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

circannuity

Looking at this almost dead bulb that stayed below ground for the whole year, I wondered whether I couldn't find a better use for the pot. It didn't look too pretty either in my living room, a pot with some mud, and some earth coloured thing sticking out. And as the guessing game about the real start of spring began (around March 2006 in S.Germany), lo and behold! This tiny mound sprouted green-stuff.

That set me thinking that I have heard of entraining in animals and plants due to light dark cycles. This allows our body to keep the 24hr day-night cycle alive (that is those of us who aren't sleep deprived and working on their computers at 02:01:02 hh:mm:ss).

It just so happened that the weekend following this amusing personal observation, I happened to be visiting the Landesmuseum Hessen in Darmstadt. The term circannual rhythms is used to describe the length-of-daylight time as an entraining mechanism for plants (seasonals) and animals (migratory birds). Some more interesting stuff I found here:
seasonality-blog.

What I still haven't understood however is:
1. When the bulbs of seasonal flowering plants are covered under the soil, they cant possibly be sensing the light. So what is it that entrains them? Is it temperature?

2. How accurate is this sensing? The "false spring" and its effect I have seen in Boston last year. It got far too warm for the season in the middle of winter, flowering started, and within a week it got miserably cold again and snowed shovelfuls. So the flowers seemed to have been to early. Maybe the plant can produce more. But what about a flock of birds and its decision to migrate hundreds of kilometres? What is the cost of that error? And how often does it happen? Are there correction mechanisms? How often does the time-of-the year detection fail?

If anybody knows the answers already, put in a comment please. Or a reference!

So now I will heed my own nighttime clock and shutdown.
Buenas noches.
c.