In theory, or supported by experimental evidence?

Carl Zimmer typically makes statements like the one below without prefacing them with “in theory.” That’s how he establishes the bias towards evolutionary theory in nearly everything he reports.
For example: “During the development of eggs and sperm, each pair of chromosomes swaps pieces of their DNA. Over the generations, long stretches of DNA get broken into smaller ones, like a deck of cards repeatedly shuffled.
Inaccurate statements like that one make it appear that the evolution of biodiversity occurs across millions of years during which accumulated mutations somehow lead to fixed changes in the amino acid substitutions that differentiate the cell types of all cells in all individuals of all different species. Accurate representations of biologically-based cause and effect include RNA-mediated events, which link ecological variation to nutrient-dependent amino acid substitutions and chromosomal rearrangements.
The amino acid substitutions and chromosomal rearrangements occur in the absence of mutations that perturb protein folding. Instead, they help to ensure biodiversity via the metabolism of nutrients to species-specific pheromones. Pheromones control the physiology of reproduction in species from microbes to man, which is how they lead from nutrient-uptake to the control of biodiversity via conserved molecular mechanisms of cell type differentiation in all species.
The alternative that Zimmer and others like him continue to tout involves a ridiculous theory that accumulated mutations somehow lead to natural selection and the evolution of biodiversity. No experimental evidence of biologically-based cause and effect suggests that is possible. Furthermore, the amino acid-dependent protein folding that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man is biophysically-constrained. Simply put, that means the Laws of Physics prevent mutation-driven evolution by placing chemical ecology in a position that ensures what Darwin called his ‘conditions of life’ have been met. Minimally, his ‘conditions of life’ have always been nutrient-dependent, which is probably why evidence of RNA-mediated events clearly links nutrient uptake to ecological adaptations.
Until 1973, most evolutionary theorists could have excused themselves from intelligent conversations about the conserved molecular biology of amino acid substitutions and cell type differentiation. However, from the time that Dobzhansky stated his creationist perspective in the terms of evolutionary theory, it has become clearer that amino acids substitutions differentiate cell types in all species. In Nothing in Biology Makes Any Sense Except in the Light of Evolution, Dobzhanksy wrote: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.”
No experimental evidence of biologically-based cause and effect suggests the single amino acids substitutions that differentiate the cell types of these primates or the cell types of any other species can arise via a mutation or the accumulation of mutations. All experimental evidence and all model organisms that sexually reproduce via ligand-specific receptor-mediated fertilization exemplifies the fact that … exosomes are the carriers of a flow of information from somatic cells to gametes…That fact, like all other facts about sex differences in cell types indicates …that somatic RNA is transferred to sperm cells, which can therefore act as the final recipients of somatic cell-derived information.
Carl Zimmer is one of two people I know about who has written a book about viruses, see A Planet of Viruses. I’m not sure what planet his information came from, since it does not appear to include anything pertinent to links between the epigenetic landscape and the physical landscape of DNA in the organized genomes of species from microbes to man. However, a book published 2 years earlier by Luis Villarreal, see Origin of group identity: viruses, addiction and cooperation, includes the mention of pheromones 79 times.
Pheromones control the physiology of nutrient-dependent reproduction in living organisms via nutrient-dependent RNA-directed DNA methylation and RNA-mediated events that link amino acid substitutions to cell type differentiation via chromosomal rearrangements in all organisms. That’s why Zimmer’s book is of much less interest to me than Villarreal’s book.
Like his articles, Zimmer seems to be stuck touting evolutionary theory at a time when others have moved forward by providing experimental evidence of biologically based facts that link microbes to man via conserved molecular mechanisms, not via mutations and natural selection that Zimmer thinks is the basis for the evolution of biodiversity. Like Villarreal’s articles, those written by other serious scientists continue to attest to that fact that Carl Zimmer’s pseudoscientific nonsense will be exposed each time new experimental evidence is published that links RNA-mediated events to increasing organismal complexity with no mention of evolutionary events whatsoever.
See also: Body Cells Transfer Genetic Info Directly Into Sperm Cells, Amazing Study Finds.
Also, on July 31, 2013 Sayer Ji wrote: “Hereditary trauma: Inheritance of traumas and how they may be mediated”
Excerpt: “Mansuy and her team have succeeded in identifying a key component of these processes: short RNA molecules. These RNAs are synthetized from genetic information (DNA) by enzymes that read specific sections of the DNA (genes) and use them as template to produce corresponding RNAs. Other enzymes then trim these RNAs into mature forms. Cells naturally contain a large number of different short RNA molecules called microRNAs. They have regulatory functions, such as controlling how many copies of a particular protein are made.
See my comments on: Scientists unmask a piece in the puzzle of how the inheritance of traumas is mediated
1) “…traumatic stress alters the amount of several microRNAs in the blood, brain and sperm – while some microRNAs were produced in excess, others were lower than in the corresponding tissues or cells of control animals. These alterations resulted in misregulation of cellular processes normally controlled by these microRNAs.”
Nutrient stress and social stress act on the same central neuronal system that links epigenetic effects of food odors and social odors called pheromones on the microRNA/messenger RNA balance and cell type differentiation to mammalian behavior.
For details, see: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
The review follows from detailed representations with cross species examples of cause and effect in my 2013 published review and it adds the required details on the physics and chemistry of protein folding.
2) Kohl’s Laws of Biology: “The ecological origin of all biological laws is apparent 1) in the context of systems biology [91]; 2) in the context of the metabolism of nutrients by microbes [157]; and 3) in the context of how the metabolism of nutrients results in species-specific pheromones that control the physiology of reproduction [158]. Taken together, the systems biology of nutrient metabolism to species-specific pheromones, which control the physiology of reproduction, can be expressed in a summary of Kohl’s Laws of Biology: 1) Life is nutrient-dependent. See for review [2, 31]. The physiology of reproduction is pheromone-controlled. See for review [30]. In the context of nutrient-dependent epigenetically-effected human reproduction, it is clearer that the epigenetic effects of human pheromones integrate neuroendocrinology and behavior [104], which includes the neuroendocrinology of mammalian behavior associated with the development of sexual preferences [159].”
RNA-sequencing / exome sequencing now link RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all organisms. Today’s news stresses the importance of RNA-mediated events to the understanding of differences between undifferentiated cancerous cell types and controlled cell type differentiation. New genome-editing technique enables rapid analysis of genes mutated in tumors. Simply put, researchers have applied what is known about RNA-mediated gene editing to help determine what goes wrong with cell metabolism processes in cancer cells. Why aren’t the theromodynamic cycles of protein biosynthesis and degradation limited by the biophysical constraints on protein folding that enable typical cell type differentiation via conserved molecular mechanisms in species from microbes to man? This rapid analysis of RNA-mediated genome editing eliminates the need for mouse models of what happens when genes are knocked out or knocked in. No need to wait for the mice to grow and manifest differences in their morphological and behavioral phenotypes as if mutations caused typical and atypical cell type differentiation as evolutionary theorist have told us occurs in the context of natural selection and the evolution of biodiversity.

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