Saturday, May 23, 2020

On The Origin Of The Home Of COVID-19 - 3

"This is our home"
I. When

When the characters in Downton Abbey say "this is our home" or "this is where I was born" they do not indicate that they built it or that their reality in their time is the same as it was when Downton Abbey was built some 400 years prior to their current reality.

Likewise, when I refer to "The Origin Of The Home of COVID-19" I do not limit it to the current reality.

II. What

The "home" referred to in this series is the original host of the original symbiotic relationship composed of the "SARS-CoV" virus type, and more specifically the "severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)".

Why I call it "SARS-CoV-2" is because it is "now designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses" (Nature-Microbiology).

The popular nickname for SARS-CoV-2 is "COVID-19" (ibid).

III. Where

The "where" of the host of the symbiotic relationship, for the purposes of this series, is the host microbe at the time of the symbiotic relationship between the host and once-symbiont but now pathogenic virus (now called COVID-19).

That "homie", that home host, then, is not a bat, cow, pig, chicken, etc., rather, it is a microbe, a single-celled biotic organism.

Thus, I will diverge from the "host" designation used in the "Nature-Microbiology" paper, i.e. "the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date" (ibid, emphasis added).

I am in good company in that divergence, because :
"...viruses can be considered as symbionts with their hosts. Symbiotic relationships encompass different lifestyles, including antagonistic (or pathogenic, the most well-studied lifestyle for viruses), commensal (probably the most common lifestyle), and mutualistic (important beneficial partners). Symbiotic relationships can shape the evolution of the partners in a holobiont, and placing viruses in this context provides an important framework for understanding virus-host relationships and virus ecology..."
(On The Origin Of The Home Of Covid-19 - 2, quoting from Symbiosis: Viruses as Intimate Partners).

IV. Who

Interestingly enough, we are talking about an original family of multiple host/virus symbiosis:
"... the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus ..."
(ibid, emphasis added). More on that in subsequent posts.

V. Why

The why of this series is to show that the current pathogenic phase of COVID-19 is not the original condition, instead it is a result of "the industry" having made war against the host microbe which changed an original symbiont virus convert into a pathogen a la:
"Like pretty much all multi-cellular organisms, humans enjoy the benefits of helpful bacteria. (As you may have heard, there are more [microbial cells] in the human body than [human cells].) These mutualistic microbes live within the body of a larger organism, and, like any good long-term houseguest, help out their hosts, while making a successful life for themselves. It’s a win-win situation for both parties.

Scientists still don’t understand exactly how these relationships began, however. To find out, a team of researchers from the University of California, Riverside, used protein markers to create a detailed phylogenic tree of life for 405 taxa from the Proteobacteria phylum—a diverse group that includes pathogens such as salmonella as well as both mutualistic and free-living species.

Those analyses revealed that mutualism in Proteobacteria independently evolved between 34 to 39 times, the researchers report in the journal Proceedings of the Royal Society B.  The team was a bit surprised to find that this happened so frequently, inferring that evolution apparently views this lifestyle quite favorably.

Their results also show that mutualism most often arises in species that were originally parasites and pathogens."
(Microbial Languages: Rehabilitation of the Unseen--2)., quoting from Smithsonian). Thus, treating what the media calls "a war against the virus" with more "war" will produce more pathogens (more victims of war).

VI. Where Do We Start?

Let's get a clue based on a post in a microbiology-specific source, which urges us to consider that we need to understand the microbiome of bats before we can better understand the various virus/microbe relationships:
"Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome."
(Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals, emphasis added). Ok, I'm game, let's check out the batosphere.

In the first post of this series we considered the gut microbiota found in domestic animals such as cows, pigs, and chickens.

But, we did not consider those microbiota very deeply, in terms of microbial hosts (but the K-4 kids evidently do).

We will dig deeper into that realm in subsequent posts.

