Complex systems biology

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.

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

• A general list of Theoretical biology/Mathematical biology references, including an updated list of actively contributing authors.
• A list of references for applications of category theory in relational biology.
• An updated list of publications of theoretical biologist Robert Rosen
• Theory of Biological Anthropology (Documents No. 9 and 10 in English)
• Drawing the Line Between Theoretical and Basic Biology, a forum article by Isidro A. T. Savillo
• Kurata, Hiroyuki; Taira, K; Kitano, H (1999). "Synthesis and Analysis of a Biological System". Genome Informatics Series (Sers 10): 352–353. OCLC 203735966.