Biology & Philosophy

, Volume 31, Issue 5, pp 639–662 | Cite as

The ontology of organisms: Mechanistic modules or patterned processes?

Article

Abstract

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles.

Keywords

Mechanisms Process ontology Evo-devo Dynamic systems theory 

References

  1. Allen G (2005) Mechanism, vitalism and organicism in late nineteenth and twentieth-century biology: the importance of historical context. Stud Hist Philos Biol Biomed Sci 36(2):261–283CrossRefGoogle Scholar
  2. Alon U (2006) An introduction to systems biology: design principles of biological circuits. Taylor & Francis, LondonGoogle Scholar
  3. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8(6):450–461CrossRefGoogle Scholar
  4. Andersen P, Emmeche C, Finnemann N, Christiansen P (eds) (2000) Downward causation: minds, bodies and matter. Aarhus University Press, AarhusGoogle Scholar
  5. Armstrong D (1997) A world of states of affairs. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  6. Bapteste E, Dupré J (2013) Towards a processual microbial ontology. Biol Philos 28(2):379–404CrossRefGoogle Scholar
  7. Bechtel W, Abrahamsen A (2005) Explanation: a mechanistic alternative. Stud Hist Philos Biol Biomed Sci 36(2):421–441CrossRefGoogle Scholar
  8. Bechtel W, Abrahamsen A (2008) From reduction back to higher levels. In: Love BC, McRae K, Sloutsky VM (eds) Proceedings of the 30th Annual Meeting of the Cognitive Science Society, pp 559–564Google Scholar
  9. Bechtel W, Abrahamsen A (2010) Dynamic mechanistic explanation: computational modeling of circadian rhythms as an exemplar for cognitive science. Stud Hist Philos Sci 41:321–333CrossRefGoogle Scholar
  10. Bhattacharya S, Zhang Q, Andersen M (2011) A deterministic map of Waddington’s epigenetic landscape for cell fate specification. BMC Syst Biol 5(85):1–11Google Scholar
  11. Brandon R (1999) The units of selection reivisted: the modules of selection. Biol Philos 14(2):167–180CrossRefGoogle Scholar
  12. Brigandt I (2007) Typology now: homology and developmental constraints explain evolvability. Biol Philos 22(5):709–725CrossRefGoogle Scholar
  13. Brigandt I (2015) Evolutionary developmental biology and the limits of philosophical accounts of mechanistic explanation. In: Braillard PA, Malaterre C (eds) Explanation in biology: an enquiry into the diversity of explanatory patterns in the life sciences. Springer, Berlin, pp 135–173CrossRefGoogle Scholar
  14. Cahoone L (2013) Ordinal pluralism as metaphysics for biology. In: Henning B, Scarfe A (eds) Beyond mechanism: putting life back into biology. Lexington Books/Rowan & Littlefield, Lanham, pp 133–146Google Scholar
  15. Callebaut W, Rasskin-Gutman D (eds) (2005) Modularity: understanding the development and evolution of natural complex systems. MIT Press, CambridgeGoogle Scholar
  16. Callebaut W, Müller G, Newman S (2007) The organismic systems approach: evo-devo and the streamlining of the naturalistic agenda. In: Sansom R, Brandon R (eds) Integrating evolution and development: from theory to practice. MIT Press, Cambridge, pp 25–92Google Scholar
  17. Canestro C, Yokoi H, Postlethwait J (2007) Nature reviews genetics. Evol Dev Biol Genomics 8(12):932–942Google Scholar
  18. Carroll S (2008) Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134(1):25–36CrossRefGoogle Scholar
  19. Carroll S, Grenier J, Weatherbee S (2001) From DNA to diversity: molecular genetics and the evolution of animal design. Blackwell Science, OxfordGoogle Scholar
  20. Corson F, Siggia ED (2012) Geometry, epistasis, and developmental patterning. Proc Natl Acad Sci USA 109(15):5568–5575CrossRefGoogle Scholar
