Skip to main content Skip to main navigation menu Skip to site footer
Type: Article
Published: 2008-12-05
Page range: 123–152
Abstract views: 42
PDF downloaded: 29

Learning from Linnaeus: towards developing the foundation for a general structure concept for morphology

Systematik und Evolution der Tiere, Institut für Biologie, FU Berlin, Königin Luise Str. 1–3, D-14195 Berlin, Germany
General Aperspectival objectivity Bio-ontology Essentialism Morphological data Linguistic problem of morphology RDF Standardization

Abstract

Morphology has fundamental problems regarding aperspectival objectivity of its data—morphological terminology is often based on homology assumptions, lacks standardization, and has problems with comparability, reproducibility, and transparency. This is astonishing given that with his sexual system Linnaeus had already established a high degree of aperspectival objectivity in morphology that unfortunately has been lost subsequently. In the first part of the article a brief introduction to the history of classification is given that provides an answer to the question why morphology only initially has been gripped by the general trend towards objectification that started in the seventeenth century. The conceptual shortcomings of Aristotle’s concept of essences and its link to the definition of species and taxa in natural philosophy play an important part in this development. The only solution to the problem of essences was to link it to the evolutionary concept of homology, which explains why morphological terminology today often rests on homology assumptions. By taking a closer look at Linnaeus’ sexual system, basic principles for developing a general structure concept for morphology are discussed, which would provide the conceptual basis for establishing a high degree of aperspectival objectivity for morphological data. The article concludes with discussing the role of data bases and ontologies for developing a data standard in morphology. A brief introduction to the basic principles of Resource Description Framework (RDF) ontologies is given. A morphological ontology has high potential for establishing a general morphological structure concept if it is developed on grounds of the following principles: morphological terms and concepts must be defined taxon-independently, homology-free, preferably purely anatomically, and if functionally only by clearly indicating the trait’s active participation in a specific biological process.

References

  1. Adanson, M. (1763) Familles des plantes. Vincent, Paris, 664 pp.

    Aldrovandi, U. (1648) Monstrorum historia. Tebaldini, Bononiae, 401 pp.

    Atran, S. (1990) Cognitive foundations of natural history: Towards an anthropology of science. Cambridge University Press, Cambridge, Mass, 360 pp.

    Appel, T. A. (1987) The Cuvier–Geoffroy Debate: French biology in the decades before Darwin. Oxford University Press US, New York, 305 pp.

    Bacon, F. (1620) Novum organum scientiarum. J. Billium, Londinii.

    Bard, J. (2003) Ontologies: formalising biological knowledge for bioinformatics. BioEssays, 25, 501–506.

    Bard, J. & Rhee, S.Y. (2004) Ontologies in biology: design, applications and future challenges. Nature Reviews Genetics, 5, 213–222.

    Beck, L.W. (1969) Early German philosophy: Kant and his predecessors. Harvard University Press, Cambridge, Mass, 567 pp.

    Beckett, D. (2004) RDF/XML syntax specification (revised). W3C recommendation published online 10 February 2004. Available from: http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/ (August 2008).

    Berners-Lee, T. (2005) Primer: Getting into RDF & Semantic Web using N3. Published online 29 June 2005. Available from: http://www.w3.org/2000/10/swap/Primer.html (August 2008).

    Bittner, T., Donnelly, M. & Smith, B. (2004) Individuals, universals, collections: on the foundational relations of ontology. In: Varzi, A. & Vieu, L. (Eds), Proceedings of the International Conference on Formal Ontology in Information Systems. IOS Press, Amsterdam, pp. 37–48.

    Blake, J. (2004) Bio-ontologies — fast and furious. Nature Biotechnology, 22, 773–774.

    Bock, G.R. & Cardew, G. (eds.) (1999) Novartis Foundation Symposium 222: Homology. John Wiley & Sons, Chichester.

    Boyd, R. (1999) Homeostasis, species, and higher taxa. In: Wilson, R. A. (Ed), Species — New interdisciplinary Essays. MIT Press, Cambridge, MA, pp. 141–185.

    Boyle, R. (1660) New experiments physico-mechanical: Touching the spring of the air and their effects. H. Hall, Oxford.

    Brazma, A. (2001) On the importance of standardisation in life sciences. Bioinformatics, 17, 113–114.

    Brickley, D. (2004) RDF Vocabulary Description Language 1.0: RDF Schema. W3C recommendation published online 10 February 2004. Available from: http://www.w3.org/TR/rdf-schema/ (August 2008).

    Brower, A.V.Z. & Schawaroch, V. (1996) Three steps of homology assessment. Cladistics, 12, 265–272.

    Cambrensis, G. (1185) History and topography of Ireland.

    Cardano, G. (1557) De vita propria.[First published 1643, Villery, Paris.]

    Cesalpino, A. (1583) De plantis libri XVI. Georgius Marescottus, Florentiae.

    Claridge, M.F., Dawah, H.A. & Wilson, M.R. (1997) Species — The units of biodiversity. The Systematics Association Special Volume Series 54. Chapman & Hall, London, 460 pp.

    Coleman, W. (1964) Georges Cuvier, zoologist: A study in the history of evolution theory. Harvard University Press, Cambridge, Mass, 212 pp.

    Cuvier, G. (1800-5) Leçons d’anatomie comparée. Baudoin, Paris.

    Cuvier, G. (1817) Le règne animal; distribué d’après son organisation; pour servir de base à l’histoire naturelle des animaux et d’introduction à l’anatomie comparée. Volume I. Deterville, Paris.

    Cuvier, G. (1825) Discours sur les révolutions de la surface du globe et sur les changements qu’elles ont produit dans le règne animal. G. Dufours et Ed. D’Ocagne, Paris et Amsterdam.

    Daston, L. (1992) Objectivity and the escape from perspective. Social Studies of Science, 22, 597–618.

    Daston, L. (1998) Fear and loathing of the imagination in science. Daedalus, 127, 16–30.

    Daston, L. & Galison, P. (1992) The image of objectivity. Representations, 40, 81–128.

    Daston, L. & Park, K. (1998) Wonders and the order of nature, 1150–1750. Zone Books, New York, 512 pp.

    Dondi, G. (1372–1374) De fontibus calidis agri Patavini consideratio. [Published 1553, Iunta, Venetiis.]

    Drake, S. (1957) Discoveries and opinions of Galileo. Doubleday, New York, 320 pp.

    Eco, U. (1988) Über Spiegel und andere Phänomene. Carl Hanser Verlag, München/Wien, 261 pp.

    Eigen, E. A. (1997) Overcoming first impressions: Georges Cuvier’s types. Journal of the History of Biology, 30, 179–209.

    Ereshefsky, M. (1997) The evolution of the Linnaean hierarchy. Biology and Philosophy, 12, 493–519.

    Farber, P.L. (1976) The type-concept in zoology during the first half of the nineteenth century. Journal of the History of Biology, 9, 93–119.

    Freudenstein, J. V. (2005) Characters, states, and homology. Systematic Biology, 54(6), 965–973.

    Fristrup, K.M. (2001) A history of character concepts in evolutionary biology. In: Wagner, G. P. (Ed), The character concept in evolutionary biology. Academic Press, San Diego, pp. 13–35.

    Galison, P. (1998) Judgement against objectivity. In: Jones, C. A. & Galison, P. (Eds), Picturing science, producing art. Routledge, New York, London, pp. 327–359.

    Gene Ontology Consortium (2006) The gene ontology (GO) project in 2006. Nucleic Acid Research, 34, D322–D326.

    Gingrich, O. (2004) The book nobody read: Chasing the revolutions of Nicolaus Copernicus. Walker Publishing Company, Inc., New York, 360 pp.

    Hall, B.K. (1994) Homology — The hierarchical basis of comparative biology. Academic Press, New York, London, 504 pp.

    Heintz, B. (2000) Die Innenwelt der Mathematik. Zur Kultur und Praxis einer beweisenden Disziplin. Springer, Wien, 318 pp.

    Heywood, V. (1985) Linnaeus — the conflict between science and scholasticism. In: Weinstock, J. (Ed.), Contemporary perspectives on Linnaeus. University Press of America, Lanham, Maryland, pp. 1–16.

    Jonston, J. (1657) Historiae naturalis de quadripedibus libri. J.J. Schipper, Amstelodami.

    Jungius, J. (1678) Isagoge phytoscopica. Vagetius, Hamburg.

    Kanz, K.T. (2002) Von der BIOLOGIA zur Biologie – Zur Begriffsentwicklung und Disziplingenese vom 17. bis zum 20. Jahrhundert. In: Hoßfeld, U. & Junker, T. (Eds), Die Entstehung biologischer Disziplinen II – Beiträge zur 10.

