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| Acquiring DNA |
It is not often that we who are now alive experience unique world wide changes in society, on this planet, during our brief sojourn.
Yet, I hazard to say that most of us alive today, whether we are aware of it or not, have lived through a major world wide change that has taken place in our civilization in our time.
I say most of us because this particular world wide change happened about 20 years ago, and continues to this day:
(A global metagenomic map of urban microbiomes, Cell 184, 3376–3393, June 24, 2021; emphasis added). This is an astonishing statistic which most of us reading this post have been a part of.
In the previous post I mentioned the difficulty facing the MetaSUB project which is a much greater difficulty than the usual collection difficulties of DNA/RNA residue collection.
One aspect of the challenge is the increased difficulty when working in an area with above and beyond naturally developed chimera quantities.
That is because the MetaSUB sample collecting area is orders of magnitude more difficult to 'sequence' (i.e. to interpret the DNA/RNA; see Fig. 2 here).
II. Chimera
Chimera in mythology are biological entities that are composed of different parts from other and different biological entities (Wikipedia).
But there is a biological concept of chimera in the science of 'genetics' too (Wikipedia).
Here on Dredd Blog another type of chimera has also been discussed, which is the type that is caused by the indiscriminate destruction of microbes.
I am in reference to microbes which are the hosts of various viruses and/or hosts to smaller microbes that live in or on them (see e.g Quantum Biology - 5, 16, 17, 18, 19).
Actual chimera detected in genetic material and interpretations thereof are not limited to scientific endeavors, there are cognitive chimera just about everywhere.
Various religions also are into cognitive chimera development, even to the point of developing chimera gods and goddesses over time:
"...it is well known that under the Roman Empire, Christianity did indeed adopt the pagan rituals of conquered peoples in an effort to help convert them. It worked pretty well as a strategy as it allowed the conquered peoples to continue a semblance of their observances as they remembered, and with time the population would be replaced with those who only knew the new traditions. This is not a secret."
(Scientific American, cf Easter Bunny). Note that this religious development of chimera gods and goddesses predates the Roman Empire, and involves not only chimera of their names, but it also involves developing chimera composed of behaviors, beliefs, and characteristics (i.e. syncretism):
"Scholars believe that Inanna and Ishtar were originally separate, unrelated deities, but were conflated with one another during the reign of Sargon of Akkad and came to be regarded as effectively the same goddess under two different names." ['Etymology' section]
"Inanna has posed a problem for many scholars of ancient Sumer due to the fact that her sphere of power contained more distinct and contradictory aspects than that of any other deity. Two major theories regarding her origins have been proposed. The first explanation holds that Inanna is the result of a syncretism between several previously unrelated Sumerian deities with totally different domains. The second explanation holds that Inanna was originally a Semitic deity who entered the Sumerian pantheon after it was already fully structured, and who took on all the roles that had not yet been assigned to other deities." ['Origins and development' section]
(Wikipedia). This wild nomenclature of cognitive chimera is a tug and pull that is still epic even after all these years (Talk:Ishtar). But I digress.
III. The Septic System Chimera
During the previous Covid-19 pandemic, and the still ongoing 'Long Covid' version, a way of predicting when a local Covid-19 outbreak would occur developed.
Researchers discovered that they could examine sewer system content at processing stations where city sewer water was processed:
"One of the hypotheses set forth in this series is that SARS-CoV-2 is a descendant of corona viruses that have been found in sewage for many years:
"These findings provide strong evidence that SARS-CoV can be excreted through
the stool/urine of patients into sewage system, thus making the sewage system a possible route of transmission."
(Concentration and detection of SARS coronavirus in sewage, Wang 2005, Journal of Virological Methods). Wang's decade and a half old research and perceptions have proven accurate some 15 years later as the descendant virus SARS-CoV-2 (which causes COVID-19) has been found in sewage systems all over the place.
