Quotations from the "Universal Common Descent" Section

Notice the identical placement of the first ellipsis. Note also the unmarked change in case of "Scientists", which means either Wiester misquoted the Framework, EE misquoted Wiester, or both. There is a long history of antievolution advocates playing "telephone" with quotes and arguments.

The quotation appears not to be the only thing borrowed from Wiester; the following conceptual summation appears to be the thrust of EE as well:

While the California Framework contains some excellent statements of what science is and how it should be taught, it treats evolution as exempt from the very principles of science it so vigorously espouses. This paper presents three examples of the Framework departing from its stated rules of science to treat evolution in a non-scientific manner. The examples chosen are: 1. Lack of definition and consistency in use of terms; 2. Failure to discuss both similarities and differences when comparing evolution to other branches of science; and 3. Failure to present evolutionary science as open to challenge and free of dogmatism.

It seems ironic that the EE authors would chose to highlight a quote that aims criticism at those who misunderstand and misrepresent natural selection.

"The recognition of a simple developmental mechanism, namely an epithelial-mesenchymal interaction, at the initiation of carapace development provides a basis for hypotheses about the rapid evolution of this body plan (Burke 1989b)."

Burke, A. C. 1989b. Development of the turtle carapace: implications for
the evolution of a novel bauplan. J. Morphol. 199: 363–378.

Note also that the authors hypothesize which proteins are involved, which inductive relationships between tissues are involved, etc.

The quote itself comes from the concluding paragraph of the paper.

"The turtle shell represents a classic evolutionary problem: the appearance of a major structural adaptation. The place of turtles amongst the other amniote groups is a classic question in systematics, due to the "instantaneous" appearance of this evolutionary novelty. The fossil record may yet provide a morphological missing link between Proganochelys and the generalized tetrapod body plan. In the meantime, the application of developmental studies to this evolutionary puzzle may help resolve these questions as to the ontogeny and phylogeny of the ancient order of Chelonia."

Notice that the full context has no hint of the "made even more difficult" concept stated by the EE authors.

Then, the context of the two quotes from Cebra-Thomas et al. 2005:

"This reptile [Proganochelys] had the characteristic derived trunk morphology now associated with turtles. Thus, the distinctive morphology of the turtle appears to have arisen suddenly. We can propose a hypothesis that may explain at least part of how this might happen. The key innovation is to getting the ribs into the dermis. Once there, variation in the population might enable some individuals to use this heterotopic placement of ribs to form a shell. If they could form a positive feedback loop between the rib and the CR (e.g., through Fgf10 and Fgf8), they could co-ordinate rib and carapace growth. When the ribs undergo normal endochodral ossification, the BMPs would induce the costal bones that form the plate of the carapace. (This may involve overpowering natural inhibitors of BMPs that are secreted by the dermis.) This mechanism, wherein the displacement of a tissue allows it to induce structures at new locations, has been proposed by Brylski and Hall (’88) to account for the rapid emergence of the fur-lined cheek pouches of pocket gophers. The compatibility of our findings with those of the turtle fossil record has been noted by paleontologists (Rieppel, ’01)."

and

"These observations indicate that the ribs act as initiation centers for the dermal ossification of costal bones. The ossifying regions of the dermis extend towards one another to eventually fuse. The data reported in the present report confirm and extend these observations and permit us to frame a hypothesis to explain the rapid origin of the turtle carapace."

[...]

The fossil record provides excellent evidence for this rapid diversification in floral form during the earliest phases of recorded flowering plant history [5]. Only 10–12 million years elapsed between the first fossil records (not, vert, similar130 Mya) and clear documentation of all of the major lines of flowering plants 1 and 6. This diversification of angiosperms occurred during a period (the Aptian, 125–112 Mya; Figure 1) when their pollen and megafossils were rare components of terrestrial floras and species diversity was low 1 and 6. Angiosperm fossils show a dramatic increase in diversity between the Albian (112–99.6 Mya) and the Cenomanian (99.6–93.5 Mya) at a global scale 7, 8, 9 and 10 (Figure 1).

(Source)

"ON THE SUDDEN APPEARANCE OF GROUPS OF ALLIED SPECIES IN THE LOWEST KNOWN FOSSILIFEROUS STRATA.

There is another and allied difficulty, which is much more serious. I allude to the manner in which species belonging to several of the main divisions of the animal kingdom suddenly appear in the lowest known fossiliferous rocks. Most of the arguments which have convinced me that all the existing species of the same group are descended from a single progenitor, apply with equal force to the earliest known species. For instance, it cannot be doubted that all the Cambrian and Silurian trilobites are descended from some one crustacean, which must have lived long before the Cambrian age, and which probably differed greatly from any known animal. Some of the most ancient animals, as the Nautilus, Lingula, etc., do not differ much from living species; and it cannot on our theory be supposed, that these old species were the progenitors of all the species belonging to the same groups which have subsequently appeared, for they are not in any degree intermediate in character.

