“Human problems aren't like mathematics, Nat. Every problem doesn't have just one answer; sometimes you get several answers—and you don't know which is the right one.”
Human problems are contrasted with mathematics in this simile. While math problems have definite answers, human issues are more complicated and multifaceted and often have more than one answer.
“These must be tiny sea animals that glow in the dark, like fireflies.”
The tiny sea animals' ability to glow in the dark is compared to the glow of fireflies. This simile draws a parallel between two different creatures that share a similar characteristic and emphasizes the brilliance of both animals.
“I will lift up my eyes unto the stars.”
The act of Bowditch looking at the stars is a metaphor for seeking guidance, hope, and perspective from something greater or more vast than himself.
The seas
Bowditch navigating across the sea is a metaphor for navigating life itself more broadly. Sailors rely on the same tools as normal, everyday individuals must deal with to navigate the challenges in their lives.