In the real world there are commercial scientists who work for and are controlled by corporations and corporate interests, and there are non-commercial scientists who do science to properly fact find, no matter what commercial corporate scientists think about it.
An example would be tobacco/cigarette company scientists versus scientists who discovered that smoking causes cancer and other sicknesses (Smoke & Fumes).
Another example would be oil company scientists versus environmental scientists who discovered that we are in theSixth Mass Extinction because of oil company activities (Smoke & Fumes).
The skepticism and criticism is borne of their failure to determine the extent of the damage that the mass-production-of-animals-for-food industry
has done by the indiscriminate overuse of antibiotics and other
chemicals that indiscriminately kill microbes and damage viruses.
IV. Today's Data & Effort
As I remarked in a previous post, I have placed "GenBank" GBFF file data into my SQL server, and have written several C++ programs to analyze the data.
That GenBank data has to do with virus genomes of coronavirus, SARS-CoV-1, and SARS-CoV-2.
Today, what the software program I am talking about does is:
(viruses with insufficient genes/nucleotides: 44,747)"
2) search for coronavirus("CO") genes in SARS-CoV-1 ("C1")viruses:
"search type: CO_in_C1 rows with 0 genes: 0 one or both genes void (no comparison): 0 matches: 4 (out of 85,350 gene comparisons)"
3) search for coronavirus("CO") genes in SARS-CoV-2 ("C2")viruses:
"search type: CO_in_C2 rows with 0 genes: 0 one or both genes void (no comparison): 0 matches: 583 (out of 2,358,998,843 gene comparisons)"
4) search for coronavirus("C1") genes in SARS-CoV-2 ("C2")viruses:
"search type: C1_in_C2 rows with 0 genes: 0 one or both genes void (no comparison): 0 matches: 0 (out of 11,295,835 gene comparisons)"
The
process involves extracting the genes of a virus, then one by one
comparing that gene with the genes of all the other viruses (On The Origin of the Genes of Viruses - 17).
The
purpose is to see if there is any gene preservation as there would be
if a gene was fit to do what an evolved gene would have to do to perform
like a well-made machine.
The result indicates that:
"0 out of 11,295,835" comparisons;
"583 out of 2,358,998,843" comparisons;
and "4 out of 85,350" comparisons.
(583
+ 4 out of 11,295,835+2,358,998,843+85,350) indicate shrapnel as the
result of damage rather than survival of the fittest gene as a result of
selection of the most fit uncertainty (The Uncertain Gene - 2).
Genieology is the "ology" of "magic words" while Genealogy is the "ology" of "just the facts ma'am".
In other words:
"Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena ... except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes." ...
"The modern evolutionary synthesis is a 20th-century union of ideas from several biological specialties which provides a widely accepted account of evolution. It is also referred to as the new synthesis, the modern synthesis, the evolutionary synthesis, millennium synthesis and the neo-Darwinian synthesis."
"The synthesis, produced between 1936 and 1947, reflects the consensus about how evolution proceeds. The previous development of population
genetics, between 1918 and 1932, was a stimulus, as it showed that Mendelian genetics was consistent with natural selection and gradual
evolution. The synthesis is still, to a large extent, the current paradigm in evolutionary biology."
"The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century."
(On The Origin of Genieology - 2). I repeat this because that practice is used to the extreme in an attempt to explain the overlapping gene (OLF) phenomenon in the coronavirus realm of virology.
In the time of WW II there was a saying "loose lips sink ships" (meaning sailors could be killed by frivolous talk), but in today's pandemic, which has seen the death of more than the soldiers who died in WW II, the saying "loose scientific lips can kill millions of innocent people" is worth consideration by the media.
II. This Series
In this series the importance of understanding the reality of the genome of viruses has been pointed out (see link at Fig. 1).
It has also been pointed out that the Covid-19 pandemic is man made:
"To meet this demand [commercialization / population growth], there are several approaches being in force like antibiotic / antimicrobial / hormonal growth promotors. But these methods also lead to major public health concerns ranging from residues to antimicrobial resistance in human population ... It
is a well-known fact that microbiota plays a pivotal role in the
gastrointestinal health in ruminant and nonruminant animals."
