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

mathematical and theoretical biology Mathematical and theoretical biology, or biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of the living organisms to investigate the principles that govern the structure, development a ...

invented by Robert Rosen concerned with

complexity Complexity characterises the behaviour of a system or model whose components interact in multiple ways and follow local rules, leading to nonlinearity, randomness, collective dynamics, hierarchy, and emergence. The term is generally used to c ...

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 interconnectivity of, and within,

biological network inference Biological network inference is the process of making inferences and predictions about biological networks. By using these networks to analyze patterns in biological systems, such as food-webs, we can visualize the nature and strength of these int ...

, and on modelling the fundamental relations inherent to life. According to Baianu ''et al''. CSB is a field that has only a partial overlap with the more conventional concepts of

complex systems theory A complex system is a system composed of many components which may interaction, interact with each other. Examples of complex systems are Earth's global climate, organisms, the human brain, infrastructure such as power grid, transportation or com ...

and

systems biology Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...

, because CSB is concerned with philosophy and human consciousness. Moreover, mathematics can model a wide range of complex systems, but this is claimed not to be relevant. Complex-adaptive-system

Complexity of organisms and biosphere

There is no satisfying definition of

in biology.Bonner, J. T. 1988. The Evolution of Complexity by Means of Natural Selection. Princeton: Princeton University Press. Seawifs global biosphere

According to Rosen, most

complex system A complex system is a system composed of many components which may interact with each other. Examples of complex systems are Earth's global climate, organisms, the human brain, infrastructure such as power grid, transportation or communicatio ...

models are not about biological subjects, such as

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...

s and organisms, although biology has been successfully modelled since the 19th century. Two approaches based on

information theory Information theory is the scientific study of the quantification, storage, and communication of information. The field was originally established by the works of Harry Nyquist and Ralph Hartley, in the 1920s, and Claude Shannon in the 1940s. ...

and

network topology Network topology is the arrangement of the elements ( links, nodes, etc.) of a communication network. Network topology can be used to define or describe the arrangement of various types of telecommunication networks, including command and contr ...

graph theory In mathematics, graph theory is the study of '' graphs'', which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of '' vertices'' (also called ''nodes'' or ''points'') which are conn ...

have been combined to model human

consciousness Consciousness, at its simplest, is sentience and awareness of internal and external existence. However, the lack of definitions has led to millennia of analyses, explanations and debates by philosophers, theologians, linguisticians, and scien ...

. Regarding

ontology In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality. Ontology addresses questions like how entities are grouped into categories and which of these entities ...

(the philosophical

metaphysics Metaphysics is the branch of philosophy that studies the fundamental nature of reality, the first principles of being, identity and change, space and time, causality, necessity, and possibility. It includes questions about the nature of conscio ...

of reality), one is assuming that there is a

hierarchy A hierarchy (from Greek: , from , 'president of sacred rites') is an arrangement of items (objects, names, values, categories, etc.) that are represented as being "above", "below", or "at the same level as" one another. Hierarchy is an important ...

of complexity levels of organization distinct from reality. Baianu ''et al''. claim that taxonomic ranks such as

order Order, ORDER or Orders may refer to: * Categorization, the process in which ideas and objects are recognized, differentiated, and understood * Heterarchy, a system of organization wherein the elements have the potential to be ranked a number of d ...

family Family (from la, familia) is a group of people related either by consanguinity (by recognized birth) or affinity (by marriage or other relationship). The purpose of the family is to maintain the well-being of its members and of society. Idea ...

genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial n ...

species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...

, etc. reflect a hierarchy of complexity levels of organization in biology. Because of their variability, ability to heal and self-reproduce, and so on, organisms are defined as ' meta-systems' of simpler systems in CSB.Metasystem Transition Theory
Valentin Turchin,

Cliff Joslyn Cliff Joslyn (born 1963) is an American mathematician, cognitive scientist, and cybernetician. He is currently the Chief Knowledge Scientist and Team Lead for Mathematics of Data Science at the Pacific Northwest National Laboratory in Seattle, Was ...

, 1993-1997 A meta-system is a system of systems.

Autopoiesis The term autopoiesis () refers to a system capable of producing and maintaining itself by creating its own parts. The term was introduced in the 1972 publication '' Autopoiesis and Cognition: The Realization of the Living'' by Chilean biologists ...

also models such a biological system of systems, however, Baianu ''et al''. claim that in biology a meta-system is not equivalent to such a system of systems. They also claim it differs from the meta-system defined in a blog by Kent D. Palmer because organisms are different from machines or robots. If, according to Hopcroft ''et al''., robots or

automata An automaton (; plural: automata or automatons) is a relatively self-operating machine, or control mechanism designed to automatically follow a sequence of operations, or respond to predetermined instructions.Automaton – Definition and Mor ...

can be defined by five qualities: states, startup state, input and output sets/alphabet and transition function, organisms are different.

Topics in complex systems biology

The following is a list of topics covered in complex systems biology: * Applicability of quantum theory to genetics. * Relational biology

Notes

References cited

* Baianu, I. C., Computer Models and Automata Theory in Biology and Medicine., ''Monograph'', Ch.11 in M. Witten (Editor), ''Mathematical Models in Medicine'', vol. 7., Vol. 7: 1513-1577 (1987),Pergamon Press:New York, (updated by Hsiao Chen Lin in 2004 * Renshaw, E., ''Modelling biological populations in space and time''. C.U.P., 1991. * Rosen, Robert.1991, ''Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life'', Columbia University Press, published posthumously: * Rosen, Robert .1970. ''Dynamical system theory in biology''. New York, Wiley-Interscience. * Rosen, Robert. 2000, ''Essays on Life Itself'', Columbia University Press. * Rosen, Robert. 2003, "''Anticipatory Systems; Philosophical, Mathematical, and Methodolical Foundations''", Rosen Enterprises publs.

Complexity of organisms and biosphere

Topics in complex systems biology

See also

Notes

References cited

Further reading