  21. Craver CF (2007) Explaining the brain: mechanisms and the mosaic unity of neuroscience. Oxford University Press, OxfordCrossRefGoogle Scholar
  22. Darden L (2007) Mechanisms and models. In: Hull D, Ruse M (eds) The Cambridge companion to the philosophy of biology. Cambridge University Press, Cambridge, pp 139–159CrossRefGoogle Scholar
  23. Darden L, Craver C (2002) Strategies in the interfield discovery of the mechanism of protein synthesis. Stud Hist Philos Biol Biomed Sci 33:1–28CrossRefGoogle Scholar
  24. Davidson E (2001) Genomic regulatory systems. In development and evolution. Academic Press, LondonGoogle Scholar
  25. Davidson E, Erwin D (2006) Gene regulatory networks and the evolution of animal body plans. Science 311(5762):796–800CrossRefGoogle Scholar
  26. Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buyila ER (2015) Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development. Front Genet. doi:10.3389/fgene.2015.00160 Google Scholar
  27. Dupré J (2013) Living causes. Proc Aristot Soc Suppl 87(1):19–38CrossRefGoogle Scholar
  28. Dupré J, O’Malley M (2007) Metagenomics and biological ontology. Stud Hist Philos Biol Biomed Sci 38(4):834–846CrossRefGoogle Scholar
  29. Edelman G, Gally J (2001) Degeneracy and complexity in biological systems. Proc Natl Acad Sci 98(24):13763–13768CrossRefGoogle Scholar
  30. Ellis G (2012) Top-down causation and emergence: some comments on mechanisms. Interface Focus 2(1):126–140CrossRefGoogle Scholar
  31. Flatt T (2005) The evolutionary genetics of canalization. Q Rev Biol 80(3):287–316CrossRefGoogle Scholar
  32. Frankel N, Davis G, Vargas D, Wang S, Payre F, Stern D (2010) Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature 466:490–493CrossRefGoogle Scholar
  33. Galis F, Metz J (2001) Testing the vulnerability of the phylotypic stage: on modularity and evolutionary conservation. J Exp Zool 291(2):195–204CrossRefGoogle Scholar
  34. Gilbert S, Bolker J (2001) Homologies of process and modular elements of embryonic construction. J Exp Zool 291(1):1–12CrossRefGoogle Scholar
  35. Greenspan R (2001) The flexible genome. Nature 2(5):383–387Google Scholar
  36. Hall B (2003) Evo-Devo: Evolutionary Developmental Mechanisms. Int J Dev Biol 47(7–8):491–495Google Scholar
  37. Hall B (2013) Epigenesis, epigenetics, and the epigenotype: toward an inclusive concept of development and evolution. In: Henning B, Scarfe A (eds) Beyond mechanism: putting life back into biology. Lexington Books/Rowan & Littlefield, Lanham, pp 345–368Google Scholar
  38. Huang S (2009) Reprogramming cell fates: reconciling rarity with robustness. BioEssays 31(5):546–560CrossRefGoogle Scholar
  39. Huang S (2012) The molecular and mathematical basis of Waddington’s epigenetic landscape: a framework for post-Darwinian biology? BioEssays 34(2):149–157CrossRefGoogle Scholar
  40. Huneman P (2010) Topological explanations and robustness in biological sciences. Synthese 177(2):213–245CrossRefGoogle Scholar
  41. Jaeger J, Monk N (2014) Bioattractors: dynamical systems theory and the evolution of regulatory processes. J Physiol 592(11):2267–2281CrossRefGoogle Scholar
  42. Jaeger J, Monk N (2015) Everything flows: a process perspective on life. EMBO Rep 16(9):1064–1067CrossRefGoogle Scholar
  43. Jaeger J, Irons D, Monk N (2012) The inheritance of process: a dynamical systems approach. J Exp Zool 318(8):591–612CrossRefGoogle Scholar
  44. Kalinka A, Varga K, Gerrard D, Preibisch S, Corcoran D, Jarrells J et al (2010) Gene expression divergence recapituates the developmental Hourglass model. Nature 468:811–814CrossRefGoogle Scholar
  45. Kaplan D (2015) Moving parts: the natural alliance between dynamical and mechanistic modeling approaches. Biol Philos 30(6):757–786CrossRefGoogle Scholar
