self-organization and biological patterns

Self-organization as a principle in generating patterns in living systems in increasingly being put forth as a general mechanism. Take for instance the following line:

A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time [1]

The same author in the review [1] goes on to say that he would like to address:

conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order.

The question that bothers me is whether such "self-organisation" needs to be invoked, and if so in what form and what extent. Why are genes and "pre-pattern" mechanisms [2] not sufficient? The book by John Maynard Smith (JMS) [2] gives some clues, I have an intuition why we need such principles, but that doesn't seem to be satisfactory or enough. JMS frames it well in the chapter titled "Information or Self-Organization" as being the contrast between "template" mechanisms that shape life as explified in the central dogma of molecular biol0gy:

dna -> rna ->proteins

as contrasted with the principles of "self-organization". That we see phenotypic effects of knoking out a gene is beyond doubt. But that we cannot explain the formation of polarized cells based on the genetic information. Or even that of the "interactome" is also becoming apparent. So what are these "principles". Are the general principles from physics already sufficient to account for these effects? How can such principles be at once adaptive and produce the same patterns?

I am still thinking of more questions and would happily post more if anybody chances upon this.

References
[1] Harold F.M. (2005) Molecules into Cells: Specifying Spatial Architecture.Microbiology and Molecular Biology Reviews, Vol. 69 (4), pp 544-564.

[2] Smith, John Maynard. (1999) Shaping Life : Genes, Embryos and Evolution. Yale University Press