Genome complexity: one DNA with six sub-codes (Introduction)

by David Turell , Monday, May 23, 2022, 15:06 (915 days ago) @ David Turell

Another way to look at all the information coded into various sub-sets of control:

https://evolutionnews.org/2022/05/in-life-one-code-or-many/

Examples follow:

"What researchers found was that not only does the sequence of the amino acids matter, but so does the speed of the process in which the amino acids are put together into a functional protein.

“'Our results uncovered a new ‘code’ within the genetic code. We feel this is quite important, as the finding uncovers an important regulatory process that impacts all biology,” said Dr. Yi Liu, Professor of Physiology.

"The researchers say that the speed of translation affects how the protein will fold. This will affect its shape, and ultimately its function. So while a point mutation may change a nucleotide in a gene without altering the amino acid its codon produces, the resulting messenger RNA may be translated at a different speed. Consequently, the protein may fold differently and have a different function — or cause disease.

"If this is a code, it rides on the genetic code. The triplet sequence will determine the amino acid used, but a different synonymous sequence will affect the protein that results. Conceivably one could say this is all one genetic code and leave it at that.

***

"The University of Copenhagen found a new function for histones, the proteins that wrap DNA and control access to genes (this compares with Wells’s “epigenetic code”). They compare their discovery to revealing “undiscovered white dots on the map.” Sounds like more information has been discovered; let’s see.

"The four core histones have so-called tails, and among other things they signal damageto the DNA and thus attract the proteins that help repair the damage. Between the histone “yarn balls” we find the fifth histone, Histone H1, but up until now its function has not been thoroughly examined.

"Using a so-called mass spectrometer, a technique developed in collaboration with fellow researchers at the Novo Nordisk Foundation Centre for Protein Research, Niels Mailand and his team have discovered that, surprisingly, the H1 histone also helps summon repair proteins.

"Scientists at the University of Barcelona, meanwhile, claim to be “Shaking up the fundamentals of epigenetics” — a bit of hyperbole, perhaps — by showing that chromatin marks do not always have the same effect on gene expression during development. From modENCODE data, they found that some genes in worms and fruit flies were highly expressed during development without the chromatin marks that the “accepted view” expects should have been there. This is a work in progress that possibly suggests deeper regulations than are currently understood.

"At Caltech, researchers found another layer of regulation in gene expression. “Cells Rhythmically Regulate Their Genes,” the headline reads...What they found was another source of informational guidance in the combinatorial code of transcription factors. It’s a time-based method of gene regulation that is “largely unexplored” —

"Previously, researchers have thought that the relative concentrations of multiple transcription factors in the nucleus determine how they regulate a common gene target–a phenomenon known as combinatorial regulation. But the new study suggests that the relative timing of the pulses of transcription factors may be just as important as their concentration.

“'Most genes in the cell are regulated by several transcription factors in a combinatorial fashion, as parts of a complex network,” says Cai. “What we’re now seeing is a new mode of regulation that controls the pulse timing of transcription factors, and this could be critical to understanding the combinatorial regulation in genetic networks.”

"...it seems fair to categorize codes separately if they contain unique information and produce unique results. Even if histones are built from DNA, once they are assembled, they no longer rely on the genetic code. They follow their own rules of tagging genes with “tails” made of other molecules. Transcription factors and their pulsations, similarly, act apart from the language of DNA triplet codons. How much more the sugar code, membrane code, and bioelectric codes that are not even made up of amino acids?

"It would be as ridiculous to lump all of these into a single genetic code as it would be to lump Morse Code into the genetic code on the grounds that the fingers of a telegraph operator contain proteins built from DNA. Codes are distinguished by the information they contain and the rules that they follow. As Jonathan Wells cogently argues, there’s more information in life than can be explained by one genetic code. He identifies “at least” six codes, never implying that the extent of coded information in life stops there."

Comment: of course, there is one master code in a zygotes' DNA. What is done here is to demonstrate sub-sections of coded controls. There are so many active processes occurring all at the same time, there must be these sub-sets of controlling coded information. Not by chance.