Ben-Naim warns that there are pitfalls in pursuing Anfinsen’s thermodynamic hypothesis. We show that the deepest one of his pitfalls is not a pitfall at all and the believing pursuing the minimum of the Gibbs free energy will lead us to the native structure. The “pitfall” came from the flawed inference of Gibbs energy function and the muddiness on concepts such as thermodynamic system and the second law of thermodynamics