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Complex systems and biology – introduction

04 Dec

What you can read in here is a set of my loose notes on complex systems and biology. I want to learn about the topic as fast as I can, so if I’m wrong anywhere, please point that to me. This post is an overview and indication of issues I’d like to cover.

Complex adaptive systems (CAS) are the heart of many phenomenas we observe every day, such as global trade, ecosystems, human body, immune system, internet and even language. Complexity of CAS does not equall to amount of information, rather it’s a indication of complex, positive and negative interactions of its components. All CAS feature a common set of dualisms:

  • distinct/connected – CAS are built of a large number of agents that interact simultaneously and independently but all together become tightly regulated system (other names: individual/system or distributed/collective)
  • robust/sensitive – CAS are pretty robust, yet at the same time are quite sensitive to initial conditions and some signals (see butterfly effect); both features are unpredictable
  • local/global – protein is a CAS, protein network is a CAS, cell is a CAS, tissue is a CAS, organism is a CAS, society is a CAS; agents of a CAS, can be CAS themselves
  • adaptive/evolving – CAS is able to adapt as a system and usually its agents are also mutually adaptive, and at the same time CAS is evolving; even if local landscape prefers simpler solutions (adaptation) CAS usually evolve toward bigger complexity

These dualisms are in some sense as artificial as wave-particle dualism. Complex system has all these features at the same time – their visibility depends only on design of a experiment. As a result, CAS present a common set of features: they are self-organizing, coherent, emergent and non-linear.

Probably the best so far representation of CAS is a network, which has a number of important features: it is scale-free (distribution of links in the network tends to follow power law), clustered (“friend of my friend is likely my friend too”) and small-world-like (diameter of a network is small, aka “six degrees of separation”). Such representation has been applied to biological complex systems, such as metabolic networks, or protein-protein interaction networks with a great success. However please remember that it’s only representation and many times people argued that scale-free networks may not be the best approximation of natural networks (see for example this recent paper).

Scale-free or not, network representation doesn’t address all dualities mentioned above, especially last two. Naturally emerging levels of organisation and relation between adaptation and evolution of complex systems are rarely studied from biological point of view, probably because we don’t have a clear idea how to reduce these phenomenas to something measurable.

In the next posts, I will try to cover other CAS representations and computational approaches to CAS modeling.

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2 Comments

Posted by on December 4, 2009 in bioinformatics

 

2 responses to “Complex systems and biology – introduction

  1. Richard Lofsted

    December 9, 2009 at 10:24

    Hello, Pawel. I hope your PhD studies have been going well. I managed only 24 units in a postgraduate systems program before “life got in the way of life.” Hopefully, your “day job” doesn’t prevent you from continuing your investigation into complex systems.
    Based on my own training and “loose notes,” I feel compelled to make a few suggestions. [1] Many dualisms can be helpful if presented as extremes of continuums. [2] Beware of simple descriptions of complex systems; even mere definitions are usually inadequate. The use of multiple models would help (too much for the conscious mind, but the subconscious mind can handle all that pretty well). [3] I found it ironic to read your words, “Naturally emerging levels of organisation and relation between adaptation and evolution of complex systems are rarely studied from biological point of view….” My reaction is such because in my second course in the systems program (M.S. level), our textbook was an anthology (Walter Buckley, editor. Modern Systems Research for the Behavioral Scientist. Chicago: Aldine Publishing Company, 1968.) whose approach to complex systems was to start with biological systems.
    That’s probably enough for now. Best of luck to you.
    Richard
    M.S., Cybernetic Systems
    San Jose State University, ’90

     
    • Pawel Szczesny

      December 9, 2009 at 10:46

      Hi Richard, I’ve actually defended more than half a year ago :).

      Thanks a lot for your comments, these are helpful suggestions. As for the third one, this was absolutely serious sentence. As a biologist in training I find complex descriptions of biological systems way too simple. For scientists studying complex systems, nature was indeed an inspiration for a long time, but rarely real knowledge about biology had been incorporated into models (one recent example I’ve seen assumed that mutations in a yeast-like organisms change dramatically 10 (!) genes at a time). “Biological point of view” means here a point of view of a biologist ;).

       
 
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