I would make a stronger statement, there is a relationship, presently unknown. We can rule out the no relationship verdict.
I would agree. As I said before, we can try to make some educated guesses about the relationship by using the degrees of difference to try and place them in a relative taxonomy. That's not conclusive, of course, but it can point us in a productive direction. And we can compare our results to morphological/cladistic taxonomies, to give us another factor in deciding the relationship.
And eventually, we can accumulate enough evidence to begin to lean in one direction or another about what the relationship is - do they share common ancestry? Did one of them just scarf up the genes from the other? Maybe they both obtained the same gene from a third source?
We'll make a materialist out of you yet.... ;)
Yes, some judgement can be made by taking other information into consideration. COGS has little cladistic trees for each COG.
This must be viewed in light of the photosynthesis experience.
As for the materialism, been there, done that.
Mat 4:4 But he answered and said, It is written, Man shall not live by bread alone, but by every word that proceedeth out of the mouth of God.