11. Taxonomy, Partonomy, and Ontology Classifying entities and discerning part-whole relations belong to the normal activity of everyday life. As soon as we describe a particular thing, we are classifying it, and as soon as we enter a house or a town, we are dividing it into parts. Such ordinary classifications and partitions have a practical purpose, and the classification and partition schemas used need not be systematic. In science, however, unsystematic classification schemas are often developed into well structured and principled general taxonomies such as the classic biological taxonomies of plants and animals. Similarly, parts and their positions in larger wholes are systematized by science into partonomies such as the anatomy of the human body and the double helix structure of the gene. 11.1 What is it that we classify and partition? In Chapters 2 and 3, we talked a little about the scientific revolution of the seventeenth century. In taxonomy (the science of classification), the revolution occurred in the eighteenth century. The Swedish botanist and zoologist Linnaeus (Carl von Linné, 1707-1778) is often regarded as the creator of modern taxonomy, with Aristotle as its ancient founding father. During medieval times, alchemists made extensive classifications of chemical substances, and herbalists made the same with respect to plants, but in neither case was a real taxonomy created. This is probably because the alchemists and the herbalists were too practically minded. With the advent of modern chemistry and botany things changed. Better organized taxonomies were created, and helped to speed up subsequent scientific development. But with the recent information explosion and the advent of the computer revolution, scientific work with the construction of taxonomies and partonomies has taken on quite a new dimension. A new stage in the need for taxonomic classifications seems to have been reached. In new disciplines such as medical informatics, bioinformatics, genomics, proteomics, and a range of similar disciplines, classificatory issues play a prominent role. 402 11.1.1 Classification of particulars and classification of classes There are two clearly distinct kinds of classifications: classifications of particulars (e.g., ‘this is a lion’, ‘this is a case of measles’, and ‘this is an example of turquoise blue’) and classifications of classes (e.g., ‘the lion is a mammal’, ‘measles is a virus disease’, and ‘turquoise blue is a color’). The term ‘particular’ is in this chapter meant to cover all cases where we normally speak of spatiotemporally specific persons, spatiotemporally specific things, or spatiotemporally specific instances of a property. Traditional taxonomies of plants, animals, and diseases are classifications of classes, whereas patient diaries and modern electronic health records rest on classifications of particulars (persons). Assertions by means of which we classify particulars – such as ‘this is a lion’, ‘this is a case of measles’, and ‘this is an example of turquoise blue’ – are worth making because the animal could have been of another kind, the patient could have had a different disease or no disease at all, and the colored object could have been of a different color. To describe a particular in front of us is to convey information about this particular by means of a classificatory term. Subject-predicate sentences such as ‘this lion is somewhat brown’ contain two classifications: one for what falls under the subject term (‘being a lion’), and one for what falls under the predicate term (‘being somewhat brown’). Implicitly, there is a classification also when we describe something negatively, as in ‘this is not a lion’, ‘he does not have the measles’, and ‘this is not turquoise blue’. In the first case, we are implicitly conveying the view that there is an animal, in the second that the person in question has either no disease at all or a disease of some other kind, and in the third that the object in question is of some other color. It seems impossible to talk about particulars without using classificatory terms. Even when we merely name something, as in the utterance ‘his name is Fido’, the context does normally indicate a classification. In this case, what is named is probably to be classified as a dog; the speaker could equally well have said ‘the name of this dog is Fido’. Such implicit classifications are necessary for communication. An utterance containing a pure ‘this’, e.g., the utterance ‘this has the name Fido’, cannot in itself possibly pick out anything in the world. Why? Since one would then not have any clue as to what the ‘this’ might refer to. The world contains at any moment an innumerable number of possible referents. Cut loose from 403 all classifications, the word ‘this’ has no communicative function at all, and the same goes for pure names. (In some corners