The Emergence of Modularity in Biological Systems

Overview

Journal Phys Life Rev

Publisher Elsevier

Specialties Biology
Biophysics

Date 2011 Mar 1

PMID 21353651

Citations 60

Authors

Dirk M Lorenz

Alice Jeng

Michael W Deem

Affiliations

Soon will be listed here.

Abstract

In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may spontaneously organize to a structured form. That is, we seek to explain how biology nucleated from among the many possibilities in chemistry. The emergence of modular organization of biological structure will be described as a symmetry-breaking phase transition, with modularity as the order parameter. Experimental support for this description will be reviewed. Examples will be presented from pathogen structure, metabolic networks, gene networks, and protein-protein interaction networks. Additional examples will be presented from ecological food networks, developmental pathways, physiology, and social networks.

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References

Collins J, Imhoff T, Grigg P . Noise-enhanced tactile sensation. Nature. 1996; 383(6603):770. DOI: 10.1038/383770a0. View

Yang A . Modularity, evolvability, and adaptive radiations: a comparison of the hemi- and holometabolous insects. Evol Dev. 2001; 3(2):59-72. DOI: 10.1046/j.1525-142x.2001.003002059.x. View

Massey R, Buckling A . Environmental regulation of mutation rates at specific sites. Trends Microbiol. 2003; 10(12):580-4. DOI: 10.1016/s0966-842x(02)02475-7. View

Chavez M, Valencia M, Navarro V, Latora V, Martinerie J . Functional modularity of background activities in normal and epileptic brain networks. Phys Rev Lett. 2010; 104(11):118701. DOI: 10.1103/PhysRevLett.104.118701. View

Meir E, von Dassow G, Munro E, Odell G . Robustness, flexibility, and the role of lateral inhibition in the neurogenic network. Curr Biol. 2002; 12(10):778-86. DOI: 10.1016/s0960-9822(02)00839-4. View

Spirin V, Mirny L . Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A. 2003; 100(21):12123-8. PMC: 218723. DOI: 10.1073/pnas.2032324100. View

He J, Deem M . Structure and response in the world trade network. Phys Rev Lett. 2011; 105(19):198701. DOI: 10.1103/PhysRevLett.105.198701. View

Nakamura Y, Itoh T, Matsuda H, Gojobori T . Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet. 2004; 36(7):760-6. DOI: 10.1038/ng1381. View

Crombach A, Hogeweg P . Evolution of evolvability in gene regulatory networks. PLoS Comput Biol. 2008; 4(7):e1000112. PMC: 2432032. DOI: 10.1371/journal.pcbi.1000112. View

10.

Singh A, Wolf D, Wang P, Arkin A . Modularity of stress response evolution. Proc Natl Acad Sci U S A. 2008; 105(21):7500-5. PMC: 2396705. DOI: 10.1073/pnas.0709764105. View

11.

Raff E, Raff R . Dissociability, modularity, evolvability. Evol Dev. 2001; 2(5):235-7. DOI: 10.1046/j.1525-142x.2000.00069.x. View

12.

Priplata A, Niemi J, Harry J, Lipsitz L, Collins J . Vibrating insoles and balance control in elderly people. Lancet. 2003; 362(9390):1123-4. DOI: 10.1016/S0140-6736(03)14470-4. View

13.

Raff R, Sly B . Modularity and dissociation in the evolution of gene expression territories in development. Evol Dev. 2001; 2(2):102-13. DOI: 10.1046/j.1525-142x.2000.00035.x. View

14.

Bogarad L, Deem M . A hierarchical approach to protein molecular evolution. Proc Natl Acad Sci U S A. 1999; 96(6):2591-5. PMC: 15812. DOI: 10.1073/pnas.96.6.2591. View

15.

Radman M, Matic I, Taddei F . Evolution of evolvability. Ann N Y Acad Sci. 1999; 870:146-55. DOI: 10.1111/j.1749-6632.1999.tb08874.x. View

16.

Kashtan N, Noor E, Alon U . Varying environments can speed up evolution. Proc Natl Acad Sci U S A. 2007; 104(34):13711-6. PMC: 1948871. DOI: 10.1073/pnas.0611630104. View

17.

Gardner A, Zuidema W . Is evolvability involved in the origin of modular variation?. Evolution. 2003; 57(6):1448-50. DOI: 10.1111/j.0014-3820.2003.tb00352.x. View

18.

Kepler T, Perelson A . Drug concentration heterogeneity facilitates the evolution of drug resistance. Proc Natl Acad Sci U S A. 1998; 95(20):11514-9. PMC: 21672. DOI: 10.1073/pnas.95.20.11514. View

19.

Price M, Dehal P, Arkin A . Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 2008; 9(1):R4. PMC: 2395238. DOI: 10.1186/gb-2008-9-1-r4. View

20.

Lipson H, Pollack J, Suh N . On the origin of modular variation. Evolution. 2002; 56(8):1549-56. DOI: 10.1111/j.0014-3820.2002.tb01466.x. View