Some bacteria self-destruct to save the colony:

https://www.sciencemag.org/news/2020/11/microbes-mystery-dna-helps-defeat-viruses-and-h...

"For several years, researchers have been adapting retrons—mysterious complexes of DNA, RNA, and protein found in some bacteria—into a potentially powerful way to alter genomes of single cell organisms. Now, biology is catching up, as two groups report evidence that, like CRISPR, retrons are part of the bacterial immune arsenal, protecting the microbes from viruses called phages.

"Last week in Cell, one team described how a specific retron defends bacteria, triggering newly infected cells to self-destruct so the virus can’t replicate and spread to others. The Cell paper “is the first to concretely determine a natural function for retrons,” says Anna Simon, a synthetic biologist at Strand Therapeutics who has studied the bacterial oddities. Another paper, which so far has appeared only as a preprint, reports a similar finding.

***

"In the 1980s, researchers studying a soil bacterium were puzzled to find many copies of short sequences of single-stranded DNA littering the cells. The mystery deepened when they learned each bit of DNA was attached to an RNA with a complementary base sequence. Eventually they realized an enzyme called reverse transcriptase had made that DNA from the attached RNA, and that all three molecules—RNA, DNA, and enzyme—formed a complex.

"Similar constructs, dubbed retrons for the reverse transcriptase, were found in many bacteria.

***

"The team then noticed that the DNA encoding retron components often accompanied a protein-coding gene, and the protein varied from retron to retron. The team decided to test its hunch that the cluster of sequences represented a new phage defense. They went on to show that bacteria needed all three components—reverse transcriptase, the DNA-RNA hybrid, and the second protein—to defeat a variety of viruses.

***

"The researchers concluded that the retron somehow “guards” another molecular complex that is the bacterium’s first line of antiviral defense. Some phages deactivate the complex, which triggers the retron to unleash the membrane-destroying protein and kill the infected cell,

***

"the group realized that next to the genes coding for a retron in a Salmonella bacterium was a gene for a protein toxic to Salmonella. The team discovered the retron normally keeps the toxin under wraps, but activates it in the presence of phage proteins."

Comment: To repeat: Bacteria edit their DNA to self-destruct and save the colony. I would ask how did this developed? Did bacteria learn this on their own or did it happen by design?

An interesting book review:

https://inference-review.com/article/from-genes-to-genomes

"Genome Chaos is a book of no small ambition. Based on his experience in cancer cytogenetics, Henry Heng invites readers to rethink the role of the genome in determining the hereditary properties of cells and organisms. He distinguishes between gene-centric and genome-based views of heredity and argues that the physical organization of the genome incorporates a higher systems level of information beyond its genes or coding sequences. For Heng, genes are rather like a parts list capable of encoding proteins and RNA that can be assembled and used in many different ways to produce cells and organisms with quite distinct properties. In making his argument, Heng challenges a number of notions about the genotype–phenotype relationship. (my bold)

"According to Heng’s genome-based perspective, evolution can be broken down into two modes. Microevolutionary change operates within species much as Charles Darwin envisaged, by “numerous, successive, slight modifications.”1 Macroevolutionary change rapidly restructures the genome to establish a new architecture, leading to new species and new phenotypes without changing the basic gene content. The transition from microevolutionary to macroevolutionary change—the period Heng labels genome chaos—occurs when there is great stress on either somatic cells, as in cancer chemotherapy, or independent organisms, as in episodes of drastic ecological change and mass extinctions.

***

"In Heng’s concept, it is the genome system properties of novel chromosome organizations and not specific gene content that drives the major steps in the evolution of all but a few exceptional cancers.

"A chapter of Genome Chaos is devoted to applying these conclusions to organismal evolution. A similar model, Heng claims, fits the punctuated nature of the fossil record and cytological observations of chromosomal differences within groups of closely related species.4 Chimpanzee and hominid gene sequences match to within 98%, but they differ with respect to a chromosome fusion and several inversions. The result is that chimpanzees (2n = 48) have a karyotype with two more chromosomes than hominids (2n = 46).

***
"Heng’s idea that genome system information is critical in taxonomic divergence has some interesting implications, notably the counter-conventional notion that the normal evolutionary function of sexual reproduction is to suppress, rather than enhance, major phenotypic variation within species. The need for meiotic chromosome pairing in the formation of gametes at each generation prevents individuals carrying germline chromosome changes from producing progeny who can pass on those changes. (my bold)

"The most controversial aspect of Heng’s argument in Genome Chaos is the claim that specific gene-based changes play a minor role in the macroevolutionary process.

***

"At numerous points throughout Genome Chaos, Heng urges researchers to reorient their thinking about basic evolutionary processes. He argues persuasively for a shift from a gene-based to a genome-based approach, a transition he describes as moving from a one-dimensional to a four-dimensional view of genomic information and function.

***

"...there is no comprehensive theory that accounts for how a given genome architecture facilitates the expression of particular phenotypes using the parts list specified by its coding sequences.

***

"Despite our current relative ignorance, we can reasonably expect that patterns will be discerned in the whole genome sequence data that will provide greater mechanistic insight into how chromosome restructuring episodes occur, with important implications both for cancer therapy and evolutionary biology.

"The case Heng makes for thinking about genomes rather than just genes is strong and convincing. By alerting the genomics community to a new scientific frontier, Genome Chaos accomplishes two important and complementary goals. It clearly demonstrates that a great deal of fundamental evolutionary biology and genetics research still needs to be done before newly acquired genomics and genome-editing technologies can be used to maximum advantage.

Comment: No gene editing noted. Instead a positive discussion to discern the 3-D interrelationships of genes to each other and to gene transcription modifiers. Note the references to how information relates to the 3-D interrelationships (in my bolds). The 3-D interrelationships themselves may actually carry information in the specific arrangement of genome parts.