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organization. The inference that the cenancestor was a rudimentary being gave aid and comfort to those of us who had always doubted that the profound differences in gene and genome structure between eukaryotic nuclei and prokaryotes were improvements or advancements wrought in the former after their emergence from among the latter. Eukaryotic nuclear genomes are after all very messy structures, with vast amounts of seemingly unnecessary "junk" DNA, difficult-to-rationalize complexities in mechanisms of transcription and mRNA modification and processing, and needless scattering of genes that often in prokaryotes would be neatly arranged into operons. It might be easiest to see nuclear genomes as in a primitive state of organization, which prokaryotes, by dint of vigorous selection for economy and efficiency ("streamlining"), have managed to outgrow.
Such a view gained credence from and lent credence to the still popular although increasingly untenable "introns early" hypothesis or "exon theory of genes" (Doolittle, 1991). In brief, the notion here is that (i) the first self-replicators were small RNAs, which became translatable into small peptides; (ii) such "minigenes" came together to form the (RNA) ancestors of modern genes, introns marking the sutures; and (iii) the subsequent history of introns has been one of loss: streamlining has removed them entirely from the genes of prokaryotes but has been less effective in eukaryotes for a variety of reasons (less intense selection, lack of transcription-translation coupling as a driving force).
The second surprise from the rRNA data is depicted in Figure 4. In addition to showing the profound division between eukaryotes (their nuclei) and prokaryotes just discussed, these data identified two deeply diverging groups, two "primary kingdoms" within the prokaryotes. Woese and Fox called the first, which included E. coli and other proteobacteria, Bacillus subtilis, mycoplasma, the cyanobacteria, and indeed all prokaryotes about which we had accumulated any extensive biochemical or molecular genetic information, the "eubacteria" (Woese and Fox, 1977). It was these organisms that Stanier and van Niel had in mind when defining the prokaryote-eukaryote dichotomy in the 1950s and 1960s and on which most of us still fashion our beliefs about prokaryotes. The second primary kingdom, the "archaebacteria ," included organisms that, although certainly not unknown to microbiologists, had been little studied at the cellular and molecular level, and whose inclusion within the prokaryotes therefore rested at that time on only the most basic of criteria (absence of a nucleus).
Archaebacteria are organisms of diverse morphology and radically different phenotypes, including the obligately anaerobic mesophilic methanogens, the aerobic and highly salt-dependent extreme halophiles, the amazing (because capable of growth up to at least 110°C)