# He sleeps at night and gets up by day

This is something that the man habitually does. Alternate translation: "He sleeps each night and gets up each day" or "He sleeps each night and gets up the next day" 

# gets up by day

"is up during the day" or "is active during the day"

# though he does not know how

"though the man does not know how the seed sprouts and grows"