Confusion About Homology

Over at EvolutionBlog there was a discussion about a creationist who took some quotes from a biology book to try and show that scientists were saying homology was both due to common ancestry and evidence for common ancestry. Let me give you an example: Suppose I say that the eyes of squids and humans are not homologous because they did not inherit this structure from a common ancestor, but then I turn around and say that the non-homologous eyes are evidence that they didn't share a (recent) common ancestor.

This is what the controversey is over, and it has taken me a while to understand just what the creationists were saying on this issue. Here was a comment I left on that post:

This is just another example of how successful Jonathan Wells has been in distorting science and spreading it from the IDers all the way to the fringe of young earth creationism. It is a confusing issue, but the way I understand it is this:

*For a structure to be homologous, it must share a deep similarity (biochemically, anatomically, and developmentally). Homologous structures may or may not have the same precise function.

*Homologous structures are then inferred as being inherited from a common ancestor.

*On the problem of convergent evolution: There are always mutliple solutions to a similar problem. For instance, one organism may move through the water by moving the tail horizontally (like whales) or vertically (like fish), or by rotating the arms (as humans do). Then again, one may "clap" their legs together in order to swim, just as frogs do. So a similar environmental pressure may occasionally produce similar features, but by comparing a large number of features, we may know whether convergent evolution has taken place. On a side note, genetics and fossils may be helpful as well in determining ancestry.