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According to Alon, "''The cell can be viewed as an overlay of at least three types of networks, which describes protein-protein, protein-DNA, and protein-metabolite interactions.''"<ref name=alon2003> Alon U (2003) [http://dx.doi.org/10.1126/science.1089072 Biological networks: the tinkerer as an engineer.] ''Science'' 301:1866-7 PMID 14512615</ref> Alon notes that cellular networks are like many human engineered networks in that they show 'modularity', 'robustness', and 'motifs':   
According to Alon, "''The cell can be viewed as an overlay of at least three types of networks, which describes protein-protein, protein-DNA, and protein-metabolite interactions.''"<ref name=alon2003> Alon U (2003) [http://dx.doi.org/10.1126/science.1089072 Biological networks: the tinkerer as an engineer.] ''Science'' 301:1866-7 PMID 14512615</ref> Alon notes that cellular networks are like many human engineered networks in that they show 'modularity', 'robustness', and 'motifs':   
<br>
<br>
:*''Modules'' comprise subnetworks with specific functions differing from those of other modules, and which typically but not invariably connect with other modules, often only at one input node and one output node. An individual module achieves its status as a distinct entity not only by its functional specificity but also by spatial specificity (e.g., ribosomes) or by chemical specificity (e.g., signal transduction networks). Modularity helps to facilitate real-time system adaptability to environmental change, as the organization of modules in the system contributes to the emergent properties of the system.<ref name=hartwell99>Hartwell LH, Hopfield JJ, Leibler S, Murray AW. (1999) [http://www.nature.com/nature/journal/v402/n6761supp/full/402c47a0.html From molecular to modular cell biology.] ''Nature'' 402:C47-C52] PMID 10591225</ref>&nbsp;&nbsp;It also facilitates evolutionary adaption, as, to select an adaptation, evolution may need tinker with just a few modules rather than with the whole system. Evolution can sometimes 'exapt' existing modules for new functions that contribute to reproductive fitness. For example, Darwin surmised that the swim bladder of skeletally heavy fish evolved as an adaptation for control of buoyancy but was exapted as a respiratory organ in certain fish and in land vertebrates. <ref name=darwinorigined1>Darwin C (1859) [http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=side&pageseq=1 ''On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life.''] 1st edition. Chap. VI, p190 “Difficulties on Theory”
*''Modules'' comprise subnetworks with specific functions differing from those of other modules, and which typically but not invariably connect with other modules, often only at one input node and one output node. An individual module achieves its status as a distinct entity not only by its functional specificity but also by spatial specificity (e.g., ribosomes) or by chemical specificity (e.g., signal transduction networks).  
**Modularity helps to facilitate real-time system adaptability to environmental change, as the organization of modules in the system contributes to the emergent properties of the system.<ref name=hartwell99>Hartwell LH, Hopfield JJ, Leibler S, Murray AW. (1999) [http://www.nature.com/nature/journal/v402/n6761supp/full/402c47a0.html From molecular to modular cell biology.] ''Nature'' 402:C47-C52] PMID 10591225</ref>&nbsp;&nbsp;It also facilitates evolutionary adaption, as, to select an adaptation, evolution may need tinker with just a few modules rather than with the whole system. Evolution can sometimes 'exapt' existing modules for new functions that contribute to reproductive fitness. For example, Darwin surmised that the swim bladder of skeletally heavy fish evolved as an adaptation for control of buoyancy but was exapted as a respiratory organ in certain fish and in land vertebrates. <ref name=darwinorigined1>Darwin C (1859) [http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=side&pageseq=1 ''On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life.''] 1st edition. Chap. VI, p190 “Difficulties on Theory”
:*Darwin wrote: “The illustration of the swimbladder in fishes is a good one, because it shows us clearly the highly important fact that an organ originally constructed for one purpose, namely flotation, may be converted into one for a wholly different purpose, namely respiration.”
:*Darwin wrote: “The illustration of the swimbladder in fishes is a good one, because it shows us clearly the highly important fact that an organ originally constructed for one purpose, namely flotation, may be converted into one for a wholly different purpose, namely respiration.”
:*Stephen Jay Gould and others dispute Darwin on the direction of exaptation between swimbladder and lung, though not the rality of exaptation:  Gould writes:  “Darwin was wrong; ancestral vertebrates had lungs… The first vertebrates maintained a dual system for respiration: gills for extracting gases from seawater and lungs for gulping air at the surface.  A few modern fishes, including the coelacanth, the African bichir Polypterus, and three genera of lungfishes, retained lungs… In two major lineages of derived bony fishes &mdash; the chondrosteans and the teleosts -- lungs evolved to swim bladders by atrophy of vascular tissue to create a more or less empty sac and, in some cases, by loss of the connecting tube to the esophagus (called the trachea in humans and other creatures with lungs). See: Gould SJ (1993) ''Eight Little Piggies: Reflections in Natural History.'' Norton, New York. ISBN 039303416X.</ref>&nbsp;<ref>[http://www.palaeos.com/Vertebrates/Lists/Glossary/GlossaryEo.html See definition of ‘exapt’]</ref>   
:*Stephen Jay Gould and others dispute Darwin on the direction of exaptation between swimbladder and lung, though not the rality of exaptation:  Gould writes:  “Darwin was wrong; ancestral vertebrates had lungs… The first vertebrates maintained a dual system for respiration: gills for extracting gases from seawater and lungs for gulping air at the surface.  A few modern fishes, including the coelacanth, the African bichir Polypterus, and three genera of lungfishes, retained lungs… In two major lineages of derived bony fishes &mdash; the chondrosteans and the teleosts -- lungs evolved to swim bladders by atrophy of vascular tissue to create a more or less empty sac and, in some cases, by loss of the connecting tube to the esophagus (called the trachea in humans and other creatures with lungs). See: Gould SJ (1993) ''Eight Little Piggies: Reflections in Natural History.'' Norton, New York. ISBN 039303416X.</ref>&nbsp;<ref>[http://www.palaeos.com/Vertebrates/Lists/Glossary/GlossaryEo.html See definition of ‘exapt’]</ref>   


