Skip to main content

Evolutionary Systems Biology: Historical and Philosophical Perspectives on an Emerging Synthesis

  • Chapter
  • First Online:
Book cover Evolutionary Systems Biology

Part of the book series: Advances in Experimental Medicine and Biology ((volume 751))

Abstract

Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Loewe L, et al. (2010) Discussion. Workshop on Evolutionary Systems Biology at the International Conference on Systems Biology, 2010. http://evolutionarysystemsbiology.org/meeting/2010-ICSB/index.html. Accessed 4 Jan 2012

  2. Rheinberger H-J (2000) Gene concepts: fragments from the perspective of molecular biology. In: Beurton PJ, Falk R, Rheinberger H-J (eds) The concept of the gene in development and evolution: historical and epistemological perspectives. Cambridge University Press, Cambridge

    Google Scholar 

  3. Pigliucci M (2003) Species as family resemblance concepts: the (dis-) solution of the species problem? BioEssays 25:596–602

    PubMed  Google Scholar 

  4. Powell A, O’Malley MA, Müller-Wille S, Calvert S, Dupré J (2007) Disciplinary baptisms: a comparison of the naming stories of genetics, molecular biology, genomics, and systems biology. Hist Philos Life Sci 29:5–32

    PubMed  Google Scholar 

  5. White M (2010) Systems biology has become meaningless. Adaptive Complexity http://www.science20.com/adaptive_complexity/systems_biology_has_become_meaningless. Accessed 4 Jan 2012

  6. Bordel S, Nookaew I (2010) Systems biology or just biology? Biotechnol J 5:1257–1260

    PubMed  CAS  Google Scholar 

  7. Wilson I (2007) Top-down versus bottom-up—rediscovering physiology via systems biology? Mol Syst Biol 3:113, doi:10.1038/msb4100154

    PubMed  Google Scholar 

  8. Kritikou E, Pulverer B, Heinrichs A (2006) All systems go! NPG focus: systems biology: a user’s guide. http://www.nature.com/focus/systemsbiologyuserguide/editorial/sysbiol-s3.html. Accessed 4 Jan 2012

  9. Cornish-Bowden A, Cárdenas ML (2005) Systems biology may work when we learn to understand the parts in terms of the whole. Biochem Soc Trans 33:516–9

    PubMed  CAS  Google Scholar 

  10. Systems biology institutes. Systems biology: a user’s guide. http://www.nature.com/focus/systemsbiologyuserguide/appendices/institutes.html. Accessed 4 Jan 4 2012

  11. List of systems biology research groups.en.wikipedia.org/wiki/List_of_systems_biology _research_groups. Accessed 4 Jan 2012

    Google Scholar 

  12. Mesarovi MD (ed) (1968) Systems theory and biology. Springer-Verlag, NY

    Google Scholar 

  13. O’Malley MA, Soyer OS (2012) The roles of integration in molecular systems biology. Stud Hist Philos Biol Biomed Sci doi:10.1016/j.shpsc.2011.10.006

    PubMed  Google Scholar 

  14. Kitano H (2002) Systems biology: a brief overview. Science 295:1662–1664

    PubMed  CAS  Google Scholar 

  15. Auffray C, Imbeaud S, Roux-Rouquié M, Hood L (2003) From functional genomics to systems biology: concepts and practices. C R Biol 326:879–892

    PubMed  CAS  Google Scholar 

  16. Cho K-H, Wolkenhauer O (2003) Analysis and modelling of signal transduction pathways in systems biology. Biochem Soc Trans 31:1503–1509

    PubMed  CAS  Google Scholar 

  17. Kell DB, Oliver SG (2004) Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. BioEssays 26:99–105

    PubMed  Google Scholar 

  18. Heinemann M, Sauer U (2010) Systems biology of microbial metabolism. Curr Opin Microbiol 13:337–343

    PubMed  CAS  Google Scholar 

  19. Ullah M, Schmidt H, Cho K-H, Wolkenhauer O (2006) Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB. IEE Proc 153:53–60

    CAS  Google Scholar 

  20. Wilkinson DJ (2009) Stochastic modelling for quantitative description of heterogeneous biological systems. Nat Rev Genet 10:122–133

    PubMed  CAS  Google Scholar 

  21. Allen RJ et al. (2011) Predicting evolution: the next challenge for systems biology. Meeting report for Modelling Microbial Evolution, January 2011, Edinburgh. http://www2.ph.ed.ac.uk/~rallen2/esi_link.html. Accessed 1 Nov 2011

  22. Boogerd FC, Bruggeman FJ, Hofmeyr J-HS, Westerhoff HV (2007) Systems biology: philosophical foundations. Elsevier, Amsterdam

