I think this aspect of the debate is a bit deceptive. Darwin may have been influenced by previous old Earth theories but it's still evolution's need for it that influenced an older Earth outlook. The deceptive part is that the idea of evolution didn't start with Darwin. He just discovered the mechanism of microevolution that allowed atheists the foundation they needed. As such the need to give the evolution model millions of years can still be said as the motivating factor for such an outlook.

Once again, you are completely wrong, EB.  Lyell's Old Earth hypothesis was itself based on James Hutton's seminal work.  Hutton was the father of modern geology, and he was working to understand his observations of rocks and fossils in light of Young Earth creationism, which was the prevailing scientific hypothesis in his time.  Hutton was not a Christian, but a deist.  Unfortunately, his writing was difficult for others to understand, and Lyell actually restated Hutton's work in a more palatable form.  Lyell was a devout Christian, the same as you and rareairpug, but he could not reconcile young Earth creationism with geology.  So he attacked the idea of the flood myth in the Bible, not creationism. 

Darwin did not discover microevolution or the "mechanism" of microevolution.  That is complete hogwash.  He developed the theory that you creationists like to call "macroevolution", and he based his theory on exhaustive studies of geographical patterns of distribution of intraspecies and extra species characteristics.  The prevailing scientific interpretation of speciation in Darwin's and Lyell's time was creationism--that species were essentially immutable, although there could be a wide range of variation within species.  Speciation itself was held to have been of divine origin, just as the Bible claimed. 

Darwin waited decades to publish his findings, primarily because he wanted to nail down every conceivable objection to the theory.  Geology and fossils played relatively little role in Darwin's theory.**  Rather he was most strongly influenced by Thomas Malthus' ideas on population growth, which gave him his idea for natural selection.  For an excellent, short, very readable biography of Darwin, see David Quammen's The Reluctant Mr. Darwin, which went into great detail on his times, the development of his theory, and his attitudes towards religion.  Although a religious skeptic, he was strongly influenced by his wife, who was a devout Christian and strong believer in the Bible.

** Hutton did actually develop a concept of natural selection that was remarkably like Darwin's, although he did not develop his idea much at all.  Darwin's grandfather also had similar ideas, but it was really Malthus who brought about Darwin's epiphany concerning natural selection as the basic mechanism behind evolution.

No one can say for certain, although the likely explanation is that conditions in the environment changed in such a way as to make the legs a liability for that niche.  Perhaps they were a hindrance in burrowing underground.  Perhaps they simply required too many resources to maintain without conveying any particular advantage to the animal.

I read the article---uniformitarianism.  I remain unconvinced.  I'll give you that there were earlier theories of a very old earth, but I'll maintain that they would never have caught fire and been promulgated as they are if not for Darwin's need for it.  By the way, what was Lyell's predicted age of earth?

It was James Ussher who came up with the original chronology from the Bible that established the Young Earth hypothesis back in the early 17th century.  James Hutton's work in geology quickly arose to challenge that hypothesis, and that was what gave birth to the modern science of geology.  Fossils became an embarrassment for Ussher, because marine fossils were found all over the Earth at very high elevations.  Hutton theorized that the Earth had a molten core (which was later verified), and that caused rock strata that were formed below sea level to be thrust up into high elevations.  All of that was well before Darwin's theory came along to explain patterns of fossils found in rock strata.

Given long periods of time, those traits that help organisms to produce more offspring are more likely than not to crowd out the less efficient producers, other things being equal.  I have no idea what you mean by "additional genetic material".  That has nothing to do with the theory of evolution, which was established before anyone became aware of the existence of genes.

So we are applying it to a physical system in this case are we not?  How is my gravity example not relevant?

You have not explained how it is relevant.  I explained why scale made sense with the theory of gravity (inverse square law) but not probability, which has to do with statistically likely or unlikely outcomes.

Your concept of how evolution works is all wrong.  It is not about sudden large scale shifts in organisms.  We are talking about small incremental shifts over huge numbers of generations.  You don't have a feel for the time scales.

You feel that a series of small changes can get you from one organism to another

Dawkins does a very good job of explaining them.  He points out that the major conceptual problem is that our longest direct experience of time is a human lifespan, but that amount of time is insignificant from a geological perspective.  He wrote a book called Climbing Mount Improbable just to tackle this one issue of how to make geologic time understandable to humans.
It is very important not to fall into Behe's trap concerning complexity.  If you juxtapose an amoeba to a vertebrate, you aren't going to see how they can have a common ancestor.  It becomes easier when you compare donkeys and horses, which can still produce offspring, even though their common ancestor is long extinct.

But Behe made the mistake of thinking that an organ could only have a single purpose, when, in fact, it can have several purposes.  Changed versions over time can gradually come to have a completely different function.  So a mousetrap might not start out as a mousetrap.  If might start out as a coat hangar that gets used for other purposes, but whose function gradually shifts to trapping mouses as it is bent into newer and newer configurations.  New functionality is an emergent property of gradual change.

You didn't answer my question. Are we applying evolution to a physical system or not?

The question could be answered differently (either "yes" or "no"), depending on what you mean by "evolution" and "physical system".  Evolution as a general concept can be modeled in a non-physical sense, e.g. in a computer simulation.  On the other hand, we are applying it to real changes in the physical world.