Genome complexity: what genes do and don't do (Introduction)

by David Turell , Monday, January 14, 2019, 13:35 (1930 days ago) @ dhw

DAVID: A careful article on the limits to what we understand about genes:
http://nautil.us//issue/68/context/its-the-end-of-the-gene-as-we-know-it

dhw: Once more my thanks for your integrity in presenting such articles.

QUOTE: "Scientists now understand that the information in the DNA code can only serve as a template for a protein. It cannot possibly serve as instructions for the more complex task of putting the proteins together into a fully functioning being, no more than the characters on a typewriter can produce a story.(David’s bold)

This, together with the two quotes that follow, presents an interesting contrast to two of your earlier statements: “…the original DNA may have contained all the info for evolution”. Your definition of intelligent information was “a complete set of instructions for cells to respond to all stimuli they must deal with.”

QUOTES: "Accordingly, even single cells change their metabolic pathways, and the way they use their genes to suit those patterns. That is, they “learn,” and create instructions on the hoof.” (dhw’s bold)

“Through the statistical patterns within the storms, instructions are, again, created de novo. The cells, all with the same genes, multiply into hundreds of starkly different types, moving in a glorious ballet to find just the right places at the right times. That could not have been specified in the fixed linear strings of DNA.”

dhw: I really don’t see how your definitions are compatible with the statements I have bolded.

Sloppy thinking and writing. My boldings above and below are my thoughts exactly.

QUOTE: " as the British biologist Denis Noble insists in an interview with the writer Suzan Mazur,1 “The modern synthesis has got causality in biology wrong … DNA on its own does absolutely nothing until activated by the rest of the system … DNA is not a cause in an active sense. I think it is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires.” (DAVID’s bold)

dhw: If DNA is not a cause and is not a set of instructions, the cell communities of which the organism is composed and which “talk to each other with storms of chemical signals” must be creating their own instructions.

QUOTE:: "In a paper in Physics of Life Reviews in 2013, James Shapiro describes how cells and organisms are capable of “natural genetic engineering.” That is, they frequently alter their own DNA sequences, rewriting their own genomes throughout life. The startling implication is that the gene as popularly conceived—a blueprint on a strand of DNA, determining development and its variations—does not really exist."

dhw: And let us not forget that James Shapiro believes that cells are intelligent organisms.

DAVID’s comment: We have a long way to go to really understand how the orchestrated layers of the genome works.

dhw: Yes, we do. And therefore we should at the very least remain open-minded on the subject of cellular intelligence versus automaticity.

DNA codes for protein but most of the so-called junk DNA provides the modifiers for gene expression. We still don 't know how it all works. It is far more complex than we demonstrate at this point. There must be integrated levels of control. Looking at a code as simply a code doesn't see the whole picture.