Lyric discussion by ikefox 

The song is indeed about two sisters. In an interview, Newsom said that the song is a deeply personal narrative to her sister:

"Like every other song on this record, "Emily" is deeply biographical. The Emily in the song is my sister, who's an astrophysicist; the narrator is myself, who is not an astrophysicist. Emily is the wanderer; she lives in Argentina and sometimes New Zealand. I'm not a wanderer, which is funny because I'm on tour half the time. I'm a home, hearth and family kind of person. It's difficult for me to make too many intelligent comments about [the symbolism in this song] because the song really is a very personal reaction to real life."

And in response to Shefik: Van Dyke Parks was only in collaboration for the production and recording, so it is unfair to call him "Joanna's producer". His task was mostly writing string parts for the orchestration, which he certainly did an excellent job of. And his role in Ys cannot be underestimated. However, the production was still mostly the work of Joanna, and the recording/mixing was headed by Jim O'Rourke, Steve Albini, and Tim Boyle (Albini recorded Joanna's vocals and harp, whereas Boyle recorded the orchestral additions. The mixing was done by O'Rourke).

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