  46. Kaplan D, Craver C (2011) The explanatory force of dynamical and mathematical models in neuroscience: a mechanistic perspective. Philos Sci 78(4):601–627CrossRefGoogle Scholar
  47. Kauffman SA (1969) Metabolic stability and epigenesis in randomly constructed nets. J Theor Biol 22(3):437–467CrossRefGoogle Scholar
  48. Kim K, Wang J (2007) Potential energy landscape and robustness of a gene regulatory network: toggle switch. PLoS Comput Biol 3(3):0565–0577CrossRefGoogle Scholar
  49. Kitano H (2004) Biological robustness. Nat Rev Genet 5(11):826–837CrossRefGoogle Scholar
  50. Laubichler MD (2010) Evolutionary developmental biology offers a significant challenge o the neo-Darwinian paradigm. In: Ayala F, Arp R (eds) Contemporary debates in the philosophy of biology. Wiley-Blackwell, Malden, pp 199–212Google Scholar
  51. Levin M (2012) Morphogenetic fields in emryogenesis, regeneration, and cancer: non-local control of complex patterning. Biosystems 109(3):243–261CrossRefGoogle Scholar
  52. Love A (2009) Typology reconfigured: from the metaphysics of essentialism to the epistemology of representation. Acta Biotheor 57(1–2):51–75CrossRefGoogle Scholar
  53. Machamer P, Darden L, Craver CF (2000) Thinking about mechanisms. Philos Sci 67(1):1–25CrossRefGoogle Scholar
  54. MacNeil L, Walhout A (2011) Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res 21(5):645–657CrossRefGoogle Scholar
  55. Mason P (2010) Degeneracy at multiple levels of complexity. Biol Theory 5(3):277–288CrossRefGoogle Scholar
  56. McCune A, Schimenti J (2012) Using genomic networks and homology to understand the evolution of phenotypic traits. Curr Genomics 13(1):74–84CrossRefGoogle Scholar
  57. McManus F (2012) Development and mechanistic explanation. Stud Hist Philos Biol Biomed Sci 43:532–541CrossRefGoogle Scholar
  58. Mitchell S (2012) Emergence: logical. Funct Dyn Synth 185(2):171–186Google Scholar
  59. Müller G (2003) Homology: the evolution of morphological organization. In: Müller GB, Newman SA (eds) Origination of organismal form: beyond the gene in developmental and evolutionary biology. MIT Press, Cambridge, pp 51–69Google Scholar
  60. Müller G, Newman SA (1999) Generation, integration, autonomy: three steps in the evolution of homology. Novartis Found Symp 222:65–73Google Scholar
  61. Mumford S (2004) Laws in nature. Routledge, LondonCrossRefGoogle Scholar
  62. Nathan M, Borghini A (2014) Development and natural kinds: some lessons from biology. Synthese 191(3):539–556CrossRefGoogle Scholar
  63. Nicholson D (2012) The concept of mechanism in biology. Stud Hist Philos Biol Biomed Sci 43(1):152–163CrossRefGoogle Scholar
  64. Owen R (1848) On the archetype and homologies of the vertebrate skeleton. John van Voorst, LondonCrossRefGoogle Scholar
  65. Raff RA (1996) The shape of life: genes, development, and the evolution of animal form. University of Chicago Press, ChicagoGoogle Scholar
  66. Rieppel O (2005) Modules, kinds, and homology. J Exp Zool 304B(1):18–27CrossRefGoogle Scholar
  67. Rosa L, Etxeberria A (2011) Pattern and process in evo-devo: descriptions and explanations. In: de Regt H, Hartmann S, Okasha S (eds) EPSA philosophy of science: Amsterdam 2009. Springer, Berlin, pp 263–274Google Scholar
  68. Rosenberg A (2001) On multiple realization and the special sciences. J Philos 98(7):365–373CrossRefGoogle Scholar
  69. Salazar-Ciudad I, Jernvall J (2013) The causality horizon and the developmental bases of morphological evolution. Biol Theory 8(3):286–292CrossRefGoogle Scholar
