phological system ignores symbioses. But bacterial consortia and protist endosymbioses irreducibly underlie evolutionary transitions from prokaryotes to eukaryotes. Although some prokaryotes [certain Gram-positive bacteria (Gupta, 1998a)] are intermediate between eubacteria and archaebacteria, no organisms intermediate between prokaryotes and eukaryotes exist. These facts render the 16S rRNA and other nonmorphological taxonomies of Woese and others inadequate. Only all-inclusive taxonomy, based on the work of thousands of investigators over more than 200 years on live organisms (Margulis and Schwartz, 1998), suffices for detailed evolutionary reconstruction (Mayr, 1998).
When Woese (1998) insists “there are actually three, not two, primary phylogenetic groupings of organisms on this planet” and claims that they, the “Archaebacteria” (or, in his term that tries to deny their bacterial nature, the “Archaea”) and the “Eubacteria” are “each no more like the other than they are like eukaryotes,” he denies intracellular motility, including that of the mitotic nucleus. He minimizes these and other cell biological data, sexual life histories including cyclical cell fusion, fossil record correlation (Margulis, 1996), and protein-based molecular comparisons (Gupta, 1998a, b). The tacit, uninformed assumption of Woese and other molecular biologists that all heredity resides in nuclear genes is patently contradicted by embryological, cytological, and cytoplasmic heredity literature (Sapp, 1999). The tubulin-actin motility systems of feeding and sexual cell fusion facilitate frequent viable incorporation of heterologous nucleic acid. Many eukaryotes, but no prokaryotes, regularly ingest entire cells, including, of course, their genomes, in a single phagocytotic event. This invalidates any single measure alone, including ribosomal RNA gene sequences, to represent the evolutionary history of a lineage.
As chimeras, eukaryotes that evolved by integration of more than a single prokaryotic genome (Gupta, 1998b) differ qualitatively from prokaryotes. Because prokaryotes are not directly comparable to symbiotically generated eukaryotes, we must reject Woese's three-domain interpretation. Yet our model greatly appreciates his archaebacterial-eubacterial distinction: the very first anaerobic eukaryotes derived from both of these prokaryotic lineages. The enzymes of protein synthesis in eukaryotes come primarily from archaebacteria whereas in the motility system (microtubules and their organizing centers), many soluble heat-shock and other proteins originated from eubacteria (Margulis, 1996). Here we apply Gupta's idea (from protein sequences) (1998a) to comparative protist data (Dolan et al., 2000) to show how two kinds of prokaryotes made the first chimeric eukaryote. We reconstruct the fusion event that produced the nucleus.