Back to Shapiro: reviews rethinking genome research (Evolution)

by David Turell , Wednesday, May 26, 2021, 23:04 (1060 days ago) @ David Turell

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.

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"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).

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"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.

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"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.

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"...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.

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"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.