I’ve already written a pair of posts about this paper, but I wanted to highlight one part, because it relates to ID. I also had to think about how it relates to what Dr. R was arguing, although it is still not totally clear to me.
This paragraph is what got me excited:
Rational design and directed evolution should not be viewed as opposing methods, but as alternate ways to produce and optimize parts, each with their own unique strengths and weaknesses. Directed evolution requires a high-throughput way to screen or select for a desired function and that functional mutants exist in the sequence space sampled. This second constraint becomes less likely as the desired function diverges further from the initial function. On the other hand, while rational design strategies can make multiple changes or large-scale alterations that incorporate scientific knowledge, these strategies are rarely precise enough to finely tune the system behaviour. Furthermore, it is difficult to know if additional optimization is possible when employing rational design. For these reasons, both methods can and should be used in conjunction and will hopefully continue to be applied in unison during the years to come.
I find this important because of what it says about how intelligent design might have worked. I think few intelligent design scientists think that everything has been controlled by a designer – there is still some room for evolution to tinker at the edges. So why did the Designer design some things, but let others evolve? I think we see the answer here. If one wants to make large changes (adding a flagellum here, an eye there), it is best to do it by designing it first. But once you have done that, it is easier to let micro-evolution optimise performance.
One of Dr. R’s criticisms is that ID presents no positive hypotheses. I disagree with him strongly, and I see this as one more example of where ID science makes positive contributions to our knowledge. If ID science can show when design is more effective than micro-evolution, it can start to focus on what functions and structures were designed.