Question: How can we think about entropy in these situations? To my knowledge all of these structures are born out of gravitational interaction. However, it would seem that the formation of these more organized structures conceptually violates the second law of thermodynamics. Is this dilemma arisen from my flawed understanding of thermodynamics or are these structures actually in a way defying an increase in entropy?

Answer: 
John Baez has a nice [article on his website](http://math.ucr.edu/home/baez/entropy.html) that goes into some detail on this question.

Broadly, your intuition is right that at face value, it looks like structured systems are born out of nearly featureless initial conditions. However, as (for instance) a gas cloud collapses into a galaxy, it heats up (see [the virial theorem](http://en.wikipedia.org/wiki/Virial_theorem), a theorem any self-respecting physicist should derive at least once). As it heats up, it radiates, and comparing the entropy of the initial cloud and that of the collapsed cloud and the emitted radiation, you'll find that entropy has *increased* overall, and the second law is safe.
The second law of thermodynamics is simply the definition of temperature. How does life, in your opinion, negate the existence of a thermodynamic temperature scale?