RNA-mediated permanent symbioses

See also: Ecological validity vs evolutionary theory

Symbiosis becoming permanent: Survival of the luckiest

Published in: Proceedings of the National Academy of Sciences (PNAS) f the United States of America

…since the 1980s, the idea that the mitochondria and plastids (chloroplasts) of eukaryotic cells arose through endosymbiosis has been about as universally accepted as such things ever are (1). However, enormous gaps remain in our knowledge about just how this happened.

My comment: Symbiosis becomes permanent via RNA-mediated biologically-based cause and effect. The enormous gaps in knowledge about how symbiosis became permanent can be attributed to claims made by supporters of the big bang cosmology industry and the evolution industry.
Industry support helps to ensure that their research is reported in the context of industry-sanctioned claims. These sanctioned claims have never included anything known to serious scientists about virus-driven pathology or nutrient-dependent RNA-mediated gene duplication and other RNA-mediated events linked to cell type differentiation in all cells of all individuals of all living genera.
Viruses were first linked to RNA-mediated cell type differentiation and ecological speciation by Greg Bear, who fact-checked his claims with people who understood biologically-based cause and effect.  See: The Darwin Code, and two book reviews in Nature Evolution rising from the grave and Living with the Neanderthals
For comparison to attempts to change the neo-Darwinian theory of evolution, here’s an example of what the theorists have missed so far.

Hepatitis B Virus Infection, MicroRNAs and Liver Disease


…large-scale studies have revealed that many host miRNAs are modulated by the virus in order to accomplish its persistence, while other miRNAs are modulated by the host in order to achieve viral clearance.

My comment: Watch what happens when industry supported researchers discover the need to report facts about biologically-based cause and effect that refute ridiculous theories.
Here are excerpts from 24 abstracts published in the context of Sackler Colloquia.
Taken together, the excerpts show there is nothing left of neo-Darwinism except the claims that evolution somehow occurs. The claim that evolution “just happens” was first made by Carl Zimmer in The Surprising Origins of Evolutionary Complexity

Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.

My comment: Ecological variation leads to ecological adaptation or mutation-driven extinction happens. That’s why neo-Darwinian theories are becoming extinct, as the pseudoscientists who have touted the nonsense of their “Just So” stories, “Just Happen” to disappear.
While trying not to admit to the fact that they are changing theories about mutations and natural selection to claims that support RNA-mediated permanent symbioses, they change the theories, perhaps hoping that no one will notice. Serious scientists have noticed that the nutrient-dependent physiology of reproduction links RNA-mediated amino acid substitutions to cell type differentiation of all cells in all individuals of all organisms. Serious scientists know that RNA-mediated DNA repair is the link from ecological variation to ecological adaptation outside the context of evolution.
Serious scientists know that neo-Darwinian theories have consistently failed to link any source of energy to cell type differentiation, and consistently failed to link virus-perturbed protein folding to that fact that viruses steal energy that cells need to reproduce.


This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

My comment: The fact that “Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development” can be placed into the context of evolutionary theories that continue to be revised to approach what is actually known about biologically-based cause and effect without revealing that evolutionary theorists know nothing. See, for examples, 24 more articles published in published in: Proceedings of the National Academy of Sciences (PNAS) f the United States of America with abstract excerpts and my comments.

Toward major evolutionary transitions theory 2.0

During transitions, new units of reproduction emerge, and establishment of such units requires high fidelity of reproduction (as opposed to mere replication).

My comment: Emerge is not a term that serious scientists use in the context of reproduction.

Major evolutionary transitions in individuality

We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions.

My comment: Ecological conditions drive all transitions.

Reproduction, symbiosis, and the eukaryotic cell

Three kinds of reproduction are distinguished, and a possible evolutionary sequence giving rise to a mitochondrion-containing eukaryotic cell from an endosymbiotic partnership is analyzed as a series of transitions between each of the three forms of reproduction.

My comment: All forms of reproduction are nutrient-dependent and biophysically constrained by RNA-mediated protein folding chemistry.

Rethinking evolutionary individuality

The case of multispecies biofilms suggests that standard reproductive requirements placed on individuality should be reconsidered. More generally, the case of multispecies biofilms indicates that accounts of individuality that focus on single-species eukaryotes are too restrictive and that a pluralistic and open-ended account of evolutionary individuality is needed.

My comment: Evolutionary individuality in the context of multispecies biofilms could be addressed in the context of nutrient-dependent pheromone-controlled physiology of reproduction in the species contained in the biofilms.

Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria

A further significant fraction of the mitochondrial proteome consists of proteins with homologs in prokaryotes, but without a robust phylogenetic signal affiliating them with specific prokaryotic lineages. The presumptive evolutionary source of these proteins is quite different in contending models of mitochondrial origin.

My comment: There is no evolutionary source of any protein. No experimental evidence suggests that proteins evolve.

Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller’s ratchet—the origin of eukaryotic recombination, or sex—might have required surprisingly little evolutionary innovation.

My comment: The evolutionary innovation that theorists thought was required has since been attributed solely to ecological adaptation, which requires no evolution of anything.

Genomic perspectives on the birth and spread of plastids

In addition to endosymbiotic gene transfer, horizontal gene transfer events occurring before, during, and after endosymbioses further confound our efforts to reconstruct the ancient mergers that forged multiple lines of photosynthetic microbial eukaryotes.

My comment:“…the ancient mergers that forged multiple lines of photosynthetic microbial eukaryotes” can be traced to the light-induced de novo creation of nucleic acids and RNA.
Mitochondrial genomes are retained by selective constraints on protein targeting

We conclude that the mitochondrial genome has been maintained to ensure the correct localization of highly hydrophobic membrane proteins. Taken together, the results suggest that selective constraints on the eukaryotic cell have played a major role in modulating the evolution of the mitochondrial genome and proteome.

My comment: The mitochrondrial genome links nutrient energy use from ecological variation to ecological adaptations via the physiology of reproduction in all living genera.

Maternal transmission, sex ratio distortion, and mitochondria

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole

Symbiotic partners enter into an evolutionary spiral that leads to irreversible codependence and associated risks. Host adaptations to symbiosis (e.g., immune-system modification) may impose vulnerabilities. Symbiont genomes also continuously accumulate deleterious mutations, limiting their beneficial contributions and environmental tolerance.

My comment: Mutations limit beneficial contributions because the are linked from perturbed protein folding to pathology.

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

We explore the evolutionary forces responsible for these patterns and argue that organelle DNA repair processes, mutation rates, and population genetic landscapes are all important factors leading to the observed convergence and divergence in organelle genome architecture.

My comment: Nutrient-dependent RNA-mediated DNA repair is essential to ecological adaptations. Mutations are linked to divergence via gene loss.

The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes

Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia

We show that the Ca. Hodgkinia genome from M. tredecim has fragmented into multiple new chromosomes or genomes, with at least some remaining partitioned into discrete cells.

My comment: Is there anything that shows how genome fragmentation could lead to speciation without RNA-mediated DNA repair?

Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

My comment: Emergence is not a term that is used by serious scientists. Placing it into the context of loss and modification of the existing, conserved traits attests to the fact that pseudoscientists have no idea at all about how gene losses and gains are linked from ecological variation to ecological adaptation.

Metabolic connectivity as a driver of host and endosymbiont integration

…our work significantly advances understanding of plastid integration and favors a host-centric view of endosymbiosis. Under this view, nuclear genes of either eukaryotic or bacterial (noncyanobacterial) origin provided key elements of the toolkit needed for establishing metabolic connections in the primordial Archaeplastida lineage.

My comment: Where did these nuclear genes come from? If they link metabolic networks to gene networks at any level of examination from atoms to ecosystems, nuclear genes cannot automagically pop into existence in any genera and then be used to explain symbiosis in all genera.

Mitochondrial ATP synthase is dispensable in blood-stage Plasmodium berghei rodent malaria but essential in the mosquito phase

Mitochondrial ATP synthase is driven by chemiosmotic oxidation of pyruvate derived from glycolysis. Blood-stage malaria parasites eschew chemiosmosis, instead relying almost solely on glycolysis for their ATP generation… Perturbation of ATP synthase completely blocks transmission to the mosquito vector and could potentially be targeted for disease control.

My comment: Viruses are linked to mutations that perturb protein synthesis because the viruses use nutrients that are required for cell type differentiation and organism-level genomic stability, which is facilitated by nutrient-dependent RNA-mediated amino acid substitutions.

Acetogenesis from H2 plus CO2 and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist

…the single-cell genome analyses revealed the endosymbiont’s potentials of the utilization of sugars for its energy requirement, and of the biosynthesis of valuable nutrients such as amino acids from the fixed nitrogen. These metabolic interactions are suitable for the dual functions of the endosymbiont and reconcile its substantial contributions in the gut.

My comment:Viruses perturb the endosymbiont’s potentials of the utilization of sugars, which are required for protein biosynthesis and fixation of amino acid substitutions that stabilize organized genomes.

