Hard Science vs the neo-Darwinian “magic box”

By: James V. Kohl | Published on: June 5, 2017

Summary: Identical nucleotide sequences link energy-dependent changes in binding sites to different amino acids in different proteins. The binding sites are conserved in the orthologous mammalian genes.

  1. The in vivo structure of biological membranes and evidence for lipid domains
  2. Scientists investigate how the sense of smell works in bacteria
  3. Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

As presciently predicted in the works of Richard Feynman and Bruce McEwen, bacteria feed on something that allows them to produce uranium isotopes in the context of their food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction. The link from a light-activated endogenous substrate in all cell types must be viewed in the context of energy-dependent feedback loops that link sunlight to the anti-entropic constraint of atomic energy in uranium isotopes. Chromosomal inheritance prevents the evolution of one species into another.

at futurism.com

See:  Scientists Have an Experiment to See If the Human Mind Is Bound to the Physical World

What it could mean is this: that the human mind (consciousness) isn’t made up of the same matter governed by physics. Furthermore, it could suggest that the mind is capable of overcoming physics with free will. This could potentially be the first time scientists gain a firm grasp on the problem of consciousness. “It wouldn’t settle the question, but it would certainly have a strong bearing on the issue of free will,” said Hardy.

The idea that the mind isn’t made up of matter, which is governed by the Laws of Physics is ridiculous. You cannot take such a ridiculous idea and make it meaningful via experiments. The experiment would be meaningless. All experiments must start with a rational hypothesis or something that is known. Then you must attempt to add scientific support for extending what is known to something that becomes known via your experiment. Otherwise, you start with a theory and add nothing more than another theory. You don’t get answers to any questions.
See for example: Did humans evolve in Europe rather than Africa? We don’t have the answer just yet

Charles Darwin believed that humans evolved in Africa, because that’s where our closest ape relatives the chimpanzees and gorillas live. And during the twentieth century he was vindicated through a combination of fossil and genetic discoveries.

Darwin placed his energy-dependent “conditions of life” first. .

While our place in the tree of life is now well established – chimpanzees being our closest relatives – the beginning of the human line millions of years ago continues to be shrouded in mystery.

Charles Darwin had a theory about how his “conditions of life” might be linked to biodiversity via natural selection. Others thought that his theory could be linked from natural selection to the evolution of humans from ape relatives. They claimed that Darwin thought humans evolved during millions of years of natural selection for small changes. De Vries (1902) defined the small changes as mutations. Biologically uninformed neo-Darwinian theorists still claim that mutation-driven evolution is supported by the fossil record and genetic discoveries.
See for comparison: Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees
Svante Paabo is one of the paleoanthropologists who has a grasp of cell biology, which links energy to RNA-mediated biodiversity via the sense of smell. When someone with his level of expertise refutes all neo-Darwinian nonsense with experimental evidence of biologically-based cause and effect, how can others justify their lack of acceptance for the facts? Paabo’s facts link natural selection for energy-dependent codon optimality to all biodiversity via the claims in Feedback loops link odor and pheromone signaling with reproduction.

See also: Engineering RGB color vision into Escherichia coli reported as: Bacterial Photography Goes Technicolor

Genetically engineered “disco bacteria” sense and respond to different colors of light, creating both stunning art in the culture dish and new possibilities for synthetic biology.

See for comparison:Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates
Who engineered the energy-dependent acquisition of RGB color vision in E. coli and full trichromatic RGB color vision in primates? What prevents the biophysically constrained loss of the engineered receptors for RGB color vision in E. coli that are linked from the de novo creation of olfactory receptor genes to the loss of the genes that coincides with the advent of RGB (Trichromatic) color vision in primates?
Pseudoscientists might claim that evolution engineers the acquisition of all morphological and behavioral traits, but they won’t make verifiable claims about biophysical constraints or loss of the genes after the genes are created. Instead, see: Mutation-Driven Evolution.
Theorists start with genes that were somehow created and then claim:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations…

