Reddit mentions of Who Am I? Where Did I Come From? (Pop-Up Book)

Great questions! (from both you and your kiddo!). I came across this article - http://www.washington.edu/news/2013/01/08/the-philosophical-child-a-book-for-when-your-child-asks-why-are-we-here/ - which recommends a book for parents, but that doesn't sound like exactly what you're looking for.

In terms of philosophical picture books, the closest thing I can think of would be I Wonder by Annaka Harris. You might also check out the Zen Shorts series, though I don't think any of them really address "nature of reality" type questions directly. Also, while not exactly a picture book, the book Is Nothing Something? might give you some good starting points for discussion. Big Questions for Little People is similar but aimed at slightly older kids. You're Here For A Reason could also be relevant, although maybe not philosophical in quite the way you're looking for.

You could also take "How am I alive?" in a more scientific direction - you might enjoy You Are Stardust and Older Than the Stars, or a simple introduction to evolution such as Our Family Tree. You could also explore simple books about the human body and discuss how her heart, lungs, brain, etc allow her to walk and talk and stay alive - something like See Inside Your Body or Outside-In - or even go into a bit more detail about how she got "in mom's tummy" with a book like Who Am I? Where Did I Come From? or Before You Were Born - or talk about past generations (i.e. mom came from HER mom's tummy!) with a book like Me and My Family Tree

Hope some of that is helpful - of course this is a discussion you can continue as she gets older, and there are lots of great books for older kids that more directly tackle different beliefs and ideas about why we are here.

My parents gave me a popup book about sex. It was called "who am I? Where did I come from?"
Edit: link to the book http://www.amazon.com/gp/aw/d/0307106187/ref=redir_mdp_mobile