    Google Scholar 

  23. Dean AM, Thornton JW (2007) Mechanistic approaches to the study of evolution. Nat Rev Genet 8:675–688

    PubMed  CAS  Google Scholar 

  24. Knight CG, Pinney JW (2009) Making the right connections: biological networks in the light of evolution. BioEssays 31:1080–1090

    PubMed  Google Scholar 

  25. Wilkins AS (2007) Between ‘design’ and ‘bricolage’: genetic networks, levels of selection, and adaptive evolution. Proc Natl Acad Sci USA 104:8590–8596

    PubMed  CAS  Google Scholar 

  26. Cain CJ, Conte DA, García-Ojeda ME, Daglio LG, Johnson L, Lau EH, Manilay JO, Phillips JB, Rogers NS, Stolberg SE, Swift HF, Dawson MN (2008) What systems biology is (not, yet). Science 320:1013–1014

    Google Scholar 

  27. Soyer OS, Goldstein RA (2011) Evolution of response dynamics underlying bacterial chemotaxis. BMC Evol Biol 11:240

    PubMed  Google Scholar 

  28. Hey J, Fitch WM, Ayala FJ (2005) Systematics and the origin of species: an introduction. Proc Natl Acad Sci USA 102 (Suppl. 1):6515–6519

    PubMed  CAS  Google Scholar 

  29. Hughes AL (2005) Gene duplication and the origin of novel proteins. Proc Natl Acad Sci USA 102:8791–8792

    PubMed  CAS  Google Scholar 

  30. Papp B, Notebaart RA, Pál C (2011) Systems-biology approaches for predicting genome evolution. Nat Rev Genet 12:591–602

    PubMed  CAS  Google Scholar 

  31. Peters RH (1976) Tautology in evolution and ecology. Am Nat 110:1–12

    Google Scholar 

  32. Wagner A (1995) Reductionism in evolutionary biology: a perceptional artefact? In: Nadel L, Stein DL (eds), SFI studies in the sciences of complexity, Vol VI. Addison-Wesley, Reading MA

    Google Scholar 

  33. Hillis DM (1999) Predictive evolution. Science 286:1866–1867

    PubMed  CAS  Google Scholar 

  34. Murray BG Jr (2000) Universal laws and predictive theory in ecology and evolution. Oikos 89:403–408

    Google Scholar 

  35. Mayr E (1961) Cause and effect in biology. Science 134:1501–1506

    PubMed  CAS  Google Scholar 

  36. Wagner A (2008) Gene duplications, robustness and evolutionary innovations. BioEssays 30:367–373

    PubMed  CAS  Google Scholar 

  37. Gutiérrez J (2009) A developmental systems perspective on epistasis: computational exploration of mutational interactions in model developmental regulatory networks. PLoS One 4(9):e6823

    PubMed  Google Scholar 

  38. Trewavas A (2006) A brief history of systems biology. Plant Cell 18:2420–2430

    PubMed  CAS  Google Scholar 

  39. Wagner A (1994) Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proc Natl Acad Sci USA 91:4387–4391

    PubMed  CAS  Google Scholar 

  40. Wagner A (1996) Does evolutionary plasticity evolve? Evolution 50:1008–1023

    Google Scholar 

  41. Davidson EH (1991) Spatial mechanisms of gene regulation in metazoan embryos. Development 113:1–26

    PubMed  CAS  Google Scholar 

  42. Davidson EH, Peterson KJ, Cameron RA (1995) Origin of bilaterian body plans: evolution of developmental regulatory mechanisms. Science 270:1319–1325

    PubMed  CAS  Google Scholar 

  43. Davidson EH (2009) Developmental biology at the systems level. Biochim Biophys Acta 1789:248–249

    PubMed  CAS  Google Scholar 

  44. Wagner GP, Altenberg L (1996) Complex adaptations and the evolution of evolvability. Evolution 50:967–976

    Google Scholar 

  45. Müller GB, Wagner GP (1996) Homology, Hox genes, and developmental integration. Am Zool 36:4–13

    Google Scholar 

  46. Wagner GP, Chiu C-H, Laubichler M (2000) Developmental evolution as a mechanistic science: the inference from developmental mechanisms to evolutionary processes. Am Zool 40:819–831

    Google Scholar 

  47. Hurst LD (1999) The evolution of genomic anatomy. Trends Ecol Evol 14:108–112

    PubMed  Google Scholar 

  48. Hurst LD, Smith NGC (1999) Do essential genes evolve slowly? Curr Biol 9:747–750

    PubMed  CAS  Google Scholar 

  49. Huynen MA, Stadler PF, Fontana W (1996) Smoothness within ruggedness: the role of neutrality in adaptation. Proc Natl Acad Sci USA 93:397–401

