Biology to a Physicist

Olfaction & the octopus and human genomes (2)

Darwinian evolution in the light of genomics

Eugene Koonin excerpt:

The distribution of evolutionary rates across sets of orthologous genes, the distribution of the sizes of paralogous gene families, the negative correlation between the expression level and the sequence evolution rate of a gene, and other relationships between key evolutionary and phenomic variables seem to be genuine universals of evolution. The simplicity of these universal regularities suggests that they are shaped by equally simple, fundamental evolutionary processes, rather than by selection for specific functions.

My comment: Selection of food links ecological variation to ecological adaptation via specific functions that are required to support the physiology of reproduction. For example, the metabolism of nutrients links the chemical appeal of food from ingestion and metabolic networks to genetic networks that are required for specie-specific survival.

The octopus genome and the evolution of cephalopod neural and morphological novelties

Abstract concluding sentences:

Finally, we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems.

Reported as only someone who was biologically uninformed could do: Octopuses ‘are aliens’, scientists decide after DNA study 

The octopus appears to be utterly different from all other animals…

My comment: The sequencing of the octopus genome links nutrient-dependent changes in the microRNA/messenger RNA of marine invertebrates to changes in crustaceans, insects, and mammals via nutrient-dependent RNA-mediated events such as gene duplication and amino acid substitutions. These RNA-mediated events link the epigenetic landscape to the physical landscape of DNA in all genera via their physiology of reproduction, which typically eliminates mutations from organized genomes. For example, unused olfactory receptor genes are eliminated or they become pseudogenes when mutations, which perturb protein folding, lead to non-functional duplicate genes.
See also: RNA-Mediated Thermoregulation of Iron-Acquisition Genes in Shigella dysenteriae and Pathogenic Escherichia coli

This study demonstrates that the expression of S. dysenteriae shuA and E. coli chuA, genes essential for the utilization of heme as a source of nutrient iron, is modulated in response to environmental temperature by a post-transcriptional regulatory mechanism. This work is the first to demonstrate temperature-dependent post-transcriptional regulation of shuA and chuA expression and the first to implicate temperature as an environmental factor controlling the production of an iron uptake system in Shigella. Finally, it is demonstrated that the observed post-transcriptional thermoregulation of both shuA and chuA expression is mediated by the activity of a conserved FourU RNA thermometer within the 5′ utr of each gene.

My comment: Organism-level thermoregulation and Darwinian evolution are based on RNA-mediated events in the context of his ‘conditions of life.’ Conditions of life, as exemplified in Shigella, are nutrient-dependent. The pseudoscientific nonsense about mutations and evolution, which was invented by population geneticists and taught to several generations of people who remain biologically uninformed, has never been supported by experimental evidence of biologically-based cause and effect. That explains why biologically uniformed researchers have not linked anything known to serious scientists about physics or chemistry to ecological adaptations, which are required for the survival of every organism and every species on this planet.
The survival of each cell type in each individual of each organism is determined by the organism’s ability to regulate thermodynamic cycles of protein biosynthesis and degradation that enable organism-level thermoregulation, which prevents the replication of viruses that damage DNA and contribute to all pathologies.
Riding the Evolution Paradigm Shift With Eugene Koonin

The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis…

My comment: Will other evolutionary theorists continue to “ride” the evolution paradigm shift until it ends with the death of us all? See Greg Bear on terrorism and ask yourself who is joking about it? If only evolutionary theorists are the jokers, please consider joining the serious scientists who are Combating Evolution to Fight Disease before its too late.
Re: “…genes essential for the utilization of heme as a source of nutrient iron…”

Amino Acid Changes in Hemagglutinin Contribute to the Replication of Oseltamivir-Resistant H1N1 Influenza Viruses


Antiviral drugs are an important defense when humans face influenza epidemics and pandemics. Our studies further our understanding of the emergence of drug-resistant viruses. Current epidemic viruses continue to evolve under selective pressure; therefore, the continuous monitoring of epidemic viruses is essential to reduce the risk of emergence of epidemics caused by drug-resistant viruses.

My comment: Drug-resistant viruses do not “emerge.” They do not “evolve.” The selective pressure that viruses are subjected to are the same ones that we are subjected to.  They will steal our iron and our life if we let the evolutionary theorists continue to ride their ridiculous neo-Darwinian paradigm.
Again, see Greg Bear on terrorism and have a nice day, or see: The Darwin Code by Greg Bear and begin to learn about counter-terrorism before evolutionary theorists lead to the death of us all.
See also: Rhesus (RH) negative blood? You may belong to the Nephilim

 The RH factor is a protein found in the human blood that is directly linked to the Rhesus Monkey.

Note: A single nutrient-dependent RNA-mediated amino acid substitution in the hemoglobin molecule differentiates the cell types of gorillas, chimpanzees, and humans. See my comments on Combating Evolution to Fight Disease.
See also: Octopus genome holds clues to uncanny intelligence
My comment: This suggests that the octopus genome also holds the key to the almost unbelievable ignorance of evolutionary theorists. See for example: Mutation-Driven Evolution. Viruses appear to have already pirated the nutrient energy that is required for intelligent thought. Unfortunately, the transgenerational epigenetic inheritance of human endogenous retroviruses (HERVs) helps to ensure the ignorance of each successive generation. If other animals could be taught to believe in the pseudoscientific nonsense of neo-Darwinian evolution, we would already be extinct. Instead, we are driving them to extinction via our ignorance of biologically-based cause and effect.
See for an alternative: Israeli Middle Schools School to Include Theory of Evolution

…learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology.
My comment: Ecological variation is linked from nutritional epigenetics to ecological adaptations via pharmacogenomics, which links metabolic networks to genetic networks via RNA-mediated events. The biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding is perturbed by viruses, which is why they are linked to pathology, except by pseudoscientists who have ignored the role that viruses play in preventing ecological adaptations or forcing organisms to adapt via theromodynamic cycles of protein biosynthesis and degradation that lead to biodiversity in their morphological and behavioral phenotypes via energy-dependent base pair changes and single amino acid substitutions.

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