Alternative splicing of pre-mRNA

More refutations of neo-Darwinian nonsense

New CRISPR–Cas systems from uncultivated microbes

In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet identified. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in E. coli. Interrogation of environmental microbial communities combined with in vivo experiments allows access to an unprecedented diversity of genomes whose content will expand the repertoire of microbe-based biotechnologies.

They discovered that energy-dependent RNA-mediated DNA methylation is the link from autophagy to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.

There results were reported as: Compact CRISPR systems found in some of world’s smallest microbes

The team also found the first CRISPR-Cas9 system in some of the world’s smallest microbes: a nano-scale member of the archaea, which is a sister group to the bacteria.

‘Sister group’ is a term used by theorists to label what they believe appears to be the closest relatives in an evolutionary tree. The authors of the article used the term domain. Carl Woese divided the close relatives into the life forms called archaea, bacteria, and eukaryote. Woese suggested that archaea and bacteria arose separately from a common ancestor.
He also suggested that the common ancestor had poorly developed genetic machinery. Initially, Woese used the term “kingdom” to name what the news report on the experimental evidence refers to as a sister group despite the fact that archaea, bacteria, and eukaryotes have been referred to in the context of three different domains of life since 1990.
Substituting the term sister group for domain clearly indicates that something has gone horribly wrong with the theories about different domains of life. By using the term domain, the researchers from Berkeley seem to be suggesting that everything reported by others who have made claims about mutations and evolution must now be revised. Use of term “sister group” is an example of how the media tailors the claims of researchers in attempts to fit back into the context of ridiculous theories.
Carl Woese claimed that archaea and bacteria were different domains of life. The media changed his claim to make archaea a sister group of bacteria. That suggests the literature from Berkeley’s domain must change all the claims to include what it known about energy-dependent ecological adaptation, which links the physiology of reproduction from autophagy to supercoiled DNA.

If they don’t make the changes, they will continue to look even more foolish than they have during the past twenty years. All  serious scientists know that supercoiled DNA protects all organized genomes from virus-driven entropy.
See also: Virus-mediated archaeal hecatomb in the deep seafloor

We show here for the first time the crucial role of viruses in controlling archaeal dynamics and therefore the functioning of deep-sea ecosystems, and suggest that virus-archaea interactions play a central role in global biogeochemical cycles.

Their evidence of virus-driven pathology links bacteria to archaea, without claims about sister groups or different domains of life. They make it clear that virus-driven energy theft in bacteria causes the bacteria to degenerate into archaea. That fact makes it clear that nutrient-dependent pheromone-controlled autophagy in bacteria causes the change in bacteria that become eukaryotes.

See for comparison: Obama Advisers Urge Action Against CRISPR Bioterror Threat

For the past two decades, the government has focused its biodefense efforts on a list of known pathogens—such as anthrax, smallpox, and Ebola—declared by the Department of Health and Human Services and Department of Agriculture to have the “potential to pose a severe threat to public health and safety.” Government-funded research on these pathogens receives special scrutiny, and the National Institutes of Health limits researchers from conducting experiments that could make certain germs, like influenza, more dangerous.

See also: Explaining major evolutionary change

A similar process is also at work in molecular evolution and helps us understand how a feature that is absolutely necessary for survival can be modified by natural selection for a different function if it is duplicated. For example, globin is a truly ancient protein. Billions of years old, it was present in the common ancestor of bacteria, plants, animals, and fungi. Globin performed an essential job: binding and carrying oxygen. You might imagine that natural selection would lock globin into that one job; however, through duplication and divergence, different copies of the globin molecule were adapted for different roles. Vertebrates rely on several different globin genes: hemoglobin carries oxygen to body tissues (though a separate globin performs this function in fetuses), myoglobin keeps a reserve supply of oxygen for muscle cells to use, and neuroglobin and cytoglobin do jobs that we don’t yet fully understand. Multiple globin genes are found all across the tree of life. In fact, some globins in deep-sea-dwelling worms are adapted for carrying both oxygen and hydrogen sulfide.

Peter Berean and other theorists consistently fail to mention that ~1200 human hemoglobin variants link energy-dependent RNA-mediated amino acid substitutions to all cell type differences in all individuals of all primate species by as little as one base pair change and fixation of one nutrient energy-dependent amino acid substitution. Peter Berean has gone one step further towards obfuscation than most pseudoscientists have been willing to take. He invented the term “bio-functional information”  which is the weasel word way to compare energy as information in the context of what is known to serious scientists.

The researchers from Berkeley and elsewhere who are touting the CRISPR technology as if it could lead to beneficial microbe-based biotechnologies have already missed the direct link from energy-dependent RNA-mediated amino acid substitutions to the prevention of all virus-driven pathology. The energy-dependent natural selection for codon-optimality that links fixation of RNA-mediated amino acid substitutions in supercoiled DNA via the physiology of reproducition is the only protection any organized genome has against virus-driven pathology.