:*''Robustness'' describes how a network is able to maintain its functionality despite environmental perturbations that affect the components. Robustness also reduces the range of network types that researchers must consider, because only certain types of networks are robust.<ref>Lenski RE ''et al.'' (2006) [http://dx.doi.org/10.1371/journal.pbio.0040428 Balancing robustness and evolvability.] ''PLoS Biol'' 4(12):e428]</ref>
*''Robustness'' refers to how a network maintains its functionality despite environmental perturbations that affect the components. Robustness also reduces the range of network types that researchers must consider, because only certain types of networks are robust.<ref>Lenski RE ''et al.'' (2006) [http://dx.doi.org/10.1371/journal.pbio.0040428 Balancing robustness and evolvability.] ''PLoS Biol'' 4(12):e428]</ref>


:*''Network motifs'' offer economy of network design, as the same circuit can have many different uses in cellular regulation, as in the case of autoregulatory circuits and feedforward loops. Nature selects motifs in part for their ability to make networks robust, so systems use motifs that work well over and over again in many different networks.<ref name=alon07nat>Alon U (2007) [http://dx.doi.org/10.1038/446497a Simplicity in biology.] ''Nature'' 446:497]</ref> In several well-studied biological networks, the abundance of network motifs &mdash; small subnetworks &mdash; correlates with the degree of robustness.<ref>Prill RJ ''et al.'' (2004) [http://dx.doi.org/10.1371/journal.pbio.0030343 Dynamic properties of network motifs contribute to biological network organization.] ''PLoS Biol'' 3:e343]</ref> Networks, like those in cells and those in neural networks in the brain,<ref>Sporns O, Kotter R (2004) [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0020369 Motifs in brain networks.] ''PLoS Biol'' 2:e369]</ref> use motifs as basic building blocks, like multicellular organisms use cells as basic building blocks. Motifs offer biologists a level of simplicity of biological functionality for their efforts to model the dynamics of organized hierarchies of networks.<ref name=alon07nat/>
*''Network motifs'' offer economy of network design, as the same circuit can have many different uses in cellular regulation, as in the case of autoregulatory circuits and feedforward loops. Nature selects motifs in part for their ability to make networks robust, so systems use motifs that work well over and over again in many different networks.<ref name=alon07nat>Alon U (2007) [http://dx.doi.org/10.1038/446497a Simplicity in biology.] ''Nature'' 446:497]</ref> In several well-studied biological networks, the abundance of network motifs &mdash; small subnetworks &mdash; correlates with the degree of robustness.<ref>Prill RJ ''et al.'' (2004) [http://dx.doi.org/10.1371/journal.pbio.0030343 Dynamic properties of network motifs contribute to biological network organization.] ''PLoS Biol'' 3:e343]</ref>  
**Networks, like those in cells and those in neural networks in the brain,<ref>Sporns O, Kotter R (2004) [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0020369 Motifs in brain networks.] ''PLoS Biol'' 2:e369]</ref> use motifs as basic building blocks, like multicellular organisms use cells as basic building blocks. Motifs offer biologists a level of simplicity of biological functionality for their efforts to model the dynamics of organized hierarchies of networks.<ref name=alon07nat/>


