Defining+properties+of+complex+systems

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TODO List
 * REF Kauffmann seminar paper
 * REF Virtual cell seminar paper: Thomas project?
 * Link/ref Dobzanksky

Defining properties of biocomplexity?
Our overview of modeling biocomplexity from a bioinformatiic (processes) perspective has lead us to the following insights about what are defining properties of biocomplexity:
 * **local interactions** of many different entities in small numbers (cf spatial individual-based models)
 * **leaky multiple levels** of organization
 * not so that they can be studied independently and plugged into each other, but have feedbacks (leaks)
 * self-organization (recognition)
 * requires a explicit effort: if don't look at screen to identify spirals, cannot understand reversal of selection
 * pre-defined multi-level models: these are defined at more than one scale and provide a nice tool to study leaky interactions
 * **interlocking timescales**: this is coupled to leaky levels
 * timescale levels interact
 * evo-eco dynamics : these are interacting and not too far apart. Thus ecological co-existence may depends on small scale evolutionary interactions (cf the wiggle in predator-prey model)
 * thus the concept fitness (which is ill-defined) is a very time dependent property
 * regulation and evolution interlock: there is not free space to choose phenotypes from, but evolutions stays within sensible states: keep something before get something new (cf Kaufmann seminar paper?)
 * **evolved and evolving systems:**
 * if we try to understand this we need not only focus on function but also how we got there
 * neutrality: is non-functional (cf virtual cell seminar paper)
 * we don't get simplest implementation: there are the dynamics of evolution and other things an organism may need to do, i.e. only relative to other things may be the simplest
 * evolutionary signatures: process of evolution can make certain biases in how organisms do things (cf feed-forward loops in regulatory networks)
 * **general attittude: modifying biocomplex systems is difficult!**
 * so lets make short cuts! (model simplifications)
 * lets focus on those phenomena which we can address without space, multi-level, interlocking, evolution (just makes things complicated!)
 * **BUT**, it is possible to target these defining properties as we have seen in this course!

Nothing in biology makes sense, expect in light of ....
As we noted before, Dobzhanksky famously pointed out that: "//Nothing in biology makes sense, except in light of evolution."// We could add now: //"Nothing in biology makes sense, except in light of self-organization//" Thus: Biology makes sense only in light of both evolution and self-organization
 * self-organization is not just //wow//
 * it might be in the way! if one wants to be well-mixed
 * we get from simple rules to complex behaviour
 * arises from local interactions
 * encompasses a micro-macro transition
 * generates non-linear dynamics

Next: How to model complex systems (Major transitions)


 * References**