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UNCHARACTERIZED LIFE. “Although non-eukaryotic microbes have long been known to be a ubiquitous and substantial component of the biosphere, the vast majority have been unculturable and thus completely resistant to study, rendering them effectively invisible. Until recently, a microscopic examination of any environment revealed a teeming, but largely mysterious prokaryotic world.” https://lnkd.in/ewnQ9Vg View in LinkedIn

HORIZONTAL ORTHOLOGS. “Most bacterial genome sequences reveal an abundance of paralogs which are often viewed as products of within-lineage duplication and divergence. However, many must be the result of the reuniting through horizontal gene transfer of orthologs that have diverged in separate lineages. Recognizing this encourages a rethinking of standard models of gene duplication and divergence.” https://lnkd.in/djKBnru View in LinkedIn

PARADIGM EVOLUTION. “When new discoveries challenge these fundamental concepts, the underlying data models must adapt or become obsolete. For example, the discovery that a gene could occur within another gene rendered obsolete any data model that was based on the fundamental assumption that genes are non-overlapping objects.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

TWO DIFFERENT KINGDOMS. “The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology. The unveiling of biological dark matter is allowing us to see, for the first time, the diversity of the entire biosphere and, to paraphrase Darwin, is providing a new view of life. Advancing and understanding that view will require major revisions to some of the most fundamental concepts and theories in biology.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

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