Skip to main content
Log in

The organism: A crucial genomic context in molecular epigenetics?

  • Published:
Theory in Biosciences Aims and scope Submit manuscript

Summary

Whereas genetics refers to the study and mapping of linear nucleotide sequences, their mutations and inheritance, epigenetics refers to the structural organization and evolution of the genome. Epigenetic studies indicate that not all heritable information leading to the phenotype is “inscribed” in the DNA base sequence. In this sense, epigenetics — as the term indicates — goes beyond genetics, thereby (1) leaving behind the gene-centered view from within molecular biology itself, and (2) urging bio-philosophers to change their focus from criticizing the central dogma to evaluating new developments in molecular research.

In the epigenetic approach, a hierarchy of genomic contexts can be revealed, consisting basically of an intracellular, an intercellular, and an organismic level. The first explorations on the organismic level suggest that under certain conditions the somatic constitution of the organism and how it stands in close interaction with its environment are to be taken into account as factors influencing the genomic constitution. Depending on the specificity of these conditions, the organism and its history and actuality can be seen as a crucial genomic context — leading to a more complex perception of the local dynamics and the structure of the genome and its consequences for development and evolution.

This “organism in the world” view fits well with the philosophical tradition of Developmental Systems Theory, although epigeneticists seek to enlarge the genetic picture of biology by gradually expanding the range of molecular processes which influence the genome, thereby decentralizing the sovereign role of the genome, without loosing track of experimental demands.

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

Access this article

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Alberts, B.; Bray, D.; Lewis, J.; Raff, M.; Roberts, K.; Watson, J. D. (1994) Molecular Biology of The Cell — third edition. Garland Publishing, New York, London.

    Google Scholar 

  • Aldridge, S. (1996) The Thread of Life: the Story of Genes and Genetic Engineering. Cambridge Univ. Press, Cambrigde.

    Google Scholar 

  • Aristotle (1943) Generation of Animals. With an English translation by A. L. Peck. William Heinemann LTD. Harvard Univ. Press, Harvard.

    Google Scholar 

  • Aristote (1961) De la Génération des Animaux. Texte établi et traduit par Pierre Louis. Recteur du l’Académie de Lyon. Les Belles Lettres, Paris.

    Google Scholar 

  • Bechtel, W.; Richardson, R. (1992) Discovering Complexity. Princeton Univ. Press, Princeton.

    Google Scholar 

  • Bender, J.; Fink, G. R. (1995) Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83: 725–734.

    Article  PubMed  CAS  Google Scholar 

  • Bhattacharya, S. K.; Ramchandani, S.; Cervoni, N.; Szyf, M. (1999) A mammalian protein with specific demethylase activity for mCpG DNA. Nature 397: 579–583.

    Article  PubMed  CAS  Google Scholar 

  • Bolker, J. A. (1995) Model systems in developmental biology. BioEssays 17: no 5, 451–455.

    Article  PubMed  CAS  Google Scholar 

  • Bonitz, H. (1955) Index Aristotelicus — Secunda Editio. Akademische Druck-U. Verlagsanstalt, Graz.

    Google Scholar 

  • Collot, V.; Rossignol, J.-L. (1999) Eukaryotic DNA methylation as an evolutionary device. BioEssays 21: 402–411.

    Article  Google Scholar 

  • Cullis, C. A. (1986) Phenotypic consequences of environmentally induced changes in plant DNA. TIG, Dec.: 307–309.

  • Dawkins, R. (1989) The Selfish Gene. New Edition. Oxford Univ. Press, Oxford, New York.

    Google Scholar 

  • De Neve, M.; De Buck, S.; De Wilde, C.; Van Houdt, H.; Strobbe, I.; Jacobs, A.; Van Montagu, M.; Depicker, A. (1999) Gene Silencing results in instability of antibody production in transgenic plants. Mol. Gen. Genet. 260: 582–592.

    Article  PubMed  Google Scholar 

  • Depew, D. J.; Weber, B. H. (1995) Darwinism Evolving: Systems Dynamics and the Genealogy of Natural Selection. MIT Press, Cambridge, Massachusetts.

    Google Scholar 

  • Elsasser, W. M. (1998) Reflections on a Theory of Organism. Holism in Biology. Johns Hopkins Univ. Press, Baltimore, London.

