Remus said:
I only had time to skim atm (I'll read it all tonight), so forgive me if I ask something that's answered in it.
What do you believe to be the driving force behind the changes? I assume that random mutation is out. Do you believe they were directly guided throughout, some part of the program so to speak, or someting else?
As rmwilliamsll notes, one of the significant differences betweeen science and theology is that theology thinks in teleological terms (things happen for a purpose) while science avoids teleological thought (things happen because of prior natural causes).
The advance of science in all areas has led to accepting that things just happen, without prior purpose. Weather, for example. People used to think that rain and drought were arranged by God for a purpose. Today we usually think of them as occurring because of meteorological causes.
Some people have asked if the tsunami was a judgment from God, but most people are prepared to attribute it to an undersea earthquake set off by tectonic motion. In times past, everyone would have asked why God caused the tsunami. No one would have questioned that it was God's purpose for it to happen and that it was intended as a message from God.
Now, I don't believe God sent the tsunami, but when we begin to explore the possible relations between God's intent and happenings in the physical world, it is an idea that cannot be ruled out. If God can act on physical process, God can certainly increase the pressure on a tectonic plate and cause it to slide so that a tsunami-inducing earthquake is set off. Who can say otherwise?
The same applies to any random event, including mutations and changes in environmental conditions which lead to favoring some mutation-induced variations and repressing others. If God acts directly on the physical world at all, these sorts of events are clearly among the events that God, with foreknowledge of their effects can manipulate to accomplish God's purpose.
It is entirely possible that God is the instigator of every event we call random. Or that God allows nature to be random most of the time, but acts on such events when His purpose calls for a particular mutation or variation or speciation. Or that God's foreknowledge so encompasses all the outcomes of evolutionary mechanisms that no intervention is required. Nature as a whole accomplishes God's purpose.
The point is that in the case of random events, neither the theologian nor the scientist can distinguish one that has been guided by God from one that has not.
In fact, that is why I see random chance as an essential ingredient of providence. It is the random aspect of creation that permits a continuing guidance by God within the laws of nature. Yet the same randomness means we can only "see" such guidance by faith. It will never rise to the threshold of being seen by scientific methods.