  70. Striedter G (1998) Stepping into the same river twice: homologues as recurring attractors in epigenetic landscapes. Brain Behav Evol 52(4–5):218–231CrossRefGoogle Scholar
  71. Tabata T (2001) Genetics of morphogen gradients. Nature 2(8):620–630Google Scholar
  72. Tickle C (2003) Patterning systems: from one end of the limb to the other. Dev Cell 4(4):449–458CrossRefGoogle Scholar
  73. Verd B, Crombach A, Jaeger J (2014) Classification of transient behaviours in a time-dependent toggle switch model. BMC Syst Biol 8(43):1–19Google Scholar
  74. Waddington CH (1957) The strategy of the genes. George Allen & Unwin, LondonGoogle Scholar
  75. Waddington CH (1969) The practical consequences of metaphysical beliefs on a biologist’s work: an autobiographical note. In: Waddington CH (ed) Towards a theoretical biology 2: sketches. Edinburgh University Press, Edinburgh, pp 72–81Google Scholar
  76. Wagner A (2005) Distributed robustness versus redundancy as causes of mutational robustness. BioEssays 27(2):176–188CrossRefGoogle Scholar
  77. Wagner G (2014) Homology, genes, and evolutionary innovation. Princeton University Press, PrincetonCrossRefGoogle Scholar
  78. Wagner G, Lynch V (2010) Evolutionary novelties. Curr Biol 20(2):R48–R52CrossRefGoogle Scholar
  79. Wagner G, Chiu C, Laubichler MD (2000) Developmental evolution as a mechanistic science: the inference from developmental mechanisms to evolutionary processes. Am Zool 40(5):819–831Google Scholar
  80. Walsh D (2013) Mechanism, emergence, and miscibility: the autonomy of evo-devo. In: Huneman P (ed) Functions: selection and mechanisms. Springer, Berlin, pp 43–65CrossRefGoogle Scholar
  81. Wang J, Zhang K, Xu L, Wang E (2011) Quantifying the Waddington landscape and biological paths for development and differentiation. Proc Natl Acad Sci USA 108(20):8257–8262CrossRefGoogle Scholar
  82. Webster G, Goodwin B (1996) Form and transformation: generative an relational principles in biology. Cambridge University Press, CambridgeGoogle Scholar
  83. Whitacre J (2010) Degeneracy: a link between evolvability, robustness and complexity in biological systems. Theor Biol Med Model 7:6CrossRefGoogle Scholar
  84. Whitacre J, Bender A (2010) Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems. Theor Biol Med Model 7(20):1–20Google Scholar
  85. Whitehead AN (1925) Science and the modern world. Cambridge University Press, CambridgeGoogle Scholar
  86. Wilkins A (2002) The evolution of developmental pathways. Sinauer Associates Inc, SunderlandGoogle Scholar
  87. Wimsatt W (2000) Emergence as non-aggregativity and the biases of reductionisms. Found Sci 5(3):269–297CrossRefGoogle Scholar
  88. Woese C (2004) A new biology for a new century. Microbiol Mol Biol Rev 68(2):173–186CrossRefGoogle Scholar
  89. Woodward J (2002) What is a mechanism? A counterfactual account. Philos Sci 3:S366–S377CrossRefGoogle Scholar
  90. Woodward J (2013) Mechanstic explanation: its scope and limits. Proc Aristot Soc Suppl 87(1):39–65CrossRefGoogle Scholar
  91. Yi T, Huang Y, Simon M, Doyle J (2000) Robust perfect adaption in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci USA 97(9):4649–4653CrossRefGoogle Scholar
  92. Zhenglong G, Steinmetz L, Gu X, Scharfe C, Davis R, Li W-H (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421(6918):63–66CrossRefGoogle Scholar
  93. Zhou JX, Aliyu MD, Huang S (2012) Quasi-potential landscape in complex multi-stable systems. J R Soc Interface 9(77):3539–3553CrossRefGoogle Scholar
  94. Zuniga A (2015) Next generation limb development and evolution: old questions, new perspectives. Development 142(22):3810–3820CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.University of OxfordOxfordUK

Personalised recommendations