    Google Scholar 

  • Fire, A.; Xu, S. Q; Montgomery, M. K.; Kostas, S. A.; Driver, S. E.; Mello, C. C. (1998) Potent and specific genetic interference by dsRNA in Caenorhabditis elegans. Nature 391: 806–811.

    Article  PubMed  CAS  Google Scholar 

  • Gilbert, S. F.; Jorgensen, E. M. (1998) Wormholes: a commentary on K. F. Schaffner’s “Genes, Behavior, and Developmental Emergentism.” Philosophy of Science 65: 259–266.

    Article  Google Scholar 

  • Griesemer, J. (1998) Turning back to go forward. Biology and Philosophy 13: 103–112.

    Article  Google Scholar 

  • Griffiths, P. E.; Gray, R. D. 1994 Developmental systems and evolutionary explanation. The Journal of Philosophy, Inc. XCI: No. 6, 277–304.

    Article  Google Scholar 

  • Griffiths, P. E.; Knight, R. D. (1998) What is the developmentalist challenge? Philosophy of Science 65: 253–258.

    Article  Google Scholar 

  • Harvey, W. (1981) Disputations Touching the Generation of Animals - Translated with introduction and notes by Gweneth Whitteridge. Blackwell Scientific Publications, Oxford.

    Google Scholar 

  • Henikoff, S.; Matzke, M. A. (1997) Exploring and explaining epigenetic effects. TIG 13: No. 8, 293–295.

    PubMed  CAS  Google Scholar 

  • Holliday, R. (1996) DNA methylation in eukaryotes: 20 years on. In: Russo, V. E. A.; Martienssen, R. A.; Riggs, A. D. (eds). Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press, New York. pp. 5–27.

    Google Scholar 

  • Hull, D. (1974) Philosophy of Biological Science. Prentice-Hall Inc., New Jersey.

    Google Scholar 

  • Jablonka, E. (1994) Inheritance systems and the evolution of new levels of individuality. J. theor. Biol. 170: 301–309.

    Article  PubMed  CAS  Google Scholar 

  • Jablonka, E.; Lamb, M. (1995) Epigenetic Inheritance and Evolution. The Lamarckian Dimension. Oxford Univ. Press, Oxford-London.

    Google Scholar 

  • Jablonka, E.; Lachmann, M.; Lamb, M. (1992) Evidence, mechanisms and models for the inheritance of acquired characters. J. Theor. Biol. 158: 245–268.

    Article  Google Scholar 

  • Jorgensen, R. A.; Atkinson, R. G.; Forster, R. L. S.; Lucas, W. J. (1998) An RNA-based information superhighway in plants. Science 279: 1486–1487.

    Article  PubMed  CAS  Google Scholar 

  • Keller, E. F. (1992) Secrets of Life, Secrets of Death. Routledge, London.

    Google Scholar 

  • Keller, E. F. (1999) Decoding the genetic program (or, some circular logic in the logic of circularity). Beurton, P. and Falk, R. (eds.) The Concept of the Gene in Development and Evolution, Cambridge Studies in Philosophy and Biology. In press.

  • Kitcher, P. (1984) 1953 and all that: a tale of two sciences. Philosophical Review 93: 335–373.

    Article  PubMed  CAS  Google Scholar 

  • Kovarick, A.; Koukalova, B.; Bezdek, M.; Opatrny, Z. (1997) Hypermethylation of tobacco heterochromatic loci in response to osmotic stress. Theor. Appl. Genet. 95: 301–306.

    Article  Google Scholar 

  • Lewin, B. (1998) The mystique of epigenetics. Cell 93: 301–303.

    Article  PubMed  CAS  Google Scholar 

  • Lewontin, R. C. (1993) The Doctrine of DNA, Biology as Ideology. Penguin Books, London.

    Google Scholar 

  • Lincoln, R.; Boxshall, G.; Clark, P. (1998) A Dictionary of Ecology, Evolution and Systematics — 2nd edition. Cambridge Univ. Press, Cambridge.

    Google Scholar 

  • Meyer, P.; Saedler, H. (1996) Homology-dependent gene silencing in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 23–48.

    Article  CAS  Google Scholar 

  • Michie, D. (1958) The Third Stage in Genetics. In: Barnett, S. A. (ed.) A Century of Darwin. Heinemann, London. pp 56–84.

