Now I'm not saying this has anything to do with Coldplay, their beliefs or whatnot, this is purely my interpretation. I think this song could be about God and his love for us, "You don't know how lovely you are", "Tell you I set you apart", "No one ever said it would be this hard", "Questions of science, science and progress/Do not speak as loud as my heart" are just some examples of idea's of God's love and knowledge, how we were made in his image, how even in the most strictest of science or logic the heart leads us, not our brains. Just an idea though.