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What I question is whether or not random mutation with natural selection is in fact the mechanism which drives evolution. I think this is (or should be) a respectable question.

It is a perfectly respectable question and one that is actively studied. However, I think it has virtually nothing to do with intelligent design. Look, the issue of random mutation is a complicated one. For example, one of the major genetic findings of the past century was that transposable elements (genetic sequences that can move from chromosome to chromosome) exist and can make for an unstable genome. A large number of spontaneous mutations have been found to be caused by the insertions of these elements and the frequency of insertion can result in multiple orders of magnitude increases in mutation rates. In addition, these elements can cause chromosome rearrangements and can even pick up other genes and carry them along. As far as I know, all organisms examined have transposable elements. How these elements impact evolutionary theories is still being assessed. What should be kept in mind is that while on average spontaneous mutation rates are relatively low, there can be periods of time, such as when a transposable element first enters a population, when rates can be very high.

One reason the observed spontaneous mutation rate is low is the organisms have evolved a very accurate means of DNA replication and very efficient mechanisms of repairing mutations. Was this always the case? Probably not, which means to me that mutation rates might have been significantly higher for different organisms in the past.

It should be noted that transposon insertions and replication errors are not random. They are sequence dependent and may even be affected by the secondary and tertiary configuration of the DNA in that region of the chromosome. How this might affect current models of evolution is also in question.

Yet the model is the one taught to undergraduate biologists, and the assumptions which the model uses are the ones taught to high school students. If there is a correct model, why isn't that the one that is taught?

Because Haldane's formulations provide an easily understandable simplification of a complex problem that provides a rough approximation of how genes behave in populations. There are more sophisticated models, but this is a controversial area as has already been noted (e.g., Kimura's neutral selection or Gould/Eldridge's puntuated equilibrium). One can think of evolution as being in roughly the same position as our understanding of gravity. The complete answer isn't known yet.

If you find a descrepancy in some set of calculations, you may well have to make a sweeping set of changes. Quantum mechanics itself is the perfect example. Quantum mechanics presents a severe challenge to the whole notion of an objective reality and/or causality.

Right, but last I checked Newtonian physics is still taught in schools, apples still fall from trees, and momentum still equals MV. For the majority of activities in the macro world, Newtonian physics provides an acceptable approximation of how the universe works. As revolutionary as quantum mechanics was, it did not invalidate Newtonian physics. Rather it provided a new perspective as to how to understand Newtonian physics. Keep in mind that quantum mechanics developed in large part because improved technology provided new data about subatomic particles.

An analogy can be made with the current state of evolutionary theory. The genome projects now provide a whole new set of tools to understand the molecular mechanisms of evolutionary change. I've no doubt that from this information a whole new set of theories will arise that could have the same impact as quantum mechanics. Undoubtedly much that is assumed now will be proved wrong or have to be significantly modified. But I'm also pretty sure that like Newtonian physics, the basic concepts of Darwinian evolution will still be valid. The body of physical evidence supporting these concepts is simply too overwhelming for them to be completely wrong.

Right now, as far as I can see, all you have is a scientific hypothesis that doesn't hold water. Sure, it explains a whole lot of stuff,...

The fact that it explains a whole lot of stuff means that it holds a lot of water. The fact that there are unanswered questions means that it is incomplete.

You want to argue intelligent design. Let's be precise about this. It is certainly possible that science could establish by empirical investigation that we had an extraterrestrial origin (say were seeded here by Vulcans). What science cannot demonstrate is whether we were designed by supernatural forces. By ID, I am assuming you mean an intelligence capable of working outside the natural laws of the universe. Just out of curiousity, how is such a supernatural ID model a better explanation than my saying "it all happened magically"? What does the assumption of intelligent design allow us to predict about the fossil record or the genetic relationship between humans and orangutangs? And how does intelligent design explain why humans have a vestigial tail bone or why the human spine is so poorly developed for upright walking that virtually everyone will experience back pain as they age?
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