The Doll As Metaphor

Gut microbiome viruses on a microbe

The doll is used as a teaching tool in many ways, and is a favorite for children, whether seen on Sesame Street as puppets, or used in the home as personal toys (The Doll As Metaphor).

Sometimes we can forget how powerful the experiences of childhood are, which can last and have a significant impact on us.

This molding of our subconscious and conscious cognition takes place across a distance beginning at the surface of our skin, going all the way down to our most abundant and mostly unknown composites:

"As a child grows, the commensal microbiota develops in a predictable succession of species that is generalizable across human populations. The developing bacteriome, the bacterial component of the microbiome, has been profiled many times, both taxonomically and in terms of metabolic functions. These profiles have provided a view of how bacterial species are structured over time. Less is known about the gut-associated eukaryotes and viruses that develop along with the bacteriome, although they are an important part of the gut ecosystem. The disruption of the bacterial succession can be pathogenic. Critical developmental milestones for the microbiota (as well as for the child) occur, in particular, during infancy and early childhood, and both medical intervention and lack of such intervention during these periods can have lifelong consequences in the composition and function of the gut ecosystem. In this section, we discuss the instances in which antibiotics are often used during development and adulthood, the effects of antibiotics on the microbiota, and the implications of such effects for health and disease."

(The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation). So, do we "Go Ask Alice" about the reality of the statement "the pills which mother gives you don't do anything at all", or do we ask ourselves about things that do "something" to us?

For example the 'pills' that are used to mass-produce the food we eat:

"The concept has been discussed in scientific journals since at least 1957 (Penicillin-Induced Lysis of Escherichia coli) and as recently as this year:

"Bactericidal antibiotics kill bacteria by perturbing various cellular targets and processes. Disruption of the primary antibiotic-binding partner induces a cascade of molecular events, leading to overproduction of reactive metabolic by-products. It remains unclear, however, how these molecular events contribute to bacterial cell death. Here, we take a single-cell physical biology approach to probe antibiotic function. We show that aminoglycosides and fluoroquinolones induce cytoplasmic condensation through membrane damage and subsequent outflow of cytoplasmic contents [including virus RNA] as part of their lethality.
...
Previous work has shown that the intracellular accumulation of promiscuously reactive metabolic by-products induces widespread cellular dysfunction and contributes to antibiotic lethality [microbe death]. However, the mechanisms underlying how reactive metabolic by-products, and the accompanying phenotypic changes, [variants, mutants] contribute to cell death have remained unclear."

(Cytoplasmic ... Damage ... Antibiotic Lethality, emphasis added). The words highlighted in red, and the words highlighted in bold, help focus on the Dredd Blog hypothesis that antibiotic chemicals used promiscuously in the mass-production-of-animals-for-food industry is causing viruses to be changed by the indiscriminate killing of microbe hosts ("around 70% of the world's total production of antibiotics is used in animal husbandry and agriculture")."

(Omicron (OMC!) - 3). This brings us to RNA viruses, such as SARS-CoV-2:

"Most emerging infectious diseases are caused by RNA viruses. Many of these that are newly found in humans have a natural mammal or bird reservoir; some are transmitted by arthropod vectors, such as mosquitos. If we do not know the reservoir host and/or vector, it is harder to identify individuals and populations at greatest risk of infection and to design an effective public health response. On page 577 of this issue, Babayan et al. report their efforts to predict the reservoir hosts and vectors of human RNA viruses by applying machine-learning algorithms to virus genome sequence data."

(Sources of human viruses). That said, the propaganda engines of Big Pharma, (who make "the pills that mother gives us" which "do anything at all"), seek to confuse us:

For example, "what are RNA viruses?" ...

"Viruses are microscopic particles that exist almost everywhere on Earth. They are present in animals, plants, and other living organisms, and they can sometimes cause diseases.

Viruses are biological entities that can only thrive and multiply in a host, which is a living organism such as a human, an animal, or a plant. Some viruses cause disease. For example, severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2, causes the disease COVID-19."

A virus may also affect one organism in one way but a different one in another. This explains why a virus that causes illness in a cat may not affect a human.

"Viruses vary in form and complexity. They consist of genetic material, DNA or RNA, with a coat of protein around it. Some have an additional coat called the envelope. This may be spiky and helps them latch onto and enter host cells. They can only replicate in a host.

In this article, we discuss in detail viruses, including how they act and how they can affect people."

(What to know about viruses, Summary). But Big Pharma does not want you to realize the reality of viruses, such as:

"Viruses, do, however, share a few features: First, they generally are quite small, with a diameter of less than 200 nanometers (nm). Second, they can replicate only within a host cell. Third, no known virus contains ribosomes, a necessary component of a cell's protein-making translational machinery."

