Toolbox murders: putting genes in their epigenetic and ecological contexts

P. Griffiths and K. Stotz: Genetics and philosophy: an introduction

A Commentary to this article is available

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.

This is a preview of subscription content, access via your institution.

Fig. 1

References

  1. Altelaar AF, Munoz J, Heck AJ (2013) Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet 14(1):35–48

    Article  Google Scholar 

  2. Barash Y et al (2010) Deciphering the splicing code. Nature 465(7294):53–59

    Article  Google Scholar 

  3. Barberousse A, Merlin F, Pradeu T (2010) Reassessing developmental systems theory. Biol Theory 5(3):199–201

    Article  Google Scholar 

  4. Bergstrom C, Rosvall M (2009) The transmission sense of information. Biol Philos 26(2):159–176

    Article  Google Scholar 

  5. Beurton P, Falk R, Rheinberger H-J (eds) (2000) The concept of the gene in development and evolution. Cambridge University Press, Cambridge

    Google 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), 166–182

  8. Burian RM (2004) Molecular epigenesis, molecular pleiotropy, and molecular gene definitions. Hist Philos Life Sci 26(1):59–80

    Article  Google Scholar 

  9. Burian RM (2005) The epistemology of development, evolution and genetics. Cambridge University Press, Cambridge

    Google Scholar 

  10. Chanock S (2012) Toward mapping the biology of the genome. Genome Res 22(9):1612–1615

    Article  Google 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):741–754

    Google Scholar 

  12. Cox J, Mann M (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem 80:273–299

    Article  Google Scholar 

  13. Craver CF (2007) Explaining the brain. Oxford University Press, Oxford

    Google Scholar 

  14. Craver CF, Bechtel W (2007) Top-down causation without top-down causes. Biol Philos 22(4):547–563

    Article  Google Scholar 

  15. Crick F (1958) On protein synthesis. Symp Soc Exp Biol 12:138–163

    Google 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 5:413–420

    Article  Google Scholar 

  18. Eisenberg D et al (2000) Protein function in the post-genomic era. Nature 405(6788):823–826

    Article  Google Scholar 

  19. Falk R (1984) The gene in search of an identity. Hum Genet 15(68):195–204

    Article  Google Scholar 

  20. Falk R (1986) What is a gene? Stud Hist Philos Sci 17:133–173

    Article  Google 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 317–348

  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 3–25

  23. Fu XD, Ares M Jr (2014) Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15(10):689–701

    Article  Google Scholar 

  24. Gerstein MB et al (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17(6):669–681

    Article  Google Scholar 

  25. Gilbert SF (2002) The genome in its ecological context. Ann N Y Acad Sci 981(1):202–218

    Article  Google Scholar 

  26. Gilbert SF, Epel D (2009) Ecological developmental biology. Sinauer Associates, Sunderland

    Google Scholar 

  27. Gilbert SF, Sarkar S (2000) Embracing complexity: organicism for the 21st century. Dev Dyn 219:1–9

    Article  Google Scholar 

  28. Godfrey-Smith P (2000) On the theoretical role of “genetic coding”. Philos Sci 67(1):26–44

    Article  Google Scholar 

  29. Griffiths PE (2001) Genetic information: a metaphor in search of a theory. Philos Sci 68(3):394–412

    Article  Google 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 175–198

    Google Scholar 

  31. Griffiths PE (2013) Lehrman’s dictum: information and explanation in developmental biology. Dev Psychobiol 55(1):22–32

    Article  Google Scholar 

  32. Griffiths PE, Gray RD (1994) Developmental systems and evolutionary explanation. J Philos 91(6):277–304

    Article  Google Scholar 

  33. Griffiths PE, Gray RD (2005) Discussion: three ways to misunderstand developmental systems theory. Biol Philos 20(2–3):417–425

