A blogger named "Efrique" left a rather critical comment about my "D.I. Youtube Propaganda 2" entry. Here is some of what he said:
DNA evidence does show that thylacines are closely related to other marsupials, but that just supports the evidence that was already there. There's plenty of evidence that thylacines are also quite different from wolves (the pouch is a dead giveaway, for starters, but there are plenty of features that are like other marsupials and unlike wolves).
Efrique, most folks who use Evolutionary Theory would suggest that the Australian "Wolf" (D.I.'s lingo, not mine) would be more closely related to its fellow marsupials than to Actual Placental Wolves. Discovery Institute's point was that homology could not always be used as evidence of common ancestry. My point is that this is caused by convergent evolution, and convergent evolution can be easily uncovered with genetic analysis. I stated this in my first paragraph and gave a reference to Dawkins' The Blind Watchmaker. Sure enough, when we analyze mitochondrial DNA of the Australian "Wolf" it turns out to be more closely related to its fellow marsupials.
I want to address another reader's comment as well:
"Homology is defined by common ancestry. If structures really are homologous, that means they are derived from an common ancestral structure."
Much of the time you could define homology by common ancestry. For instance, have you ever seen the diagram comparing the bone structures of various creatures? A lot of these examples could be backed up with fossil evidence showing that they are descended from a single ancestral structure.
However, homology is often used to mean similarity. Kenneth Miller has written an article about the bacterial flagellum, and he names the Type Three Secretory System as homologous to it. This clearly means that the two structures are merely similar to one another, since their isn't (as far as I know) any fossil evidence that the two are related!
Similarity can be useful when trying to pinpoint common ancestry. Now, the reason that homology at a biochemical or genetic level is useful is because, basically, two populations are not likely to evolve the same structure the same way. At the biochemical/genetic level, there are many ways to build the same thing. For instance, over half of the genes in a banana do the same thing as the genes in a human being, but the genes are not the same. For another example, their is genetic drift. Letters in our genetic code can be substituted and they still work just fine. Clearly, there is more than one way to build a structure at the genetic and/or biochemical level. This tells us that two populations will most likely be distinct genetically and biochemically when undergoing convergent evolution. Sure enough, this prediction holds true with Placental and Marsupial Mammals, with the Banana and the Human, with the whale and the fish, and so on.