Biologists puzzled by evolved RNAs and decaying DNA

By: James V. Kohl | Published on: November 11, 2014

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella (December, 2013)

Excerpt) “The ancestral angiosperm-wide genome duplication apparent in the Amborella genome not only serves as a genetic marker for the origin of extant angiosperms, but it may also have set in motion a series of events as numerous genes evolved novel functions, eventually leading to modern flowering plants.”

See also: The Amborella Genome and the Evolution of Flowering Plants

Excerpt) “Evolution of Small RNAs
More than 56,000 discrete loci generating apparent regulatory small RNAs 20 to 24 nucleotides (nt) in size were identified by analysis of small RNA-seq data (17). Most small RNA loci had features consistent with those of heterochromatic small interfering RNAs (siRNAs) (24), indicating that heterochromatic siRNAs were present in the MRCA of all angiosperms. We also identified 124 MIRNA loci corresponding to 90 distinct families; 27 of these microRNA (miRNA) families, including 5 newly discovered ones, were likely present in the ancestral angiosperm.”

In the context of evolved small RNAs, this was reported, 11 months later as:

Gene-Hoarding Shrub Puzzles Biologists

Foreign mitochondrial genes outnumber the Amborella plant’s own six to one

Excerpt 1)  “Judging by accumulated mutations, the transfers appear to have happened tens of millions of years ago. “It’s like Amborella is a museum full of ancient DNA that is just decaying away,” Palmer says.”
My comment: If Palmer’s claim is true, genetic entropy, which he suggests is manifested in “…DNA that is just decaying away,” could be placed into the context of cell type differentiation. For example, light-induced amino acid substitutions in plants link nutrient-dependent amino acid substitutions in animals and the differentiation of all cell types in all individuals of all species. However, cell type differentiation cannot be placed into the context of genetic entropy because tens of millions of years are not required for a nutrient-dependent amino acid substitution to create changes in morphological and behavioral phenotypes. Only a few generations are required. Amino acid substitutions link the epigenetic landscape to the physical landscape of DNA in organized genomes via their ability to stabilize protein folding. If it took more than a few generations for the stability of DNA to arise, biodiversity could not arise.
Excerpt 2) “But because it’s more stable in its evolution, we can actually observe it better and it doesn’t erase the footprints of those insertions as fast.”
My comment: What insertions? He appears to be claiming the amino acid substitutions that stabilize the organized genome are akin to accumulated mutations in DNA that is just decaying away. See, for comparison, Kochman (2012) Evolution of gonadotropin-releasing hormone (GnRH) structure and its receptor.
“It should be stressed that the surprising total conservation of GnRH II’s primary structure, from bony fish to man, appears to be a result of the excellent coordinated evolutionary selection of amino acids participating in binding, activation and configuration such that its structure cannot be improved by substitution with any natural amino acid at any position.”
My comment: The nutrient-dependent RNA-directed DNA methylation and RNA-mediated events that link fixation of amino acid substitutions and pheromone-controlled biodiversity in species from microbes to man appears to also have arisen in the context of a link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of plants via conserved molecular mechanisms. Kochman places these conserved molecular mechanisms into the context of “…selection of amino acids participating in binding, activation and configuration…”
Selection for amino acids appears to occur in this context: “… the sense of smell developed in order to identify amino acid-like chemical substances soluble in water. The ability to determine molecules floating in the air is an adaptation of that original mechanism. That claim was cited in this context: Evolutionists Cannot Account for the Origin of the Sense of Smell on page 106 of The Miracles Of Smell And Taste.
The author adds: “In brief, what Caprio, an evolutionist researcher, wants to say is that single-celled organisms unknowingly released chemical substances; that predators detected these and hunted them. In addition to being exceptionally illogical, his conjecture fails to answer how the sense of smell came into existence. Absolutely no information is provided about the sensory systems that enabled predators to detect their single-celled prey. No explanation is offered of how the sensory systems came into being that permitted single-celled organisms to detect their enemies’ scents and thus survive. Neither are we told what “evolutionary” mechanisms entered the equation during the construction of this extraordinarily complex mechanism.”
Conserved molecular mechanisms that link amino acid substitutions to DNA stability in species from microbes to man appear to have been established in plants during the same time that Palmer and many others seem to think “evolutionary” mechanisms established a link to cell type differentiation that somehow evolved in the context of “…DNA that is just decaying away…”  For contrast, in my model, the link from nutrient-dependent protein biosynthesis and degradation in plants to nutrient-dependent protein biosynthesis and degradation in animals appears to be exemplified by the effects of odors produced by flowering plants that attract animals. The result is a form of assisted reproduction in flowering plants, which is closely linked to the accumulation of foreign mitochondrial genes via nutrient-uptake. Nutrient-uptake is also essential in other plants that incorporate the DNA of other organisms into their organized genome.
For example, even the ‘corpse flower’ attracts some insect species.
Excerpt 3) “Before the Amborella discovery the plant known to have squirreled away the most foreign mitochondrial genes was Rafflesia, a parasitic plant that makes the lurid-colored and notorious “corpse flower,” so called for its putrescent smell. (It also happens to be the world’s largest flower.)”
My comment: In Rafflesia arnoldii, “To pollinate successfully, the flies and/or beetles must visit both the male and female plants, in that order.” That fact seems to eliminate random mutations and decaying ancient DNA from claims about evolutionary events linked to biodiversity. It also appears to replace those claims with experimental evidence of RNA-mediated events that link plant and animal reproduction from the nutrient-dependent pheromone-controlled reproduction of bacteria via the conserved molecular mechanisms of nutrient-dependent RNA-mediated amino acid substitutions that arise in the context of the de novo creation of odor receptor genes and receptor-mediated behaviors in Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
Excerpt 4) “That makes it [Rafflesia arnoldii] an important organism for studying Darwin’s “abominable mystery” – the sudden evolution of flowering plants.”
My comment: Indeed, the flowering organism links ecological variation to the de novo creation of odor receptor genes via nutrient-dependent RNA-mediated amino acid substitutions. The substitutions are linked from protein biosynthesis and degradation to cell type differentiation in all cells of all species via ecological adaptations manifested in morphological and behavioral diversity. Biodiversity exemplifies the fact that ecological variation leads to ecological speciation via conserved molecular mechanisms, which are controlled by the physiology of nutrient-dependent reproduction.
That fact links Darwin’s nutrient-dependent ‘conditions of life’ to the controlled physiology of reproduction via sympatric speciation in species from microbes to man, and also to the killer whales at the top of the aquatic food chain. See for example: Tracking niche variation over millennial timescales in sympatric killer whale lineages.
Excerpt: “Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].”
See for comparison: Genetic mutation Nature Education
Excerpt: “…mutations provide the “raw material” upon which the mechanisms of natural selection can act.
My comment: There are huge differences between ideas about mutations and facts about ecological variation in the context of the “raw material” of biodiversity. Ecological adaptations are bio-physically constrained by nutrient uptake linked to thermodynamic cycles of protein biosynthesis and degradation. If the thermodynamic cycles were not biophysically constrained, the epigenetic landscape could not stabilize the physical landscape of DNA in the organized genomes of species from microbes to man via RNA-mediated events that link amino acid substitutions to cell type differentiation.
An alternative is suggested by Palmer and others. The alternative is: mutations, which destabilize organized genomes and result in uncontrolled cell type differentiation or perturbed protein folding, also alter the ability of cells to eliminate dysfunctional proteins in genes that are no longer useful. But Palmer and others suggest the mutations are somehow linked to the evolution of biodiversity before they are left behind  as if they were in “…a museum full of ancient DNA that is just decaying away.” That suggestion does not make sense in the context of anything currently known about physics, chemistry, or molecular biology.

