Advertisement

Biology & Philosophy

, Volume 31, Issue 1, pp 125–142 | Cite as

Toolbox murders: putting genes in their epigenetic and ecological contexts

P. Griffiths and K. Stotz: Genetics and philosophy: an introduction
  • T. Pradeu
Review Essay

Abstract

Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what I consider as the two main theses of the book, namely: (i) genes are better conceived as tools; (ii) genes become causes only in a context. I situate these two theses in the wider perspective of developmental systems theory. This leads me to emphasize that Griffiths and Stotz reflect very well an on going process in genetics, which I call the “epigenetization” of genetics, i.e., the growing interest in the complex processes by which gene activation is regulated. I then make a factual objection, which is that Griffiths and Stotz have almost entirely neglected the perspective of ecological developmental biology, and more precisely recent work on developmental symbioses, and I suggest that this omission is unfortunate in so far as an examination of developmental symbioses would have considerably strengthened Griffiths and Stotz’s own conclusions.

Keywords

Gene Genetics Epigenetics Development Information Symbiosis 

References

  1. Altelaar AF, Munoz J, Heck AJ (2013) Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet 14(1):35–48CrossRefGoogle Scholar
  2. Barash Y et al (2010) Deciphering the splicing code. Nature 465(7294):53–59CrossRefGoogle Scholar
  3. Barberousse A, Merlin F, Pradeu T (2010) Reassessing developmental systems theory. Biol Theory 5(3):199–201CrossRefGoogle Scholar
  4. Bergstrom C, Rosvall M (2009) The transmission sense of information. Biol Philos 26(2):159–176CrossRefGoogle Scholar
  5. Beurton P, Falk R, Rheinberger H-J (eds) (2000) The concept of the gene in development and evolution. Cambridge University Press, CambridgeGoogle Scholar
  6. Brigandt I, Love AC (2008) Reductionism in biology. In: Zalta EN (ed) The Stanford Encyclopedia of Philosophy. http://plato.stanford.edu/entries/reduction-biology/
  7. Burian RM (1995) Too many kinds of genes? Reprinted in Burian (2005), 166–182Google Scholar
  8. Burian RM (2004) Molecular epigenesis, molecular pleiotropy, and molecular gene definitions. Hist Philos Life Sci 26(1):59–80CrossRefGoogle Scholar
  9. Burian RM (2005) The epistemology of development, evolution and genetics. Cambridge University Press, CambridgeGoogle Scholar
  10. Chanock S (2012) Toward mapping the biology of the genome. Genome Res 22(9):1612–1615CrossRefGoogle Scholar
  11. Chen M, Manley JL (2009) Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 10(11):741–754Google Scholar
  12. Cox J, Mann M (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem 80:273–299CrossRefGoogle Scholar
  13. Craver CF (2007) Explaining the brain. Oxford University Press, OxfordCrossRefGoogle Scholar
  14. Craver CF, Bechtel W (2007) Top-down causation without top-down causes. Biol Philos 22(4):547–563CrossRefGoogle Scholar
  15. Crick F (1958) On protein synthesis. Symp Soc Exp Biol 12:138–163Google Scholar
  16. Darden L, Tabery J (2009) Molecular biology. In: Zalta EN (ed) The Stanford Encyclopedia of Philosophy. http://plato.stanford.edu/entries/molecular-biology/
  17. Eberl G (2005) Inducible lymphoid tissues in the adult gut: recapitulation of a fetal developmental pathway? Nat Rev Immunol 5:413–420CrossRefGoogle Scholar
  18. Eisenberg D et al (2000) Protein function in the post-genomic era. Nature 405(6788):823–826CrossRefGoogle Scholar
  19. Falk R (1984) The gene in search of an identity. Hum Genet 15(68):195–204CrossRefGoogle Scholar
  20. Falk R (1986) What is a gene? Stud Hist Philos Sci 17:133–173CrossRefGoogle Scholar
  21. Falk R (2000) The gene: a concept in tension. In: Beurton PJ, Falk R, Rheinberger H-J (eds) The concept of the gene in development and evolution. Cambridge University Press, Cambridge, pp 317–348Google Scholar
