I posted this question on another website, but I've yet to find the name of the book. I remember some very specific details, but nothing I can type into a search engine (I've tried).
Here are the details I remember:
The book might be part of a series of books that follow this quirky space captain.
It takes place in universe where people are in contact with many types aliens
The story begins with an entire "council" of thin bird like aliens turning into glass, this has something to do with some "virus" or "disease" related to entropy some how, and the fact that the silica they turn into is the lowest entropy state.
The story follows an alien that can shoot spines out of his back at some point. There is some romantic relationships between him and a human woman. She dies by turning into glass and he gets arrested, sent to some prison ship and mutilated so that he can't shoot spines anymore.
All the while, the space captain is going on quirky adventurous trying to solve the whole mystery about why people are turning into glass. Also, at some point he visits a "graveyard" ship full of dead aliens, which is being overseen by another alien that gives him a tour around.
Lastly, the book was most likely published between 1999-2007, although I'm not 100% sure (it was definitely modern, though).