Thursday, June 23, 2022

On The Origin of the Genes of Viruses - 18

Acquiring DNA
In virology, the acquisition of genomes has many nomenclature problems.

One "LUCY problem" ("this was followed by arguments for splitting the wealth of specimens into different species given the wide range of variation") is endemic to genetic analysis of all sorts.

I guess "LUCY goosy" could be just another way of saying "some things never change it would seem":

"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 the Genes of Viruses - 17). In other words ("Since at least the 17th century"), since at least January 1, 1601 to December 31, 1700.

I say that because among other things:

"At least six small alternative-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and functional inferences.

(Conflicting and ambiguous names ... in the SARS-CoV-2 genome). There are several reasons for the phenomena, besides inferior nomenclature practices:

"1) technicians improperly collected otherwise good samples, 
2) technicians were given bad samples,
3) chemicals damaged the host cell causing chimeric hosts and/or viruses,
4) proton tunneling caused a mutation,
5) natural change took place."

(On The Origin Of The Home Of COVID-19 - 31). We should also note that if the host bacteria is not known it adds to the problem:

"Easy to see though, plaque as­says for counting phages do not work if ... the host bacteria are ... not known."

 (Polony Method, emphasis added). Time after time the SARS-CoV-2 host cell/microbe is never mentioned ... instead the meta-host ("host of the host") is mentioned (e.g. human, mink, bat, etc.).

Over and over, someone has to waste some time to figure out what is up with all of these "different samenesses" in the data that finds its way into GenBank and similar repositories.

Imagine the confusion that is caused if we take too much for granted:

"Obtaining virus genome sequence directly from clinical samples is still a challenging task due to the low load of virus genetic material compared to the host DNA, and to the difficulty to get anaccurate genome assembly."

(A complete protocol for whole-genome sequencing). NOTE: That is a problem even when a pure sample of genetic material is at hand, because it is a problem if the host is not known and therefore not described.

But, as with polio virus detection on a mass scale, the SARS-CoV-2 detection on a mass scale uses sewage treatment plant locations:

"Although wastewater monitoring has been used to track polio and other pathogens for decades, the COVID-19 pandemic has led to an explosion of interest. The technique takes advantage of the fact that SARS-CoV-2 replicates in the digestive system and is shed in high quantities, often before symptoms appear. (The virus is also detected in urine, though not as consistently.) That provides an inexpensive way to monitor infections in thousands or even millions of people without pesky nose or throat swabs, or to predict where cases might be about to surge and hospitals risk getting overburdened. The genetic sequences of the shed virus can also provide hints about how it is evolving.

Scientists in the Netherlands, which has had a nationwide network of wastewater monitoring for decades, were among the first to show fragments of SARS-CoV-2 virus in wastewater samples could accurately reflect its levels in the community (see graphic, below)."

(Signals from the sewer, 2022; cf. On The Origin Of The Home Of COVID-19 - 19, 2020). However the improper nomenclature being used in virology papers is only a small microcosm when compared to the "in-the-field" problems that arise to also be a bar to comprehension:

"Last January, a team of researchers searching for the coronavirus in New York City’s wastewater spotted something strange in their samples. The viral fragments they found had a unique constellation of mutations that had never been reported before in human patients — a potential sign of a new, previously undetected variant [a.k.a. dead bodies of microbes and viruses] ... because wastewater samples contain an amalgamation of lineages circulating in the sewer-shed, it is not possible to reconstruct individual genomes using standard methods."

 (The Doll As Metaphor - 4, quoting NY Times). The less-than-professional nomenclature development should be addressed in all cases.

However, as regular Dredd Blog readers know, suggested corrections are resisted (It's In The GenBank - 4).

It is a long and winding road still (On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17).

The previous post in this series is here.

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