[ahayes]

Those two sources cannot be combined to conclude that fish lack genes for the immune system that humans and coral both have. We have many genes for the immune system that neither coral nor fish have.

Let's try to analyze this. You say:

1. Coral have some immune genes humans have.
2. Ray-finned fish do not have some immune genes that humans have.
3. Therefore, the lineage leading to humans cannot have gone through ray-finned fish.

I pointed out one glaring flaw with your argument already--the line of human descend did not go through ray-finned fish! The first ray-finned fish was our evolutionary cousin, not our evolutionary grandfather. Therefore any secondary modifications in ray-finned fish, such as the different gene expression patterns of Hox genes in ray-finned fish forelimbs, do not have any bearing on tetrapod evolution.

The second major flaw is a more subtle assumption. You are truly saying:

1. Coral have some immune genes humans have.
2. Ray-finned fish do not have some immune genes that humans have and the missing genes are present in coral.
3. Therefore, the lineage leading to humans cannot have gone through ray-finned fish.

The problem here is that you don't know which genes are present in each and which genes are missing. You're making an ungrounded assumption that the missing genes in fish are present in corals. As a matter of fact I went through the major Toll-like receptors mentioned in the paper and everyone one of them is present in the ray-finned fish, and thus present in the lobe-finned fish and throughout our lineage as well.

The reason that ray-finned fish do not have some immune genes that we have is because there was considerable innovation in the immune system in mammalian evolution. These new immune genes are not shared by fish nor coral.

[Southack]

"I pointed out one glaring flaw with your argument already--the line of human descend did not go through ray-finned fish!"

The flaw is glaring, but it is in your rebuttal, not in my argument.

My argument isn't limited to "ray-finned fish." That's your red herring.

My argument encompasses *all* fish from all Ages and all Branches. It's complete and unlimited.

[Southack]

"The reason that ray-finned fish do not have some immune genes that we have is because there was considerable innovation in the immune system in mammalian evolution. These new immune genes are not shared by fish nor coral."

Coral and humans do share immune genes, it's the Fish that are missing some of those genes.

"Among the 25 percent of human genes without counterparts in Fugu (Puffer Fish) are key genes involved in the human immune system and metabolic regulation."

Prof Miller says another surprise has been that coral shares many genes with humans, including those related to the development of immune systems