Year: 2022

OLD HAT. “Traditional models for prokaryotic evolution based on clonality and periodic selection are inadequate to describe the process of prokaryotic evolution at the species level and that treelike phylogenies are inadequate to represent the pattern of prokaryotic evolution at any level.” https://lnkd.in/djKBnru View in LinkedIn

TWO UNIVERSES. “We could resolve the “species problem” (perhaps by dismissing it), appreciate the real differences in tempo and mode between prokaryote and “higher” eukaryote evolution, let unraveling of the complex histories of genes and genomes supersede the quest for one true “organismal phylogeny,” develop new models for diversification of prokaryotic niches and definitions of adaptedness, and, at the level of the gene, propose new scenarios for evolution of novel function.” https://lnkd.in/djKBnru View in LinkedIn

THE PROKARYOTIC WORLD. “Embracing gene transfer promises a broad and radical revision of the prokaryotic evolutionary paradigm. This will come from a fusion of population genetics, molecular genetics, epidemiological and environmental genomics, microbial ecology, and molecular phylogeny, fields that have developed mostly in isolation from each other.” https://lnkd.in/djKBnru View in LinkedIn

ADDING NOT REPLACING “Although we have presented the new view as if it were antithetical to traditional understandings of prokaryotic evolution, in the long run we endorse a synthesis that will acknowledge gene exchange and clonality, weblike and treelike behavior, and adaptation and the evolution of new function by many modes.” https://lnkd.in/djKBnru View in LinkedIn

THIS ENDS this important paper that repositions the evolution of prokaryotes versus eukaryotes in the light of promiscuous gene transfer. The biological world view was overly vertebrate-centric, and generalized nature from this perspective. In fact, vertebrates are a very minor group compared to the microbial world. This important contribution has adjusted that view accordingly. When combined with the curious mechanisms from the plant world, we have a less pear-shaped view of the natural world. View in LinkedIn

THIS NEW SECTION is a treatment of an extraordinarily important paper on biological dark matter and an emerging new paradigm in biology. I will cite extensively from this paper on biological dark matter by RJ Robbins, L Krishtalka, and JC Wooley. It is a suitable companion to the previous paper on horizontal gene transfer. https://lnkd.in/ewnQ9Vg View in LinkedIn

TWO SCALES OF BEING. “Biology, like physics, has a fundamental duality—the classical macroscale eukaryotic realm vs. the quantum microscale microbial realm—with the two realms differing profoundly, and counter-intuitively, from one another. Just as classical physics is emergent from and cannot explain the microscale realm of quantum physics, so classical biology is emergent from and cannot explain the microscale realm of prokaryotic life.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

TWO SETS OF RULES. “The two realms occupy fundamentally different mega-niches: eukaryotes interact primarily mechanically with the environment, prokaryotes primarily physiologically. Further, many foundational tenets of classical biology simply do not apply to prokaryotic biology.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

WE IGNORE HALF OF NATURE. “Classical biology describes the familiar, macroscale realm of multi-cellular eukaryotic organisms, which constitute a highly derived and constrained evolutionary subset of the biosphere, unrepresentative of the vast, mostly unseen, microbial world of prokaryotic life that comprises at least half of the planet’s biomass and most of its genetic diversity.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

CLASSICAL GENETICS “held that genes, arranged on chromosomes like beads on a string, were the fundamental units of mutation, recombination, and heredity. Then, molecular analysis showed that there were no fundamental units, no beads, no string.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn