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MICROBIAL DARK MATTER. “Now, metagenomic tools are forcing a recognition that there are no completely objective individuals, no unique lineages, and no one true tree. The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

“CLASSICAL BIOLOGY asserts that individual organisms and species are fundamental units of ecology, evolution, and biodiversity, composing an evolutionary history of objectively real, lineage-defined groups in a single-rooted tree of life.” 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

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

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

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

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

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

MACROEVOLUTION. “Darwin's finches, which show such dramatic change on short time-scales, continue to appear much as they did millions of years ago. Macroevolution may thus require progressive change in the environment that takes evolution consistently in one direction (such as increased body size). It is important to note, however, that this may sometimes be a gradual process, interspersed with many temporary reversals of direction.” https://lnkd.in/dAmAVYa View in LinkedIn

ONLY A CHINK OF REALITY. “These discoveries are showing that the full biosphere is substantially more complex than previously conceived and that a conception of nature based only on the biology of multicellular eukaryotes (MCEs) is decidedly inadequate. Attempting to understand and describe the entire biosphere using concepts based only on the biology of MCEs is like trying to understand all vertebrates by studying only hummingbirds.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn