If Ellie is Daniel's mother then that opens up the possibility that Widmore could be the father. Timeline on the island, 50's would fit. Daniel and Penny half (or even full) siblings?
Then things get confusing.
Widmore funded Daniel's research. Daniel's mother is working with Ben, yet Widmore appears to know her whereabouts, i.e. that she is in LA. Does he know that she is working with Ben? Surely Ben knows the connection between the 2? Was Daniel born on the island? Did Widmore lead the orginal coup on the island (he comes across as a bit snotty, "no-one knows the island better than me") and was ousted by Ben or did he and Ellie leave the island?
Also could ghost boy and Dharma man be related?
So many questions .......