  22. Fogle T (2000) The dissolution of protein coding genes in molecular biology. In: Beurton PJ, Falk R, Rheinberger H-J (eds) The concept of the gene in development and evolution. Cambridge University Press, Cambridge, pp 3–25Google Scholar
  23. Fu XD, Ares M Jr (2014) Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15(10):689–701CrossRefGoogle Scholar
  24. Gerstein MB et al (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17(6):669–681CrossRefGoogle Scholar
  25. Gilbert SF (2002) The genome in its ecological context. Ann N Y Acad Sci 981(1):202–218CrossRefGoogle Scholar
  26. Gilbert SF, Epel D (2009) Ecological developmental biology. Sinauer Associates, SunderlandGoogle Scholar
  27. Gilbert SF, Sarkar S (2000) Embracing complexity: organicism for the 21st century. Dev Dyn 219:1–9CrossRefGoogle Scholar
  28. Godfrey-Smith P (2000) On the theoretical role of “genetic coding”. Philos Sci 67(1):26–44CrossRefGoogle Scholar
  29. Griffiths PE (2001) Genetic information: a metaphor in search of a theory. Philos Sci 68(3):394–412CrossRefGoogle Scholar
  30. Griffiths PE (2006) The fearless vampire conservator: Philip Kitcher, genetic determinism and the informational gene. In: Neumann-Held EM, Rehmann-Sutter C (eds) Genes in development: re-reading the molecular paradigm. Duke University Press, Durham, pp 175–198CrossRefGoogle Scholar
  31. Griffiths PE (2013) Lehrman’s dictum: information and explanation in developmental biology. Dev Psychobiol 55(1):22–32CrossRefGoogle Scholar
  32. Griffiths PE, Gray RD (1994) Developmental systems and evolutionary explanation. J Philos 91(6):277–304CrossRefGoogle Scholar
  33. Griffiths PE, Gray RD (2005) Discussion: three ways to misunderstand developmental systems theory. Biol Philos 20(2–3):417–425CrossRefGoogle Scholar
  34. Griffiths PE, Knight RD (1998) What is the developmentalist challenge? Philos Sci 65(2):253–258CrossRefGoogle Scholar
  35. Griffiths PE, Neumann-Held EM (1999) The many faces of the gene. Bioscience 49(8):656–662CrossRefGoogle Scholar
  36. Griffiths PE, Stotz K (2006) Genes in the postgenomic era. Theor Med Bioeth 27(6):499–521CrossRefGoogle Scholar
  37. Hooper LV et al (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291(5505):881–884CrossRefGoogle Scholar
  38. Hull D (1974) Philosophy of biological science. Prentice-Hall Inc, Englewood CliffsGoogle Scholar
  39. Jablonka E, Raz G (2009) Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Q Rev Biol 84(2):131–176CrossRefGoogle Scholar
  40. Keller EF (2000) The century of the gene. Harvard University Press, CambridgeGoogle Scholar
  41. Kim MS et al (2014) A draft map of the human proteome. Nature 509(7502):575–581CrossRefGoogle Scholar
  42. Kitcher P (1984) 1953 and all that: a tale of two sciences. Philos Rev 93:335–373CrossRefGoogle Scholar
  43. Kitcher P (2001) Battling the undead: how (and how not) to resist genetic determinism. In: Singh R, Krimbas K, Paul D, Beatty J (eds) Thinking about evolution: historical, philosophical and political perspectives. Cambridge University Press, Cambridge, pp 369–414Google Scholar
  44. Lewontin R (2000) The triple helix: gene, organism, and environment. Harvard University Press, CambridgeGoogle Scholar
  45. Maienschein J (2005) Epigenesis and preformationism. In: Zalta EN (ed) The Stanford Encyclopedia of Philosophy. http://plato.stanford.edu/entries/epigenesis/
  46. Matlin AJ, Clark F, Smith CW (2005) Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6(5):386–398CrossRefGoogle Scholar
  47. McFall-Ngai M (2002) Unseen forces: the influence of bacteria on animal development. Dev Biol 242:1–14CrossRefGoogle Scholar
  48. McFall-Ngai M et al (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci 110:3229–3236CrossRefGoogle Scholar
  49. Morange M (1998) A history of molecular biology. Harvard University Press, CambridgeGoogle Scholar
  50. Moss L (2003) What genes can’t do. MIT Press, CambridgeGoogle Scholar
  51. Noble D (2006) The music of life: biology beyond genes. Oxford University Press, OxfordGoogle Scholar
