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

........................................................................................................................................................................ 124 Introduction ..................................................................................................................................................................... 124 The historical burden of essentialism .............................................................................................................................. 125 Aristotle and essentialism ........................................................................................................................................ 125 Naturalness, essences, and the epistemic role of observation............................................................................ 127 The influence of medieval hermetism ...................................................................................................................... 127 Paradoxographies and early encyclopaedists..................................................................................................... 128 Naturalness, essences, and the epistemic role of observation............................................................................ 129 Emancipation from the ancient heritage ................................................................................................................... 129 The discovery of the ‘New World’ and the collections of pharmacists and physicians .................................... 130 Bacon’s empirical facts ...................................................................................................................................... 130 Naturalness, essences, and the epistemic role of observation............................................................................ 131 The age of classification ........................................................................................................................................... 132 Naturalness, essences, and the epistemic role of observation........................................................................... 133 Causal reasoning and the role of function in classification....................................................................................... 133 Development of the laboratory method ............................................................................................................. 133 Causal reasoning ................................................................................................................................................ 134 The role of functional morphology in classification.......................................................................................... 134 Naturalness, essences, and the epistemic role of observation............................................................................ 135 The problem with essences and its unsatisfactory solution ............................................................................................ 136 Morphological terminology and homology—the downside of the solution ............................................................ 138 What can we learn from Linnaeus .................................................................................................................................. 138 Linnaeus’ morphological structure concept .............................................................................................................. 138 Developing a general structure concept for morphology ................................................................................................ 140 What is 'structure'? .................................................................................................................................................... 140 Basic principles for developing a structure concept ................................................................................................. 141 Foundations of a morphological structure concept ................................................................................................... 141 What is the structure of a morphological trait?.................................................................................................. 142 Data bases, ontologies, and data standards ..................................................................................................................... 142 The role of data bases in biology .............................................................................................................................. 142 Morphological data bases .................................................................................................................................. 143 Ontologies for standardizing structure concepts ...................................................................................................... 143 An introduction to resource description framework (RDF) ontologies ............................................................ 144 Defining concepts in RDF ................................................................................................................................. 144 Defining relations in RDF.................................................................................................................................. 146 Using an ontology for inferences ....................................................................................................................... 146 Ontology as a structure concept ......................................................................................................................... 147 A morphological ontology can provide a general morphological structure concept ............................................... 148