Junk DNA goodbye!: a new article says there is none (Introduction)

by David Turell , Thursday, November 21, 2019, 01:19 (1830 days ago) @ David Turell

This claims that there are overriding patterns to DNA which constitute an overall genetic code which controls DNA in a different organization and functional way:

https://www.advancedsciencenews.com/that-junk-dna-is-full-of-information/

"It should not surprise us that even in parts of the genome where we don’t obviously see a “functional” code (i.e., one that’s been evolutionarily fixed as a result of some selective advantage), there is a type of code, but not like anything we’ve previously considered as such. And what if it were doing something in three dimensions as well as the two dimensions of the ATGC code?

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"Hence a sequence of DNA can code for a protein and, in addition, for something else. This “something else”, according to Giorgio Bernardi, is information that directs the packaging of the enormous length of DNA in a cell into the relatively tiny nucleus. Primarily it is the code that guides the binding of the DNA-packaging proteins known as histones. Bernardi refers to this as the “genomic code”—a structural code that defines the shape and compaction of DNA into the highly-condensed form known as “chromatin”.

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"As Bernardi reviews, synthesizing his and others’ groundbreaking work, in the core sequences of the eukaryotic genome, the GC content in structural organizational units of the genome termed “isochores” increased during the evolutionary transition between so-called cold-blooded and warm-blooded organisms. And, fascinatingly, this sequence bias overlaps with sequences that are much more constrained in function: these are the very protein-coding sequences mentioned earlier, and they—more than the intervening non-coding sequences—are the clue to the “genomic code”.

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"These regions of DNA may then be regarded as structurally important elements in forming the correct shape and separation of condensed coding sequences in the genome, regardless of any other possible function that those non-coding sequences have: in essence, this would be an “explanation” for the persistence in genomes of sequences to which no “function” (in terms of evolutionarily-selected activity), can be ascribed (or, at least, no substantial function).

"A final analogy—this time much more closely related—might be the very amino acid sequences in large proteins, which do a variety of twists, turns, folds etc. We may marvel at such complicated structures and ask “but do they need to be quite so complicated for their function?” Well, maybe they do in order to condense and position parts of the protein in the exact orientation and place that generates the three-dimensional structure that has been successfully selected by evolution. But with a knowledge that the “genomic code” overlaps protein coding sequences, we might even start to become suspicious that there is another selective pressure at work as well."

Comment: What is being described in the very complex original article are 'isochores' which are sections of the DNA which are similar in structure and are packed in chromatin as recognized sections. So we again see the 3-D aspect of DNA being critical, and the importance of 'junk' DNA as defining Darwinian evolution by chance and mistake as flying out the window, resulting in a recognition that all of DNA and its organization are most likely designed, purposeful, and not a slap-dash chance structure predicted by Darwin's theory.