Critique of evolutionary theory

for my Evolution capstone course, we are each supposed to bring in an argument against evolution which according to the professor will fall into 1 of 3 categories.  I know I've heard this before but I don't remember what they were.  Anyway, I'm sure most of the examples that students will bring in will be from intelligent design advocates associated with the religious right.  However, according to Kenneth Miller, in his book Only a theory, many of the creationist arguments that come from the religious right were actually borrowed from the extreme academic left.  Case in point, a recent book that Nature called a "misguided attack on evolution", What Darwin Got Wrong by philosopher Jerry Fodor is a great example.  His central argument is that natural selection cannot tell the difference between adaptive traits and freeloader traits.  I have addressed this topic at length in previous posts and I believe it is a pretty inane claim coming from such a supposedly sophisticated philosopher.  I don't believe that there is a meaningful distinction between a selfish freeloading trait and a truly adaptive trait (see my last few posts on this topic.)
Another claim he makes is that evolution is a historical process and as such isn't truly testable.  I like the way that Nick Lane addresses this claim in his book Life Ascending in his chapter on the evolution of the vertebrate eye.  He points out that when investigating the evolution of a particular phenotype, we actually can make specific predictions.  It doesn't matter that the process actually occurred long ago.  The fact is, we can make predictions about how some structure evolved and we can confirm or falsify these claims as the data comes in from genome sequences and other sources.  For example, we can make the claim that the vertebrate eye evolved by the process of natural selection.  The common ancestor of invertebrate chordates and vertebrates did have a retina.  In fact, the sea squirt today has a retina but no lens.  So, to confirm this claim we would need to show that the specialized lens proteins that exist in the vertebrate eye were already present in this common ancestor.  What is important to note here is that these kinds of claims are definitely falsifiable.  If these apparently specialized proteins just appeared out of thin air, that would be a huge blow to natural selection.  Potentially, if such a pattern emerged, then evolution by natural selection could be falsified.  But, according to Lane, this is not what was found.  He explains that vertebrate eye crystallin proteins were sequenced in the 80s and all of the proteins used to construct the vertebrate eye can be found in other parts of the body fulfilling other completely unrelated tasks.  In fact, in the sea squirt which does not have a lens over its retina, some of these crystallin proteins are performing other functions nearby in the brain. This example is not isolated of course and there are many different ways that predictions can be made about the path that natural selection has taken which can then be tested as data becomes available.  Fodor's criticism is indeed misguided.