But, since we are now focusing on bats, let's consider the microbiota in bat digestive systems (please excuse a few misuses of "host" in the following sources, which are otherwise quite helpful):

"When you think about bats and what they eat, does the thought of blood come to mind? Only a very small fraction of bats in the world actually survive off of the blood of other animals. The diet for the bat depends on what species you are talking about. Approximately 70% of bats consume insects and small bugs. They are referred to as insectivores. Most of the rest consume fruits and they are called frugivores ... Those that feed on bugs and insects are opportunistic. They will consume anything that they come into contact with ... A bat typically will consume about 1/3 of its own body weight in food per night ... There are two types of insects that bats consume. Most people assume they only eat those that are in the air. Those are called aerial insects and this action can take place with lightening fast speed. They usually use their tail to capture the prey and then they will stop and consume it ... Other types of insects are considered ground dwelling insects. The bats have to swoop down and get them. They often will remain on the ground long enough to consume them and then they continue on again. There are bats that don’t use their tail for catching food though. Instead, they capture it in their teeth. The method that is used depends on the particular species of bat being discussed ... A very small number of bat species also feed on vertebrates. They are said to be the carnivores of the bat world. They consume frogs, lizards, small birds, and also other species of bats. Fish also make great meals for these types of bats. Only the Vampire Bat specifically feeds only on blood for survival."
(BatWorlds). Bats eat insects (which are "the enemy") to kill according to "the insecticide industry" members such as Monsanto, and those "enemies" (a.k.a. bat food) are everywhere:
"Many species [of bats] also inhabit more urban areas like farms, barns, pastures, parks, suburbs, and even cities."
(Animals/Bat). Accordingly, there are many viruses implicated which will aid the ongoing research:

"Bats, which comprise about 20% of the mammal world, have many microbe types which are likely hosts to viruses"
(Bats, Bacteria, and Bat Smell: Sex-Specific Diversity of Microbes in a Sexually Selected Scent Organ).
"The identification of dermatophytic fungi, isolated from the skins of cave-dwelling bat species, is necessary to distinguish pathogenic (disease-causing) microbes from those that are innocuous. This distinction is an essential step for disease diagnoses, early detection of the presence of microbial pathogens prior to symptom development, and for discrimination between microbes that are present on the skins of hibernating bats."
(Discrimination between Pseudogymnoascus destructans, other Dermatophytes of Cave-dwelling Bats, and related innocuous Keratinophilic Fungi based on Electronic-nose/GC Signatures of VOC-Metabolites produced in Culture). Since  microbes are the bona fide hosts of our research, notice this too:

"Microorganisms play a crucial role in maintaining the delicate ecological balance of the earth. They revitalize the soil by recycling the minerals and nutrients of decaying matter, and many are essential to the healthy growth of plants. Microorganisms also affect our lives more directly in the manufacture of such items as food products, detergents, antibiotics and antitumor drugs.

A marvelous symbiosis exists between these organisms and bats. Bacteria in the mammalian intestinal tract aid in the breakdown and digestion of food. These organisms possess enzymes capable of degrading a vast array of substances. Countless microbes are regularly excreted along with waste products, and together with soil organisms, they constitute the microbial population of a bat guano deposit.
(Bats, Bacteria and Biotechnology). Looking further into this subject matter, note that some research has hypothesized an interesting, and perhaps unique characteristic of the environment/ecosystem impact on bats:

"Bats may be very susceptible to environmental change -- if they have a transient microbiome, they might not have the most stable defense mechanisms," says Lutz. 'Human-caused disturbances to the environment are a very important issue. Bats may be extra-fragile and more at risk.'"
(Bats don't rely on gut bacteria the way humans do). That article points out the short length of bat intestines compared to other mammals and that they therefore have a more vulnerable gut microbiota population.

VII. Closing Comments

The gravamen of the situation is that bats have a diet that is susceptible to being contaminated by toxins from pesticides and herbicides.

Many of them live in human habitats where anti-biotic, anti-insect, and anti-plant chemicals are consistently sprayed into their habitat, and ours.

