At the beginning of Part I, we mentioned Oparin's bold idea that the transition to life would be based on a gradual and spontaneous increase of molecular complexity – and we added that indeed, there are quite a few processes of self-organization in nature that bring about an increase of molecular complexity in perfect agreement with thermodynamics. This is what we will see in this third part of the book, devoted to order and organization in biological systems.
Self-organization has to do with the ordered increase of structural complexity – but obviously increasing the size alone would not be enough to proceed towards life. Another property must be considered when smaller parts assemble to constitute a larger entity: emergence – namely, the arising of novel properties. Novel, in the sense that they are not present in the constituting parts. Although self-organization and emergence go hand in hand, for heuristic reasons they will be discussed in this book as separate chapters. We will see also that the notions of self-organization and emergence do not refer only to static, equilibrium systems, but are also present in dynamic systems far from equilibrium – a quite particular and very important aspect of life. A particular combination of self-organization and emergence gives rise to self-reproduction, which will also be discussed in Part III.
After the general comments, let us start with self-organization processes, considering first the terminology. The terms self-assembly and self-organization are often used synonymously, depending on the author. For example, Whitesides uses the term self-assembly (Whitesides and Boncheva, 2002; Whitesides and Grzybowski, 2002). I consider this term too general, and I will use instead the term self-organization.
Some of the self-organization processes take place with a negative free energy change without any hindrance from kinetic activation energy barriers – and as such they can be considered “spontaneous.” The attribution of spontaneity to processes that occur because of the concomitance of a negative free energy change and low activation energy barriers may be controversial for some: in fact, in some classic physicochemical textbooks, the term spontaneous characterizes a reaction that has a negative free energy change regardless of the kinetic constraints – i.e., regardless of whether it happens – a definition that I will ignore in this book.