Protein isoforms do not evolve

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A Conversation With Peter Coveney [5.7.15] Introduction by: John Brockman
Excerpt:

I will perform the right number of experiments to make measurements of, say, the time series evolution of a given set of proteins. From those data, when things are varying in time, I can map that on to my deterministic Popperian model and infer what’s the most likely value of all the parameters that would be Popperian ones that would fit into the model. It’s an intelligent interaction between them that’s necessary in many complicated situations.

My comment: In one week, Brockman’s interviews takes us from nutrient-dependent alternative splicing, RNA editing, and the production of many distinct protein isoforms to the claims about the time series evolution of a given set of proteins. No experimental evidence of biologically-based cause and effect suggests that protein isoforms evolve.
isoforms: isomeric forms of the same protein, with slightly different amino acid sequences, but with the same activity.
See also: A universal trend of amino acid gain and loss in protein evolution
Excerpt:

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:  A universal trend that emerged before the last universal common ancestor of all extant organisms cannot be linked to the amino acid compositions of proteins that Peter Coveney places into the context of “… the time series evolution of a given set of proteins.” However, 1) the de novo creation of amino acids has been placed into 2) the context of amino acid substitutions that differentiate the cell types of all individuals of all genera.
1) Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
2) Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Clearly, theorists are struggling with their attempts at Making Sense of the Chemistry That Led to Life on Earth at the same time that Ancient DNA Tells a New Human Story that is linked to RNA-mediated metabolic and genetic networks in all genera by their physiology of reproduction. This suggests that the theorists are ignoring an atoms to ecosystems model while focusing on theories of evolution.  See for example: Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution.
See also: Junk DNA: A Journey Through the Dark Matter of the Genome
The bits of gobbledygook between the parts of a gene that code for amino acids were originally considered to be nothing but nonsense or rubbish. They were referred to as junk or garbage DNA, and pretty much dismissed as irrelevant. … But we now know that they can have a very big impact. (pp. 17-18)
RNA-mediated amino acid substitutions are linked from top-down nutrient-dependent causation to many aspects of cell type differentiation. See also: New Book on “Junk DNA” Surveys the Functions of Non-Coding DNA
Excerpt:

Preventing mutations by separating out gene-coding DNA.
Controlling telomere length that can serve as a “molecular clock” that helps control aging.
Forming the loci for centromeres.
Activating X chromosomes in females.
Producing long non-coding RNAs which regulate Hox genes or regulating brain development, or serving as attachment points for histone-modifying enzymes helping to turn genes on and off.
Serving as promoters or enhancers for genes, or imprinting control elements for “the expression of the protein-coding genes.”
Producing RNA which acts “as a kind of scaffold, directing the activity of proteins to particular regions of the genome.”
Producing RNAs which can fold into three-dimensional shapes and perform functions inside cells, much like enzymes, changing the shapes of other molecules, or helping to build ribosomes. As she notes: “We’ve actually known about these peculiar RNA molecules for decades, making it yet more surprising that we have maintained such a protein-centric vision of our genomic landscape.” (p. 146)
Serving as tRNA genes which produce tRNA molecules. These genes can also serve as insulators or spacers to stop transcription from spreading from gene to gene.
Development of the fingers and face; changing eye, skin, and hair color; affecting obesity.
Gene splicing and generating spliceosomes.
Producing small RNAs which also affect gene expression.

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