The view of the cell as an overlay of mathematically-definable dynamic networks can reveal how a living system can exist as an improbable, intricate, self-orchestrated dance of molecules.<ref>Alon U (2007) ''An Introduction to Systems Biology: Design Principles of Biological Circuits.'' Boca Raton: Chapman and Hall/CRC</ref> The 'overlay of networks' view also suggests how the concept of self-organized networks can extend to all higher levels of living systems.
The view of the cell as an overlay of mathematically-definable dynamic networks can reveal how a living system can exist as an improbable, intricate, self-orchestrated dance of molecules.<ref>Alon U (2007) ''An Introduction to Systems Biology: Design Principles of Biological Circuits.'' Boca Raton: Chapman and Hall/CRC</ref> The 'overlay of networks' view also suggests how the concept of self-organized networks can extend to all higher levels of living systems.

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...networks are now widely recognized not only as outcomes of complex interactions, but as key determinants of structure, function, and dynamics in systems that span the biological, physical, and social sciences...
   —Joshua S. Weitz et al.[1]


Biological networks resemble many types of man-made networks, in particular those types of man-made networks consisting of diverse structures and functions, like the World Wide Web, a collection of parts, the parts themselves differing in type, with multiple copies of each type, parts capable of interconnecting, the interconnections tying all the parts together into a whole entity with a particular architecture made up of subtructures and modules of subtructures, the interconnected parts capable of interacting, the interactions capable of producing particular changes in the structure of each other or in the structures' properties, enabling intercommunication with signals that convey information, the whole structure a functional unit designed for a purpose.

Biological networks differ from such man-made networks as the World Wide Web, however, in having no human designer or initiating human engineer. Biological networks emerged from extra-human nature by organic evolutionary processes, their foundational network-as-a-whole a biological cell, the cell an overlay of differing types of networks, a computationally-enabled information-processing bio-computer, designed basically to live and reproduce itself, self-assembling and self-organizing, autonomously functioning, capable of exhibiting behaviors/functions/properties not in practice predictable or explicable, capable of cooperating with other cells to generate multicellular structures that can intelligently and consciously design networks, inorganic as well as organic ones.

Overview

See also: Systems biology

We have a new continent to explore and will need maps at every scale to find our way.
  —Dennis Bray[2]


Networks represent (i.e., 're-present') a system as 'nodes' (also referred to as 'vertices') and interactions among the nodes (also referred to as 'edges' or 'arrows' or 'links').[3] For example, in a spoken sentence, words and phrases make up the nodes, and the interconnections of syntax (subject-to-predicate, preposition-to-object of preposition, etc.) make up the links. Intracellular molecular networks represent specific functions in the cell; genes and proteins make up the nodes, and their interactions make up the edges or arrows. The network of the nervous system has neuron nodes and axons and dendrites edges. The Internet has a network of HTML files and links pointing between them. Many networks accept inputs of one kind and return outputs of a different kind.

One finds networks everywhere in biology, from intracellular signaling pathways, to intraspecies cooperative networks, to ecosystem food webs. Humans deliberately construct social networks of individuals working (more or less) to a common purpose, such as the U.S. Congress; they also construct networks of electronic parts to produce, for example, mobile phones; and networks of sentences and paragraphs to express messages, including this very article. Researchers view the World Wide Web as a network, and study its characteristics and dynamics.[4] [5]

According to Alon, "The cell can be viewed as an overlay of at least three types of networks, which describes protein-protein, protein-DNA, and protein-metabolite interactions."[6] Alon notes that cellular networks are like many human engineered networks in that they show 'modularity', 'robustness', and 'motifs':