In fact, in the USA it is a preferred method of SARS-COV-2 detection now:
"Sampling wastewater is therefore sampling a mix of the total population in the sewershed, and encompasses the large proportion of infected individuals that do not get tested, because they are not or only mildly symptomatic, are reluctant to get tested, are not included in the testing policy or have less access to testing. As a consequence, sewage surveillance better represents the true SARS-CoV-2 circulation in the population. Sewage surveillance is the systematic collection, analysis and interpretation of data on SARS-CoV-2 RNA in wastewater to observe (and provide an early warning of) trends in COVID-19 in the communities. Sewage surveillance has been shown to be sensitive and fast enough to provide an early warning of increasing SARS-CoV-2 in cities. This is important information to support stratified lockdown decisions. Sewage surveillance is aimed to monitor the circulation of SARS-CoV-2 communities; large communities such as inhabitants of a large city, or smaller communities, such as nursing homes, university or office campuses, prisons, and so on. It is a very cost-efficient tool for population surveillance, and also a noninvasive tool, which does not require repeated sampling of individuals (such as nursing home inhabitants) to survey for (absence of) SARS-CoV-2 circulation in that community."
(On The Origin Of The Home Of COVID-19 - 19). But to be more specific, it was also discovered that some of the samples were composed in whole or in part of chimera viruses.
More on that in a bit, but the chimeric phenomena evidently shows up in other places too:
"The following three links evince a recent back and forth between two research teams concerning what causes "chimeric" (mixed) genome readings and illustrates some of the weaknesses in current virology research (Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues; No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues, Response to Parry et al.: Strong evidence for genomic integration of SARS-CoV-2 sequences and expression in patient tissues)."
(Some Of My Best Friends Are Germs - 2, emphasis added). "The ayes have it" on the issue of whether or not genetic chimera exist:
We must take this and related issues very seriously:
"Assembly pipelines often result in viral genomes contaminated with host genetic material, some of which are currently deposited into public databases ... For years now the study of viruses and their genetic composition has been important in their identification and classification. Especially in these times of the pandemic turmoil, accurate knowledge of a virus’ exact genetic composition can help identify its strengths and weaknesses allowing us to track its evolution and assist in the development of vaccines and antiviral agents. The reconstruction of these genomic sequences is called the assembly process, a bioinformatics approach which can be complicated and full of pitfalls. This work identifies one such issue, concerning artifacts introduced in viral genomes from the new technologies of nucleic acid sequencing. The proposed algorithm helps alleviate this problem by tentatively removing these problematic regions while keeping the vast majority of the genetic information required to produce a more complete viral genome. This work is anticipated to assist in the submission of higher integrity and accuracy viral genomes in public databases used for novel virus identification and characterization ... Open databases, such as GenBank, while they contain most of the current sequences, are poorly curated regarding the integrity and the accuracy of the submitted sequences. Indeed, various reports have highlighted contamination of sequences with bacterial moieties that were erroneously incorporated in the final assembly. Such errors are especially important as they result in false positive identification of viruses that happen to contain in their proposed viral genomes parts of host DNA or RNA."
(ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach, emphasis added)...
(It's In The GenBank - 4; cf. It's In The GenBank - 2). Ok, "so what about the septic system chimera, Dredd?", you may still be wondering:
"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.
(Signals from the sewer, emphasis added, 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, emphasis added, quoting NY Times). The less-than-professional nomenclature development should be addressed in all cases."
(On The Origin of the Genes of Viruses - 18). Passing "the smell test" is a very old but easy to attain standard which applies in this case too.
IV. Closing Comments
This reminds me of the time when a detective asked a suspect "Why do you rob banks?", to which the suspect replied "that's where the money is".
While I applaud the MetaSUB organization's attempts to "make perfect" with "make do" on the streets and other public places of the world's cities ("where the public DNA is"), I also caution them about being too self-assured.
Interpretation of chimera is to be avoided in the best-case scientific endeavors.
The next post in this series is here, the previous post in this series is here.
Various experts on human genetics (the first speaker in the video is Dr. Robert Morris Sapolsky, Professor at Stanford University; cf. epigenetics):