  52. Noble D (2008) Genes and causation. Philoso Trans R Soc A 366(1878):3001–3015CrossRefGoogle Scholar
  53. Oyama S (1985) The ontogeny of information: developmental systems and evolution. Cambridge University Press, CambridgeGoogle Scholar
  54. Oyama S (2000) Causal democracy and causal contributions in developmental systems theory. Philos Sci 67:S332–S347CrossRefGoogle Scholar
  55. Oyama S, Griffiths P, Gray R (eds) (2001) Cycles of contingency: developmental systems and evolution. MIT Press, CambridgeGoogle Scholar
  56. Pennisi E (2001) Behind the scenes of gene expression. Science 293:1064–1067CrossRefGoogle Scholar
  57. Pennisi E (2013) How do microbes shape animal development? Science 340:1159–1160CrossRefGoogle Scholar
  58. Portin P (1993) The concept of the gene: short history and present status. Q Rev Biol 68(2):173–223CrossRefGoogle Scholar
  59. Pradeu T (2010) The organism in developmental systems theory. Biol Theory 5(3):216–222CrossRefGoogle Scholar
  60. Pradeu T (2011) A mixed self: the role of symbiosis in development. Biol Theory 6:80–88CrossRefGoogle Scholar
  61. Pradeu T (2012) The limits of the self: immunology and biological identity. Oxford University Press, New YorkCrossRefGoogle Scholar
  62. Robert JS (2004) Embryology, epigenesis and evolution: taking development seriously. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  63. Rosenberg A (1985) The structure of biological science. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  64. Rosenberg A (2006) Darwinian reductionism. University of Chicago Press, ChicagoCrossRefGoogle Scholar
  65. Sarkar S (1992) Models of reduction and categories of reductionism. Synthese 91:167–194CrossRefGoogle Scholar
  66. Sarkar S (1998) Genetics and reductionism. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  67. Sarkar S (2005) Molecular models of life: philosophical papers on molecular biology. MIT Press, CambridgeGoogle Scholar
  68. Schaffner K (1993) Discovery and explanation in biology and medicine. University of Chicago Press, ChicagoGoogle Scholar
  69. Shea N (2007) Representation in the genome and in other inheritance systems. Biol Philos 22:313–331CrossRefGoogle Scholar
  70. Shin SC et al (2011) Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signaling. Science 334:670–674CrossRefGoogle Scholar
  71. Stappenbeck TS, Hooper LV, Gordon JI (2002) Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci USA 99:15451–15455CrossRefGoogle Scholar
  72. Stotz K (2006) Molecular epigenesis: distributed specificity as a break in the Central Dogma. Hist Philos Life Sci 28(4):527–544Google Scholar
  73. Stotz K (2012) Murder on the development express: who killed nature/nurture? Biol Philos 27:919–929CrossRefGoogle Scholar
  74. Strange K (2005) The end of “naive reductionism”: rise of systems biology or renaissance of physiology? Am J Physiol Cell Physiol 288:C968–C974CrossRefGoogle Scholar
  75. Waddington CH (1955) Mechanisms of development. Nature 4480(178):477–478Google Scholar
  76. Wang ET et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476CrossRefGoogle Scholar
  77. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63CrossRefGoogle Scholar
  78. Waters CK (2007) Causes that make a difference. The Journal of Philosophy 104(11):551–579CrossRefGoogle Scholar
  79. Weber M (2005) Philosophy of experimental biology. Cambridge University Press, CambridgeGoogle Scholar
  80. West MJ, King AP (1987) Settling nature and nurture into an ontogenetic niche. Dev Psychobiol 20(5):549–562CrossRefGoogle Scholar
  81. Woodward J (2003) Making things happen: a theory of causal explanation. Oxford University Press, New YorkGoogle Scholar
  82. Woodward J (2010) Causation in biology: stability, specificity, and the choice of levels of explanation. Biol Philos 5(3):287–318CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.CIRID, CNRSUniversity of BordeauxBordeauxFrance
  2. 2.IHPST, CNRSPanthéon-Sorbonne UniversityParisFrance

Personalised recommendations