(On The Origin Of The Home Of COVID-19). When antibiotics ("anti" means against, "biotic" means life) kill, maim, and hurt microbes which replicate viruses, the ribosomes of those microbes are damaged in varying degrees.
“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said. ...
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically
interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
...
The most complex molecular machines are found within cells.
...
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.
Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped." (On The Origin of the Genes of Viruses). ...
"As viruses are obligate intracellular pathogens they cannot replicate without the machinery and metabolism of a host cell. [microbe] Although the [replication] of viruses differs greatly between species and category of virus, there are six basic stages that are essential for [pathogenic] viral replication." (On The Origin of the Genes of Viruses - 14).
This has monumental implications for understanding the overlapping gene (OLG) phenomenon.
The media does not seem to grasp the fact that when one does an examination of viruses during a pandemic, one must first answer the question "has this genome been damaged or malformed because its microbe host was damaged by antibiotics and other anti-life chemicals?" ("around 70% of the world's total production of antibiotics is used in [the mass-production-of-animals-for-food industry]", Antibiotics and the Foods We Eat).
In the GenBank ".gbff" files of some genomes, one runs across statements which indicate some grasp of that research-question requirement (e.g. "join(242..12379,12379..20415" and "/ribosomal_slippage").
However, explanations of that list of "joins" or overlaps and "slippage" is very slight, even though such aberrations are shown to be pervasive as shown in the two appendices to today's post.
III. Data In The Appendices
The appendices (Appendix One, Appendix Two) detail the location and quantity of genes within viruses as depicted in genetic reports provided by researchers (e.g. GenBank).
I have separated them by the Country where the virus was found.
Notice that from one virus to another, gene beginning location within the nucleotide sequences ('actg' list) and gap locations vary, even when the number of genes and/or overlap location is the same.
Notice that the number of overlaps does not necessarily increase with time, so, among other things, the 'viruses are learning to save more space over time' magic is non-sensible (truth: gene overlap and location is hap-hazard and erratic).
Notice the other evidence that belies the 'magic words' explanations that the viruses 'decided' to save space with gene overlap.
IV. Closing Comments
"Parts are parts."
Parts of genomes have been found on the surface of microbes:
"Typically, the nuclear genome encoded RNAs (ngRNA) are not expected to be present on the surface of eukaryotic cells with intact cell membranes ... [except for 'leakage'] To confirm that the Surface-FISH signals are not a result of RNA leakage from damaged cell membranes,
we combined Malat1 Surface-FISH with a transmission-through-dye (TTD)
microscopic analysis, where only live cells with intact membranes are
fluorescently labeled ... signals appeared on cells with perfectly intact membranes ... [thus, their techniques] suggest the presence of specific nuclear-encoded transcripts on the surface of intact live cells."
(Nuclear-encoded RNA on the cell surface, emphasis added). That is why I recommend that virologists be required to take a class, during their education, on TCR:
"Traffic collision reconstruction [TCR] is the process of investigating, analyzing, and drawing conclusions about the causes and events during a vehicle collision. Reconstructionists conduct collision analysis and reconstruction to identify the cause of a collision and contributing factors including the role of the driver(s), vehicle(s), roadway and general environment. Physics and engineering principles are the basis for these analyses and may involved the use of software for calculations and simulations. Collision reconstruction is sometimes used as the basis of expert witness testimony at trials."
(Wikipedia, emphasis added). Deformed genes in a world of antibiotics, and other overused-to-the-point-of-toxicity chemicals, have made a vast junkyard of evidence showing that the virology of pandemics is inordinately variant.
The next post in this series is here, the previous post in this series is here.
'Country': where the virus was found; 'version': the virus' GenBank id; 'OLG': overlapping genes; '#OLG': number of OLG in listed virus; 'date Collected': 0000-00-00 means unknown; 'OLG @ pos': OLG list positions; 'gene count': number of genes in listed virus;
