Organisation, its omni-presence, preservation and dependence, is possible the distinctive aspect of biological phenomena. Achieving a consensus about what is organisation and how can it be used to generate biological explanations would greatly benefit the development of (theoretical) biology.
Often "organized" can be seen as "improbable to occur by chance". The formalism to use then is entropy.
I Think you can find hints in René Thom (catastroph theory and forms growth), Ilya Prigogine (auto-organisation, dissipative structures) and Classical theory of entropy.
Thank you both for your comments and excuse me for this late reply, but I have been off -wires and -nets. Since mid 1950's till early 1990's a rich, thoughtful, and outstanding literature has been developed that investigated life phenomena and organisation following the lines you proposed. They are strongly grounded on ideas immanent from General System Theory, Dynamical Systems, Cybernetics. Why they have fallen short to their initial promises have been thoroughly analysed by R. Rosen (Life Itself, 1991; Essays on Life Itself, 2000).
To the best of my knowledge though, none of them handles the idea of organisation in a way other than intuitive, less say defining it, either implicitly or explicitly. Not in the sense of "having the right things at their proper places at the right time" (cf F.M. Harold, doi:10.1128/MMBR.69.4.544-564.2005). Failure to comply to organisation in this sense is a major upheaval for most life phenomena stating with proteins, the building blocks of life phenomena (http://publications.nigms.nih.gov/insidelifescience/protein-folding-gone-wrong.html).
Information in biology has a rich story as well. I shall comment on it soon.
The enterprise modelling framework called 'Projective Analysis' (or PAN) provides a structure for organisation that is consistent with the reflexivity in Rosen's categorical model, with the third order cybernetics in Maturana's later work and with the Lacanian/Freudian accounts of consciousness. It also provides a full set of computational tools for eliciting, composing and analysing people's models of the organisations they inhabit and for indicating the 'holes' in these models. See the papers and blogs at www.brl.com and www.asymmetricdesign.com.
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