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important to set the conceptual stage, 
which was being constructed during the early 1960s. 
A seminal paper of this period was by Ehret (1960) 
and entitled “Organelle systems and biological 
organization”. Influenced by systems theory , cell 
biology , and the emerging field of molecular bio-
logy , Ehret imagined cells to be constructed of a 
series of levels of organization – from molecules to 
 macromolecular aggregates to organelles to enve-
lope systems (= cells). He concluded – 
 Within this reference frame of understanding, the cell 
ceases to occupy a central location as a fundamental unit 
of life. It appears, instead, as a special case among the 
single- and multiple-envelope systems that comprise all 
forms of life. (p. 122) 
 This perspective had a liberating effect for it 
demanded that we not constrain our view to the 
importance of cellular characters, but look “below” 
the cell at features that might be just as significant 
to an understanding of the common descent of 
protists. Ehret and McArdle (1974) then imagined 
the Paramecium cell to be constructed of levels, the 
simpler ones integrating to build more complex levels. 
In the context of the ciliate cortex, these levels 
can be imagined as macromolecule (i.e. tubulin ), 
 suborganelle or macromolecular aggregate (i.e., 
 microtubule ), unit organelle (i.e., kinetosome , 
 cilium , microtubular ribbon ), organellar complex 
(i.e., kinetid ), and organellar system (i.e., locomotory 
system or kinetome ) (Lynn, 1981; also see Chapter 
2 for definitions). 
 A number of scientists had imagined cells and 
organisms to be built in a series of increasingly com-
plex levels of organization and had concluded that 
this important property constrained morphological 
variation, especially at the lower levels of biological 
organization. In other words, if one constructs some-
thing of bricks of a certain shape that are assem-
bled in a precise sequence, changing the ultimate 
arrangement has less drastic consequences than 
changing the shape of each brick. Bronowski (1970) 
had termed this the principle of stratified stability : 
“the building up of stable configurations does have a 
direction, the more complex built on the next lower, 
which cannot be reversed in general” (pp. 242–243). 
Independently, Lynn (1976a, 1981) called it the 
 principle of structural conservatism : the conserva-
tion of structure through time is inversely related to 
the level of biological organization. Thus, if the cili-
ate cortex and infraciliature were conceived as being 
constructed of repeating and highly integrated units, 
then there should be strong selection on preserving 
this unit structure (i.e., the kinetid ) to construct the 
cortical system (Fig. 1.3). Lynn and Small (1981) 
then argued that this principle gave us an approach 
to examining the comparative ultrastructure of the 
ciliate cortex and to infer common descent: structur-
ally similar kinetids should be homologues, limited 
to vary by the “selective forces” of stratified stability 
or structural conservatism. 
 In the 21st century, this may all seem self-evident.
However, there was one major conceptual problem 
with it at the time – the idea of ‘ organic design ’. 
Pantin (1951, 1966) and Grimstone (1959) had 
argued that microtubules , basal bodies or kineto-
somes , and the cilium were of such low complex-
ity that they could conceivably have evolved many 
times, unlike “the more complex and improbable 
metazoan organs which, determined by a far more 
numerous set of genes, appear to have arisen only 
once” (p. 277, Grimstone, 1959), and “it seems 
highly improbable that the unique assemblage of 
genetic factors which ensures the development of a 
 pentadactyl limb would ever be selected independ-
ently on two separate occasions” (p. 144, Pantin, 
1951). Thus, from this view, similarities in kinetids 
would have arisen by a non-adaptive process, rather 
than as a result of natural selection . Instead, these 
structures were determined by thermodynamics 
and “by physical and spatial properties of matter 
rather than by functional needs … of a transcen-
dental rather than adaptive origin” (p. 4, Pantin, 
1966). Yet, a little over a decade later, the flagellum 
of Chlamydomonas was reported to have at least 
170 polypeptides (Huang, Piperno, & Luck, 1979) 
and the cilium of Paramecium to have at least 125 
polypeptides (Adoutte et al., 1980), and this picture 
has become even more complex in the intervening 
decades. Thus, these organelles are clearly not 
simple, but indeed are extremely highly ordered 
complexes. It is therefore reasonable to conclude 
that their structural complexity is as much a result 
of natural selection as the organs of metazoa or the 
 pentadactyl limb . 
 With this conceptual perspective, Small and 
Lynn (1981) applied structural conservatism to 
make sense of the diversity of ciliate kinetids . They 
also relied on the notion that somatic structures are 
more highly conserved than oral ones (Gerassimova 
& Seravin, 1976; Lynn, 1976a, 1976c). One reason 
lies in the development of somatic and oral regions. 
The duplication of somatic kinetids in ciliates 
usually occurs closely adjacent to pre-existing 
kinetids, called cytotaxis or structural guidance 
(Frankel, 1991), and this may place severe con-
straints on the variability of the components. On 
the other hand, the organellar complexes of the oral 
region are not as intimately linked to pre-existing 
organelles and also, as more complex structures, 
there is a higher potential for change, at least in 
size and shape. Another reason that oral structures 
Fig. 1.3. The hierarchical organization of the ciliate cortex. The fundamental component of the cortex is the dikinetid, 
an organellar complex here composed of seven unit organelles, which are the two kinetosomes, two cilia (not shown), 
transverse (T) and postciliary (Pc) microtubular ribbons, and the kinetodesmal fibril (Kd). In a patch of cortex, the 
microtubular ribbons and kinetodesmal fibrils of adjacent kinetids are closely interrelated. The interrelated kinetids 
comprise the components of the next higher level in the hierarchy, the organellar system called the kinetome. Two 
major cortical organellar systems are the somatic region or kinetome and the oral region, functioning in locomotion 
and feeding, respectively. (from Lynn & Small, 1981.)
1.3 The Age of Ultrastructure (1970–1990) 7
8 1. Introduction and Progress in the Last Half Century
are more variable is that even slight structural 
alterations, if they resulted in increased capture 
and ingestion rates, would directly affect growth 
and reproductive rates, enhancing relative fitness and 
fixation of new variants. Thus, Lynn (1979b) 
concluded “somatic over oral”, meaning that 
somatic structures have in general a “deeper” 
phylogenetic signal than oral ones. 
 The consistent application of these principles 
(i.e., structural conservatism and somatic over oral) 
resulted in the proposal of eight major classes by 
Small and Lynn (1981) (Table 1.3). During the Age 
of Ultrastructure , the classification was refined by 
Small and Lynn (1985) and Lynn and Small (1990), 
the latter revision beginning to consider the early 
results of molecular genetic research. Overall, 
 somatic kinetids were used to identify mono-
phyletic clades, called classes, and this approach 
often placed genera that had been assigned to dif-
ferent, older higher taxa together. The colpodeans 
provide a most dramatic example: Sorogena was 
a gymnostome ; Colpoda was a vestibuliferan ; 
Cyrtolophosis was a hymenostome ; and Bursaria
was a heterotrich (Fig. 1.4)! 
 Small and Lynn (1981, 1985) divided the phylum 
into three subphyla, based on ultrastructural features 
of the cortex: for the somatic cortex – the overlap-
ping postciliary microtubular ribbons – for the 
Subphylum Postciliodesmatophora (Gerassimova