Wow. That was a fantastic part. My theory on the reason for the title was correct. The 'doubt' is over the owner of the 'seed'. How will they prove who it is? I'm sure they will want to know, but that means DNA tests and what is Clark going to say at that point.
In fact, why hasn't he told her already. They've been dating for weeks. And it's not even the off/on complicated dating of season 2/Dan 'cause you can forgive Clark for not telling Lois during those circumstances. Instead, I get the impression that this is going very well. Especially as they just told each other I love you. Which, was just wonderful, by the way. I loved it. Just ... tell her Clark, tell her already!
I figured at least a few people might realize that "seed" should be taken quite literally.
Why hasn't Clark said anything? Fear, plus they've only really just started to get comfortable in their relationship and admit their love. And now with the baby coming, he's going to feel like he really can't say anything - how can he throw in "hey, guess what? I'm Superman," when Lois is faced with what to do about the baby? (Read: He's not going to want to pressure her into feeling like she has to keep it because it might be Superman's kid.)
Glad you enjoyed this installment!
