Joined: June 2005
That Scopes quote cannot possibly be true for the simple reason that by 1925, both classical Newtonian gravitation and the concept of "aether" had already been disproven, in 1915 and 1905, respectively. Thus, I do not know where or when you found that quote, but neither of those concepts were seriously accepted by scientists at the time of the Scopes trial.
As for how one would determine the difference between "Common Design" and common descent, let's make a really simple hypothesis and test it out:
Let's look at birds and bats for a second. Both fly using wings, so one could conclude that if they were a product of "common design," then their wings should be structurally very similar, since they were "designed" to perform very similar tasks. On the other hand, if their wings were a product of descent with modification from ancestors within their separate classes, we should see very distinct differences.
Now, looking at their wings, we see a very serious difference almost instantaneously: Birds' wings are modified from arms, and in fact retain many of the structures found in all terrestrial vertebrate arms, but modified for flight. Bats' wings, on the other hand, are modified fingers with webbing in between, not arms. While their fingers are similar to other terrestrial vertebrates, they are modified for flight, but in a completely different manner from birds.
Furthermore, one would expect that the collarbones for both animals would be similar, since both were "designed" for flight, right? Well, not really. For starters, birds' collarbones have a particular "wishbone" shape, whereas bats' collarbones are shaped more similarly to those of other mammals. Furthermore, the bones of birds are structured differently on their interior, with hollow crevices, whereas again, bats' bones resemble those of other mammals. One would also expect that their skulls would be more similar to each other, were they designed, since the strains of flight are similar. But no, again, we find that birds' skulls are built more similarly to those of reptiles, with two fenestral openings and multiple jawbones, while bats' skulls are similar to mammals, with one fenestral opening and one jaw bone.
So, looking at this evidence, we can conclude that it does not match what we would expect if these two species were designed. Designed flying animals would be more similar to each other than to walking animals. The evidence does, however, support a conclusion that birds and bats evolved from separate classes of walking animals, independently gaining the ability to fly. Incidentally, when examining insect wings, we find that they are structurally very different from either bat or bird wings, a profound difference which makes no sense if flying animals were all designed, but fits perfectly with the theory that they evolved from walking animals from a completely different phylum.
Thus we find that the observed evidence disconfirms a design hypothesis, but is consistent with a hypothesis of descent with modification.