These models argue some version of the idea that the cilium evolved from a symbiotic[?] spirochete that attached to a primitive eukaryote or archaebacterium. The modern version of the hypothesis was first proposed by Lynn Margulis as Sagan (1967) (Margulis was the first wife of the late Carl Sagan). The hypothesis, though very well publicized, was never widely accepted by the experts, in contrast to Margulis' successful arguments for the symbiotic origin of mitochondria and chloroplasts.
The only real point in favor of the symbiotic hypothesis is that there apparently actually are eukaryotes that use symbiotic spirochetes as their motility organelles (for example, inside termite guts). While this is a flabbergasting example of co-option and the creativity and flexibility of biological systems, none of the proposed homologies that have been reported between cilia and spirochetes have stood up to further scrutiny. The homology of tubulin[?] to the bacterial replication/cytoskeletal protein FtsZ would seem to clinch the case against Margulis, as FtsZ is apparently found native in archaebacteria, providing an endogenous ancestor to tubulin (as opposed to Margulis' hypothesis, that an archaebacterium acquired tubulin from a symbiotic spirochete).
At present the symbiotic hypothesis for the origin of cilia seems to be basically a pet idea of Margulis and a few of her associates. Margulis is, though, still strongly promoting and publishing a revised version of her hypothesis (Margulis' 1998 book Symbiotic planet: a new look at evolution[?] has some frank autobiographical comments about her stubborn support of the symbiotic hypothesis for the origin of the cilium).
The cilium developed from pre-existing components of the eukaryotic cytoskeleton (which has tubulin, dynein[?], and nexin[?], used for other functions of course) as an extension of the mitotic spindle apparatus. The connection can still be seen, first in the various early-branching single-celled eukaryotes that have a microtubule basal body[?], where microtubules on one end form a spindle-like cone around the nucleus, while microtubules on the other end point away from the cell and form the cilium. A further connection is that the centriole, involved somehow (scientists are unsure of the purpose of the centriole) in the formation of the mitotic spindle in many (but not all) eukaryotes, is homologous to the cilium, and in many cases is the basal body from which the cilium grows.
An obvious intermediate stage between spindle and cilium would be a non-swimming appendage made of microtubules with a selectable function like increasing surface area, helping the protozoan to remain suspended in water, increasing the chances of bumping into bacteria to eat, or serving as a stalk attaching the cell to a solid substrate. One can't argue that such a non-swimming appendage is merely convenient imagination or unlikely to be selectable, as modern protists with analogous non-swimming microtubular appendages do exist and find them perfectly useful, the axopodia[?] of phylum Actinopoda[?] on genus Raphidiophrys[?] being an oft-cited example.
Regarding the origin of the individual protein components, an interesting paper on the evolution of dyneins (Gibbons, 1995; see also Asai and Koonce, 2001) shows that the more complex protein family of cilial dynein has an obvious ancestor in a simpler cytoplasmic dynein (which itself appears to be a result of a four-fold duplication of a smaller motif). Recently, long-standing suspicions that tubulin was homologous to FtsZ (based on very weak sequence similarity and some behavioral similarities), were impressively confirmed in 1998 by the independent resolution of the 3-dimensional structures of the two proteins.
An obvious approach to the evolutiuon of the bacterial flagellum is suggested by the fact that a subset of flagellar components can serve a function as a Type III transport system[?]. Admittedly, all currently known nonflagellar Type III transport systems are for injecting toxins into eukaryotic cells, and are therefore presumably descended from the flagellum, which is likely older than eukaryotes. However, the Type III transport system still proves that the flagellum did not have to come about all at once, as a subset of components has a selectable function. That all known nonflagellar Type III transport systems are disease mechanisms is not shocking as the Type III secretion system was only discovered in 1994 and as our scientific study of eubacteria is significantly biased towards disease-causing organisms for obvious good reasons. We have another rather spectacular case of co-option, where a motility organelle has evolved into a "complex weapon for close combat."
The recently elucidated archaeal flagellum is analogous, not homologous, to the bacterial one. In addition to no sequence similarity being detected between the genes of the two systems, the archaeal flagellum appears to grow at the base rather than the tip, and is about 15 nanometers (nm) in diameter rather than 20. Sequence comparison indicates that the archaeal flagellum is homologous to Type IV pili[?] (pili are nonmotile filamentous structures outside the cell) and better yet, to twitching motility systems, which allow the cell to crawl along a surface. These systems are in turn homologous to the Type II transport system[?], which is the conclusion of the general secretory pathway.
In recent years, the Discovery Institute (DI), a conservative thinktank based in Seattle, has spearheaded the Intelligent Design (ID) movement. In the main, this movement advocates the "Renewal of Science and Culture" (the DI has a Center with exactly this title) through the assertion of intelligent design as an explanatory force in biology.
Biochemist Michael Behe, of the Discovery Institute, wrote a 1996 book entitled Darwin's Black Box[?], in which he claimed that "irreducibly complex[?]" (IC) systems, systems which require several parts to function, were either impossible (or very unlikely) to reach via natural evolutionary mechanisms, and therefore must have been designed by an intelligence. Behe's first two major example systems were the eukaryotic flagellum/cilium and the bacterial flagellum. Behe asserted that scientists had no idea how such structures evolved. This argument has been wildly popular among anti-evolutionists, who in particular have latched onto the bacterial flagellum as an icon of ID. For the Intelligent Design movement, the bacterial flagellum has now become the equivalent of the eye in 19th century debates.
However, as described above, there are plausible models for the incremental natural evolution of all known forms of flagellum. Testable outlines exist for the origin of each of the three motility systems, and avenues for further research are clear; for prokaryotes, these avenues include the study of secretion systems in free-living, nonvirulent prokaryotes. In eukaryotes, the mechanisms of both mitosis and cilial construction, including the key role of the centriole, need to be much better understood. A detailed survey of the various nonmotile appendages found in eukaryotes is also necessary. Finally, the study of the origin of all of these systems would benefit greatly from a resolution of the questions surrounding deep phylogeny -- what are the most deeply branching organisms in each domain, and what are the interrelationships between the domains?