Ecological adaptation vs neo-Darwinian nonsense (3)

By: James V. Kohl | Published on: February 19, 2019

See for comparison to Kohl’s Laws of Biology / Darwin’s conditions of life, which require links from the creation of energy to light-activated changes in protons that link the potential of hydrogen (pH) to biophysically constrained viral latency via gene transfer and sympatric speciation.
lateral gene transfer  Items: 1 to 20 of 11319
horizontal gene transfer  Items: 1 to 20 of 10009
See for an example of how the creation of energy is portrayed in the context of the microRNA-mediated emergence of small RNAs: Origin, Evolution, and Loss of Bacterial Small RNAs (4/9/18)

Drawing guidance from the study of eukaryotic microRNAs, it would be useful to more broadly characterize sRNA emergence and loss dynamics in a large number of bacterial genomes, enabling us to quantify the rates at which they emerge, evolve and persist. Studying sRNAs in the context of these evolutionary forces will help us better understand not only sRNA emergence and change, but also how these elements fit in the larger context of bacterial posttranscriptional regulation and adaptation to environmental stress.

For comparison to the automagical emergence, evolution, and persistence of small RNAs, and the loss dynamics in organized genomes, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model (6/14/13)

…the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, ; Duvarci, Nader, & LeDoux, ; Griggs et al., ; Monahan & Lomvardas, ) in adaptive evolution will certainly be discussed in published works that will follow.

See also: Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella (2013)

We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms.

The six genome equivalents of foreign mitochondrial DNA link lateral gene transfer / horizontal gene transfer from Kohl’s Laws of Biology / Darwin’s conditions of life to all biodiversity on Earth via the light-activated assembly of the nucleic acid-microRNA-peptide nanocomplex in: Plant MicroRNAs in Cross-Kingdom Regulation of Gene Expression (7/10/18)

…miRNA has huge potential to work as a major factor to influence biological functions in the host. There is no doubt that in the future, the identification, confirmation, and analysis of more miRNA molecules, as well as a greater understanding of miRNA-mediated cross-kingdom regulation, will result in the application of miRNAs for the diagnosis, prognosis, and treatment of human diseases; crop improvement by increasing disease resistance; and the pharmacological study of traditional Chinese medicines.

Every aspect of Cross-Kingdom Regulation of Gene Expression has been placed into the context of light-activated microRNA biogenesis in plants via Exploring fast proton transfer events associated with lateral proton diffusion on the surface of membranes (2/12/19)

1) Proton diffusion (PD) across biological membranes is a fundamental process in many biological systems, such as in aerobic respiration or in the photosynthesis process.

2)  Here, we suggest an experimental technique to study the very fast PD events taking place upon the photoinduced release of a proton on the surface of the membrane.

3) We show that the diffusion, as well as the interaction between protons on the surface and protons in bulk media can be influenced by the nature of the membrane’s lipids.

4) Our probe is composed of a photoacid that serves as our light-induced proton source for the initiation of the PD process. We use our probe to follow PD, and its pH dependence, on the surface of lipid vesicles… [with or without a phosphate group].

For comparison, see: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation” (1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

The microRNA-mediated synthesis of RNA also requires the phosphate group.

The sugar-phosphate backbone forms the structural framework of nucleic acids, including DNA and RNA. … DNA and RNA are composed of nucleotides that are linked to one another in a chain by chemical bonds, called ester bonds, between the sugar base of one nucleotide and the phosphate group of the adjacent nucleotide.

Watch as the light-activated assembly of the nucleic acid-microRNA-peptide nanocomplex (the L-ANC) links the creation of sunlight to all biodiversity in:
Lateral transfers of large DNA fragments spread functional genes among grasses PNAS (2/19/19)
Reported as: How our plants have turned into thieves to survive (2/18/19)

Lateral gene transfer allows organisms to bypass evolution and skip to the front of the queue by using genes that they acquire from distantly related species.

“Grasses are simply stealing genes and taking an evolutionary shortcut,” said Dr. Luke Dunning.