Consequently, if the theory be true, it is indisputable that before the lowest Cambrian stratum was deposited long periods elapsed, as long as, or probably far longer than, the whole interval from the Cambrian age to the present day; and that during these vast periods the world swarmed with living creatures. Here we encounter a formidable objection; for it seems doubtful whether the earth, in a fit state for the habitation of living creatures, has lasted long enough. Sir W. Thompson concludes that the consolidation of the crust can hardly have occurred less than twenty or more than four hundred million years ago, but probably not less than ninety-eight or more than two hundred million years. These very wide limits show how doubtful the data are; and other elements may have hereafter to be introduced into the problem. Mr. Croll estimates that about sixty million years have elapsed since the Cambrian period, but this, judging from the small amount of organic change since the commencement of the Glacial epoch, appears a very short time for the many and great mutations of life, which have certainly occurred since the Cambrian formation; and the previous one hundred and forty million years can hardly be considered as sufficient for the development of the varied forms of life which already existed during the Cambrian period. It is, however, probable, as Sir William Thompson insists, that the world at a very early period was subjected to more rapid and violent changes in its physical conditions than those now occurring; and such changes would have tended to induce changes at a corresponding rate in the organisms which then existed.

To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer. Several eminent geologists, with Sir R. Murchison at their head, were until recently convinced that we beheld in the organic remains of the lowest Silurian stratum the first dawn of life. Other highly competent judges, as Lyell and E. Forbes, have disputed this conclusion. We should not forget that only a small portion of the world is known with accuracy. Not very long ago M. Barrande added another and lower stage, abounding with new and peculiar species, beneath the then known Silurian system; and now, still lower down in the Lower Cambrian formation, Mr Hicks has found South Wales beds rich in trilobites, and containing various molluscs and annelids. The presence of phosphatic nodules and bituminous matter, even in some of the lowest azotic rocks, probably indicates life at these periods; and the existence of the Eozoon in the Laurentian formation of Canada is generally admitted. There are three great series of strata beneath the Silurian system in Canada, in the lowest of which the Eozoon is found. Sir W. Logan states that their "united thickness may possibly far surpass that of all the succeeding rocks, from the base of the palaeozoic series to the present time. We are thus carried back to a period so remote, that the appearance of the so-called primordial fauna (of Barrande) may by some be considered as a comparatively modern event." The Eozoon belongs to the most lowly organised of all classes of animals, but is highly organised for its class; it existed in countless numbers, and, as Dr. Dawson has remarked, certainly preyed on other minute organic beings, which must have lived in great numbers. Thus the words, which I wrote in 1859, about the existence of living beings long before the Cambrian period, and which are almost the same with those since used by Sir W. Logan, have proved true. Nevertheless, the difficulty of assigning any good reason for the absence of vast piles of strata rich in fossils beneath the Cambrian system is very great. It does not seem probable that the most ancient beds have been quite worn away by denudation, or that their fossils have been wholly obliterated by metamorphic action, for if this had been the case we should have found only small remnants of the formations next succeeding them in age, and these would always have existed in a partially metamorphosed condition. But the descriptions which we possess of the Silurian deposits over immense territories in Russia and in North America, do not support the view that the older a formation is the more invariably it has suffered extreme denudation and metamorphism.

The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained. To show that it may hereafter receive some explanation, I will give the following hypothesis. From the nature of the organic remains which do not appear to have inhabited profound depths, in the several formations of Europe and of the United States; and from the amount of sediment, miles in thickness, of which the formations are composed, we may infer that from first to last large islands or tracts of land, whence the sediment was derived, occurred in the neighbourhood of the now existing continents of Europe and North America. This same view has since been maintained by Agassiz and others. But we do not know what was the state of things in the intervals between the several successive formations; whether Europe and the United States during these intervals existed as dry land, or as a submarine surface near land, on which sediment was not deposited, or as the bed of an open and unfathomable sea."

"What appeared to be a nice progression when relatively few data were available now appears to be much more complex and much less gradualistic. So Darwin's problem has not been alleviated in the last 120 years and we still have a record which does show change but one which can hardly be look upon as the most reasonable consequence of natural selection."

The way this is quoted made me think that I would find it in the last page or two of the article. So I looked there first. It turns out this comes in the second paragraph of the article. Basically, EE has taken a rhetorical question posed to help introduce the purpose of the study and turned it into a conclusion. One additional point needs to be made. This paper studies the morphospace of four groups of marine invertebrates: trilobites, blastozoans, blastoids, and crinoids, yet EE tries to use this as a statement about the entire fossil record - a questionable extrapolation at best.

It should be noted that this comes in a section defending species selection.