  • Modules comprise subnetworks with specific functions differing from those of other modules, and which typically but not invariably connect with other modules, often only at one input node and one output node. An individual module achieves its status as a distinct entity not only by its functional specificity but also by spatial specificity (e.g., ribosomes) or by chemical specificity (e.g., signal transduction networks).
    • Modularity helps to facilitate real-time system adaptability to environmental change, as the organization of modules in the system contributes to the emergent properties of the system.[7]  It also facilitates evolutionary adaption, as, to select an adaptation, evolution may need tinker with just a few modules rather than with the whole system. Evolution can sometimes 'exapt' existing modules for new functions that contribute to reproductive fitness. For example, Darwin surmised that the swim bladder of skeletally heavy fish evolved as an adaptation for control of buoyancy but was exapted as a respiratory organ in certain fish and in land vertebrates. [8] [9]
  • Robustness refers to how a network maintains its functionality despite environmental perturbations that affect the components. Robustness also reduces the range of network types that researchers must consider, because only certain types of networks are robust.[10]
  • Network motifs offer economy of network design, as the same circuit can have many different uses in cellular regulation, as in the case of autoregulatory circuits and feedforward loops. Nature selects motifs in part for their ability to make networks robust, so systems use motifs that work well over and over again in many different networks.[11] In several well-studied biological networks, the abundance of network motifs — small subnetworks — correlates with the degree of robustness.[12]
    • Networks, like those in cells and those in neural networks in the brain,[13] use motifs as basic building blocks, like multicellular organisms use cells as basic building blocks. Motifs offer biologists a level of simplicity of biological functionality for their efforts to model the dynamics of organized hierarchies of networks.[11]

The view of the cell as an overlay of mathematically-definable dynamic networks can reveal how a living system can exist as an improbable, intricate, self-orchestrated dance of molecules.[14] The 'overlay of networks' view also suggests how the concept of self-organized networks can extend to all higher levels of living systems.

Small world networks

Holding reference: [15]

References and notes cited in text as superscripts

  1. ↑ Weitz JS, Benfey PN, Wingreen NS. (2007) Evolution, Interactions, and Biological Networks. PLoS Biol 5(1): e11.
  2. ↑ Bray D. (2003) Molecular Networks: The Top-Down View. Science 301:1864-1865.
  3. ↑ Barabási A-L, Albert R. (1999) Emergence of Scaling in Random Networks. Science 286:509-511.
  4. ↑ Barabási AL (2002) Linked: The New Science of Networks. Cambridge, Mass: Perseus Pub. ISBN 0-7382-0667-9
  5. ↑ Watts DJ. (2007) A twenty-first century science. Nature 445:489
  6. ↑ Alon U (2003) Biological networks: the tinkerer as an engineer. Science 301:1866-7 PMID 14512615
  7. ↑ Hartwell LH, Hopfield JJ, Leibler S, Murray AW. (1999) From molecular to modular cell biology. Nature 402:C47-C52] PMID 10591225
  8. ↑ Darwin C (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. 1st edition. Chap. VI, p190 “Difficulties on Theory”
    • Darwin wrote: “The illustration of the swimbladder in fishes is a good one, because it shows us clearly the highly important fact that an organ originally constructed for one purpose, namely flotation, may be converted into one for a wholly different purpose, namely respiration.”
    • Stephen Jay Gould and others dispute Darwin on the direction of exaptation between swimbladder and lung, though not the rality of exaptation: Gould writes: “Darwin was wrong; ancestral vertebrates had lungs… The first vertebrates maintained a dual system for respiration: gills for extracting gases from seawater and lungs for gulping air at the surface. A few modern fishes, including the coelacanth, the African bichir Polypterus, and three genera of lungfishes, retained lungs… In two major lineages of derived bony fishes — the chondrosteans and the teleosts -- lungs evolved to swim bladders by atrophy of vascular tissue to create a more or less empty sac and, in some cases, by loss of the connecting tube to the esophagus (called the trachea in humans and other creatures with lungs). See: Gould SJ (1993) Eight Little Piggies: Reflections in Natural History. Norton, New York. ISBN 039303416X.
  9. ↑ See definition of ‘exapt’
  10. ↑ Lenski RE et al. (2006) Balancing robustness and evolvability. PLoS Biol 4(12):e428]
  11. ↑ 11.0 11.1 Alon U (2007) Simplicity in biology. Nature 446:497]
  12. ↑ Prill RJ et al. (2004) Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 3:e343]
  13. ↑ Sporns O, Kotter R (2004) Motifs in brain networks. PLoS Biol 2:e369]
  14. ↑ Alon U (2007) An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton: Chapman and Hall/CRC
  15. ↑ Watts DJ, Strogatz SH. (1998) Collective dynamics of 'small-world' networks. Nature 393:440-442.
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