    PubMed  CAS  Google Scholar 

  50. Schuster P, Fontana W (1999) Chance and necessity in evolution: lessons from RNA. Physica D 133:427–452

    CAS  Google Scholar 

  51. Ancel LW, Fontana W (2000) Plasticity, evolvability, and modularity in RNA. J Exp Zool B Mol Dev Evol 288:242–283

    CAS  Google Scholar 

  52. Stearns SC, Magwene P (2003) The naturalist in a world of genomics. Am Nat 161:171–180

    PubMed  Google Scholar 

  53. Medina M (2005) Genomes, phylogeny and evolutionary systems biology. Proc Natl Acad Sci USA 102:6630–6635

    PubMed  CAS  Google Scholar 

  54. Koonin EV, Wolf YI (2006) Evolutionary systems biology: links between gene evolution and function. Curr Opin Biotechnol 17:481–487

    PubMed  CAS  Google Scholar 

  55. Siegal ML, Promislow DEL, Bergman A (2007) Functional and evolutionary inference in gene networks: does topology matter? Genetica 129:83–103

    PubMed  CAS  Google Scholar 

  56. Pallen MJ, Wren BW (2007) Bacterial pathogenomics. Nature 449:835–842

    PubMed  CAS  Google Scholar 

  57. Lu C, Zhang Z, Leach L, Kearsey MJ, Luo ZW (2007) Impacts of yeast metabolic network structure on enzyme evolution. Genome Biol 8:407 doi:10.1186/gb-2007–8–8–407

    PubMed  Google Scholar 

  58. Chen B-S, Wu W-S (2007) Underlying principles of natural selection in network evolution: systems biology approach. Evol Bioinform Online 3:245–262

    PubMed  Google Scholar 

  59. Leclerc RD (2008) Survival of the sparsest: robust gene networks are parsimonious. Mol Syst Biol 4:213

    PubMed  Google Scholar 

  60. Loewe L (2009) A framework for evolutionary systems biology. BMC Syst Biol 3:27 doi:10.1186/1752–0509–3–27

    PubMed  Google Scholar 

  61. Koonin EV (2009) Darwinian evolution in the light of genomics. Nucleic Acids Res 37:1011–1034

    PubMed  CAS  Google Scholar 

  62. Leclerc RD (2009) Evolution, robustness, and the cost of complexity. Dissertation, Yale University (ProQuest Document ID 305040556)

    Google Scholar 

  63. Richards CL, Hanzawa Y, Katari MS, Ehrenreich IM, Engelmann KE, Purugganan MD (2009) Perspectives on ecological and evolutionary systems biology. Annu Plant Rev 35:331–351

    CAS  Google Scholar 

  64. Ratmann O, Andrieu C, Wiuf C, Richardson S (2009) Model criticism based on likelihood-free inference, with an application to protein network evolution. Proc Natl Acad Sci USA 106:10576–10581

    PubMed  CAS  Google Scholar 

  65. Wolf YI, Gopich IB, Lipman DJ, Koonin EV (2010) Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes. Genome Biol Evol 2:190–199

    PubMed  Google Scholar 

  66. Loewe L, Hill WG (2010) The population genetics of mutations: good, bad and indifferent. Philos Trans R Soc Lond B Biol Sci 365:1153–1167

    PubMed  Google Scholar 

  67. Soyer OS (2010) The promise of evolutionary systems biology: lessons from bacterial chemotaxis. Sci Signal 3:pe23

    Google Scholar 

  68. Park SG, Choi SS (2010) Expression breadth and expression abundance behave differently in correlations with evolutionary rates. BMC Evol Biol 10:241 doi:10.1186/1471-2148-10-241

    PubMed  Google Scholar 

  69. Barton MD, Delneri D, Oliver SG, Rattray M, Bergman CM (2010) Evolutionary systems biology of amino acid biosynthetic cost in yeast. PLoS One 5(8):e11935. doi:10.1371/journal.pone.0011935

    PubMed  Google Scholar 

  70. de Hoon MJL, Eichenberger P, Vitkup D (2010) Hierarchical evolution of the bacterial sporulation network. Curr Biol 20:R735–R745

    PubMed  Google Scholar 

  71. Wang Y, Franzosa EA, Zhang Y-S, Xia Y (2010) Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Res 38:5959–5969

    PubMed  CAS  Google Scholar 

  72. Wang Z. 2010. Evolutionary systems biology. Dissertation, University of Michigan http://gradworks.umi.com/34/29/3429306

  73. Zera AJ (2011) Microevolution of intermediary metabolism: evolutionary genetics meets metabolic biochemistry. J Exper Biol 214:179–190

