This is not a “debate”, it’s some comments that I …

Comment on Dr. Nick Matzke Explains the Evolution of Complexity by Nick (Matzke).

This is not a “debate”, it’s some comments that I randomly posted on your blog, which you have fairly weirdly strung together into a single piece and then called a “debate”. That’s all you.

You still aren’t getting the difference between a “functional island” as measured by blasting a protein with multiple simultaneous mutations, and the reality, which is a web (even within a single function), the strands of which are gradually explored by a step-by-step process of various sorts of substitutions, including compensatory ones, and which would essentially never return to the starting point, or even be constrained within the region of sequences-similar-enough-to-be-identified-by-BLAST. The web covers a far, far greater area of the sequence landscape than your little island. There’s not much point in discussing more complex issues if we can’t resolve simple points like this.

Re: flagellum — the word “Pallen” does not appear in your webpage, and the homology-and-unessentiality table from that paper is not discussed.

Recent Comments by Nick (Matzke)

Dr. Jason Rosenhouse “Among the Creationists”

My model does not ignore compensatory mutation at all. The effect of compensatory mutations is simply to reverse the random walk of a sequence back onto the original island from which it started. That’s all. Compensatory mutations do not help to reduce the average time required to find a qualitatively novel island within sequence space.

You’re not getting the basics. After a slightly deleterious substitution, followed by a compensatory mutation, you are not returning to where you started, you have moved to a different place in sequence space. The compensatory mutation makes the sequence more different from the original sequence, not more similar to it. The “space” we are talking about is sequence space, unless you want to abandon all your previous arguments.