“They are acting as a sponge, absorbing useful genetic information from their neighbours to out compete their relatives and survive in hostile habitats without putting in the millions of years it usually takes to evolve these adaptations.”

Note, the requirement for the creation of sunlight was removed in this report on the theft of genes.
Also note the confusion in the claims that:

  1. Plants simply steal genes.
  2. Grasses act as a sponge.
  3. They adapt.

Clearly, plants did not evolve to steal genes. No species has ever evolved in any hostile habitats that would require the theft of genes from other species. All individuals of all species have adapted to survive in the context of the energy-dependent creation of “Keystone Genes,” which enable ecological adaptations across ecosystems.
Keystone Genes (2018)

This opinion article discusses how single genes can have pronounced ecological effects through changes in community structure and/or ecosystem processes.

For example, luciferases are ecologically important genes.
See: luciferase + microRNA Items: 1 to 20 of 9843
The creation of microRNAS has been linked to the creation of luciferase genes via microRNA sponges.
See: microRNA+sponge Items: 1 to 20 of 778
For example: Insights into the biogenesis and potential functions of exonic circular RNA  (2/14/19)

The competitive endogenous RNA (ceRNA) hypothesis posits that transcripts with shared microRNA binding sites compete for post-transcriptional control.

Others have also linked the creation of sunlight from light-activated microRNA biogenesis to biophysically constrained viral latency as an example of the ecological importance of luciferase and the competitive endogenous RNA (ceRNA) hypothesis of energy-dependent post-transcriptional control.
See:  Endogenous microRNA sponges: evidence and controversy (4/4/16)
See: Introduction: Special issue on species interactions, ecological networks and community dynamics – Untangling the entangled bank using molecular techniques
See also: Flower‐visitor communities of an arcto‐alpine plant—Global patterns in species richness, phylogenetic diversity and ecological functioning

Local communities assemble as a function of both stochastic and deterministic processes (Götzenberger et al., 2012; Gravel, Canham, Beaudet, & Messier, 2006; Leibold & McPeek, 2006; Weiher et al., 2011). These assemblies are a result of neutral processes, historical processes such as speciation, species dispersal, abiotic environmental factors and biotic interactions (Götzenberger et al., 2012; Weiher et al., 2011). As an outcome of these assembly processes, the number, abundance, identities and traits of the species present in local communities vary in space and/or time.

For comparison, see: The self-organizing fractal theory as a universal discovery method: the phenomenon of life

…application of the new discovery method to life sciences reveals that moving electrons represent a keystone physical force (flux) that powers, animates, informs, and binds all living structures-processes into a planetary-wide, multiscale system of electron flow/circulation, and that all living organisms and their larger-scale organizations emerge to function as electron transport networks that are supported by and, at the same time, support the flow of electrons down the Earth’s redox gradient maintained along the core-mantle-crust-ocean-atmosphere axis of the planet.

The creation of sunlight must be linked to the claim that a keystone physical force animates a planetary-wide multiscale system of electron flow/circulation, which links the creation of the sun’s anti-entropic virucidal energy to epigenetic effects on “keystone genes.” Top-down causation occurs in the context of links from the Virus-mediated archaeal hecatomb in the deep seafloor to  Eukaryotic plankton diversity in the sunlit ocean.
I reiterate: the creation of the sun’s anti-entropic virucidal energy is required to link all biophysically constrained energy-dependent life on earth to the physiology of reproduction in all living genera.
Please revisit Darwin’s claims about the “abominable mystery” of the sudden appearance in the fossil record of flowering plants.
See: The meaning of Darwin’s ‘abominable mystery’
If you do not agree that the creation of the sun is the link to solving his ‘abominable mystery’ via the physiology of reproduction in grasses and flowering plants, see:
A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation

…plants alter microRNA (miRNA) biogenesis in response to light transition.

See also: The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

In the last few decades, sperm have been reported to carry both RNA and microRNA to the fertilized zygote [17], [18]. MicroRNA (miRNA) are important regulators in translation, and their altered expression often leads to disease or cancer.

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