Does anyone here understand the implications of your final question, "Where have all the transitionals gone?" I have not read any proper treatment of the question, though it may exist in a post here, somewhere.
i've posted the answer to this question a number of times.
here it is again:
The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly** and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable.
- The Biological Big Bang model for the major transitions in evolution.htm
i think what you need to understand is, how can koonin make such a peer reviewed statement such as "no intermediate grades are detectable" in connection with animal phyla.
the "soft body" explanation doesn't cut it, because to make such a comment requires the assumption that all phyla had to arrive at once instead of descending from one another.
furthermore, the record MUST be complete enough for koonin to make such a statement.
goulds PE hypothesis falls into the same sort of thing, and it has been accepted as a valid evolutionary theory.
i also believe gould was talking about the exact same thing as koonin, the missing transitionals between animal phyla.
of course, you'll either ignore this post, or brush it aside like it was never presented, or resort right back to the mainstream explanation which koonin says (and gives references for) is unreliable.
koonin dismisses the mainstream explanation of "this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal" as unreliable and gives the following reference for doing so:
Welch JJ, Fontanillas E, Bromham L. Molecular dates for the "cambrian explosion": the influence of prior assumptions. Syst Biol. 2005;54:672–678. doi: 10.1080/10635150590947212.
** koonins original phrase was ready made, and the reviewers calls him on it, thus:
"In each major class of biological objects, the principal types emerge "ready-made", and intermediate grades cannot be identified." Ouch, that will be up on ID websites faster than one can bat an eye.
Here I do not really understand the concern. I changed "ready-made" to "abruptly", to avoid any ID allusions and added clarifications but, beyond that, there is little I can do because this is an important sentence that accurately and clearly portrays a crucial and, to the very best of my understanding, real feature of evolutionary transitions.
we aren't talking about one animal phyla, but ALL of them.
ALL of them appear in the record as "ready made".
for the life of me, i cannot understand how you can possibly say phyla descended from one another.