of philosophy, especially those linked to Saul Kripke (b. 1940), there is much talk about a kind of pure names called ‘rigid designators’; but such a designator is always introduced by a ‘description used to fix its reference’.) Assertions by means of which we classify classes – such as ‘the lion is a mammal’, ‘measles is a virus disease’, and ‘turquoise blue is a color’ – are worth making because it is often possible and expedient to convey in one stroke information about whole collections of particulars. All the three examples above have the linguistic form ‘A is B’ (in informatics, it is often written ‘A is_a B’), and should in what follows be read ‘the class A belongs as a subclass to the class B’ or ‘the class B subsumes class A’. One connection between classifications of classes and classifications of particulars is the necessity that if (i) class A belongs to class B, and (ii) a certain particular is classified as being an A, then (iii) it has to be classified as being a B, too. Necessarily, if Leo is a lion, and lions are mammals, then Leo is a mammal; if patient Joan has the measles, and measles is a viral disease, then patient Joan has a viral disease; if this spot is turquoise blue, and turquoise blue is a color, then this spot is colored. So far, so simple; but what then do we more precisely mean by ‘class’? First, the term must not be conflated with the more specific biological term ‘class’ that occurs in the hierarchy of biological taxa: ‘species’, ‘genus’, ‘family’, ‘order’, ‘class’, ‘phylum’, ‘kingdom’. Second, neither should it be conflated with the broader term ‘class’ that is used in some programming languages. The general concept of ‘class’ is today normally defined (e.g., in Wikipedia, spring 2007) as follows: • class =def. a collection of entities between which there are similarity relations. This general definition being accepted, there is much to say about how different kinds of similarity relations constitute different kinds of classes. We will only talk about classes of spatiotemporal particulars (not about classes of abstract objects such as ‘the class of prime numbers’), but the term ‘class’ will here never be used to refer to spatially or temporally bounded collections. A class in our sense has, in contradistinction to 404 bounded collections such as ‘the lions in the Copenhagen zoo’, ‘the hitherto living dinosaurs’, or ‘measles patients in the year 2000’, no predetermined limits in space and/or time. The class of lions, the class of patients, and the class of blue property instances are open in the sense that if a new lion is born, a person suddenly becomes a patient, and something is painted blue, then these individuals and instances are automatically members of the corresponding classes. Conversely, if, for example, the lion species becomes extinct, it still makes good sense to talk of the class of lions. (To those familiar with set theory, we have to add that classes cannot be identified with sets in the way that sets are defined in standard set theory. One reason for this is that there is only one ‘empty set’, i.e., a set without a member, but there are many ‘empty classes’. For example, ‘the class of mermaids’ and ‘the class of offspring of two mules’ are two different empty classes, but ‘the set of mermaids’ and ‘the set of offspring of two mules’ is one and the same set: the empty set.) When we are classifying we are using classificatory terms and the concepts that come with the terms, but we are nonetheless classifying the classes that the concepts refer to. A concept is for us, to make this clear, merely the meaning that a term shares with synonymous terms. People often and easily conflate the use of terms and concepts in taxonomies with talk about these terms and concepts. Certainly, terms and concepts are talked about and classified in linguistics. But in all other traditional empirical sciences the terms and concepts are used in order to classify what they refer to, their referents. Because of this unhappy conflation of ‘using terms’ and ‘talking about terms’, we must spend some time on the relationship between language (terms and concepts) and reality (classes of particulars), as this relationship is not always as straightforward as it may appear to the un-philosophical eye. What, for instance, do we classify when we classify classes of cells as being ‘epithelial’ and ‘neural’, respectively? There are not only two logically possible answers to this question: that we either classify only the concepts ‘epithelial cell’ and ‘neural cell’, or we must have an ability to see directly and to carve, infallibly, nature at the joint where the class of epithelial cells is distinguished from the class of neural cells. Since the realist fallibilism we have defended (Chapter 3.5) applies to taxonomy, 405 informatics, and the information sciences, both these answers are ruled out.