    Jahrestagung der DGGTB in Berlin 2001, Verhandlungen zur Geschichte und Theorie der Biologie, Volume 9. VWB Verlag, Berlin, pp. 9–30.

    Kukla, R. (2006) Objectivity and perspective in empirical knowledge. Episteme: A Journal of Social Epistemology, 3, 80–95.

    Lankester, E.R. (1870) On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreements. Annals and Magazine of Natural History, (series 4) 6, 34–43.

    Larson, J.T. (1967) Linnaeus and the natural method. Isis, 58, 304–320.

    Linnaeus, C. (1735) Systema naturae sive Regna tria naturae. Systematice proposita per Classes, Ordines, Genera, & Species. Theodor Haak, Lugduni Batavorum.

    Linnaeus, C. (1737) Genera plantarum. Salvius, Holmiae.

    Linnaeus, C. (1751) Philosophia botanica. Kiesewetter, Stockholm.

    Locke, J. (1689/1979) An essay concerning human understanding. Oxford University Press, Oxford.

    Manola, F. & Miller, E. (2004) RDF Primer, W3C Recommendations published online 10 February 2004. Available from: http://www.w3.org/TR/rdf-primer/ (August 2008).

    Mayden, R.L. (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. In: Claridge, M. F., Dawah, H. A. & Wilson, M. R. (Eds), Species: The units of biodiversity. Chapman & Hall, London, pp. 381–424.

    McGuiness, D.L. & van Harmelen, F. (2004) OWL Web Ontology Language Overview. W3C recommendation published online 10 February 2004. Available from: http://www.w3.org/TR/owl-features/ (August 2008).

    Mery, J. (1718) Sur un exomphale monstrueuse. HARS, Année 1716. Paris.

    Montecatini, U. da (1471) De balneis mineralibus et artificialibus. [Publ. 1950, Olschki, Firenze.]

    Müller-Wille, S. (1999) Botanik und weltweiter Handel. Zur Begründung eines Natürlichen Systems der Pflanzen durch Carl von Linné (1707–78). Studien zur Theorie der Biologie, Band 3. Verlag für Wissenschaft und Bildung, Berlin.

    Nagel, T. (1986) The view from nowhere. Oxford University Press, Oxford, 255 pp.

    Newton, I. (1687) Philosophiae naturalis principia mathematica. Societas Regia, Londini.

    Olivi, G.B. (1584) De reconditis et praecipuis collectaneis ab onestissimo et solertissimo Francisco Calceolari Veronesi in Musaeo adservatis. Zanfrettus, Venetiis.

    Owen, R. (1843) Lectures on comparative anatomy and physiology of the invertebrate animals delivered at the Royal College of Surgeons. Longman, Brown, Green and Longmans, London, 689 pp.

    Panchen, A.L. (1999) Homology – history of a concept. In: Bock, G. R. & Cardew, G. (Eds), Homology, Novartis Foundation Symposium 222. John Wiley & Sons, Chichester, pp. 5–18.

    Pennisi, E. (2003) Modernizing the tree of life. Science, 300, 1692–1697.

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

    Pleijel, F. & Rouse, G.W. (2000) Least-inclusive taxonomic unit: a new taxonomic concept for biology. Proceedings of the Royal Society of London, Series B: Biological Sciences, 267, 627–630.

    Porter, T. (1992) Objectivity as standardization: The rhetoric of impersonality in measurement, statistics, and cost–benefit analysis. Annals of Scholarship, 9, 19–59.

    Pullan, W. (2000) Structuring structure. In: Pullan, W. & Bhadeshia, H. (Eds), Structure in science and art. Cambridge University Press, Cambridge, pp. 1–8.

    Ramírez, M.J., Coddington, J.A., Maddison, W.P., Midford, P.E., Prendini, L., Miller, J., Griswold, C.E., Hormiga, G., Sierwald, P., Scharff, N., Benjamin, S.P. & Wheeler, W.C. (2007) Linking of digital images to phylogenetic data matrices using a morphological ontology. Systematic Biology, 56, 283–294.

    Ray, J. (1703) Methodus plantarum emendata et aucta. Smith and Walford, London.

    Riedl, R. (2000) Strukturen der Komplexität – Eine Morphologie des Erkennens und Erklärens. Springer, Berlin, 367 pp.

