Why are Australian marsupials more closely related?

Dr. Nathaniel T. Jeanson does a great job laying out the differences between evolutionary hypotheses and creation hypotheses in his new article New Genetic Findings Tackle the Toughest Evolutionary Questions.  Evolutionary theory predicts that Australian marsupials should be more closely related to each other than placentals even though they have similar adaptations.  The fossil record shows marsupials migrating from North America to South America to Antarctica, and finally settling in Australia which became a genetically isolated continent.

Just like the fossil record and taxonomy predicted, genetics established that a marsupial mole is more closely related to a kangaroo than a European placental mole.   This seems like an open and shut case.  Three lines of evidence seem to demonstrate that the Theory of Evolution best explains Australian marsupial diversity.  

In his article, Jeason fields probably the second most common creationist apologetic to this conclusion.  "Perhaps wombats and kangaroos are similar at the protein level because the sequences that were compared between these two species play a role in marsupial physiology."  Jeason does a great job of explaining why this is not probably the case.  The proteins that are used for this genetics testing perform the same function in cells.  It would be useless to test a protein that could vary depending on the length of an animal's nose.  The ones with similar noses would appear more closely related.  

After explaining this, Jeason goes on to say that this is exactly his hypothesis.  First, he tried to model genetic variation over time and determined that under that model marsupials should appear more distantly related than closer.  Then he had the following insight.

This negative result was actually the first step toward discovering new insights into DNA function, and it turned the tables on the evolutionary argument. By eliminating the hypothesis of functionally neutral change over time, I was able to clearly identify the hole in modern molecular biology thinking. Though each protein has historically been thought to perform a single function inside the cell—like energy transformation—these negative results required a modification to this rule. Combined with preliminary data from the secular literature, these results suggest that each protein might perform several functions. For example, proteins involved in energy transformation in fish might also play a role in fin formation and underwater respiration. It’s as if a light switch were designed not only to control electricity but also to simultaneously support the ventilation system, maintain the foundation, and repair the roof.

Hypothesizing multi-functional proteins stretches the imagination and even seems to strain credulity. But the Master Designer has no such intelligence limitations, and He appears to have designed numerous proteins for multiple purposes.2

 He goes on to say that genetic relationships strongly correlate with taxonomic relationships.  According to him this provides another line of evidence.  So who has the better hypothesis?  The evolutionary hypothesis is held up by the fossil record, taxonomy, and genetics.  Plus it is predictive.  Jeason's hypothesis is held up by maybe taxonomy and does not explain the fossil record.  Also Jeason even admits that he at this junction has not found any other functions for these proteins.  He is just hypothesizing that they might be there.  Jeason hints that he may provide more evidence at a later date.

In a future issue we’ll tell you about a startling discovery we made when comparing genetic similarity among members of the same kind.

There was already over 80 comments, so I thought that I would respond here.  Someone in the comments is hailing this as the "right answer".  This same person says that the evolutionary explanation has been "refuted".  Let's be clear, Jeason has not demonstrated that he has the "right answer" and has not "refuted" the evolutionary explanation.  He has merely guessed that the proteins used in genetic testing have many other functions.  Until he manages to demonstrate these functions for these proteins he has not refuted anything.

Let's address one last comment.

This is not really anymore of a challenge than explaining similarities between a kangaroo and a kangaroo rat.  Convergent evolution produces similar traits through similar mechanisms.  In fact, the stinky striped possum is related closely to the Sugarglider.  As far as I can tell, unlike a skunk, striped possums stink, but do not spray.  Even Lightner places them into the "Gliding and striped possum kind".  So according to AiG, they are the same kind as a gliding marsupial.