DNA codes for protein but we still do not know what runs life:

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

"The existence of a powerful code-script seemed to be confirmed with the discovery of the structure of DNA by Watson and Crick in 1953. They revealed how the sequences of components (called nucleotides) in DNA could serve as a template—a code—for a protein, much as a typewriter sequences letters to form words. 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.

***

"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.

"This can seem confusing to those of us indoctrinated in the idea that there must be a set of genetic instructions prior to development: If not in the DNA code, then where? By the 1980s, research findings started to turn that notion on its head.

***

"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. 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.

"Some have likened the process to an orchestra without a conductor. Physiologist Denis Noble has described it as Dancing to the Tune of Life (the title of his recent book). 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.

***

"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, “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.”

***

"But more evolved functions—and associated diseases—depend upon the vast regulatory networks mentioned above, and thousands of genes. Far from acting as single-minded executives, genes are typically flanked, on the DNA sequence, by a dozen or more “regulatory” sequences used by wider cell signals and their dynamics to control genetic transcription.

"This explains why humans seem to have only a few more genes than flies or mice (around 20,000), while a carrot has 45,000! There is no correlation between the complexity of living things and the number of genes they have. But there is a correlation with the evolving complexity of regulatory networks. Counting genes to understand the whole is like judging a body of literature by counting letters. It can’t be done.

***

"More startling has been the realization that less than 5 percent of the genome is used to make proteins at all. Most produce a vast range of different factors (RNAs) regulating, through the network, how the other genes are used.

"Increasingly, we are finding that, in complex evolved traits—like human minds—there is little prediction from DNA variation through development to individual differences. The genes are crucial, of course, but nearly all genetic variations are dealt with in the way you can vary your journey from A to B: by constructing alternative routes. “Multiple alternative pathways … are the rule rather than the exception,” reported a paper in the journal BioSystems in 2007.

***

" we can now understand why the same genetic resources can be used in many different ways in different organs and tissues. Genes now utilized in the development of our arms and legs, first appeared in organisms that have neither. Genes used in fruit flies for gonad development are now used in the development of human brains. And most genes are used in several different tissues for different purposes at the same time.

"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."

Comment: the whole system of genetic controls is still a giant black box.

dhw: The question is not whether DNA editing happens, but whether your God’s “information/instructions used by the cell” means a specific, 3.8-billion-year-old programme for every single change in the history of evolution, switched on automatically by the cell when conditions require or allow it – which seems to me extremely unlikely – or a mechanism which enables the cell to change itself autonomously, i.e. to devise its own programme as conditions change. Shapiro clearly believes in the latter.

DAVID: The only issue here is I believe God gave the cells that mechanism.

I’ve read this through several times, and I’m still not sure that I dare to celebrate. Can it really be true that you have jettisoned the hypothesis of the first cells containing a 3.8-billion-year old programme for every change, and are now in favour of an autonomous mechanism whereby cells change in response to changing conditions? (I have always allowed for your God being the inventor of the mechanism.) This may be a red letter day in the history of the AgnosticWeb!

Quotes from “Genome complexity: DNA tiny part of the controls”: "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. 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.

"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."

Once more I must thank you for your admirable integrity in offering us an article which supports the hypothesis you have so long resisted. It even uses my own favourite analogy of ant colonies. Shapiro champions cellular intelligence, and I don’t see how any organism that “learns” and creates instructions on the hoof (as opposed to being preprogrammed) can be seen as an automaton.

DAVID (under “Gulls change wing shape”): Helps them glide and fly in different ways:
https://techxplore.com/news/2019-01-zoologists-reveal-gulls-wing-morph.html

DAVID: It is not known if the original gulls had this ability from the beginning or developed it over time. If it wasn't present in the beginning they had trouble hunting over the oceans so one can wonder how they survived until they developed these adaptations of elbow joints which require exact design.

dhw: Perhaps they initially found plenty of food close at wing (like pre-whales having plenty of food close at leg) but then conditions changed and they had to hunt further afield, which occasioned the changes made by the cell communities that constitute the wings and their connections.