    Google Scholar 

  • Moore, J. A. (1987) Science as a way of knowing — Developmental Biology. American Zoologist 27: 415–573.

    Google Scholar 

  • Oyama, S. (1985) The Ontogeny of Information. Cambridge Univ. Press, Cambridge, London.

    Google Scholar 

  • Oyama, S. (1993) How shall I name thee? The construction of natural selves. Theory and Psychology 3 (4): 471–496.

    Article  Google Scholar 

  • Palauqui, J.-C.; Elmayan, T.; Pollien J.-M.; Vaucheret, H. (1997) Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions. The EMBO Journal 16: No. 5, 4738–4745.

    Article  PubMed  CAS  Google Scholar 

  • Palauqui, J. C.; Vaucheret, H. (1998) Transgenes are dispensable for the RNA degradation step of cosuppression. Procl. Natl. Acad. Sci. USA 95: 9675–9680.

    Article  CAS  Google Scholar 

  • Palauqui, J. C. & Balzerque, S. (1999) Activation of systemic acquired silencing by localised introduction of DNA. Curr. Biol. 9: 59–66.

    Article  PubMed  CAS  Google Scholar 

  • Pinto-Correia, C. (1997) The Ovary of Eve. Egg and Sperm and Preformation. The Univ. of Chicago Press, Chicago.

    Google Scholar 

  • Richards, E. J. (1997) DNA methylation and plant development. TIG 13, No. 8, 319–323.

    PubMed  CAS  Google Scholar 

  • Russo, V. E. A.; Martienssen, R. A.; Riggs, A. D. (eds.). 1996. Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press, New York.

    Google Scholar 

  • Salthe, S. N. (1993) Development in Evolution: Complexity and Change in Biology. MIT Press, Cambridge MA.

    Google Scholar 

  • Saunders, P. T.; Ho, M.-W. (1984) Beyond Neo-Darwinism: an Introduction to the New Evolutionary Paradigm. Academic Press, London.

    Google Scholar 

  • Schaffner, K. F. (1998) Genes, behavior, and developmental emergentism: one process, indivisible? Philosophy of Science 65, 209–252.

    Article  Google Scholar 

  • Tabara, H.; Grishok, A.; Mello, C. C. (1998) RNAi in C. elegans: soaking in the genome sequence. Science 282: 430–431.

    Article  PubMed  CAS  Google Scholar 

  • Timmons, L.; Fire, A. (1998) Specific interference by ingested dsRNA. Nature 395: 854.

    Article  PubMed  CAS  Google Scholar 

  • Voinnet, O.; Baulcombe, D. C. (1997) Systemic signaling in gene silencing. Nature 389: 553.

    Article  PubMed  CAS  Google Scholar 

  • Voinnet, O.; Vain, P.; Angell, S.; Baulcombe, D. C. (1998) Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 95: 177–187.

    Article  PubMed  CAS  Google Scholar 

  • Von Sternberg, R. (2000) Genomes, form, epigenetic influences on inheritance, and morphological attractors: the case for teleomorphic recursivity. In Chandler, J.; Van de Vijver, G. (eds.) Volume on Closure. New York Academy of Sciences. In press.

  • Waddington, C. H. (1956) Principles of Embryology. Allen and Unwin, London.

    Google Scholar 

  • Waddington, C. H. (1949) The genetic control of development. Symp. Soc. Exp. Biol. 2: 145–154.

    Google Scholar 

  • Weber, B. H. & Depew, D. J. (1999) Developmental systems, Darwinian Evolution, and the Unity of Science. In Griffiths, P.; Oyama, S. (eds.) Cycles of Contingency. MIT Press, in press.

  • Wimsatt, W. C. (1998) Simple systems and phylogenetic diversity. Philosophy of Science 65: 267–275.

    Article  Google Scholar 

  • Wolffe, A. P. (1994) Inheritance of chromatin states. Developmental Genetics 15: 463–470.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Linda Van Speybroeck.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Van Speybroeck, L. The organism: A crucial genomic context in molecular epigenetics?. Theory Biosci. 119, 187–208 (2000). https://doi.org/10.1007/s12064-000-0016-2

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12064-000-0016-2

Key words

Navigation