Mutagenesis: Replacing facts with theories

By: James V. Kohl | Published on: January 10, 2015

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Never mind the selfish gene – ribosomes are the missing link

Excerpt: “All cells share three organelles, or internal structures, besides gene-containing chromosomes: ribosomes which contain the machinery for translating genetic information into the proteins that perform the cell’s work; a cell membrane that selectively permits materials in and out; and acidocalcisomes, which store and regulate the ions that drive the chemical reactions of life.”
In his criticisms of my model of cell type differentiation, Andrew Jones (aka anonymous_9001 in discussions on phys.org) ignored all of the above. See: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model. Simply put, he ignored everything known about what drives the chemical reactions of life. Adding another insult to the intelligence of all serious scientists, he recently claimed: “The work you detail rarely has anything to do with the claims you make.” See for comparison his 2012 Carthage College Department of Biology thesis: Jones, Andrew Lipid Encapsulation of Self Replicating Ribozymes
The work he did for his thesis supports the ridiculous claims he has made about a series of my published works and the relevance of the works I cited to support my claims. He could have included a reference to his thesis, or to other works on mutagenesis for comparison to my model. Instead, he concluded: “James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.”
Here is the concluding sentence from my review Nutrient-dependent/pheromone-controlled adaptive evolution: a model: “Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.”
The question arises: Why didn’t Andrew Jones compare his ideas from mutagenesis experiments to the facts about RNA-mediated cell type differentiation that I detailed? The answer is obvious. Mutagenesis experiments start with a definition of “mutation.” The assumption is made that everything downstream from the definition is relevant to what is currently known about thermodynamic cycles of protein biosynthesis and degradation. For comparison, I will emphasize this fact:

Controlled thermodynamic cycles are required for organism-level thermoregulation.

What is currently known about molecular epigenetics and the bio-physically constrained chemistry of protein folding is exemplified as organism-level thermoregulation in species from microbes to man. What is known links atoms to ecosystems; thermodynamics to organism-level thermoregulation; and morphological phenotypes to behavioral phenotypes in the context of increasing organismal complexity. In my model, for example, the epigenetic landscape is linked to the physical landscape of DNA in organized genomes via nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species via their pheromone-controlled physiology of reproduction. The claim that ribosomes are the missing link between the epigenetic landscape and the physical landscape of DNA in organized genomes integrates facts about the nutrient-dependent chemical reactions of life that I detailed in my model.
Anyone who wonders why no one has tried to compare their ideas about evolution to my model of how ecological variation leads to nutrient-dependent pheromone-controlled ecological adaptations can read the thesis by Andrew Jones, or they can look at the conclusion from a textbook on Mutation-driven evolution, which was published on the same day as my 2013 review. The textbook conclusion is: “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.” (p. 199). In the context of that ridiculous conclusion, Andrew Jones’ ridiculous conclusion makes sense: “Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered.”

I reiterate: “All cells share three organelles, or internal structures, besides gene-containing chromosomes: ribosomes which contain the machinery for translating genetic information into the proteins that perform the cell’s work; a cell membrane that selectively permits materials in and out; and acidocalcisomes, which store and regulate the ions that drive the chemical reactions of life.”

I think the most important thing to remember about that fact is that professor Masatoshi Nei and the recent graduate, Andrew Jones, continue to ignore the physical and chemical constraints on the biology of life.

Instead, they make claims about constraint-breaking mutations and abiogenesis research. They appear to think their definitions and assumptions may someday link physics to prebiotic chemistry and life.

If you want to know what your descendants are being taught to believe about the chemical reactions of life, ASK THEM.

Many of them, like Andrew Jones, are being taught to believe in pseudoscientific nonsense. Your descendants may be the future of scientific progress, and none will be made by evolutionary theorists.

See for comparison: Division of labor in transhydrogenase by alternating proton translocation and hydride transfer reported in the “Editor’s Summary” as “Both bacteria and mitochrondria produce NADPH for amino acid biosynthesis and to remove reactive oxygen species.” Also reported in Mitochondrial Enzyme Detailed.

Excerpt: “We suspect that the passage of the proton is what somehow causes this flipping of the domain III structures.”

My comment: As other serious scientists continue to add details about links from the sun’s biological energy to light-induced amino acid substitutions in plants and animals that link nutrient-dependent pheromone-controlled cell type differentiation via bio-physically constrained protein folding and the molecular epigenetics of RNA-mediated events we detailed in our 1996 Hormones and Behavior review, remember what evolutionary theorists are trying to do who think they can link prebiotic chemistry and life via constraint-breaking mutations. Also, remember that in this report: Quantum biology: Algae evolved to switch quantum coherence on and off , the claim was reasserted that “…a genetic mutation has led to the insertion of an extra amino acid that changes the structure of the protein complex, disrupting coherence.”

If you wonder how a genetic mutation could lead to a light-induced amino acid substitution, see How Genes Work and this definition of “amino acid” substitution: “Substitution is a type of mutation where one base pair is replaced by a different base pair. The term also refers to the replacement of one amino acid in a protein with a different amino acid.” For more confusion about the difference between mutations and amino acid substitutions, listen as Christopher P. Austin, M.D. defines Substitution. Until you learn that the dogma of DNA to RNA and cell type differentiation has been replaced by facts about nutrient-dependent RNA-mediated events you will probably have a skewed view about cellular life that has nothing to do with physics, chemistry, or molecular biology because it is based on the pseudoscientific nonsense taught as evolutionary theory.

See for comparison: Baverstock, K. (2013) Life as physics and chemistry: A system view of biology. Prog Biophys Mol Biol. 111; 108-115

Abstract: Cellular life can be viewed as one of many physical natural systems that extract free energy from their environments in the most efficient way, according to fundamental physical laws, and grow until limited by inherent physical constraints. Thus, it can be inferred that it is the efficiency of this process that natural selection acts upon. The consequent emphasis on metabolism, rather than replication, points to a metabolism-first origin of life with the adoption of DNA template replication as a second stage development. This order of events implies a cellular regulatory system that pre-dates the involvement of DNA and might, therefore, be based on the information acquired as peptides fold into proteins, rather than on genetic regulatory networks. Such an epigenetic cell regulatory model, the independent attractor model, has already been proposed to explain the phenomenon of radiation induced genomic instability. Here it is extended to provide an epigenetic basis for the morphological and functional diversity that evolution has yielded, based on natural selection of the most efficient free energy transduction. Empirical evidence which challenges the current genetic basis of cell and molecular biology and which supports the above proposal is discussed.