When Darwin was theorizing about the mechanism that would drive his theory he called it "natural selection." He also believed that the cell, the "building block" of all life, was nothing more than a blob of protoplasm. Given his ignorance about the inner workings of the cell and the existence and complexity of the DNA language by which the cell operates, we can't blame him for basing his evidence on what we now call phenotype (think "phenomenon") -- or the observable traits by which we recognize an organism. In Darwin's mind, the physical traits were what varied among populations and those that were beneficial to the organism were more successful in surviving. They conferred an advantage that allowed the most robust variant to carry on. It's where we got the term "survival of the fittest," though, as I understand it, Darwin never used that term. And it's why species that looked alike were assumed to be members of the same branch of the family tree.
The key is that Darwin concentrated on what the organism looked like but he had no idea what physical mechanism could actually make such a thing work. We now know that that phenotype is an "expression" of genotype (think genetics), and that the genetic differences are what make different species different. This more recently learned fact has changed the game considerably and led to what we call Neo-Darwinism -- the The Neo-Darwinists work on completely different assumptions than Darwin worked under.
This advance in scientific knowledge has been breathtaking in scope and explanatory power -- but that doesn't mean it helps Darwinism. Though we now know that genetic variation can be the object on which natural selection works, this new discovery requires that Darwinism first explain the origin of the genetic code itself. How is it that such a rich and powerful information system can arise from a purely mechanistic process?
Not only that, but how does Darwinism explain the fact that similar looking organisms are not genetically related? Stephen J. Gould was fond of saying that Evolution's randomness demands that, if it were possible to start over again, would never turn out the way it has in the actual world we live in. Computer models meant to verify this claim have proved that Gould was indeed correct. Yet we have discovered completely unrelated organisms that have acquired physical traits (eyes, sensory receptors etc.) that are exactly the same. Somehow, Evolution would seem to have reached the same end under completely different circumstances. Conversely, genetics have shown us that Neanderthals, always proposed as human precursors and our distant relatives (and still equated with politically conservative males), are completely distinct from us in the only way that matters under a Darwinistic explanation -- their genetic makeup.
More hauntingly, a purely naturalistic understanding of Evolution would be deterministic. That is, natural selection acting on purely random mutations, would be the only means to determine who we are, what we think, and where we are going. There could be no such thing as free will. Yet human experience tells us that such a thing is ridiculous. Our thoughts, hopes, fears and imaginings can be about things that have never happened -- and never will. We can change what we believe and alter the course of our lives. Twins don't end up in the same place. Genetics, in other words, does not determine everything about us. For one thing, it cannot explain our ability to reason. The irony is that, if it did, we would have no reason to accept the claims of Evolutionists about reality as being any more reliable than our own.