In the end: calories in, calories out. Humanity hasn't defeated the laws of thermodynamics.

I think is a simplistic and problematic view of it. We are complicated machines. We can't process all types of input efficiently and without side effects. Any type of machine works differently depending on the source of energy. I can't put diesel fuel in my car and expect it to run the same way that it does on gas. Diesel fuel has energy just like gas but there is more to it than that.