Antithetical conclusions (5)

By: James V. Kohl | Published on: August 20, 2016

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Something is antithetical when it is in complete and utter opposition to the character of something.
For example, see:
Small population size? It doesn’t have to mean that species can’t adapt to environmental change.

A new study shows that small populations of species can still adapt and respond to natural selection.

Natural selection for energy-dependent codon usage in the context of the physiology of reproduction is the only way known to serious scientists for a species to ecologically adapt. Theorists place natural selection first. They place natural selection into the context of neo-Darwinian evolution. Selection occurs for beneficial mutations.
Serious scientists place ecological variation first. For example, Darwin insisted the his “conditions of life” must be placed before natural selection. He seemed to intuitively know that others would bastardize his theory, which linked ecological variation to ecological adaptation. Neo-Darwinian theorists bastardized his theory when they used deVries definition of ‘mutation’ and their assumptions to portray evolution as if natural selection could link the mutations to increasing organismal complexity. In the context of neo-Darwinian nonsense, theorists can prove virtually anything. But theorists are not scientists, which makes the following statement a lie.
See also: Ducks evolved from Norfolk, scientists prove

The scientists expect to conclude that ducks and residents of Norfolk are indeed close relatives.

In the context of this report, that suggests the distant relatives lived or went camping in an area that is ~one to two or miles closer to the sun.
See: 10,500 year old camp site discovered in Kashmir

“It was a small flat area with snow-covered peaks, dry barren land with loose rocks all around and a gushing stream within the deep western gorges – an ideal place for camping in a picturesque setting,” the ministry noted.

The ministry failed to note that camping at 14,000 ft above sea level requires ecological adaptation to lower levels of oxygen. Adaptation requires the selection for nutrient energy-dependent codon usage via RNA-mediated protein folding chemistry, which is biophysically constrained by the physiology of reproduction in all human populations.
SARCASM ALERT: Perhaps the people who camped in Kashmir evolved from hummingbirds, not ducks.
See: Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
Alternatively, since people are mammals, perhaps they evolved from deer-mice.
See: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
But, see for comparison: Nothing in Biology Makes Any Sense Except in the Light of Evolution

“…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).”

Dobzhansky (1973) linked cell type differentiation in 3 primate species to what Bazzini et al., (2016) refer to as the amino acid optimality code.

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

However, this is what Dobzhansky (1973) claimed had been brought into the context of the light of evolution:

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.

Here’s information on what is currently known to serious scientist about the code.
codon: a series of three adjacent bases in one polynucleotide chain of a DNA or RNA molecule, which codes for a specific amino acid.
All serious scientists have since linked energy-dependent changes in what is known about the code from natural selection for codon usage to amino acid substitutions and the de novo creation of G protein-coupled receptors (GPCRs). They have linked the GPCRs to receptor-mediated nutrient-dependent pheromone-controlled biophysically constrained RNA-mediated protein folding chemistry. The biophysically constrained chemistry of energy-dependent protein folding chemistry links fixation of RNA-mediated amino acid substitutions to the stability of all organized genomes via the physiology of reproduction.
All serious scientists also know that virus-driven energy theft links mutations to all pathology by preventing fixation of RNA-mediated amino acid substitutions that differentiate cell types in all individuals of all living genera.
Unfortunately, scientists who did not take Dobzhansky’s claims seriously are forced to eliminate what is known about codon usage and RNA-mediated protein folding chemistry from their representations of biologically-based cause and effect. They must continue attempts to portray the assembly of proteins as if it automagically occurred in the context of their ridiculous theories.
For example, see: First 3-D map of cell-building protein linked to cancer

Dr Lucet said in healthy cells, DCLK1 can control its own function, ensuring it only assembles microtubules at the right time. “We can think of the kinase domain of DCLK1 being an inbuilt controlling unit for the protein,” she said. “The kinase domain sits separately from the part of the protein that assembles microtubules, and can switch microtubule assembly on or off as needed.
“The complexity of having these two different components in one protein has, until now, hindered our understanding of how DCLK1 functions normally and what goes wrong in cancer. We decided to focus on just the regulatory kinase domain of DCLK1, because we knew that this is the part of DCLK1 that is often altered in cancers,” Dr Lucet said.
The team created a detailed map of the DCLK1 kinase domain using the Australian synchrotron, providing new information about how the part of the protein functioned, Dr Patel said.
“By looking at the structure of the kinase domain at the atomic level, we can now understand the effect of cancer-associated mutations located in this region,” she said. “These mutations can lead to a non-stop microtubule building by DCLK1, and consequently chaotic cell division that is a hallmark of cancer.

Biochemical and Structural Insights into Doublecortin-like Kinase Domain 1 (Subscription required)

Abstract excerpt:

This structure also allowed for the mapping of cancer-causing mutations within the kinase domain, suggesting that a loss of kinase function may contribute to tumorigenesis.

Continued

See: Antithetical conclusions (6)