After the energy-dependent de novo creation of genes, genomic conservation continues to be nutrient energy-dependent and biophysically constrained by the physiology of pheromone-controlled reproduction in all living genera. Chromosomal inheritance prevents the evolution of one species into another — unless it occurs via magic traits. In the context of mutation-driven evolution species must have magic traits.
See for example: Evolution on the fast lane—One flounder species became two

“The answer may lay in so called magic traits, meaning traits that are under selection which at the same time cause reproductive isolation as a byproduct. In theory, selection on such traits could play a central role in rapid speciation events. The mating strategies and reproductive traits of the two flounder species could act as magic traits,” clarifies Momigliano.

See for comparison: Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

Reported as: Living fossil challenges thinking on brain evolution

Despite its appearance, amphioxus is not a fish. It has a primitive spinal cord which runs down its back, but no clearly defined face, no bones or jaws and a small brain with a single light-sensing “frontal eye”. It has changed so little for hundreds of millions of years that it has been described as a “living fossil”.

See for comparison to the report of a hundreds of million years-old “living fossil:” Bacteria evolve over a weekend  (video)
Serious scientists know that the bacteria that reportedly “evolved” adapted to ecological variation in their food supply. Adaptation is nutrient energy-dependent and pheromone controlled via the physiology of reproduction in all living genera. It occurs over-the-weekend in P. fluorescens, but it is still reported to be mutation-driven evolution by biologically uninformed theorists.
Biologically uniformed theorists also make claims like those found here: The Physics of Everything

For comparison: This is the Physics of Everything, outside the context of the magic of evolution in the context of magic traits.

See: The in vivo structure of biological membranes and evidence for lipid domains

This approach relies on tuning the isotopic content of hydrogen within the membrane, and other parts of the bacterium, to generate neutron scattering spectra exclusively from the membrane. Using this approach, we confirmed that the structure of the B. subtilis membrane is lamellar and has an average hydrophobic thickness of 23.9 ± 0.9 Ångstroms (Å).

Average hydrophobic thickness cannot be linked from energy-dependent changes in the cell membrane to biophysically constrained cause and effect via the pheromone-controlled physiology of reproduction in any organism.
See for comparison: Scientists investigate how the sense of smell works in bacteria

…the signaling and inactive states differ only very slightly at the nitrate-binding site – by 0.5-1 angstroms, which is approximately one fifth of the size of the ion itself (1 angstrom is 10-10 meters). However, when this ion binds to the sensor, it causes huge changes in the protein: The helices of different monomers begin to move in different directions, like pistons. These “pistons” transmit the small change of 0.5-1 angstroms through the membrane, and their outer ends shift by approximately 2.5 angstroms in different directions. Inside the cell, in the HAMP domain, these shifts are converted into the rotation of two parts of NarQ relative to each other. Ultimately, the positions of the output helices change by as much as 7 angstroms, thus completing the signal transmission.

Serious scientists do not link average hydrophobic thickness from the sense of smell in bacteria to all biophysically constrained energy-dependent biodiversity via the physiology of reproduction in species from microbes to humans. Serious scientists link the energy-dependent changes from angstroms to ecosystems in the context of RNA-mediated amino acid substitutions in supercoiled DNA.
See: Structural diversity of supercoiled DNA

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

The metabolic processes are energy-dependent and biophysically constrained.

For another example of biogenic metabolic processes, see: Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

This was reported as: A new twist on uranium’s origin story, by CSU scientists

In recent years, scientists had uncovered new evidence that bacteria – living microorganisms – could generate a different kind of reduced uranium that is non-crystalline and has very different physical and chemical properties.

…using new techniques including synchrotron radiation-based spectroscopy and isotope fingerprinting. They found that up to 89 percent of the uranium from their 650-foot-deep samples wasn’t crystalline uraninite at all, but rather, a non-crystalline uranium that was bound to organic matter or inorganic carbonate. Most of the uranium they found in that unmined site is estimated to be 3 million years old, and formed via reduction by microorganisms – microbes that respire not on oxygen, but on uranium.