    Article  Google Scholar 

  34. Griffiths PE, Knight RD (1998) What is the developmentalist challenge? Philos Sci 65(2):253–258

    Article  Google Scholar 

  35. Griffiths PE, Neumann-Held EM (1999) The many faces of the gene. Bioscience 49(8):656–662

    Article  Google Scholar 

  36. Griffiths PE, Stotz K (2006) Genes in the postgenomic era. Theor Med Bioeth 27(6):499–521

    Article  Google Scholar 

  37. Hooper LV et al (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291(5505):881–884

    Article  Google Scholar 

  38. Hull D (1974) Philosophy of biological science. Prentice-Hall Inc, Englewood Cliffs

    Google 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):131–176

    Article  Google Scholar 

  40. Keller EF (2000) The century of the gene. Harvard University Press, Cambridge

    Google Scholar 

  41. Kim MS et al (2014) A draft map of the human proteome. Nature 509(7502):575–581

    Article  Google Scholar 

  42. Kitcher P (1984) 1953 and all that: a tale of two sciences. Philos Rev 93:335–373

    Article  Google 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 369–414

    Google Scholar 

  44. Lewontin R (2000) The triple helix: gene, organism, and environment. Harvard University Press, Cambridge

    Google 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):386–398

    Article  Google Scholar 

  47. McFall-Ngai M (2002) Unseen forces: the influence of bacteria on animal development. Dev Biol 242:1–14

    Article  Google Scholar 

  48. McFall-Ngai M et al (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci 110:3229–3236

    Article  Google Scholar 

  49. Morange M (1998) A history of molecular biology. Harvard University Press, Cambridge

    Google Scholar 

  50. Moss L (2003) What genes can’t do. MIT Press, Cambridge

    Google Scholar 

  51. Noble D (2006) The music of life: biology beyond genes. Oxford University Press, Oxford

    Google Scholar 

  52. Noble D (2008) Genes and causation. Philoso Trans R Soc A 366(1878):3001–3015

    Article  Google Scholar 

  53. Oyama S (1985) The ontogeny of information: developmental systems and evolution. Cambridge University Press, Cambridge

    Google Scholar 

  54. Oyama S (2000) Causal democracy and causal contributions in developmental systems theory. Philos Sci 67:S332–S347

    Article  Google Scholar 

  55. Oyama S, Griffiths P, Gray R (eds) (2001) Cycles of contingency: developmental systems and evolution. MIT Press, Cambridge

    Google Scholar 

  56. Pennisi E (2001) Behind the scenes of gene expression. Science 293:1064–1067

    Article  Google Scholar 

  57. Pennisi E (2013) How do microbes shape animal development? Science 340:1159–1160

    Article  Google Scholar 

  58. Portin P (1993) The concept of the gene: short history and present status. Q Rev Biol 68(2):173–223

    Article  Google Scholar 

  59. Pradeu T (2010) The organism in developmental systems theory. Biol Theory 5(3):216–222

    Article  Google Scholar 

  60. Pradeu T (2011) A mixed self: the role of symbiosis in development. Biol Theory 6:80–88

    Article  Google Scholar 

  61. Pradeu T (2012) The limits of the self: immunology and biological identity. Oxford University Press, New York

    Google Scholar 

  62. Robert JS (2004) Embryology, epigenesis and evolution: taking development seriously. Cambridge University Press, Cambridge

    Google Scholar 

  63. Rosenberg A (1985) The structure of biological science. Cambridge University Press, Cambridge

    Google Scholar 

  64. Rosenberg A (2006) Darwinian reductionism. University of Chicago Press, Chicago

    Google Scholar 

  65. Sarkar S (1992) Models of reduction and categories of reductionism. Synthese 91:167–194

    Article  Google Scholar 

  66. Sarkar S (1998) Genetics and reductionism. Cambridge University Press, Cambridge

    Google Scholar 

  67. Sarkar S (2005) Molecular models of life: philosophical papers on molecular biology. MIT Press, Cambridge

    Google Scholar 

  68. Schaffner K (1993) Discovery and explanation in biology and medicine. University of Chicago Press, Chicago

    Google Scholar 

  69. Shea N (2007) Representation in the genome and in other inheritance systems. Biol Philos 22:313–331

    Article  Google Scholar 

  70. Shin SC et al (2011) Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signaling. Science 334:670–674

    Article  Google 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 99:15451–15455

    Article  Google Scholar 

  72. Stotz K (2006) Molecular epigenesis: distributed specificity as a break in the Central Dogma. Hist Philos Life Sci 28(4):527–544

    Google Scholar 

  73. Stotz K (2012) Murder on the development express: who killed nature/nurture? Biol Philos 27:919–929

    Article  Google 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–C974

    Article  Google Scholar 

  75. Waddington CH (1955) Mechanisms of development. Nature 4480(178):477–478

    Google Scholar 

  76. Wang ET et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476

    Article  Google Scholar 

  77. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63

    Article  Google Scholar 

  78. Waters CK (2007) Causes that make a difference. The Journal of Philosophy 104(11):551–579

    Article  Google Scholar 

  79. Weber M (2005) Philosophy of experimental biology. Cambridge University Press, Cambridge

    Google Scholar 

  80. West MJ, King AP (1987) Settling nature and nurture into an ontogenetic niche. Dev Psychobiol 20(5):549–562

    Article  Google Scholar 

  81. Woodward J (2003) Making things happen: a theory of causal explanation. Oxford University Press, New York

    Google Scholar 

  82. Woodward J (2010) Causation in biology: stability, specificity, and the choice of levels of explanation. Biol Philos 5(3):287–318

    Article  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to T. Pradeu.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Pradeu, T. Toolbox murders: putting genes in their epigenetic and ecological contexts. Biol Philos 31, 125–142 (2016). https://doi.org/10.1007/s10539-014-9471-x

Download citation

Keywords

  • Gene
  • Genetics
  • Epigenetics
  • Development
  • Information
  • Symbiosis