DAVID: You are still using environmental changes to push evolution, but some one or some thing has to do the designing for the large body changes.

Yes of course I am. Fins would not be much use if the pre-whale hadn’t taken to the water. You have just agreed that the ‘some thing’ is the cells themselves containing the mechanism which enables them to change autonomously as conditions change (provided God invented the mechanism).

Another review:

https://www.quantamagazine.org/scientists-catch-jumping-genes-rewiring-genomes-20210512/

"For more than a decade, Feschotte has pointed to transposons as the ultimate innovators in eukaryotic genomes. Transposons are genetic elements that can copy themselves and insert those copies throughout the genome using a splicing enzyme they make. Feschotte may have finally found the smoking gun he has been looking for: As he and his colleagues recently reported in Science, these jumping genes have fused with other genes nearly 100 times in tetrapods over the past 300 million years, and many of the resulting genetic mashups are likely to encode transcription factors.

"David Adelson, chair of bioinformatics and computational genetics at the University of Adelaide in Australia, who was not involved with the study, said, “This study provides a good mechanistic understanding of how these new genes can form, and it squarely implicates the transposon activity itself as the cause.”

"Scientists have long known that transposons can fuse with established genes because they have seen the unique genetic signatures of transposons in a handful of them, but the precise mechanism behind these unlikely fusion events has largely been unknown. By analyzing genes with transposon signatures from nearly 600 tetrapods, the researchers found 106 distinct genes that may have fused with a transposon. The human genome carries 44 genes likely to have been born this way.

"The structure of genes in eukaryotes is complicated, because their blueprints for making proteins are broken up by introns. These noncoding sequences are transcribed, but they get snipped out of the messenger RNA transcripts before translation into protein occurs. But according to Feschotte’s new study, a transposon can occasionally hop into an intron and change what gets translated. In some of these cases, the protein made by the fusion gene is a mashup of the original product and the transposon’s splicing enzyme (transposase).

***

"Cosby described the 106 fusion genes described in the study as the “tiniest tip of the iceberg.” Adelson agreed and explained why: Events that randomly create fusion genes for functional, non-harmful proteins rely on a series of coincidences and must be exceedingly rare; for the fusion genes to spread throughout a population and withstand the test of time, nature must also positively select for them in some way. For the researchers to have found the examples described in the study so readily, transposons must surely cause fusion events much more often, he said.

***

"Transposons comprise a hefty chunk of eukaryotic DNA, yet organisms take extreme measures to carefully regulate their activity and prevent the havoc caused by problems such as genomic instability and harmful mutations. These dangers made Adelson wonder if fusion genes sometimes endanger orderly gene regulation. “Not only are you perturbing one thing, but you’re perturbing this whole cascade of things,” he said. “How is it that you can change expression of all these things and not have a three-headed bat?” Cosby, however, thinks it’s unlikely that a fusion gene leading to harmful morphogenic changes would readily propagate through a population.

"Damon Lisch, a plant geneticist at Purdue University who studies transposable elements and was not involved with the study, said he hopes this study pushes back against a widespread but misguided notion that transposons are “junk DNA.” Transposable elements generate tremendous amounts of diversity and have been implicated in the evolution of the placenta and the adaptive immune system, he explained. “These are not junk — they’re living little creatures in your genome that are under very active selection over long periods of time, and what that means is that they evolve new functions to stay in your genome,” he said.

"Though this study highlights the mechanism underlying transposase fusion genes, the vast majority of new genetic material is thought to form through genetic duplication, in which genes are accidentally copied and the extras diverge through mutation. But a large quantity of genetic material does not mean that new protein functions will be significant, said Cosby, who is continuing to investigate the function of the fusion proteins.

“'Evolution is the ultimate tinkerer and ultimate opportunist,” said David Schatz, a molecular geneticist at Yale University who was not involved with the study. “If you give evolution a tool, it may not use it right away, but sooner or later it will take advantage of it.'” (my bold)

Comment: The last paragraph treats evolution as if if is a personage. Why not simply God in action?