Nutrient-dependent trophic analogs (2)

Nutrient-dependent trophic analogs
The claim that Microbes are trophic analogs of animals has not yet been placed into the context of RNA-mediated events that link amino acid substitutions to cell type differentiation in all individuals of all living genera over-the-weekend.
See, for example:  Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Excerpt from the editors summary: 

The mutated bacteria regained the lost flagella, and motility, within 4 days. Two stereotypical mutations diverted an evolutionarily related regulator that normally controls nitrogen uptake to control flagella biosynthesis. The mutations increased the levels of the co-opted regulator, then altered its specificity for the flagella pathway.

Journal article excerpt:

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).

My comment: The claim that two point mutations linked to amino acid substitutions via a kinase sensor and a DNA binding domain can be placed into the context of what neo-Darwinian theorists are taught about how the evolution of functional nutrient-dependent structures occurs outside the context of the physiology of reproduction.
For example, evolutionary theorists may be taught to believe this: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.
If they accept what they are taught to believe, they never become serious scientists who must link atoms to ecosystems via experimental evidence of biologically-based cause and effect before entering discussions with other serious scientists.  None of the serious scientists I have encountered, and none of the intelligent medical professionals I have known have ever made a claim about emergence that is comparable to this:

We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms.

My comment: All the serious scientists and intelligent medical professionals that I have encountered would laugh at the fact that the excerpt above came from the article with the abstract that claimed Amino acid composition of proteins varies substantially between taxa and, thus, can evolve.

Claims that emergence and the idea that whatever emerged then evolved are claims based on unsupported pseudoscientitic nonsense. However, the simple-minded claims are not possible to discuss with anyone who believes they are true. They will not take the time to learn the difference between mutation-driven evolution and how ecological variation must link atoms to ecosystems in the context of RNA-mediated amino acid substitutions that are fixed in the organized genomes of all living genera via their physiology of reproduction.
In the real world of the medical laboratory, the nutrient-dependent RNA-mediated amino acid substitutions link microRNAs and adhesion proteins to ecological adaptations in the context of supercoiled DNA, which protects organized genomes from virus-driven entropy. Thermodynamic cycles of protein biosynthesis and degradation are explained in the context of experimental evidence that is used to develop the assays for cell type differentiation that link nutritional epigenetics to healthy longevity and viruses to pathology that often requires pharmacogenomic intervention to restore the innate immune system’s ability to establish and maintain organism-level thermoregulation in the context of ecological variation.

See:  A LAMP to see in the molecular darkness

My comment: Loop-mediated isothermal amplification (LAMP) reaction complexity is a challenge to explain even to well-trained medical laboratory scientists.  John Brunstein accepted the challenge in the context of his series of articles in the Medical Laboratory Observer, which is a trade publication for medical laboratory professionals. His explanation of the LAMP reaction includes aspects of thermodynamic cycles that link spectral energy to protein biosynthesis and degradation via the ability to monitor energy changes across the visible color spectrum and beyond. That ability is a requirement to measure what serious scientists know happens because they know that thermodynamic cycles of protein biosynthesis and degradation must link atoms to ecosystems.
Brunstein notes that “…within the space constraints of this column it would not be possible to clearly explain in detail how the method functions.”  For comparison, others have claimed that base-composition pressures on nutrient-dependent protein structure and function automagically link RNA-mediated amino acid substitutions to the evolution of biodiversity because it is obvious to them that different species have different evolved proteins.  That is the premise for this textbook conclusion: “…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).”
It is pointless to attempt to discuss how serious scientists link atoms to ecosystems with anyone who accepts claims about constraint-breaking mutations linked to biodiversity, or anyone who is unwilling to learn how RNA-mediated amino acid substitutions are linked to cell type differentiation in all individuals of all living genera.
For contrast, A LAMP to see in the molecular darkness can be linked to the claim that Nothing in Biology Makes Any Sense Except in the Light of Evolution

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds. E. Margoliash, W. M. Fitch, and others
have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

My comment: The claim about knowing the DNA code was made in 1973 in the same article that claimed “…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” (p. 127).”
The claims about the two mutations that led to the evolution of the bacterial flagellum were made earlier this year by biologically uninformed science idiots who have been taught to believe in neo-Darwinian nonsense.

  1. They are not afraid to show others what they have been taught to believe, and
  2. serious scientists are not afraid to politely ridicule them.


Some evolutionary theorists are not afraid to mention that “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…” But no neo-Darwinian theorist has explained how mutations and evolution explain evolution of the bacterial flagellum over-the-weekend.
For comparison, see the complexity that Brunstein tries to detail: A LAMP to see in the molecular darkness

We start from the idea that single-stranded DNA can, when an end of a strand has a sequence which is the reverse complement of a distal sequence on the same strand, fold around to pair the end to the internal sequence in a structure known as a hairpin. (Figure 1A). If the end in question is a 3′ strand end, and the complementarity proceeds right to the 3′ nucleotide, then the hairpin can act as a point of DNA polymerase initiation allowing for extension of the 3′ end back up the hairpin stem, converting the originally single stranded DNA molecule into now an extended double strand (with one end having paired 3′ and 5′ ends, like a conventional DNA double strand, while the other end has a small single stranded loop which is the actual hairpin bend; see Figure 1B). The molecule has in effect, in the presence of nothing more than a DNA polymerase, nucleotides, and a suitable buffer, amplified itself by very nearly a factor of two.

My comment: When you are ready to look under the metaphorical lamp-post for the keys to what serious scientists know about RNA-mediated cell type differentiation, start by looking in the lab. That’s where the serious scientists can be found and you won’t find any serious scientist who make claims about evolution that are based on claims that the amino acid composition of proteins varies between taxa that thus, can evolve. The amino acid composition of proteins varies because it is nutrient-dependent and the physiology of reproduction is linked to ecological speciation without the neo-Darwinian nonsense that is included in claims made by theorists, like Eugene Koonin, which were replaced soon after I published my 2013 review of RNA-mediated amino acid substitutions and cell type differentiation in species form microbes to humans, with examples across all living genera.
For example, Koonin and others are now touting A virocentric perspective on the evolution of life.
I think that he is biologically uninformed, and would not understand the complexity of this representation of molecular machinery.

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Carl Zimmer ranks right up there with Eugene Koonin with his claims about viruses.
Excerpt: Antibiotics, once considered wonder drugs, are becoming increasingly ineffective against bacterial disease. Misuse of the drugs has led to bacterial resistance that could pose a threat to public health. The solution to this problem could be something that most people usually try to avoid: viruses.
At a time when serious scientists are linking atoms to ecosystems, nutritional epigenetics to pharmacogenomics, and the epigenetic landscape to the physical landscape of DNA via energy-dependent base pair substitutions and single amino acid substitutions that link the conserved molecular mechanisms of RNA-mediated cell type differentiation in species from microbes to man, why do we have any pseudoscientists or science journalists who are still touting ridiculous theories?

Clinical applications:

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