Sherwin starts this section with a quote from Douglas Futuyuma lauding the advancements in molecular biology in the light of evolution. He follows up with a quote from another paper stating that "Even with the appropriate genes, the molecular tree of life is difficult to interpret." (Erwin, et al, 1997).
It is true that because of the variable mutations rates in different genes, phylogeny can be difficult to interpret, but not impossible. However, this appears to be yet another case of a creationist quoting out of context. This quote was taken from section2 (of the online version- more in a moment) of the work in question. In keeping with the context, Erwin, et al state: "Choosing appropriate genes to study can be difficult, however, because different genes evolve at different rates. If the changes in sequence are too few, there is not enough difference among species to resolve the branching pattern on an evolutionary tree; too many changes overwhelm or "saturate" the DNA, so that any original similarities resulting from common ancestry are lost. Thus, for example, a gene that changes rapidly enough to be useful for examining the differences between two recently separated species of mice evolves too rapidly to be appropriate for examining the difference between the ancestor of a mouse, an earthworm and a fly, which lived over half a billion years ago. Even with the appropriate genes, the molecular tree of life is difficult to interpret. For one thing, many of the phyla appear to have branched within a relatively short period of time." (Erwin, et al, 1997, section 2).
Soon afterward they address the problems and the measures taken to overcome them. "More than 100 different numerical techniques have been developed to counter such problems, and whereas many of the divergences among phla remain uncertain, others seem to be well established by the new molecular analysis." (Erwin, et al, 1997, section 2).
Oddly, this is the only paper from which Sherwin quotes where there is no title given in the references. The title is "The Origin of Animal Body Plans", and it appeared in the March-April 1997 issue of American Scientist. As you may have guessed, not only does this paper have nothing to do with cetacean evolution, but the problems addressed in ascertaining molecular phylogenies are, as stated, different than those of determining relationships of more recently diverged taxa. Erwin, et al's paper has to do with the "Cambrian Explosion", an event that happened somewhere in the vicinity of 500 million years prior to the divergence of whales from their terrestrial relatives.
Fortunately for us all, the wonderful folks at American Scientist freely offer the full text of "The Origins of Animal Body Plans" at their website, and I cannot recommend it enough. It is a fantastic piece, full of great information (including the evolution of "new" structures), and readable enough for just about anyone to thoroughly enjoy (And misquote too!)
His next quote (Sherwin, 1998, ref. 13), seems to be more of a commentary on the Linnean classification system in light of molecular phylogenies and is a bit confusing.
In the paper in question (Janke, et al, 1994), there are indeed some surprises and some problems regarding the phylogenies of mammalian clades with the inclusion of a marsupial (opossum), including an indication for an earlier divergence time of rats and mice, and a closer relationship between primates and ungulates, than primates with rodents (which is in contrast to some phylogenetic work, but in agreement with others), and a further strengthening of the relationship between carnivores and ungulates (Ferungulata).
However, nowhere in the paper "cited" by Sherwin did the quote "These results reveal a large discordance between morphological and molecular measures of similarity. Rats and mice are classified in the same family, while cows and whales are classified in different orders. Perhaps molecular sequences are not necessarily giving an accurate picture of ancestry." appear.
This discrepancy leads one to ponder the possible scenarios. First, that Sherwin picked out this quote, for what it said and not what it meant, from a list of out of context quotes from "evolutionists" that are common in print and electronic media today, and that the reference to it was mistaken. Next, the quote could be entirely fabricated, which is unlikely in view of the former scenario. The wording of the quote suggests that it does exist in a publication somewhere, however, not in the one cited. Regardless, it seems clear that Sherwin very likely just did not read "The Marsupial Mitochondrial Genome and the Evolution of Placental Mammals", but also the paper from which the quote was taken.
I do not have Gatesy's paper (Sherwin, 1998, ref. 14) that Sherwin quoted from. However, in a later work by the same author (Gatesy, 1998), cited earlier, he also commented on the problem regarding "morphology vs. molecules", and the need for more evidence from the fossil record to better resolve the issue. This, of course, does not mean that whales did not evolve from ungulate ancestors, but questions from which of the other two groups of paraxonians they evolved from, mesonychians or artiodactyls.
Clearly, there are several aspects of the origin and evolution of cetaceans that are in need of more evidence and clarification, from the fossil record, and physiological and molecular research. However, impenetratable roadblocks exist only for those that insist upon blinding themselves to the ever-mounting evidence.
Sherwin's "Scientific Roadblocks to Whale Evolution" offers neither scientific evidence against the evolution of, or for the special creation of, the Cetacea. The use of quotes gleaned out of otherwise sound (and/or irrelevant) scientific literature for what they say and not what they mean is a desperate attempt at concealing the baselessness of creation "science". Furthermore, it is obvious that the entire article was concocted as an editorial on the objection to evolutionary biology in general, not on scientific grounds, but in the light of a very narrow religious viewpoint, and exhibits both shoddy research into, and a lack of knowledge of the subject at hand.
It is truly sad that so many people have and will come away after reading this article not just terribly misinformed, but without learning anything of the remarkable past, the natural history, or the physical adaptations of one of the most unique group of animals ever to have inhabited this planet, whales.
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