Biology Direct (15 September 2014) OPEN ACCESS
Excerpt (with my emphasis): “Widespread occurrence of phage sequences in almost all studied M. abscessus complex isolates suggests that the rate of prophage invasion is faster than the rate of mutation, implying rapid evolution of M. abscessus.”
My comment: The faster rate of prophase invasion suggests ecological adaptations occur more rapidly than evolution. That may be why no experimental evidence of biologically-based cause and effect suggests that evolution of biodiversity somehow occurs via mutations and natural selection; the processes are too slow to be linked to extant ecologically-adapted biodiversity. Also, the Wikipedia summary (below) does not support ideas about the evolution of biodiversity. It supports the concept of chemically-induced RNA-mediated events that can now be linked from nutrient-dependent chromosomal rearrangements in microbes (e.g., Mycobacterium spp.) to explanations of RNA-mediated species diversity in primates via conserved molecular mechanisms.
RNA-mediated events link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. See Kohl (2013) for review.
For example, UV light-induced amino acid substitutions in plants and nutrient-dependent amino acid substitutions in animals are biophysically constrained, which suggests that the role of RNA-mediated events and amino acid substitutions in cell type differentiation extends from viruses to primates in the context of thermodynamic cycles of protein biosynthesis and degradation that lead to more efficient organism-level thermoregulation via the Laws of Physics.
Wikipedia: “A prophage is a bacteriophage (often shortened to “phage”) genome inserted and integrated into the circular bacterial DNA chromosome or existing as an extrachromosomal plasmid. This is a latent form of a phage, in which the viral genes are present in the bacterium without causing disruption of the bacterial cell.
Upon detection of host cell damage, such as UV light or certain chemicals, the prophage is excised from the bacterial chromosome in a process called prophage induction. After induction, viral replication begins via the Lytic Cycle. In the lytic cycle, the virus commandeers the cell’s reproductive machinery. The cell may fill with new viruses until it lyses or bursts, or it may release the new viruses one at a time in a reverse endocytotic process. The period from infection to lysis is termed the latent period. A virus following a lytic cycle is called a virulent virus. Prophages are important agents of horizontal gene transfer, and are considered part of the mobilome. All families of bacterial viruses with circular (single-stranded or double-stranded) DNA genomes or replicating their genomes through a circular intermediate (e.g., Caudovirales) have temperate members.”
Addendum: “… the synergistic use of tissue diagnostic techniques and microbiology is paramount to render an accurate diagnosis.” (Patel, Rhodes, Spicknall, & Mortensen, 2014)
That fact cannot be ignored if medical practitioners are ever able to escape the ignorance touted by theorists and their ridiculous ideas about mutations, natural selection, and the evolution of biodiversity. We no longer have the option to believe in pseudoscientic nonsense and must begin to treat diseases and disorders in the context of what they are: failed ecological adaptation. See also: Combating Evolution to Fight Disease and RNA and dynamic nuclear organization.
Patel, R., Rhodes, J., Spicknall, K. E., & Mortensen, J. (2014). Case Twenty NIne: The synergistic role of microbiology and pathology. Journal of Continuing Education Topics & Issues, 16 (3), 88-92.
The ever-more antagonistic Roy Niles continues his attacks and on May 15, 2015 he asked
“Can you even tell me what scientists have got wrong about the reasons that proteans are folded at all?
My response: Nutrient-dependent RNA-mediated protein folding protects all cell types from the damage to their DNA caused by viral microRNAs. Biophysically constrained RNA-directed DNA methylation links thermodynamic cycles of protein biosynthesis and degradation to RNA-mediated amino acid substitutions that stabilize the organized genomes of all genera.
See other comments by Roy Niles on The Strange Inevitability of Evolution. No matter what he is told about how ecological variation leads to ecological adaptations via the conserved molecular mechanisms of cell type differentiation in all genera, Roy refuses to accept the truth. Ecological adaptation is inevitable because organisms and species adapt or become extinct. They do not evolve into other species. Only the biologically uninformed and intellectually handicapped believe in the pseudoscientific nonsense about the evolution of increasing organismal complexity via mutations — or whatever other ideas theorists think sound convincing enough to convince others who were taught to believe in “evolution for dummies.”