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Why is it so important whose baby it is, biologically? (Besides the Kryptonite, of course)
Clark acts like Christopher is his son. Christopher believs Clark is his father. He loves him like his son. So why should that play a role in what happens in five years? How could that make a difference to Clark?
I agree that Clark's feelings for Chris shouldn't be contingent on whether or not Clark is the biological father. Being adopted himself, twice over, I think Clark realizes there is more to blood than being a father.

However, I do see two reasons why the paternity of Chris should be resolved:
1. First, because Chris being biologically Clark's answers two of his main questions: (1) can I have children with Earth women; and (2) I'm no longer alone on this planet.

2. I think the more important reason is that Chris deserves a right to know. It will be hard, when Chris grows up and begins to ask questions, for Lois to tell him she has no idea as to who his father is.

The important distinction between Clark and Chris is that Clark couldn't search for his birth-father. This option is available to Chris, however.