We agree with this. There were two sorts of manipulations: to the environment and to the genetics. You and Behe point to both types of manipulation as examples of “guidance” and intelligent design, which render the experiment irrelevant. I do not think this is a valid conclusion.
What were the manipulations? There were two types of manipulations: genetic and environmental. You and Behe objected to both manipulations.
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External Environment. The investigators placed the cells in an environment where they would benefit from evolving new functions. This simulates what is already happening in the wild, in a controlled laboratory setting. In what sense is “placing the bacterial in a environment where it will be rewarded for innovating” grounds for dismissing the capacity of these cells to evolve new functions?
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Internal Genetics. the genetic manipulations are merely so that the researchers could better measure and study the evolutionary process, but they do not actually altering the mechanism. A good analogy might be tagging a wild animal with a radio transmitter, and then releasing him back into the wild to track his movements. Yes, there is an immense amount of designed technology in the transmitter, but this just helps us observe what the wild animal does on its own, without directing him. It does not appear the manipulations alter or direct the course of the evolutionary mechanism, so why is this a valid objection?
It does not appear you have even begun to answer these questions.
I disagree. It was not observed without careful experimental work. It seems to be the full truth to say that these new functions evolved by natural evolutionary mechanisms, in a context designed to give researchers visibility into what happens at a genetic level. We see evidence of this mechanism of evolution in the wild too, but we can’t track it as easily. We need the genetic manipulations to directly observe the innovation, but not to direct it.
We have not yet even considered the implications for Axe’s (and your) understanding of enzyme function. This experiment, it would appear, should be impossible if you were both right. You’ve produced calculations that demonstrate this experiment is impossible. I will let others press you on this, but this experiment appears to be just as challenging to Axe’s understanding of sequence space as this one: Beta-Lactamase, Antibody Enzymes, and Sequence Space.