I made a huge theory/speculation/explanation post in the last episode Disqus section, in reply to both Pearl and Donovan. Then, I made a slight "unconscious" wish on the BH forum that was hopefully be "picked up" by a certain someone. And, I just feel that this episode made a small attempt on answering this, but it definitely isn't enough.
Rood was speaking of the big DK's wishes. Meredith would've known better, even if he's restrained/captive by the Tower. He still had the power to stop any of this, but he didn't do anything because of his one mind-set thinking. The human experimentation phase started after the Tower was built. That's my whole reasoning behind supporting the Meredith =/= big DK.
Until Yong gives us a full proper backstory/flashback, it's going to be a wild ride in the theory section. :)