I've read through the article and the thread, but let me address this point. I consider intelligent design a real possibility, provided it is in its truest form. There are those (both for and against it) that pervert it into something it's really not--or at least---shouldn't be. I myself subscribe to a version of it, though I also think the evidence for evolutionary theory is overwhelming. In other words, evolution clearly takes place...but where did it begin?
Secondly, who is to say evolution itself is not guided by a higher power?
Ironically, the best example is the very experiment to which you linked. An intelligent creature, that being a man, began
the experiment. The bacteria didn't show up in the lab on their own. They didn't throw a shitload of proteins and amino acids and what not into a jar and voila!
I also think that the article overstates what actually happened. OMG! A mutation!
But sometime around the 31,500th generation, something dramatic happened in just one of the populations the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.
So the bacteria organized themselves into a higher life form, then (any type of higher life form?). Is there evidence this may happen after say, 1,000,000 generations? It just seems like a very small change, even if it is "random."