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.


  1. My blue collar brain struggles to understand, but tiny bits of knowledge seep in, and after awhile, BOOM, all life is outstanding. It does give a sense of wonder; that which I felt as a youth while scanning the night sky.

  2. Well rocco, now that you have experienced what every researcher experiences when they first look at a new subject, jump in. Absorb it all. Become a gray literature aficionado. Welcome aboard.