    Rieppel, O. (1993) The conceptual relationship of ontogeny, phylogeny, and classification – the taxic approach. Evolutionary Biology, 27, 1–32.

    Russell, E.S. (1916) Form and function: a contribution to the history of animal morphology. John Murray, London, 394 pp.

    Salthe, S.N. (1985) Evolving hierarchical systems: their structure and representation. Columbia University, New York, 343 pp.

    Salthe, S.N. (1993) Development and evolution: complexity and change in biology. MIT Press, Cambridge, Mass, 368 pp.

    Savonarola, M. (1448–1449) De balneis seu thermis naturalibus omnibus Italiae. [Publ. 1845, Andreas Belfortis, Ferrariae.]

    Scotland, R.W., Olmstead, R.G. & Bennet, J.R. (2003) Phylogeny reconstruction: The role of morphology. Systematic Biology, 52, 539–548.

    Shapin, S. (1996) The Scientific Revolution. University of Chicago Press, Chicago, 218 pp.

    Shapin, S. & Schaffer, S. (1985) Leviathan and the air pump: Hobbes, Boyle and the experimental life, including a translation of Hobbes, Dialogus Physicus De Natura Aeris. Princeton University Press, Princeton NJ, 456 pp.

    Spedding, J., Ellis, R.L. & Heath, D.D. (1857–1874) The works of Francis Bacon. 14 volumes. Longman, Green, Longman & Roberts, London.

    Stamos, D.N. (2005) Pre-Darwinian taxonomy and essentialism – a reply to Mary Winsor. Biology and Philosophy, 20, 79–96.

    Stein, L.D. (2003) Integrating biological databases. Nature Reviews Genetics, 4, 337–345.

    Stevens, P.F. (1997) Mind, memory and history: How classifications are shaped by and through time, and some consequences. Zoologica Scripta, 26, 293–301.

    Stevens, R., Goble, C.A. & Bechhofer, S. (2000) Ontology-based knowledge representation for bioinformatics. Briefings in Bioinformatics, 1, 398–414.

    Strickland, H.E. (1840a) On the true method of discovering the natural system in zoology and botany. Annals and Magazine of Natural History, 6, 184–186.

    Strickland, H.E. (1840b) Observations upon the affinities and analogies of organized beings. Magazine of Natural History, 4, 219–226.

    Tournefort, J.P. de (1694) Elemens de botanique. Imprimerie Royale, Paris.

    Valentine, J.W. & May, C.L. (1996) Hierarchies in biology and paleontology. Paleobiology, 22, 23–33.

    Vogt, L. (in press) The future role of bio-ontologies for developing a general data standard in biology – Chance and challenge for zoo-morphology. Zoomorphology.

    Vogt, L., Bartolomaeus, T. & Giribet, G. (submitted) The linguistic problem of morphology – Challenges to the future role of morphology in phylogenetics.

    von Sachs, J. (1875) Geschichte der Botanik. Oldenburg, München.

    Wang, X., Gorlitsky, R. & Almeida, J.S. (2005) From XML to RDF: how semantic web technologies will change the design of 'omic' standards. Nature Biotechnology, 23, 1099–1103.

    Wheeler, Q.D. & Meier, R. (2000) Species concepts and phylogenetic theory: a debate. Columbia University Press, New York, 256 pp.

    Whewell, W. (1840) Philosophy of the inductive sciences. J.W. Parker, London.

    Wilson, R.A. (ed.) (1999) Species — New interdisciplinary essays. MIT Press, Cambridge, Mass, 349 pp.

    Wimsatt, W.C. (1976) Reductionism, levels of organization, and the mind–body problem. In: Globus, G., Maxwell, G. & Savodnik, I. (Eds), Consciousness and the brain: A scientific and philosophical inquiry. Plenum Press, New York, pp. 202–267.

    Wimsatt, W.C. (1994) The ontology of complex systems: Levels, perspectives, and causal thickets. Canadian Journal of Philosophy, Supplemental Volume 20, 207–274.

    Winsor, M.P. (2003) Non-essentialist methods in pre-Darwinian taxonomy. Biology and Philosophy, 18, 387–400.

    Winsor, M.P. (2006a) Linnaeus’s biology was not essentialist. Annals of the Missouri Botanical Garden, 93, 2–7.

    Winsor, M.P. (2006b) The creation of the essentialism story: an exercise in metahistory. History and Philosophy of the Life Sciences, 28, 149–174.