I think the fact that fish have TLR-4 but use it for something else is evidence for, not against, common descent. The fish immune system recognizes the presence of endotoxins, of course, just using a different mechanism: "
Our analysis also suggests that beta-2 integrins, a group of well-conserved ancient molecules, may play a primary role in the LPS recognition by the piscine immune system." Why would we all have the same parts if we were going to use them for different things, unless we all had a common ancestor?
What is it you
do think happened?
"Why would we all have the same parts if we were going to use them for different things, unless we all had a common ancestor? What is it you do think happened?" - Ha Ha Thats Very Logical Information Theory implies that new uses for old coding routines is due to intelligent design (or redesign), not happenstance.
We certainly see the same code used for entirely different purposes in computer programming, for instance.