a Patient in Korea with COVID-19", Osong Public Health Research and Perspectives, 2020 Feb; 11(1): 3-7
 John Archibald, Genomics A Very Short Introduction, Oxford University Press, 2018, p. 101. A superb and up-to-date introduction to the wide field of genomics.
 Victor M Corman et.al., "Detection of 2019 Novel Coronavirus (2019-nCoV) by Real-Time RT-PCR", Euro Surveillance, 2020 Jan 23; 25(3).
 Oude Munnik, B.B. et.al., "Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands", bioRxiv, April 25, 2020.
 Ranjit Sah et.al., "Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal", American Science for Microbiology, Microbiology Resource Announcements Mar 2020, 9 (11).
 Nextstrain, Real-time tracking of pathogen evolution. Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. It provides a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Its goal is to aid epidemiological understanding and improve outbreak response. It contains real-time information about the prevalence and spread of SARS-CoV-2, Seasonal Influenza, the West Nile Virus, Mumps, Zika, West-African Ebola, Dengue, Avian Influenza, Measles, Enterovirus and Tuberculosis. Have fun!
 We will analyse Stefan Lanka's view of viruses and their supposed non-existence in Part 7 of this series.
YouTube channel of Andrew Kaufman
YouTube channels critiquing Andrew Kaufman / London Real
Part 5 | Part 6 | Part 7 | Part 8