Not really. Thermodynamics isn't just one thing. Proteins are brilliant examples of this. You would think that a organic molecules coming together (order from chaos) would be unfavourable, right? Well... it's not so. This is because the interactions between molecules (hydrogen bonds, ionic, cation-pi, hydrophobic interactions, etc.) are far more favourable thermodynamically, than the unfavourable thermodynamics that come from becoming more ordered. Now, I could talk all day about aspects of proteins where ordered structures are more favoured than disordered... but I think you will get the idea with this post.