See also: Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

Our results corroborate the prevalence of non-canonical splice-sites and a tendency towards unidirectionality of gene orientation in dinoflagellates. We identified a surprisingly large repertoire of proteins involved in molecule transfer in dinoflagellates, but also highlight enrichment of domains involved in the transport of carbon and nitrogen in the Symbiodinium lineage. We also find evidence for substantial differences of these domains between Symbiodinium species, which may provide a genomic basis to explain physiological differences and contribute to host-symbiont specificity. The large amount of intraspecific gene duplications in Symbiodinium putatively represents an alternate mechanism to increase transcript and protein levels in the absence of strong transcriptional control of gene expression.

It is refreshing to see that some researchers now report that nutrient energy-dependent alternative splicings of RNA link the pheromone-controlled physiology of reproduction to the physiological differences that contribute to host-symbiont specificity. Each time serious scientists fail to make a claim about mutations and evolution everybody is one step closer to eliminating the pseudoscientific nonsense of neo-Darwinian theory from any further consideration whatsoever.
See for comparison, the most recent obfuscation of facts that are make to fit the misrepresentations of theorists:
Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome

The intrinsically disordered regions of eukaryotic proteomes are enriched in short linear motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate interactions by providing binding sites for peptide binding domains. The vast majority of SLiMs remain to be discovered highlighting the need for experimental methods for their large-scale identification. We present a novel proteomic peptide phage display (ProP-PD) library…

Motif-mediated interactions is the “Weasel Word Way” (WWW) to obfuscate the fact the RNA-mediated protein folding chemistry is the energy-dependent link to the biophysically constrained order of eukaryotic proteomes.
I think I coined the term “Weasel Word Way” above, since I have not seen anyone else use it to describe how claims are made by theorists. Weasel words are words or phrases used in an ambiguous manner. Motif-mediated interactions makes it appear that the interactions are not energy-dependent and biophysically constrained by the physiology of reproduction.
See for comparison from 2002: An integrated vector system for cellular studies of phage display-derived peptides

Library construction and screening is performed using an optimized type 3 phage display vector, mJ(1), which is shown to accept peptide libraries of at least 23 amino acids in length.

I’ve tried to explain how the peptide libraries of amino acids link biophysically constrained RNA-mediated protein folding chemistry to energy-dependent changes in the microRNA/messenger RNA balance and amino acid substitutions, supercoiled DNA and cell type stability. Few people seem willing to accept the fact that virus-driven energy theft causes all pathology.
When I find an article like this, which was published in 2002, I realize the situation may be hopeless. You cannot explain facts about RNA-mediated cell type differentiation to theorists, even after physicists, chemists, and molecular biologists have already linked energy as information to all biodiversity. Theorists believe in mutation-driven evolution, and nothing is likely to change their ridiculous beliefs.
AXM mutagenesis: an efficient means for the production of libraries for directed evolution of proteins
Proteins do not evolve. Evolve is a WWW to claim that biodiversity is not energy as information-dependent
Use of micro-emulsion technology for the directed evolution of antibodies
Anti-bodies do not evolve. Energy as information is the key to ecological adaptation in all living genera. No species evolves into another species. All species adapt to virus-driven energy theft via nutrient uptake and the physiology of reproduction, or the species becomes extinct leaving only the fluorescence in its DNA to link the cause of extinction to virus-driven energy theft.

Here, they reported that two RNA-mediated amino acid substitutions were mutations so they could link virus-driven energy theft to evolution instead of linking energy as information to ecological adaptation.

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

After 96 hours of incubation of AR2 and Pf0-2x at room temperature on SMM, two breakout mutations were visible, conferring first slow (AR2S and Pf0-2xS) and then fast (AR2F and Pf0-2xF) spreading over the agar surface (Fig. 1A). The AR2F strain produces flagella, but we could not detect flagella in electron microscopy samples for AR2S (Fig. 1B). Genome resequencing revealed a single-nucleotide point mutation in ntrB in strain AR2S, causing an amino acid substitution within the PAS domain of the histidine kinase sensor NtrB [Thr97→Pro97 (T97P)] (13). The fast-spreading strain AR2F had acquired an additional point mutation in the σ54-dependent EBP gene ntrC, which alters an amino acid (R442C) within the DNA binding domain (Table 1 and table S2).

See also: Carl Woese was wrong

See also: Store and Supply: How the Brain Saves Time

This study reveals a completely new regulatory mechanism for the brain”, declares Scheiffele. “The results provide us with a further explanation of how neurons steer rapid plasticity processes.
The conserved molecular mechanisms of energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution have been linked from microRNA flanking sequences to learning and memory in the context of changes that link angstroms to ecosystems via the physiology of reproduction.
The claim that this is a new regulatory mechanism is foolish. They have simply linked changes in the microRNA/messenger RNA balance to experience-dependent adaptations in the cell types of all individuals of all living genera via RNA-mediated amino acid substitutions.

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