Thankful, the talk is over. It went okay, didn't stumble too much and most importantly, got a few laughs.
The main questions where about the things that I thought they would be. First, was the question about the apparent circularity of the definition; I thought to take this out, because I knew it might cause trouble, but it produces a much more unwieldy definition. A second, was the question about orphan functions --- genes with new functions or functions of duck-billed platypus. My answer is that all things have homologues even if they don't exist any more.
Not sure people were entirely convinced; if you look at the axiomatisation, then my feeling is that it doesn't make much difference anyway. You build your process hierarachy; functions and roles then just drop out because they are defined. So you don't need to answer questions about homology when building the ontology at all; just when thinking about the instances.
Should have made that point. Damn.