Punctuated Equilibrium explains only small evolutionary changes.  This means that Punctuated Equilibrium does not necessarily solve the bigger problem regarding the sudden appearance of higher taxa.  This, I think, should give us pause, for it tends to limit the applicability of Punctuated Equilibrium to the level of the lower taxa, and leaves us still curious about the higher taxa.  Eldredge himself hinted at the matter, speaking about Phacops rana,

 

Hardly prodigious, this degree of anatomical retooling falls well within the bounds of "micro-evolution" – loosely speaking, the kind and degree of relatively minor change that marks the difference between closely related species.[1]

 

     The sudden appearance of new and completely unparalleled forms is the great problem.  Where are the missing links from archosaurs to pterosaurs?  From mustelids to sea lions?  From Ediacaran fauna to the Cambrian Explosion?  Punctuated Equilibrium seems to only address small changes from species to species – not from order to order, class to class, or phylum to phylum, and therefore does not answer the most pressing question about the origin of higher taxa.  The examples of Punctuated Equilibrium that can be garnered from the fossil record – the snails, the conodonts, the trilobites – all these are examples of minor species-level changes.  Although Punctuated Equilibrium is an excellent framework for explaining small evolutionary changes at the level of the lower taxa, it is not necessarily directly pertinent to the bigger problem regarding the sudden appearance of higher taxa.

     If the change brought from a punctuation event is small, as every indication testifies, then an accumulation of Punctuated Equilibrium cycles are required before a quantum leap from one phylum, class, or order can be realized.   And if these punctuations are most often separated by long periods of stasis, then would not the emergence of new phyla, classes, and orders be, as a matter of the big picture, gradual? 

     The accomplishments of multiple Punctuated Equilibrium cycles over time should therefore yield a gradual advancement not too different from what Darwin originally envisioned – a slow and steady progress, characterized by punctuations, yes, but each of such a small scale and with such infrequency as to be barely distinguishable from the "big picture" of phyletic gradualism.  The alternation between stasis and punctuation yields a very slow rate of progress over time.  It still falls short of explaining the sudden emergence of the higher taxa.  For even though a punctuation at the level of species or genus, such as Phacops was, could be quite speedy; however, the subsequent period of stasis is not speedy, and therefore if we wish to use the framework of Punctuated Equilibrium to explain, for example, how the trilobite's relatives became spiders, we must assume it happened over a long period of time, for a large number of punctuations followed by periods of stasis must have occurred to make it happen.

     Notice that both Darwinism and Punctuated Equilibrium yield an overall pattern of gradual evolution.  Even though Punctuated Equilibrium is characterized by fits and starts, it still necessarily takes a long time to accomplish significant evolutionary change at the magnitude of higher taxa.  That is because stasis separates punctuations, and because punctuations only accomplish small amounts of change.  Both traditional Darwinism and Punctuated Equilibrium contrast sharply with what the fossil record actually demands, for the fossil record frequently does not allow for the gradual evolution of higher taxa.

     However, if we postulate that several punctuations occurred in rapid succession, then perhaps we have an answer.  For if the punctuations were very numerous and followed each other in quick succession, occurring with greater frequency, and with shorter periods of stasis intervening between them, this might explain the sudden appearance of the higher taxa. We might call it "Punctuated Punctuationalism," in which the "Equilibrium" part of the process is skipped or greatly abbreviated.  If this model works in tandem with Punctuated Equilibrium, then rapid succession of punctuations is followed by long periods wherein punctuations are comparatively infrequent.  If this is the case, we might interpose a staircase upon the quantum leap, such that sudden leaps are explained by the summation of smaller punctuation events. 

     Yet for this to happen, one must consider the series of population bottlenecks that would follow each punctuation event, for the bottlenecks would rapidly deplete the gene pool and make species vulnerable to further selective pressures.  As with the case of the dark and light colored moths mentioned earlier, the more selection kills off the ill-adapted members of a species, the more that species looses its genetic variety.  The more it looses its variety, the less able it is to make further adaptations. 

     Moreover, every time a species is nearly killed off in a bottleneck, the population declines, which significantly increases the chances of inbreeding.  This brings harmful recessive alleles to the surface, where they kill their carriers and thus exterminate even more variety from the gene pool.  The mutations that enable evolution to occur get killed off before transposable elements can reshuffle them and make them useful.

     The question is, can the mechanics of population genetics support a series of population bottlenecks associated with several punctuations in rapid succession, and still retain enough genetic variety to effect a mega-evolutionary transition on the order of magnitude required to explain the sudden appearance of higher taxa? 

     Yet even if it were genetically plausible, we are still left with another question – what caused the series of punctuations in rapid succession to begin with?