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Network, degeneracy and bow tie. Integrating paradigms and architectures to grasp the complexity of the immune system.

Tieri P, Grignolio A, Zaikin A, Mishto M, Remondini D, Castellani GC, Franceschi C - Theor Biol Med Model (2010)

Bottom Line: Recently, the network paradigm, an application of graph theory to biology, has proven to be a powerful approach to gaining insights into biological complexity, and has catalyzed the advancement of systems biology.In this perspective and focusing on the immune system, we propose here a more comprehensive view to go beyond the concept of network.We start from the concept of degeneracy, one of the most prominent characteristic of biological complexity, defined as the ability of structurally different elements to perform the same function, and we show that degeneracy is highly intertwined with another recently-proposed organizational principle, i.e. 'bow tie architecture'.

View Article: PubMed Central - HTML - PubMed

Affiliation: Interdept, Center Luigi Galvani for Bioinformatics, Biophysics and Biocomplexity (CIG), University of Bologna, Via F, Selmi 3, 40126 Bologna, Italy. p.tieri@unibo.it

ABSTRACT
Recently, the network paradigm, an application of graph theory to biology, has proven to be a powerful approach to gaining insights into biological complexity, and has catalyzed the advancement of systems biology. In this perspective and focusing on the immune system, we propose here a more comprehensive view to go beyond the concept of network. We start from the concept of degeneracy, one of the most prominent characteristic of biological complexity, defined as the ability of structurally different elements to perform the same function, and we show that degeneracy is highly intertwined with another recently-proposed organizational principle, i.e. 'bow tie architecture'. The simultaneous consideration of concepts such as degeneracy, bow tie architecture and network results in a powerful new interpretative tool that takes into account the constructive role of noise (stochastic fluctuations) and is able to grasp the major characteristics of biological complexity, i.e. the capacity to turn an apparently chaotic and highly dynamic set of signals into functional information.

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Example of a technological structure organized as a bow tie. Aerial view of the Bologna freight marshalling yard, clearly showing a structure analogous to a bow tie. Wagons arrive from a variety of sources (left bow); to facilitate control and sorting out operations, they are driven through a narrowing: few rails under strict supervision to ensure the maximal capability for control and decision-making; from here they are dispatched to a plethora of new destinations (right bow). Again, the narrowing (the 'core' surveillance station) allows economical and effective regulation to be taken and exercised on a variety of inputs (train provenances) and to yield a quantity of outputs (new destinations). Inspired by Needham [122], p. 170, Figure forty five. Image from Google Maps.
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Figure 3: Example of a technological structure organized as a bow tie. Aerial view of the Bologna freight marshalling yard, clearly showing a structure analogous to a bow tie. Wagons arrive from a variety of sources (left bow); to facilitate control and sorting out operations, they are driven through a narrowing: few rails under strict supervision to ensure the maximal capability for control and decision-making; from here they are dispatched to a plethora of new destinations (right bow). Again, the narrowing (the 'core' surveillance station) allows economical and effective regulation to be taken and exercised on a variety of inputs (train provenances) and to yield a quantity of outputs (new destinations). Inspired by Needham [122], p. 170, Figure forty five. Image from Google Maps.

Mentions: This kind of architecture has been observed in the structural organization of organisms throughout the biological scale as well as in technological and dynamical systems where the management, control and restriction of incoming inputs become central, e.g. metabolic networks [5,40,41], signalling networks [42], TCR signaling [6], pathways of oxygen signalling and energy of the hypoxia-inducible factor cascade [43], the Internet [44], large technological installations (see Figure 3); it also accounts for the dynamics of socio-political phenomena [45], so it may be considered wide-ranging [5].


Network, degeneracy and bow tie. Integrating paradigms and architectures to grasp the complexity of the immune system.

Tieri P, Grignolio A, Zaikin A, Mishto M, Remondini D, Castellani GC, Franceschi C - Theor Biol Med Model (2010)

Example of a technological structure organized as a bow tie. Aerial view of the Bologna freight marshalling yard, clearly showing a structure analogous to a bow tie. Wagons arrive from a variety of sources (left bow); to facilitate control and sorting out operations, they are driven through a narrowing: few rails under strict supervision to ensure the maximal capability for control and decision-making; from here they are dispatched to a plethora of new destinations (right bow). Again, the narrowing (the 'core' surveillance station) allows economical and effective regulation to be taken and exercised on a variety of inputs (train provenances) and to yield a quantity of outputs (new destinations). Inspired by Needham [122], p. 170, Figure forty five. Image from Google Maps.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2927512&req=5

Figure 3: Example of a technological structure organized as a bow tie. Aerial view of the Bologna freight marshalling yard, clearly showing a structure analogous to a bow tie. Wagons arrive from a variety of sources (left bow); to facilitate control and sorting out operations, they are driven through a narrowing: few rails under strict supervision to ensure the maximal capability for control and decision-making; from here they are dispatched to a plethora of new destinations (right bow). Again, the narrowing (the 'core' surveillance station) allows economical and effective regulation to be taken and exercised on a variety of inputs (train provenances) and to yield a quantity of outputs (new destinations). Inspired by Needham [122], p. 170, Figure forty five. Image from Google Maps.
Mentions: This kind of architecture has been observed in the structural organization of organisms throughout the biological scale as well as in technological and dynamical systems where the management, control and restriction of incoming inputs become central, e.g. metabolic networks [5,40,41], signalling networks [42], TCR signaling [6], pathways of oxygen signalling and energy of the hypoxia-inducible factor cascade [43], the Internet [44], large technological installations (see Figure 3); it also accounts for the dynamics of socio-political phenomena [45], so it may be considered wide-ranging [5].

Bottom Line: Recently, the network paradigm, an application of graph theory to biology, has proven to be a powerful approach to gaining insights into biological complexity, and has catalyzed the advancement of systems biology.In this perspective and focusing on the immune system, we propose here a more comprehensive view to go beyond the concept of network.We start from the concept of degeneracy, one of the most prominent characteristic of biological complexity, defined as the ability of structurally different elements to perform the same function, and we show that degeneracy is highly intertwined with another recently-proposed organizational principle, i.e. 'bow tie architecture'.

View Article: PubMed Central - HTML - PubMed

Affiliation: Interdept, Center Luigi Galvani for Bioinformatics, Biophysics and Biocomplexity (CIG), University of Bologna, Via F, Selmi 3, 40126 Bologna, Italy. p.tieri@unibo.it

ABSTRACT
Recently, the network paradigm, an application of graph theory to biology, has proven to be a powerful approach to gaining insights into biological complexity, and has catalyzed the advancement of systems biology. In this perspective and focusing on the immune system, we propose here a more comprehensive view to go beyond the concept of network. We start from the concept of degeneracy, one of the most prominent characteristic of biological complexity, defined as the ability of structurally different elements to perform the same function, and we show that degeneracy is highly intertwined with another recently-proposed organizational principle, i.e. 'bow tie architecture'. The simultaneous consideration of concepts such as degeneracy, bow tie architecture and network results in a powerful new interpretative tool that takes into account the constructive role of noise (stochastic fluctuations) and is able to grasp the major characteristics of biological complexity, i.e. the capacity to turn an apparently chaotic and highly dynamic set of signals into functional information.

Show MeSH
Related in: MedlinePlus