Gene Silencing by Small RNAs (B1)

Summary of Meeting:
The impact of small non-coding RNAs has profoundly touched the fields of development and cell biology, functional genomics, human disease and drug therapy. This mode of gene regulation is not restricted to eukaryotes; bacteria utilize small RNAs, notably those made from CRISPR loci that silence the expression of bacteriophages, transposons and plasmids. There are still many gaps in our knowledge of the mechanisms used by small RNAs, particularly newly discovered RNAs. It has become clear that this field of study needs an annual forum to enable rapid dissemination of new discoveries between researchers. Overall, the goals of this proposed meeting are: (1) to foster the scientific development of junior investigators by promoting their interaction with established investigators, and (2) to allow for mixing and sharing of ideas between biochemists, molecular biologists, geneticists and systems biologists working in the field. We hope this will synergize ideas and method breakthroughs in small RNA mechanisms.
Meetings to discus breakthroughs that help others to understand the role of RNA-mediated mechanisms in cell type differentiation should probably be attended by evolutionary theorists, especially any that continue to claim that mutations lead to the evolution of biodiversity when it has become obvious that nutrient uptake and the pheromone-controlled physiology of nutrient-dependent reproduction link Diet as driver and constraint in human evolution.
Similarly, evolutionary theorists should address the claims made in the current extant literature on biologically-based cause and effect. Yesterday, results from Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers were reported as Study suggests a unified model for how DNA is read, offering insight into how genes evolve.
Scientific progress cannot be made when journalists or scientists report that genes evolve. The de novo creation of genes is nutrient-dependent and they arise in the context of what is currently known about how nascent RNA links the microRNA/messenger RNA balance from RNA-directed DNA methylation to RNA-mediated cell type differentiation by amino acid substitutions in species from microbes to man. The amino acid substitutions clearly link genetic networks to metabolic networks via the pheromone-controlled physiology of nutrient-dependent reproduction, not via mutations.

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