This means that we can reasonably hypothesize that these behaviors are anti-host to the point of killing symbiotic relationships and thereby creating pathogenic behavior as symbiotic hosts die and release "homeless" viruses into a strange world (for them).

In other words, the catastrophe of the Anthropogenic era is the ongoing Sixth Mass Extinction which, like the Fifth Mass Extinction, adversely impacts symbiotic relations (What Did The Mass Extinctions Do To Viruses and Microbes?).

The next post in this series is here, the previous post in this series is here.

Thursday, May 21, 2020

On The Origin Of The Home Of COVID-19 - 2

Viruses outnumber stars
I. Which Came First

The logic of cosmology's "Big Bang Hypothesis" (BBH) is clear enough to be understood in several fundamental ways (The New Paradigm: The Physical Universe Is Mostly Machine).

The BBH timeline indicates that there was a "B.C.", that is, there was a time before carbon.

In the B.C. age there was no carbon, and thus no carbon based life forms such as single-celled microbes.

It was the abiotic age:
Dr Clarke said: “There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become livingeverything up to that point is chemistry.[e.g. atoms, molecules: molecular machines]”
“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.
(Putting A Face On Machine Mutation - 3). Thus, following the logic of the BBH, the carbon-based life-form age would have to have begun after the emergence of carbon, which came about thusly:
"Formation of the carbon atomic nucleus requires a nearly simultaneous triple collision of alpha particles (helium nuclei) within the core of a giant or supergiant star which is known as the triple-alpha process, as the products of further nuclear fusion reactions of helium with hydrogen or another helium nucleus produce lithium-5 and beryllium-8 respectively, both of which are highly unstable and decay almost instantly back into smaller nuclei. This happens in conditions of temperatures over 100 megakelvin and helium concentration that the rapid expansion and cooling of the early universe prohibited, and therefore no significant carbon was created during the Big Bang. Instead, the interiors of stars in the horizontal branch transform three helium nuclei into carbon by means of this triple-alpha process. In order to be available for formation of life as we know it, this carbon must then later be scattered into space as dust, in supernova explosions, as part of the material which later forms second, third-generation star systems which have planets accreted from such dust. The Solar System is one such third-generation star system."
(On the Origin of the Genes of Viruses - 5, quoting Wikipedia & NASA). In one sense this complicates the search for the origin of the "home" of viruses, that is, "where they came from".

But, in another sense it simplifies the origin of symbiotic viruses in terms of the symbiotic relationship between single cell carbon based life forms (microbes) and viruses.

Abiotic viruses emerged first during the abiotic age (pre-carbon), then much later microbes emerged in the biotic age (post-carbon).

Some of the abiotic age machines were 'dynamos' (The Uncertain Gene - 10).

But the saga doesn't stop there, no, viruses "aren't what they used to be" as told in the oldie textbooks:
"Virus infection involves coordination of a series of molecular machines, including entry machines, replication machines, assembly machines, and genome packaging machines, leading to the production of infectious virions.
Although viruses had been considered as merely dull, static containers, and protectors of genomes, this false concept was replaced by the realization that viruses are beautiful intricate machines, essential to biological evolution, capable of invading cells, stealthily avoiding the protective barriers of the host, usurping the host's synthetic machinery for their own survival and able to self assemble into complex molecular machines. Indeed it has become apparent that the capabilities of viral machines far exceed those to the simple enzymes first studied in the mid-twentieth century. This book is a partial description of some of the amazing things accomplished by viruses in infecting a host and replicating themselves [the host cell's replication machines replicate viruses]."
(On the Origin of the Genes of Viruses - 7, quoting from "Viral Molecular Machines").

II. Then Came Symbiosis

How the viruses (in the abiotic age's last BC days) reacted to emerging biotic cells as they came on the scene is anybody's guess I suppose.

But most would agree that the relationship would have been incremental, the ultimate relationship eventually developing last (simple to complex), which would be symbiosis.

