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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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Related in: MedlinePlus

Degeneracy, pluripotentiality and bow tie. The concept of bow tie integrates the concepts of degeneracy and pluripotentiality: figuratively, a bow tie structure (many-few-many) (1c) appears from the overlapping of degeneracy (many-to-one) (1a) and pluripotentiality (one-to-many) (1b).
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Figure 2: Degeneracy, pluripotentiality and bow tie. The concept of bow tie integrates the concepts of degeneracy and pluripotentiality: figuratively, a bow tie structure (many-few-many) (1c) appears from the overlapping of degeneracy (many-to-one) (1a) and pluripotentiality (one-to-many) (1b).

Mentions: A bow tie architecture shows the ability to accept a wide range of inputs (in Figure 1 the left, input wing) and convert them to a reduced set of universal building blocks (the knot, or core). Here, assembly protocols act on these basic modular building blocks, eventually restoring and fanning out a wide variety of outputs (the right bow). It is interesting to note that the bow tie can be interpreted as the combination of two degenerate systems coupled through a single central element, suggesting that the two concepts of degeneracy and bow tie share a similar conceptual and architectural design, i.e. the many-to-one (degeneracy) and one-to-many (pluripotentiality) paradigm (Figure 2).


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)

Degeneracy, pluripotentiality and bow tie. The concept of bow tie integrates the concepts of degeneracy and pluripotentiality: figuratively, a bow tie structure (many-few-many) (1c) appears from the overlapping of degeneracy (many-to-one) (1a) and pluripotentiality (one-to-many) (1b).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Degeneracy, pluripotentiality and bow tie. The concept of bow tie integrates the concepts of degeneracy and pluripotentiality: figuratively, a bow tie structure (many-few-many) (1c) appears from the overlapping of degeneracy (many-to-one) (1a) and pluripotentiality (one-to-many) (1b).
Mentions: A bow tie architecture shows the ability to accept a wide range of inputs (in Figure 1 the left, input wing) and convert them to a reduced set of universal building blocks (the knot, or core). Here, assembly protocols act on these basic modular building blocks, eventually restoring and fanning out a wide variety of outputs (the right bow). It is interesting to note that the bow tie can be interpreted as the combination of two degenerate systems coupled through a single central element, suggesting that the two concepts of degeneracy and bow tie share a similar conceptual and architectural design, i.e. the many-to-one (degeneracy) and one-to-many (pluripotentiality) paradigm (Figure 2).

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