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

by David Turell , Sunday, February 24, 2019, 19:00 (1888 days ago) @ David Turell

A great article on changing concepts on the true role of genes. To set the scene b e sure to read the very learned concepts, especially this one:

Yelloguy: "I think the article makes a very good case of flipping the old way of thinking that the genes are the blueprint to an organism's development, to a new way of thinking that genes are a small subset of the database available, and that the blueprint lies elsewhere." I think he uses the term 'blueprint' broadly to imply information and controls.

http://nautil.us//issue/68/context/its-the-end-of-the-gene-as-we-know-it

"We’ve all seen the stark headlines: “Being Rich and Successful Is in Your DNA” (Guardian, July 12); “A New Genetic Test Could Help Determine Children’s Success” (Newsweek, July 10); “Our Fortunetelling Genes” make us (Wall Street Journal, Nov. 16); and so on.

"The problem is, many of these headlines are not discussing real genes at all, but a crude statistical model of them, involving dozens of unlikely assumptions. Now, slowly but surely, that whole conceptual model of the gene is being challenged.

"We have reached peak gene, and passed it.

***

"In a famous paper in 1911, Wilhelm Johannsen warned against doing that. We do not know, he said, how those inferred, but invisible, factors can possibly carry such complex information. But Johannsen was ignored, for reasons, as it turned out, more to do with ideology than biology.

***

"So the accepted “central dogma” could be conceived as the one-way flow of information from the code in the gene:

"DNA template → proteins → developing characteristics;

as if production of the words alone is tantamount to writing the whole “book” of a complex being.

***

"So the hype now pouring out of the mass media is popularizing what has been lurking in the science all along: a gene-god as an entity with almost supernatural powers. Today it’s the gene that, in the words of the Anglican hymn, “makes us high and lowly and orders our estate.”

"In her 1984 book, The Ontogeny of Information, the philosopher of science Susan Oyama warned, “Just as traditional thought placed biological forms in the mind of God, so modern thought finds ways of endowing the genes with ultimate formative power.”

"The long-suppressed logic of Johansenn that has stalked the gene-god for decades has come home to roost. 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.

***
"Genes are used as templates for making vital resources, of course. But directions and outcomes of the system are not controlled by genes. Like colonies of ants or bees, there are deeper dynamical laws at work in the development of forms and variations.

***

"It is most stunningly displayed in early development. Within hours, the fertilized egg becomes a ball of identical cells—all with the same genome, of course. But the cells are already talking to each other with storms of chemical signals. 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.

"So it has been dawning on us is that there is no prior plan or blueprint for development: Instructions are created on the hoof, far more intelligently than is possible from dumb DNA. That is why today’s molecular biologists are reporting “cognitive resources” in cells; “bio-information intelligence”; “cell intelligence”; “metabolic memory”; and “cell knowledge”—all terms appearing in recent literature.1,2 “Do cells think?” is the title of a 2007 paper in the journal Cellular and Molecular Life Sciences.3 On the other hand the assumed developmental “program” coded in a genotype has never been described.

"It is such discoveries that are turning our ideas of genetic causation inside out. We have traditionally thought of cell contents as servants to the DNA instructions. But, 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.” (my bold)

Comment: See next entry to continue. My bias has had me skip his references to RNA world beginning. My bold above is my agreement with Noble.