One of the most powerful evidences for evolution is some of the details of the protein cytochrome c on Talk Origins. This is their baby, it's original research. This protein is present in all living things. An interesting property common to all amino acids, is that mutations have little effect on function. Indeed, even within species, most amino acid mutations do nothing. This is called protein functional redundancy (PFR) and is present in all known proteins and genes. What that means when we are talking about protein cytochrome c, is that no matter what the specific configurations or mutations are present they all work the same, with minor differences in electron transport ability.
Cytochrome c doesn't just work in a wide variety of configurations, it also is essential for life. Remarkably, experiments have shown that if you knock out the cytochrome c gene of a yeast, and replace it with human cytochrome c it works the same. If that wasn't stunning enough, yeast cytochrome c differs from human cytochrome c over 40% of the protein. This is an incredible testament to its redundancy; a consequence being there is no particular reason for any given configuration to have any advantages over another. If evolution is false, we would not expect to see any correlation between species and cytochrome c, or all species would have the same cytochrome c. Furthermore, we observe that only about 30 of the 100 amino acids are even required for the protein to function. If that wasn't enough, any number of the amino acids can be replaced by many other functionally equivalent ones.
So evolution is very vulnerable here. It would be remarkably easy to fail this delicate test. There are a total of 2.3×1093 possible functional cytochrome c sequences. There are more functional cytochrome c sequences than there are atoms in the universe. Yet chimpanzees and humans have the same cytochrome c sequences. The chance of this happening outside of a hereditary process is 10-93 probability (that's 1 one over a number starting with one that has 93 zero's behind it--tiny number.) It doesn't stop there; when we compare protein sequences with other species, we find that the cytochrome c sequences match the phylogenetic tree arranged by morphological and physiological characteristics. This provides an independent confirmation of the validity of the phylogenetic and hereditary tree of life. A back of the napkin calculation (multiplying the probability 10^-93 by some geometrically shrinking number times the number of species, accounting for broader genetic drift across more distantly related species) of the probability of this occurrence by random chance, absent a ancestral relationship, I find is no better than 10-100.