    CAS  Google Scholar 

  74. Foster KR (2011) The sociobiology of molecular systems. Nat Rev Genet 12:193–203

    PubMed  CAS  Google Scholar 

  75. Huvet M, Toni T, Sheng X, Thorne T, Jovanovic G, Engle C, Buck M, Pinney JW, Stumpf MPH (2010) The evolution of the phage shock protein response system: interplay between protein function, genomic organization, and system function. Mol Biol Evol 28:1141–1155

    PubMed  Google Scholar 

  76. Thompson JD, Linard B, Lecompte O, Poch O (2011) A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One 6(3):e18093 doi:10.1371/journal.pone.0018093

    PubMed  CAS  Google Scholar 

  77. Shimizu KK, Kudoh H, Kobayashi MJ (2011) Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology. Ann Bot 108:777–787

    PubMed  CAS  Google Scholar 

  78. Papp B, Szappanos B, Notebaart RA (2011) Use of genome-scale metabolic models in evolutionary systems biology. In: Castrillo JI, Oliver SG (eds), Yeast Systems Biology, Meth Mol Biol 759:483–497

    CAS  Google Scholar 

  79. Koonin EV (2005) Systemic determinants of gene evolution and function. Mol Syst Biol doi:10.1038/msb4100029

    PubMed  Google Scholar 

  80. Systems Biology Discussion Group (2008) Convergent revolution: evolutionary systems biology. http://www.nyas.org/Publications/Ebriefings/Detail.aspx?cid=4723f666--6bc9--4efe-a7a5--02b029d35639. Accessed 4 Jan 2012

  81. Evolutionary systems biology: Meetings. http://evolutionarysystemsbiology.org/meeting/index.html

  82. Streelman JT, Kocher TD (2000) From phenotype to genotype. Evol Dev 2:166–173

    PubMed  CAS  Google Scholar 

  83. Benfey PN, Mitchell-Olds T (2008) From genotype to phenotype: systems biology meets natural variation. Science 320:495–497

    PubMed  CAS  Google Scholar 

  84. Koonin EV (2011) Are there laws of genome evolution? PLoS Comput Biol 7(8):e1002173

    PubMed  CAS  Google Scholar 

  85. Tirosh I, Bilu Y, Barkai N (2007) Comparative biology: beyond sequence analysis. Curr Opin Biotechnol 18:371–377

    PubMed  CAS  Google Scholar 

  86. DeLuna A, Vetsigian K, Shoresh N, Hegreness M, Colón-González M, Chao S, Kishony R (2008) Exposing the fitness contribution of duplicated genes. Nat Genet 40:676–681

    PubMed  CAS  Google Scholar 

  87. Hurst LD, Pál C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5:299–310

    PubMed  CAS  Google Scholar 

  88. Levasseur A, Pontarotti P, Poch O, Thompson JD (2008) Strategies for reliable exploitation of evolutionary concepts in high throughput biology. Evol Bioinform Online 4:121–137

    PubMed  CAS  Google Scholar 

  89. Carmel L, Koonin EV (2009) A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes. Genome Biol Evol. doi:10.1093/gbe/evp038

    PubMed  Google Scholar 

  90. Tirosh I, Barkai N (2011) Inferring regulatory mechanisms from patterns of evolutionary divergence. Mol Syst Biol 7:530 doi:10.1038/msb.2011.60

    PubMed  Google Scholar 

  91. Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8(7):e1000414

    PubMed  Google Scholar 

  92. Wapinski I, Pfiffner J, French C, Socha A, Thompson DA, Regev A (2010) Gene duplication and the evolution of ribosomal protein gene regulation in yeast. Proc Natl Acad Sci USA 107:5505–5510

    PubMed  CAS  Google Scholar 

  93. Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ (2009) Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol 7(6):e1000134

    PubMed  Google Scholar 

  94. Wang Z, Liao B-Y, Zhang J (2010) Genomic patterns of pleiotropy and the evolution of complexity. Proc Natl Acad Sci USA 107:18034–18039

    PubMed  CAS  Google Scholar 

  95. Teusink B, Westerhoff HV, Bruggeman FJ (2010) Comparative systems biology: from bacteria to man. Wiley Interdiscip Rev Syst Biol Med 2:518–532

    PubMed  CAS  Google Scholar 

  96. Cork JM, Purugganan MD (2004) The evolution of molecular genetic pathways and networks. BioEssays 26:479–484

    PubMed  CAS  Google Scholar 

  97. Proulx SR, Promislow DEL, Phillips PC. 2005. Network thinking in ecology and evolution. Trends Ecol Evol 20:345–353

    PubMed  Google Scholar 

  98. Feist AM, Palsson BØ (2008) The growing scope of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26:659–667

    PubMed  CAS  Google Scholar 

  99. Schuetz R, Keupfer L, Sauer U (2007) Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 3:119

    PubMed  Google Scholar 

  100. Oberhardt MA, Puchalka J, dos Santos VAPM, Papin JA (2011) Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PLOS Comput Biol 7(3):e1001116

