Self-assembly and self-organisation are important concepts in both nanotechnology and biology, but the distinction between them isn’t readily apparent, and this can cause considerable confusion, particularly when the other self-word – self-replication- is thrown into the mix.
People use different definitions, but it seems to me that it makes lots of sense to reserve the term self-assembly for equilibrium situations. As described in my book Soft Machines, the combination of programmed patterns of stickiness in nanoscale objects and constant Brownian motion mean that on the nanoscale complex 3-dimensional structures can assemble themselves from their component parts with no external intervention, purely driven by the tendency of systems to minimise their free energy in accordance with the second law of thermodynamics.
We can then reserve self-organisation as a term for those types of pattern forming system which are driven by a constant input of energy. A simple prototype from physics are the well-defined convection cells you get if you heat a fluid from below, while in chemistry there are the beautiful patterns you get from systems that combine some rather special non-linear chemical kinetics with slow diffusion – the Belousov-Zhabotinsky reaction being the most famous example. A great place to read about such systems is the book by Philip Ball – The self-made tapestry – pattern formation in nature (though Ball doesn’t in fact make the distinction I’m trying to set up here).
Self-assembly is pretty well understood, and it’s clear that at small length scales it is important in biology. Protein folding, for example, is a very sophisticated self-assembly process, and viable viruses can be made in the test-tube simply by mixing up the component proteins and nucleic acid. Self-organisation is much less well understood; it isn’t entirely clear that there are universal principles that underly the many different examples observed, and the relevance of the idea in biology is still under debate. There’s a very nice concrete example of the difference between the two ideas reported in a recent issue of Physical Review Letters (abstract here, full PDF preprint here). These authors consider a structural feature of living cells – the pattern of embedded proteins in the cell membrane – and ask, with the help of mathematical models, whether this pattern is likely to arise from equilibrium self-assembly or non-equilibrium self-organisation. The conclusion is that both processes can lead to patterns such as the ones observed, but that self-assembly leads to smaller scale patterns which take longer to develop.
One thing one can say with certainty – living organisms can’t arise wholly from self-assembly, because we know that in the absence of a continuous supply of energy they die. In summary, viruses self-assemble, but elephants (perhaps) self-organise.