Trans-kingdom RNA interactions (3)

By: James V. Kohl | Published on: September 6, 2019

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Intracellular innate immune surveillance devices in plants and animals 12/2/16
Excerpts:

1) In plants and animals, innate immunity involves both cell surface receptors (1) and intracellular receptors of the NLR [nucleotide binding domain (NBD) and leucine-rich repeat (LRR)] superfamily (2–4). NLRs play critical roles in organismal health in both plants and animals; absence or dysfunction can result in organ failure and death (Fig. 1).

2) The NBD falls within the STAND [signal transduction adenosine triphosphatase (ATPases) with numerous domains] AAA⁺ ATPase superfamily, which typically includes Walker A (P-loop) and Walker B motifs involved in nucleotide binding and hydrolysis (20, 21).

3) Thus, plant and animal NLRs likely evolved from distinct ancestral NBD lineages based on differential expansion from a common ancestor of these STAND AAA⁺ ATPases (27).

The Creation of sunlight and water links the Creation of signal transduction adenosine triphosphatase (ATPases) from the nucleotide binding domain to the intracellular receptors of the NLR. Light-activated signal transduction is clearly required for the nucleotide binding and hydrolysis that links hydrogen atom transfer in supercoiled DNA to trans-kingdom responses to environmental stimuli, which are required to link the Creation of hydrophobic supercoiled DNA to the physiology of reproduction and species survival in all living genera on Earth.
The ridiculous claim that plant and animal NLRs base pair – receptor interactions automagically evolved is not supported by any experimental evidence of top-down energy-dependent Creation. That evidence has been bastardized for presentation to biologically uninformed science idiots who believe in ridiculous theories that require energy to emerge from the void before it is linked to the magic of how evolution must link ecologically relevant sensory input to all biodiversity in species from microbes to mammals.
See for instance: Lipid Encapsulation of Self Replicating Ribozymes

Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered.

See for comparison: MicroRNA based feedforward control of intrinsic gene expression noise 8/30/19
The preprint was published as Buffering gene expression noise by microRNA based feedforward regulation 4/28/18

The quasi-steady state (QSS) approximation often leads to formulation of simplified models that can be more amenable to exact characterisation [39–43].

Here we apply these methodologies to analyse a reaction-kinetics model of a feedforward loop.

The feedforward loop links their approximation to the claims of Ariel Bazzini in Genome-Wide Study Reveals a Novel Regulatory Pathway: Translation Affects mRNA Stability in a Codon-Dependent Manner 6/26/19
See also: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition 7/19/16

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

A paralog one of a pair of two genes that supposedly are derived from the same ancestral gene. That ancestral gene has not been found. Most theorists realize it will never be found, if only because they know that genes do not create themselves.
Claims about self-replicating ribozymes, promoters, enhancers, spacers, QTLs, non-homologous end joining, et al., have been linked from mutation-driven evolution to all biodiversity on Earth. But claims that energy-dependent sequence changes in paralogs link food energy-dependent pheromone-controlled sympatric speciation to the biogenesis of all diversity via the amino acid optimality code have been used to refute the pseudoscientific nonsense touted by neo-Darwinian theorists and Big Bang cosmologists.

See: Integrated mobile genetic elements in Thaumarchaeota 3/18/19
Eugene Koonin and Mart Krupovic are among others who have placed the diversity of mobile genetic elements such as biophysically constrained human endogenous retroviruses into the context energy-dependent ecological adaptations and sympatric speciation.
See for comparison: Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea 7/18/19

…viral predation has a profound impact on thaumarchaeal functioning and mortality, thereby regulating global biogeochemical cycles.

A universal trend of amino acid gain and loss in protein evolution 2/10/05

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

Feedback loops link odor and pheromone signaling with reproduction 11/18/05

[The feedback loops] …may reflect a strategy wherein GnRH neurons can modify diverse functions in order to coordinate the internal state of the animal and its behavior with reproduction in order to optimize reproductive success.

Fourteen more years of scientific progress have failed to link mutations to the evolution of anything except pathology. During the same time, the food energy-dependent pheromone-controlled physiology of reproduction has linked the Creation of sunlight and water to biophysically constrained viral latency and the genesis of all biodiversity via microRNA biogenesis, which prevents the virus-driven degradation of messenger RNA that links mutations to all pathology.