    PubMed  CAS  Google Scholar 

  101. de Silva E, Stumpf MPH (2005) Complex networks and simple models in biology. J R Interface 2:419–430

    Google Scholar 

  102. Stumpf MPH, Kelly WP, Thorne T, Wiuf C (2007) Evolution at the system level: the natural history of protein interaction networks. Trends Ecol Evol 22:366–373

    PubMed  Google Scholar 

  103. Wagner A (2011) Genotype networks shed light on evolutionary constraints. Trends Ecol Evol 26:577–584

    PubMed  Google Scholar 

  104. Babu MM, Teichmann SA, Aravind L (2006) Evolutionary dynamics of prokaryotic transcriptional networks. J Mol Biol 358:614–633

    Google Scholar 

  105. Lozada-Chávez I, Janga SC, Collado-Vides J (2006) Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res 34:3434–3445

    PubMed  Google Scholar 

  106. Tan K, Shlomi T, Feizi H, Ideker T, Sharan R (2007) Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci USA 104:1283–1288

    PubMed  CAS  Google Scholar 

  107. Sharan R, Ideker T (2006) Modelling cellular machinery through biological network comparison. Nat Biotechnol 24:427–433

    PubMed  CAS  Google Scholar 

  108. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8:450–461

    PubMed  CAS  Google Scholar 

  109. Kashtan N, Alon U (2005) Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci USA 102:13773–13778

    PubMed  CAS  Google Scholar 

  110. Mazurie A, Bottani S, Vergassola M (2005) An evolutionary and functional assessment of regulatory network motifs. Genome Biol 6:R35 doi:10.1186/gb-2005–6–4-r35

    PubMed  Google Scholar 

  111. Cordero OX, Hogeweg P (2006) Feed-forward loop circuits as a side effect of genome evolution. Mol Biol Evol 23:1931–1936

    PubMed  CAS  Google Scholar 

  112. Presser A, Elowitz MB, Kellis M, Kishony R (2008) The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. Proc Natl Acad Sci USA 105:950–954

    PubMed  CAS  Google Scholar 

  113. Oikonomou P, Cluzel P (2006) Effects of topology on network evolution. Nat Phys 2:532–536

    CAS  Google Scholar 

  114. Wagner A (2003) How the global structure of protein interaction networks evolves. Proc R Soc Lond B 270:457–466

    CAS  Google Scholar 

  115. Burda Z, Krzywicki A, Martin OC, Zagorski M (2011) Motifs emerge from function in model gene regulatory networks. Proc Natl Acad Sci USA 108:17263–17268

    PubMed  CAS  Google Scholar 

  116. Borenstein E, Kupiec M, Feldman MW, Ruppin E (2008) Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci USA 105:14482–14487

    PubMed  CAS  Google Scholar 

  117. Borenstein E, Feldman MW (2009) Topological signatures of species interactions in metabolic networks. J Comput Biol 16:191–200

    PubMed  CAS  Google Scholar 

  118. Barabási A-L, Oltvai ZN (2004) Understanding the cell’s functional organization. Nat Rev Genet 5:101–113

    PubMed  Google Scholar 

  119. Hahn MW, Conant GC, Wagner A (2004) Molecular evolution in large genetic networks: does connectivity equal constraint? J Mol Evol 58:203–211

    PubMed  CAS  Google Scholar 

  120. Albert R (2005) Scale-free networks in cell biology. J Cell Sci 118: 4947–4957

    PubMed  CAS  Google Scholar 

  121. Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314:1938–1941

    PubMed  CAS  Google Scholar 

  122. Ratmann O, Wiuf C, Pinney JW (2009) From evidence to inference: probing the evolution of protein interaction networks. HFSP J 3:290–306

    PubMed  CAS  Google Scholar 

  123. Davidson EH (2011) Evolutionary bioscience as regulatory systems biology. Dev Biol 357:35–340

    PubMed  CAS  Google Scholar 

  124. Bayer TS (2010) Using synthetic biology to understand the evolution of gene expression. Curr Biol 20:R772–R779

    PubMed  CAS  Google Scholar 

  125. Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C (2011) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol 7:515 doi:10.1038/msb.2011.46

    PubMed  Google Scholar 

  126. Ibarra RU, Edwards JS, Palsson BØ (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420:186–189

    PubMed  CAS  Google Scholar 

  127. Pál C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37:1372–1375

    PubMed  Google Scholar 

  128. Pfeiffer T, Soyer OS, Bonhoeffer S (2005) The evolution of connectivity in metabolic networks. PLoS Biol 3(7):e228

    PubMed  Google Scholar 

  129. Isalan M, Lemerle C, Michalodimitrakis K, Beltrao P, Horn C, Raineri E, Garriga-Canut M, Serrano L (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840–845