Why chloroplasts and mitochondria retain their own genomes and genetic systems: Colocation for redox regulation of gene expression

These copies gave rise to nuclear chromosomal genes that encode cytosolic proteins and precursor proteins that are synthesized in the cytosol for import into the organelle into which the endosymbiont evolved. What accounts for the retention of genes for the complete synthesis within chloroplasts and mitochondria of a tiny minority of their protein subunits? One hypothesis is that expression of genes for protein subunits of energy-transducing enzymes must respond to physical environmental change by means of a direct and unconditional regulatory control—control exerted by change in the redox state of the corresponding gene product.

My comment: That is not a hypothesis. The response to changes in the epigenetic landscape are controlled by the availability of nutrients that regulate the control of gene products.

An ancestral bacterial division system is widespread in eukaryotic mitochondria

…we confirm a mitochondrial localization of these proteins by their heterologous expression in Saccharomyces cerevisiae. The discovery of a proteobacterial-like division system in mitochondria of diverse eukaryotic lineages suggests that it was the ancestral feature of all eukaryotic mitochondria and has been supplanted by a host-derived system multiple times in distinct eukaryote lineages.

My comment: The mitochondrial localization of proteins is nutrient-dependent and pheromone-controlled in the context of the physiology of reproduction in species from microbes to man. Saccharomyces cerevisiae exemplifies that fact at the advent of sexual reproduction in unicellular microbes. Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus (Runge and Zakian, 1996; Wu and Haber, 1995).

Integration of plastids with their hosts: Lessons learned from dinoflagellates

After their endosymbiotic acquisition, plastids become intimately connected with the biology of their host. For example, genes essential for plastid function may be relocated from the genomes of plastids to the host nucleus, and pathways may evolve within the host to support the plastid.

My comment: Plastids are intimately linked to the synthesis and storage of food, but their is no experimental evidence of biologically-based cause and effect that suggests that genes essential for plastid function evolved. There is no experimental evidence that suggests any genes evolved or that any proteins evolved.

Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses

Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. …we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research.

My comment: No experimental evidence of biologically-based cause and effect suggests that metabolic cooperation evolved. Symbiosis is linked from the sun’s biological energy to nutrient-dependent RNA-mediated gene duplication via metabolic networks that link the epigenetic landscape to the physical landscape of DNA via RNA-mediated amino acid substitutions that differentiate all cell types of all individuals of all living genera via the physiology of reproduction. Instead, the honeybee model organism of nutrient-dependent pheromone-controlled life history transitions is linked to the life history transitions of humans by a single amino acid substitution during the transition from adolescence to adulthood. See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism

Although no significant correlations between soil variables and symbiotic persistence were found, nitrogen and phosphorus leaf contents were positively correlated with legumes in a state of high symbiotic persistence. This pattern suggests that highly demanding nutrient lifestyles are associated with more stable partnerships, potentially because they “lock” the hosts into symbiotic dependency. Quantitative reconstruction methods are emerging as a powerful comparative tool to study broad patterns of symbiont loss and retention across diverse partnerships.

My comment:Lead and manganese leaf contents were linked by evolutionary theorists to differences in fawn and pepper-colored moths by what they claimed were naturally selected mutations due to bird predation. The demanding nutrient requirements of females were linked to the pheromone-controlled physiology of reproduction in males. It became obvious that fixation of mutations never occurred in that context because the pepper-colored moths became fawn colored when industrial pollution was limited.

Endosymbiosis and its implications for evolutionary theory

Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis…. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation.

My comment: The late Lynn Margulis argued against neo-Darwinian evolutionary theory. She never argued against Darwin’s theory, which put his ‘conditions of life’ first.  This attempt to pervert her legacy is unconscionable. She clearly stated her argument against neo-Darwinian theory by addressing the credibility of those who invented it.  [W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. Assumptions, made but not verified, were taught as fact.

Eukaryogenesis, how special really?

Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet…. Overall, we question whether premises of existing theories about the uniqueness of eukaryogenesis and the greater evolutionary potential of eukaryotes have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was “special,” any such notion has more than rhetorical value.

My comment: Existing theories about the uniqueness of eukaryogenesis failed to consider the role of ecological variation and virus-perturbed ecological adaptations that require nutrient-dependent RNA-mediated repair to prevent genomic entropy.
This series of abstracts linked above contains nothing but more pseudoscientific nonsense that fails to address any aspect of how biophysically constrained nutrient-dependent protein folding and fixation of RNA-mediated amino acid substitutions links what is known by serious scientists from ecological variation to ecological adaptations via conserved molecular mechanisms of cell type differentiation in all living genera.

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