Quick guide for the uninitiated: Just what the hell is Bill Cole, @colewd, droning on about?
For the most part Bill is simply blathering. Once again he name drops some scientist, or some subject, that isn’t really relevant to the Howe diagram(thread about that here) and what Bill is demanding to account for it.
ID-proponent and biochemist Michael Behe and David Snoke(Behe & Snoke 2004) had an exchange with biologist Michael Lynch (Lynch 2005) about divergence of duplicate genes, in which Behe & Snoke made different starting assumptions from Lynch. These assumptions made a huge difference to the rate at which duplicate genes could evolve and diverge. This is not directly related to the Howe diagram.
Bill one day sees the Howe diagram, in which it is implied that four species have evolved different numbers of novel genes (that are presumed to mostly not derive from divergence of duplicates) since they split off from their common ancestors.
These genes are not detected as orthologous to genes in the other three species by various criteria, which means they’re probably not diverged duplicates. So they’re “novel” genes in a certain sense. That means they’re probably the result of other forms of novel gene formation than duplication and divergence: fusions of fragments of other genes, frameshift mutations, HGT, genes evolving de novo from non-coding DNA and stuff like that.
To Bill this is a huge problem. Because Bill thinks new genes evolving is miraculously improbable (he rejects all the above mechanisms as being capable of generating any significant number of genes on the available timescales), so when he sees this is nevertheless implied to have occurred by the Howe diagram he thinks this means the shared relationship of the species in the diagram couldn’t possibly be true. That is, if the genes couldn’t have evolved, then the species that have them can’t have evolved from common ancestor either. Never mind that this doesn’t logically follow even if the premise is true, Bill isn’t strong on logic.
On a related note, and a very important one, it isn’t actually known how many of the putative novel genes in the Howe diagram are actually genuine novel genes. Nobody knows what any of them do, if anything. Nobody knows whether they affect fitness or whether they’re even expressed. There can exist an ORF in a piece of DNA that never gets expressed, or is only expressed at a very low level that doesn’t have a function. Bill doesn’t know of or understand any of this. He just seems a number on a figure and goes with it.
Anyway. He demands a “population genetics model” to account for the new genes in the diagram having evolved. It’s not really clear what he means by that.
Bill now name-drops Behe and Lynch, for reasons. The exchange they had has next to nothing to do with the Howe diagram, because the novel genes in that diagram are generally not though to owe to divergence of duplicate genes. So neither of their models or assumptions are really relevant to what Bill is asking for. All Bill knows is that Lynch is a population geneticist, he did something that has something to do with the evolution of new genes or new functions or… something, and he thinks he can score points by mentioning him and the fact that he interacted with Michael Behe.
I suppose Bill might think that because it is very unlikely that the novel genes in the Howe diagram are diverged duplicates, somehow in Bill’s mind Behe and Lynch’s exchange is relevant in showing this, with what Bill calls their “stochastic models” (Bill thinks saying those two terms in a sentence sounds clever and technical).
Bill understands nothing. He doesn’t understand the evidence for common descent. He doesn’t understand the logic of historical inference. He doesn’t know what models are. He doesn’t know what population genetics is. These ideas and concepts just exist in this strange hazy state in his mind and he somehow thinks they’re all related in ways he can’t articulate. So he always just writes these incoherent responses that we, correctly, tell him amount to word salad. Perhaps somewhere deep in Bill’s subconscious there’s a coherent idea he wants to express, but he lacks the capacity to put it into text.
Believe me when I say we’ve all been trying for years to get Bill to understand what the words he uses mean. And how these topics relate (and how they don’t) and how and why he doesn’t make sense.