(The Origins of Viruses, Nature). Viruses absolutely do not reproduce themselves, so let's be clear that Big Pharma does not want you to know that.

The origins of what you "know/believe" about viruses can be different, depending on who you trust, because Big Pharma is a Big Fibber:

"In short, viruses can replicate and create other viruses."

(Big Pharma, Our Industry, emphasis added). FALSE. The truth is that viruses are replicated inside microbes by the microbe's complex replication machinery that Big Pharma's antibiotics kill (Some Of My Best Friends Are Germs - 2).

First Step?

"The human endogenous intestinal microflora is an essential “organ” in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features remain poorly described. We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity. A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms. We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease."

(Diversity of the human intestinal microbial flora, emphasis added). Which brings up today's appendices and the results of first step searches in them.

Much of the mass-produced food we consume originates in the "cattle factories" where beneficial microbes are relentlessly slaughtered, so research into the nature of their microbiome is useful:

"Over the past decade it has become clear that mammals live in symbiosis with their abundant resident microbes. Advances in culture-independent techniques (eg, 16S ribosomal RNA [rRNA] sequencing) have enabled detection and quantification of bacterial species that are difficult or impossible to detect by culture-based methods. These advances in the field of molecular techniques, in particular metagenomics, have led to the definition of the animal microbiota, a term that refers to the complex microbial ecosystems in and on bodies of animals. Like other body sites, the respiratory tract of cattle is colonized by a variety of different bacterial microbiotas directly after birth. Composition and diversity of these microbiotas have been recently associated with respiratory health in cattle.

...

The diversity of bacteria on earth is vast, comprising 55 phyla. The cattle respiratory tract is inhabited predominantly by 5 of these phyla (Proteobacteria, Firmicutes, Tenericutes, Actinobacteria, and Bacteroidetes..."

(Respiratory Bacterial Microbiota in Cattle). It's the kill anything that moves thingy that is destroying helpful microbes.

Today's appendices are (A, C1, C2, C3, C4, H, I-M1, M2, P1, P2, R-S1, S2-X), which show results of searches on the DNA of microbes found in animal microbiomes.

I have taken a look inside some of the DNA of various microbes the authors above ("Respiratory Bacterial Microbiota in Cattle") mentioned.

I searched their DNA for "the mother of all SARS-CoV-2" RNA segments and genes.

Those results in today's appendices are in this format:

"1) microbe version: NZ_CP033460.1 results:
 
    microbe nucleotide size: 2,691,850
    Wuhan bp percent of microbe bp: 1.11%
    complete Wuhan genes in microbe: 0
    Wuhan SARS-CoV-2 bp in microbe nucleotides: 25,680
    percent of Wuhan bp in microbe DNA: 85.88%"

The unique id of each microbe (e.g. "NZ_CP033460.1") is the official identity of that particular microbe (which you can look up here by entering that ID).

The "microbe nucleotide size: 2,691,850" is the number of ACGT base pairs (bp) in that microbe's DNA.

The "Wuhan bp percent of microbe bp: 1.11%" indicates the percentage size of the SARS-CoV-2 virus's bp compared to the microbe's bp size (yes microbes are vastly larger than the virus);

The "complete Wuhan genes in microbe: 0" indicates whether a complete SARS-CoV-2 gene was located in the microbe's DNA (there were none).

The "Wuhan SARS-CoV-2 bp in microbe nucleotides: 25,680" indicates how many ACGT's of the virus were found in the microbe. This is performed by an incremental search for ten bp, moving to the following ten bp, until the end of the virus bp was reached (see the ten pair layout at the bottom of the page here).

The "percent of Wuhan bp in microbe DNA: 85.88%" indicates how much (percent) of the Wuhan SARS-CoV-2 virus bp nucleotide RNA is located inside the microbe DNA (this is an astounding percentage for most of the microbes).

It is an understatement to say there is much still to learn in the realm of genomics (The Human Microbiome Congress, The Germ Theory - of Government):

"Microbes may indeed be subtly changing our brain early on — and for what purposes we cannot yet say ... the mere fact that microorganisms can shape our minds brings up many more questions about how humans develop their identity ... these findings call for a complete re-examination of human physiology and immunology. Attributes that were assumed to be human traits have been shown to result from human–microbe interactions."

(The Skulls They Are A Changin'). But, let us not make "dolls" out of microbes and viruses by using "magic words" to describe what they do.

The next post in this series is here.