***Why does this imply what you say? This is purely a difference in opinion. I say this looks like the creator using the same building blocks over and over. And if they work, why not?***
I think what you are saying is actually an insult to God. By suggesting that God uses the same genetic building blocks is innocent enough, but what about the vast number of parasites that have evolved in our biosphere? Is God being efficient when he uses the same genetic code in the creation of parasites? Perhaps God, in your view, is a tyrannical being who enjoys these kind of sadistic pleasures of seeing his creatures go at it and harm each other?
Sam, try to understand this very basic fact. God is Love. God does not torture. God is always trying to inspire goodness and peace and harmony in the world. He doesn't do this by actively seeking to create parasites and viruses that do a better job of causing mayhem.
***And out of this great multitude of mutations, how many are benificial? Any? You make it sound like mutations are commonplace, and beneficial. They are neither.***
Firstly, most mutations are not regulatory gene mutations. When regulatory genes mutate, they cause significant changes in an organism. Often these regulatory gene changes are detrimental, which is a good thing, otherwise there would be no stability to evolution. On the other hand, when environments or an organisms conditions change (e.g., new predators move into the area, etc), then a regulatory gene mutation which once before might have provided no adaptive advantage for breeding, might all of a sudden provide a great deal of advantage. In those select cases, the regulatory gene mutation provides a great deal of advantage. For example, here is an example of a regulatory gene mutation dealing with biological clocks which in certain times and places, might be helpful:
Genetic mutations of course take many generations to sow themselves, but evolution provides plenty of time for this sowing given that thousands of generations can fit inside a mere 100,000 years. When you have millions of years as a mere 'tick' of geological time, these regulatory genetic mutations are able to help species evolve and adapt to changing environments. Sometimes the environmental changes are too rapid (such as the K-T extinction), so in many of those cases the regulatory genetic mutations do not happen fast enough to 'save' the genus or family.