    PubMed  CAS  Google Scholar 

  130. Philippe N, Crozat E, Lenski RE, Schneider D (2007) Evolution of global regulatory networks during a long-term experiment with Escherichia coli. BioEssays 29:846–860

    PubMed  Google Scholar 

  131. Jenkins DJ, Stekel DJ (2010) De novo evolution of complex, global and hierarchical gene regulatory mechanisms. J Mol Evol 71:128–140

    PubMed  CAS  Google Scholar 

  132. Poelwijk FJ, de Vos MGJ, Tans SJ (2011) Tradeoffs and optimality in the evolution of gene regulation. Cell 146:462–470

    PubMed  CAS  Google Scholar 

  133. Yokobayashi Y, Weiss R, Arnold FH (2002) Directed evolution of a genetic circuit. Proc Natl Acad Sci USA 99:16587–16591

    PubMed  CAS  Google Scholar 

  134. François P, Hakim V (2004) Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci USA 101:580–585

    PubMed  Google Scholar 

  135. Haseltine EL, Arnold FH (2007) Synthetic gene circuits: design with directed evolution. Annu Rev Biophys Biomol Struct 36:1–19

    PubMed  CAS  Google Scholar 

  136. Davidson EA, Windram OPF, Bayer TS (2012) Building synthetic systems to learn nature’s design principles. In: Soyer OS (ed) Evolutionary systems biology, Springer, NY

    Google Scholar 

  137. Wang Z, Zhang J (2011) Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci USA 108:E67–E76

    PubMed  Google Scholar 

  138. Dekel E, Mangan S, Alon U (2005) Environmental selection of the feed-forward loop circuit in gene-regulation networks. Phys Biol 2:81–88

    PubMed  CAS  Google Scholar 

  139. Lynch M (2007) The evolution of genetic networks by non-adaptive processes. Nat Rev Genet 8:803–813

    PubMed  CAS  Google Scholar 

  140. Camas FM, Poyatos JF (2008) What determines the assembly of transcriptional network motifs in Escherichia coli? PLoS One 3(11):e3657

    PubMed  Google Scholar 

  141. Fernández A, Lynch M (2011) Non-adaptive origins of interactome complexity. Nature 474:502–505

    PubMed  Google Scholar 

  142. Koonin EV, Wolf YI (2010) Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet 11:487–498

    PubMed  CAS  Google Scholar 

  143. Rodrigues JFM, Wagner A (2009) Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Comput Biol 5(12):e1000613

    Google Scholar 

  144. Bergman A, Siegal ML (2003) Evolutionary capacitance as a general feature of complex gene networks. Nature 424:549–552

    PubMed  CAS  Google Scholar 

  145. Soyer OS, Pfeiffer T (2010) Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Comput Biol 6:e1000907

    PubMed  Google Scholar 

  146. Poyatos JF (2011) The balance of weak and strong interactions in genetic networks. PLoS One 6(2):e14598

    PubMed  CAS  Google Scholar 

  147. Kaneko K (2009) Relationship among phenotypic plasticity, phenotypic fluctuations, robustness, and evolvability; Waddington’s legacy revisited under the spirit of Einstein. J Biosci 34:529–542

    PubMed  Google Scholar 

  148. Ciliberti S, Martin OC, Wagner A (2007) Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Comput Biol 3(2):e15

    PubMed  Google Scholar 

  149. Wagner A (2005) Distributed robustness versus redundancy as causes of mutational robustness. BioEssays 27:176–188

    PubMed  CAS  Google Scholar 

  150. Wagner A (2005) Robustness, evolvability and neutrality. FEBS Lett 579:1772–1778

    PubMed  CAS  Google Scholar 

  151. ten Tusscher KH, Hogeweg P (2011) Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability. PLoS Comput Biol 7(10):e1002208

    PubMed  Google Scholar 

  152. Solé RV, Valverde S (2007) Spontaneous emergence of modularity in cellular networks. J R Soc Interface 5:129–133

    Google Scholar 

  153. Kashtan N, Parter M, Dekel E, Mayo AE, Alon A (2009) Extinctions in heterogeneous environments and the evolution of modularity. Evolution doi:10.1111/j.1558–5646.2009.00684.x

    PubMed  Google Scholar 

  154. Snel B, Huynen MA (2004) Quantifying modularity in the evolution of biomolecular systems. Genome Res 3:391–397

    Google Scholar 

  155. Crombach A, Hogeweg P (2008) Evolution of evolvability in gene regulatory networks. PLoS Comput Biol 4(7):e1000112

    PubMed  Google Scholar 

  156. Kreimer A, Borenstein E, Gophna U, Ruppin E (2008) The evolution of modularity in bacterial metabolic networks. Proc Natl Acad Sci USA 105:6976–6981

