One decade is hardly a ripple in respect to biological evolutionary time, but can be significant in regard to the evolution of concepts based on new experimental discoveries. Despite the popularity of the simple idea that a single macromolecule, namely 16S rRNA, is a repository of the evolutionary history of bacteria and can serve as a "Rosetta Stone" for classification, I and several others considered this notion to be an egregious oversimplification. Moreover, changing the names of well-characterized bacterial species on the basis of 16S RNA sequence differences struck me as a particularly objectionable practice. These considerations led me to publish two satires (Gest, 1999/2000) which in the fullness of time can be seen to have struck the bull's eyes of their targets. An editorial sidebar in the year 2000 satire noted:

"The following satire is based on Howard Gest's view that the evolutionary history of bacteria was more complex than commonly supposed and cannot be traced with accuracy using 16SrRNA sequences as the sole criterion. Indeed, during recent years, a number of reports summarizing new research findings, including evidence suggesting the widespread occurrence of lateral gene transfer, cast doubt on the validity of bacterial evolutionary phylogeny based on rRNA trees. Gest emphasizes that rRNA sequences will probably prove to be useful eventually for identifying certain kinds of taxonomic relationships, but will not serve to provide an unambiguous evolutionary phylogeny of bacteria. Accordingly, he argues that changing the names of numerous well-known genera and species on the basis of rRNA sequences is premature and counterproductive to formulation of a logical, scientific scheme of bacterial relationships and classification." "Gest's Postulates" (1999) relate to actual free-living bacteria, and refer to "virtual bacteria" reported to exist in natural sources as indicated by detection of 16S rRNA sequences ("virtuals" are sometimes referred to by the cognoscenti as "computer bacteroids"). The "Postulates" prescribe some penalties for investigators who publish only 16s rRNA sequences and fail to isolate corresponding live organisms within a reasonable length of time.

The satires referred to have now been reproduced on the Internet via the agency of the Scholarworks Program of Indiana University. They can be accessed at: https://scholarworks.iu.edu/dspace/handle/2022/3848.

To appreciate the naivete of the 16S RNA "Rosetta Stone" hypothesis in the light of new developments, I recommend that readers of Microbe study an important recent issue (12 August 2009) of the Philosophical Transactions of the Royal Society (Biological Sciences). The theme of the issue is "The network of life: genome beginnings and evolution." A paper by Doolittle and a contribution from Lake's laboratory are of special significance. Conventional "trees-of-life" representations for evolution of bacterial species have clearly become very dubious because of "mobile elements that can shuttle genetic material within and between related sets of organisms" (see Ragan, McInerney, and Lake, p. 2169-2175).

The new views elaborated in the Royal Society theme issue make it clear that changing the names of bacterial genera and species based on 16S RNA differences was a retrograde development. The important reasons underlying the great significance which attaches to a stable and generally accepted nomenclature of bacterial genera and species are discussed in my 2003 essay "Names of bacteria and their evolutionary relationships" (Microbiology 149:1956-1958, 2003).

It is obvious that we can expect much more knowledge to come from research on actual bacteria that grow, exchange genes, multiply, and cause chemical changes in the biosphere, than from speculations based on disembodied partial16S RNA sequences of unknown origin that float as phantoms in the memories of computers.

Howard Gest
Indiana University, Bloomington
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