Like many others, I watched the recent debate between Bill Nye and Ken Ham with a queer mixture of awe and déjà vu. Who knew that 89 years later, we'd still be litigating the Scopes trial? As someone trained in the sciences, I find it horrifying that there are college-educated people in the U.S. (and around the world) who believe the earth is 6,000 years old; and yet at the same time, I have a certain amount of discomfort, myself, with evolutionary theory—not because it demeans the nobility of man or denies the Bible, or anything of that sort, but because it's such an incomplete and unsatisfying theory on purely scientific grounds. (Many physicists feel much the same way about quantum theory.)
It always amazes me that creationists do so litte research on Darwinism before attacking it. Darwin's theory is subject to some very legitimate scientific criticisms. Biologists are, by and large, painfully aware of the theory's shortcomings.
Darwin's landmark work was called The Origin of Species, yet it doesn't actually explain in detail how speciation happens (and in fact, no one has seen it happen in the laboratory, unless you want to count plant hybridization or certain breeding anomalies in fruit flies). Almost everything in evolutionary theory is based on "survival of the fittest," a tautology that explains nothing. ("Fittest" means most able to survive. Survival of the fittest means survival of those who survive.) The means by which new survival skills emerge is, at best, murky. Of course, we can't expect Darwin himself to have proposed detailed genetic or epigenetic causes for speciation, given that he was unaware of the work of Mendel, but the fact is, even today we have a hard time figuring out how things like a bacterial flagellum first appeared.
When I was in school, we were taught that mutations in DNA are the driving force behind evolution, an idea that is now thoroughly discredited. The overwhelming majority of non-neutral mutations are deleterious (reducing, not increasing, survival). This is easily demonstrated in the lab. Most mutations lead to loss of function, not gain of function. Evolutionary theory, it turns out, is great at explaining things like the loss of eyesight, over time, by cave-dwelling creatures. It's terrible at explaining gain of function.
It's also terrible at explaining the speed at which speciation occurs. (Of course, The Origin of Species is entirely silent on the subject of how life arose from abiotic conditions in the first place.) It doesn't explain the Cambrian Explosion, for example, or the sudden appearance of intelligence in hominids, or the rapid recovery (and net expansion) of the biosphere in the wake of at least five super-massive extinction events in the most recent 15% of Earth's existence.
Of course, the fact that classical evolutionary theory doesn't explain these sorts of things doesn't mean we should abandon the entire theory. There's a difference between a theory being wrong and being incomplete. In science, we cling to incomplete theories all the time. Especially when the alternative is complete ignorance.