They linked the nutrient energy-dependent pheromone-controlled physiology of reproduction in bacteria and all other living genera to the creation of differences in the 238U to 235U isotope ratio. The differences in the 238U to 235U isotope ratio discriminate between the abiotic and biotic transformation of uranium. But, they placed their findings on abiogenesis into the context of ridiculous theories of evolution and ignored everything  known to serious scientists about the energy-dependent biotic transformation of uranium and all energy-dependent biogenesis.

For any example of how placing their results into the context of abiogenesis supports ridiculous theories about emergence and evolution, see: Uranium–lead dating

The method relies on two separate decay chains, the uranium series from 238U to 206Pb, with a half-life of 4.47 billion years and the actinium series from 235U to 207Pb, with a half-life of 710 million years.

For comparison, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

This was reported as: Evolutionary Rewiring: Strong selective pressure can lead to rapid and reproducible evolution in bacteria

NtrC shares 30 percent amino acid identity with FleQ… the re-evolved flagella enabled the bacteria to access food supplies…

Natural selection for food energy-dependent codon optimality links ultraviolet light (UV) to the nutrient energy-dependent pheromone-controlled physiology of reproduction in P. fluorescens, which links UV light to the weekend resurrection of the flagellum because P. fluorescens fluoresces with exposure to UV light.

Differences in the nutrient energy-dependent RNA-mediated amino acid substitutions link differences in supercoiled DNA to the protection of all organized genomes from viruses. Virus-driven energy theft causes the degradation of messenger RNA, which links mutations to all pathology.

See Feynman’s comments about food energy:


Could any other physicist but Feynman have guessed that bacteria feed on something that allows them to produce uranium isotopes in the context of their food energy-dependent biophysically constrained pheromone-controlled physiology of reproduction?

Could any other molecular biologist but Bruce McEwen have linked an endogenous substrate from the energy-dependent biophysically constrained pheromone controlled physiology of reproduction to all biodiversity in all living genera?

See also: The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes

Binding sites of miR-619-5p in the 3’UTRs of all human target genes are also present in the 3’UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes.

CONCLUSIONS:(with my emphasis)

The majority of miR-619-5p binding sites are located in the 3’UTRs but some genes have miRNA binding sites in the 5’UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins. The binding sites of miR-619-5p in 3’UTRs, 5’UTRs and CDSs are conservative in the orthologous mammalian genes.

To help differentiate between evolution and adaptation in the context of natural selection for food energy-dependent codon optimality in the context of the physiology of pheromone-controlled reproduciton, see: Metrics of assay accuracy

Neo-Darwinian evolution occurs only in the context of this “Magic Box” example. Each time you look at the “+” sign on the box, you are taught to believe in evolution.

For comparison, see: The Emerging View of Aging as a Reversible Epigenetic Process

This evidence supports the idea that progressive epigenetic dysregulation may be the key driver of organismal aging and challenges the conventional view of aging as an irreversible process. The model of aging as an epigenetic process provides an elegant explanation of a number of age-related processes difficult to explain by conventional theories of aging.

Conventional theories of aging have failed to link the nutrient energy-dependent pheromone-controlled physiology of RNA-mediated protein folding chemistry to all biodiversity via biophysically constrained chromosomal inheritance. That’s how conventional theories left all of humanity waiting for cures that will never become available. Biologically uninformed theorists still do not know how protein folding chemistry is linked from changes in the microRNA/messenger RNA balance to healthy longevity via cell type differentiation or from the virus-driven degradation of messenger RNA to mutations and all pathology.
See: Genome editing: That’s the way the CRISPR crumbles
Review of A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution This title will be released on June 13, 2017.

Not since the atomic bomb has a technology so alarmed its inventors that they warned the world about its use.

June 14, 2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

 June 14, 2013 Mutation-Driven Evolution

(1) Mutation is the source of all genetic variation on which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors.

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