    PubMed  CAS  Google Scholar 

  157. Phillips PC (2008) Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9:855–867

    PubMed  CAS  Google Scholar 

  158. Moore JH, Williams SM (2005) Traversing the conceptual divide between biological and statistical epistasis: systems biology and more modern synthesis. BioEssays 27:637–646

    PubMed  CAS  Google Scholar 

  159. Gjuvsland AB, Hayes BJ, Omholt SW, Carlborg Ö (2007) Statistical epistasis is a generic feature of gene regulatory networks. Genetics 175:411–420

    PubMed  Google Scholar 

  160. MacLean RC, Hall AR, Perron GG, Buckling A (2010) The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nat Rev Genet 11:405–414

    PubMed  CAS  Google Scholar 

  161. Forde SE, Beardmore RE, Gudelj I, Arkin SS, Thompson JN, Hurst LD (2008) Understanding the limits to generalizability of experimental evolutionary models. Nature 455:220–223

    PubMed  CAS  Google Scholar 

  162. Wagner GP, Zhang J (2011) The pleotropic structure of the genotype-phenotype map: the evolvability of complex organisms. Nat Rev Genet 12:204–213

    PubMed  CAS  Google Scholar 

  163. Tyler AL, Asselbergs FW, Williams SM, Moore JH (2009) Shadows of complexity: what biological networks reveal about epistasis and pleiotropy. BioEssays 31:220–227

    PubMed  Google Scholar 

  164. Knight CG, Zitzmann N, Prabhakar S, Antrobus R, Dwek R, Hebestreit H, Rainey PB (2006) Unraveling adaptive evolution: how a single point mutation affects the protein coregulation network. Nat Genet 38:1015–1022

    PubMed  CAS  Google Scholar 

  165. Snitkin ES, Segrè D (2011) Epistatic interaction maps relative to multiple metabolic phenotypes. PLoS Genet 7(2):e1001294

    PubMed  CAS  Google Scholar 

  166. Conrad TM, Lewis NE, Palsson BØ (2011) Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol 7:509

    PubMed  Google Scholar 

  167. Nam J, Dong P, Tarpine R, Istrail S, Davidson EH (2010) Functional cis-regulatory genomics for systems biology. Proc Natl Acad Sci USA 107:3930–3935

    PubMed  CAS  Google Scholar 

  168. Bains W (2008) Technological speculations and science. Biosci Hypotheses 1:177–178

    Google Scholar 

  169. Eddy SR (2005) ‘Antedisciplinary’ science. PLoS Comput Biol 1(1):e6

    PubMed  Google Scholar 

  170. Johnson NA (2007) The micro-evolution of development. Genetica 129:1–5

    PubMed  Google Scholar 

  171. Wilkins AS (2002) The evolution of developmental pathways. Sinauer, Sunderland MA

    Google Scholar 

  172. Alonso CR, Wilkins AS (2005) The molecular elements that underlie developmental evolution. Nat Rev Genet 6:709–715

    PubMed  CAS  Google Scholar 

  173. Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P (2006) Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 443:594–597

    PubMed  CAS  Google Scholar 

  174. Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 8:93–103

    PubMed  CAS  Google Scholar 

  175. Moses AM, Landry CR (2010) Moving from transcriptional to phospho-evolution: generalizing regulatory evolution? Trends Genet 26:462–467

    PubMed  CAS  Google Scholar 

  176. Freschi L, Courcelles M, Thibault P, Michnick SW, Landry CR (2011) Phosphorylation network rewiring by gene duplication. Mol Syst Biol 7:504 doi:10.1038/msb.2011.43

    PubMed  Google Scholar 

  177. Jaeger J (2011) The gap gene network. Cell Mol Life Sci 68:243–274

    PubMed  CAS  Google Scholar 

  178. Sommer RJ (2009) The future of evo-devo: model systems and evolutionary theory. Nat Rev Genet 10:416–422

    PubMed  CAS  Google Scholar 

  179. Haag ES, Lenski RE (2011) L’enfant terrible at 30: the maturation of evolutionary developmental biology. Development 138:2633–2637

    PubMed  CAS  Google Scholar 

  180. Fontana W (2002) Modelling ‘evo-devo’ with RNA. BioEssays 24:1164–1177

    PubMed  CAS  Google Scholar 

  181. Tinbergen N (1963) On aims and methods of ethology. Z Tierpsychol 20:410–433

    Google Scholar 

  182. Carroll SB (2008) Evo-devo and an explanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25–36

    PubMed  CAS  Google Scholar 

  183. Huang S (2011) The molecular and mathematical basis of Waddington’s epigenetic landscape: a framework for post-Darwinian biology? BioEssays 34:149–157

    PubMed  Google Scholar 

  184. Pigliucci M, Müller GB (2010) Evolution—the extended synthesis. MIT Press, Cambridge

    Google Scholar 

  185. Rose MR, Oakley TH (2007) The new biology: beyond the modern synthesis. Biol Direct 2:30 doi:10.1186/1745–6150–2–30

    PubMed  Google Scholar 

  186. Klitgord N, Segrè D (2011) Ecosystems biology of microbial metabolism. Curr Opin Biotechnol 22:1–6

    Google Scholar 

  187. Tagkopoulos I, Liu Y-C, Tavozoie S (2008) Predictive behavior within microbial genetic networks. Science 320:1313–1317

    PubMed  CAS  Google Scholar 

  188. Raes J, Letunic I, Yamada T, Jensen LJ, Bork P (2011) Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol 7:473 doi:10.1038/msb.2011.6

    PubMed  Google Scholar 

  189. Ernebjerg M, Kishony R (2011) Dynamic phenotypic clustering in noisy ecoystems. PLoS Comput Biol 7(3):e1002017

    PubMed  CAS  Google Scholar 

  190. Collins FS, Green ED, Guttmacher AE, Guyer MS, et al. (2003) A vision for the future of genomics research. Nature 422:835–847

    PubMed  CAS  Google Scholar 

  191. Butcher EC (2005) Can cell systems biology rescue drug discovery? Nat Rev Drug Discov 4:461–467

    PubMed  CAS  Google Scholar 

  192. Clermont G, Auffray C, Moreau Y, Rocke DM, Dalevi D, et al. (2009) Bridging the gap between systems biology and medicine. Genome Med 1:88 doi:10.1186/gm88

    PubMed  Google Scholar 

  193. O’Malley MA, Stotz K (2011) Intervention, integration and translation in obesity research: genetic, developmental and metaorganismal perspectives. Philos Ethics Humanit Med 6:2. doi:10.1186/1747–5341–6–2

    PubMed  Google Scholar 

  194. Gatenby RA, Gillies RJ, Brown JS (2010) The evolutionary dynamics of cancer prevention. Nat Rev Cancer 10:526–527

    PubMed  CAS  Google Scholar 

  195. Baquero F, Coque TM, de la Cruz F (2011) Ecology and evolution as targets: the need for novel eco-evo drugs and strategies to fight antibiotic resistance. Antimicrob Agents Chemother 55:3649–3660

    PubMed  CAS  Google Scholar 

  196. Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417–433

    PubMed  CAS  Google Scholar 

  197. Lambert G, Estévez-Salmeron, Oh S, Liao D, Emerson BM, Tisty TD, Austin RH (2011) An analogy between the evolution of drug resistance in bacterial communities and malignant tissues. Nat Rev Cancer 11:375–382

    PubMed  CAS  Google Scholar 

  198. Pujol A, Mosca R, Farrés J, Aloy P (2009) Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci 31:116–123

    Google Scholar 

  199. Auffray C, Chen Z, Hood L (2009) Systems medicine: the future of medical genomics and healthcare. Genome Med 1(1):2.1–2.11

    Google Scholar 

  200. Williams GC, Nesse RM (1991) The dawn of Darwinian medicine. Q Rev Biol 66:1–22

    PubMed  CAS  Google Scholar 

  201. Poyatos JF, Carnero A (2004) Non-neutral role of replicative senescence in tissue homeostasis and tumorigenesis. J Theoret Biol 230:333–341

    CAS  Google Scholar 

  202. Poyatos JF, Hurst LD (2004) How biologically relevant are interaction-based modules in protein networks? Genome Biol 5:R93

    PubMed  Google Scholar 

  203. Poyatos FJ, Hurst LD (2006) Is optimal gene order impossible? Trends Genet 22:420–423

    PubMed  CAS  Google Scholar 

  204. Thomas PD, Mi H, Lewis S (2006) Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol 11:4–11

    Google Scholar 

  205. Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B (2007) Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res 34:W645–W650

    Google Scholar 

  206. Mi H, Guo N, Kejariwal A, Thomas PD (2007) PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res 35:D247–D252

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The research for this chapter was funded by the Australian Research Council in the form of a Future Fellowship held at the University of Sydney. The referees and editor are gratefully acknowledged for their assistance in improving this chapter.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Maureen A. O’Malley .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

O’Malley, M.A. (2012). Evolutionary Systems Biology: Historical and Philosophical Perspectives on an Emerging Synthesis. In: Soyer, O. (eds) Evolutionary Systems Biology. Advances in Experimental Medicine and Biology, vol 751. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-3567-9_1

Download citation

Publish with us

Policies and ethics