So, as of now scientists clearly realize that the notion of viruses as enemies of carbon based life forms is archaic and wrong:
"Viruses must establish an intimate relationship with their hosts and vectors in order to infect, replicate, and disseminate; hence, viruses can be considered as symbionts with their hosts. Symbiotic relationships encompass different lifestyles, including antagonistic (or pathogenic, the most well-studied lifestyle for viruses), commensal (probably the most common lifestyle), and mutualistic (important beneficial partners). Symbiotic relationships can shape the evolution of the partners in a holobiont, and placing viruses in this context provides an important framework for understanding virus-host relationships and virus ecology. Although antagonistic relationships are thought to lead to coevolution, this is not always clear in virus-host interactions, and impacts on evolution may be complex. Commensalism implies a hitchhiking role for viruses—selfish elements just along for the ride. Mutualistic relationships have been described in detail in the past decade, and they reveal how important viruses are in considering host ecology. Ultimately, symbiosis can lead to symbiogenesis, or speciation through fusion, and the presence of large amounts of viral sequence in the genomes of everything from bacteria to humans, including some important functional genes, illustrates the significance of viral symbiogenesis in the evolution of all life on Earth."
(Symbiosis: Viruses as Intimate Partners). However, there remains a rancid nomenclature still in use by the commentariat and by many scientists:
"Symbiosis is a concept fraught with misunderstanding, and the literature is full of various definitions. Here we use the original definition of symbiosis as described by Frank and de Bary in the nineteenth century from their studies on lichen. The two critical aspects of this definition are that the entities must be in an intimate relationship, living in or on one another, and that the entities must be dissimilar (1). Symbiotic relationships are not necessarily beneficial; antagonistic symbioses also are common, and for viruses, commensal relationships, where there is no observable cost to the host, are probably the most common. Symbiotic relationships fall on a continuum between mutualistic and antagonistic, where the environment affects the placement of the holobiont on the continuum, a relationship known as conditional mutualism (Figure 1)(2, 3). Although some definitions of symbiosis use the term parasitism instead of antagonism, this further muddies the waters; all viruses, and indeed many other symbiotic microbes, are parasitic, meaning they benefit from their hosts by acquiring nutrients from them. This does not mean that they cannot also be commensal or mutualistic; these distinctions depend on whether or not the benefits outweigh the costs. Finally, mutualism does not necessarily imply symbiosis. For example, just because humans eat fruit and thus are involved in seed distribution, humans and fruiting plants do not live in an intimate relationship (in or on one another), and hence, even though the relationships are mutualistic, they are not symbiotic."
(ibid). The rancid nomenclature mentioned in that quote is typical historical behavior (e.g. Modern Evolutionary Synthesis).

But, as pointed out in the first post of this series, it (understanding the reality of the virus world) is exacerbated to new lows by commercialism.

Just as bad, the term "war" is still being used by the commentariat of the media and the government as it has always been to describe virus/host interaction.

Still, the truth tellers struggle to make reality better known:
"Viruses are the most abundant and diverse biological entities on the planet. Recent biodiversity surveys in desert, ocean, soil, mammalian gut, and plant ecosystems have uncovered an abundance of viruses in every ecosystem and life form examined. These ecological surveys also highlight a common misconception about virus biology: In spite of their ubiquitous incidence, most viruses produce no recognizable symptoms associated with disease. Interactions among viruses and their respective hosts are dynamic and variable and constitute important forces shaping populations."
(ibid, emphasis added). "If it bleeds it leads" is a sacrament of both McTell news and corrupt government.

III. Closing Comments

I have isolated 63,626 scientific papers that focus on viruses in general, then filtered them with the keywords "SARS" and "symbiotic", which "boiled" the scientific papers I am reviewing down to 2,640.

Saying that the "Origin Of The Home Of Covid-19" is "the abiotic age prior to the emergence of carbon based life forms" or "the Earth's ecosystem" is not sufficient to detail the reality.

So, stay tuned as I try to follow the trail, then tell you where it may be leading.

The next post in this series is here, the previous post in this series is here.