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DOUBTFUL SPECIES UTILITY. “By comparison, current data suggest a 30 % overlap in gene content between humans and mice. That is, there may be more genetic similarity between a randomly selected human and a randomly selected mouse than there is between two bacterial cells of the same “species.” Clearly, a species concept that encompasses that much genetic variation is not compatible with the species concept as generally applied to multi-cellular eukaryotes.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

HERETICS FIRST. “Not surprisingly, Woese’s work was originally doubted, even ridiculed, by many biologists. One referred to him as “a crank, who was using a crazy technique to answer an impossible question”. Subsequent improvements in sequencing technology, however, allowed the confirmation of a three-domain biosphere, of which the two prokaryotic realms are essentially alien to classical biology. Now, the three-domain view is well established, even at the level of introductory textbooks.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

STRAINS VERSUS SPECIES. “This is a stunning amount of variation within one “species” of bacteria. (Strains in the genus Shigella are now regarded as E. coli variants that need reclassification). If only strains currently named E. coli are considered, the number of core gene families rises from 993 to 1472, a slight increase of 6 % to 9 % of the total pan-genome.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

TUMOR-LIKE GENOMES. “In many cases, a typical individual bacterial cell carries less than 50 % of the genes found in the species’ pan-genome—a level of genomic plasticity that in multi-cellular eukaryotes is only seen in highly unregulated tumors.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

CORE, FLEX AND PAN GENOME. “Early bacterial whole-genome sequencing efforts discovered that whenever a particular “species” was re-sequenced, new genes were found that had not been detected earlier—entirely new genes, not merely new alleles. This led to the concepts of the bacterial core-genome, the set of genes found in all members of a particular “species”, and the flex-genome, the set of genes found in some, but not all members of the “species”. Together these make up the species’ pan-genome.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

PAN GENOME. “Although the enforced stability of genomic content is ubiquitous among multi-cellular eukaryotes, the opposite is proving to be the case among prokaryotes, which exhibit remarkable and adaptive plasticity of genomic content.” https://lnkd.in/ewnQ9Vg View in LinkedIn

UNPROTECTED GENOMES. “The enforced stability of genomic content in multi-cellular eukaryotes is necessary for maintaining a non-pathological multi-cellular, differentiated condition. Curiously, this critical attribute is not on any of the lists of essential eukaryotic pre-adaptations necessary for the evolution of multi-cellularity. This absence may be a result of the pervasive multi-cellular eukaryotes-centricity of much classical biology thinking.” https://lnkd.in/ewnQ9Vg View in LinkedIn

MALFUNCTIONS AND DISEASE. “Among multi-cellular eukaryotes, when genetic or genomic changes produce significant adverse effect, many of the resulting problems are produced by perturbations in development, or disruptions of a complicated bit of physiology necessary to accomplish some critical function in differentiated somatic tissue.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

MENDELIAN GENE FLOW. “Following the rediscovery of Mendel’s work, the study of these processes came to be known as transmission genetics, thereby linguistically capturing the implicit notion that, barring rare mutation, a new individual acquires new genetic material only through the active transmission of that material across generations (of individuals) via the cellular processes of meiosis, gametogenesis, and fertilization.” https://lnkd.in/ewnQ9Vg View in LinkedIn

VERTICAL INHERITANCE. “In classical multi-cellular eukaryotes biology, organisms acquire new hereditary material precisely once, when genetic material is transmitted from parent to progeny during the formation of the zygote. This produces a genetically novel cell that will form the clonal basis for the new Weismannian individual to come.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn