The heart of the issue is that we cannot drive a wedge between faith and reason. I believe wholeheartedly that there cannot be any contradiction between the two. The scientific method, based on reason, seeks to discover truths about the nature of the created order and how it operates, whereas faith deals with spiritual truths. The truths of science and faith are complementary: they deal with very different questions, but they do not contradict each other because the spiritual order and the material order were created by the same God.
The question of evolution goes to the heart of this issue. If belief in evolution means simply assenting to microevolution, small changes over time within a species, I am happy to say, as I have in the past, that I believe it to be true. If, on the other hand, it means assenting to an exclusively materialistic, deterministic vision of the world that holds no place for a guiding intelligence, then I reject it.
What Sam wants to do is redefine evolution and rule out common descent. Now there are many who, like me for instance, would affirm both common descent and divine involvement. That has always been the foundation of theistic evolution.
Sam feels the need to protect human dignity. I agree human dignity is important, but affirming common descent need not degrade that dignity. What it does is affirm our connectedness to our context and calls us to be careful with the environment in which we live. And that there are arguments as to how evolution took place doesn't deny that it did. Sam mentions punctuated equilibrium as a challenge to traditional Darwinism. As I understand it, Stephen Jay Gould consistently denied that his theory should be taken as a challenge to evolution, only the manner in which it took place. So Sam has confused the issues.
If faith and reason are to be kept together we must not be afraid of science, and if science challenges our faith then we must of course consider how it affects faith. I simply can't deny the facts of evolution and so my understanding of the way in which God is present in creation must adapt (that's a good evolutionary term).
While no stone should be left unturned in seeking to discover the nature of man’s origins, we can say with conviction that we know with certainty at least part of the outcome. Man was not an accident and reflects an image and likeness unique in the created order. Those aspects of evolutionary theory compatible with this truth are a welcome addition to human knowledge. Aspects of these theories that undermine this truth, however, should be firmly rejected as an atheistic theology posing as science.
I'm saddened by this paragraph, because Sam affirms the scientific method and then basically says that if it doesn't agree with his faith perspective then the results of science must be rejected as atheistic theology. He has let ideology get the best of him!