Complex systems biology

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Complex systems biology (CSB) is a branch or subfield of mathematical and theoretical

biology concerned with complexity of both structure and function in biological organisms, as well as
the emergence and evolution of organisms and species, with emphasis being placed on the complex
interactions of, and within, bionetworks,[1] and on the fundamental relations and relational
patterns that are essential to life.[2][3][4][5][6] CSB is thus a field of theoretical sciences aimed at
discovering and modeling the relational patterns essential to life that has only a partial overlap
with complex systems theory,[7] and also with the systems approach to biology called systems
biology; this is because the latter is restricted primarily to simplified models of biological organization
and organisms, as well as to only a general consideration of philosophical or semantic questions
related to complexity in biology.[citation needed] Moreover, a wide range of abstract theoretical complex
systems are studied as a field of applied mathematics, with or without relevance to biology,
chemistry or physics.

Network Representation of a Complex Adaptive System

Contents
[hide]

1Complexity of organisms and biosphere

2Topics in complex systems biology
o 2.1Related journals
3CBS societies and institutes
4See also
5Biographies
6Further reading
7Notes
o 7.1References cited
8External links
Complexity of organisms and biosphere[edit]
A complete definition of complexity for individual organisms, species, ecosystems, biological
evolution and the biosphere has eluded researchers, and still is an ongoing issue.[3][8]

Most complex system models are often formulated in terms of concepts drawn from statistical
physics, information theory and non-linear dynamics; however, such approaches are not focused on,
or do not include, the conceptual part of complexity related to organization and topological attributes
or algebraic topology, such as network connectivity of genomes, interactomes and biological
organisms that are very important.[6][9][10] Recently, the two complementary approaches based both
on information theory, network topology/abstract graph theory concepts are being combined for
example in the fields of neuroscience and human cognition.[7][11] It is generally agreed that there is
a hierarchy of complexity levels of organization that should be considered as distinct from that of the
levels of reality in ontology.[7][12][13]The hierarchy of complexity levels of organization in the biosphere
is also recognized in modern classifications of taxonomic ranks, such as: biological domain and
biosphere, biological kingdom, Phylum, biological class, order, family, genus and species. Because
of their dynamic and composition variability, intrinsic "fuzziness", autopoietic attributes, ability to self-
reproduce, and so on, organisms do not fit into the 'standard' definition of general systems, and they
are therefore 'super-complex' in both their function and structure; organisms can be thus be defined
in CSB only as 'meta-systems' of simpler dynamic systems[7][14] Such a meta-system definition of
organisms, species, 'ecosystems', and so on, is not equivalent to the definition of a system of
systems as in Autopoietic Systems Theory,;[15] it also differs from the definition proposed for example
by K.D. Palmer in meta-system engineering,[16] organisms being quite different from machines
and automata with fixed input-output transition functions, or a continuous dynamical system with
fixed phase space,[17]contrary to the Cartesian philosophical thinking; thus, organisms cannot be
defined merely in terms of a quintuple A of (states, startup state, input and output sets/alphabet,
transition function),[18] although 'non-deterministic automata', as well as 'fuzzy automata' have also
been defined. Tessellation or cellular automata provide however an intuitive, visual/computational
insight into the lower levels of complexity, and have therefore become an increasingly popular,
discrete model studied in computability theory, applied mathematics, physics, computer science,
theoretical biology/systems biology, cancer simulations and microstructure modeling. Evolving
cellular automata using genetic algorithms[19][20][21] is also an emerging field attempting to bridge the
gap between the tessellation automata and the higher level complexity approaches in CSB.

Topics in complex systems biology[edit]

Animated Molecular Model of a DNA double helix

Telomerase structure and function

A Complex Signal Transduction Pathway

The following is only a partial list of topics covered in complex systems biology:

Organisms and species relations and evolution

Interactions among Species
Evolution theories and population genetics
Population genetics models
Epigenetics
Molecular evolution theories
Quantum biocomputation
Quantum genetics[22]
Relational biology[4][23][24][25]
Self-reproduction[26] (also called self-replication in a more general context)
Computational gene models
DNA topology
DNA sequencing theory
Evolutionary developmental biology
Autopoiesis
Protein folding
Telomerase conformations and functions in vivo
Epigenetics
Interactomics[27][28]
Cell signaling
 Signal transduction networks
Complex neural nets
Genetic networks
Morphogenesis
Digital morphogenesis
Complex adaptive systems
Topological models of morphogenesis
Population dynamics of fisheries
Epidemiology
Theoretical ecology
Immune system
Related journals[edit]

Acta Biotheoretica
Bioinformatics
Biological Theory
BioSystems
Bulletin of Mathematical Biology
Ecological Modelling
Journal of Mathematical Biology
Journal of Theoretical Biology
Mathematical Biosciences
Medical Hypotheses
Theoretical and Applied Genetics
Theoretical Biology and Medical Modelling