One major problem with Darwinian evolutionary theory is the fact that during his time he was operating on extremely limited understanding.
In Darwins time it was still believed that the atom was the smallest and most basic building block of matter.
In fact, based on discoveries made in the last century, "Darwins Hypothesis" is a better term than "Darwins Theory" because a theory must be based on sound scientific concepts.
Irreducable complexity has all but destroyed the entire concept of Darwinian evolution as well. You see, there is a point at which the complexity of an organism cannot be reduced, (De-Evolved) without making it impossible for that organism to have existed in the first place.
Bacterial flagellum is just one example of this. Bacterial flagellum is an organic propellar and motor assembly attached to the rear of many small bacteria. It is made up of over 40 individual components, each one equally necessary for it to function.
It simply could not have evolved. If any one of it's components is not in place the entore locomotion device would be unable to function and the bacteria would die.
Again, these (and thousands of other) facts were unknown during Darwins time.
I will agree that he had a pretty good theory, but it hasn't withstood 100 years of scientific discoveries.
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