Aristotle also studied animals and classified them according to method of reproduction, as did Linnaeus later with plants. Aristotle's animal classification was soon made obsolete by additional knowledge and was forgotten.
The philosophical classification is in brief as follows. Primary substance is the individual being; for example, Peter, Paul, etc. Secondary substance is a predicate that can properly or characteristically be said of a class of primary substances; for example, man of Peter, Paul, etc. The characteristic must not be merely in the individual; for example, being skilled in grammar. Grammatical skill leaves most of Peter out and therefore is not characteristic of him. Similarly man (all of mankind) is not in Peter; rather, he is in man.
Species is the secondary substance that is most proper to its individuals. The most characteristic thing that can be said of Peter is that Peter is a man. An identity is being postulated: "man" is equal to all its individuals and only those individuals. Members of a species differ only in number but are totally the same type.
Genus is a secondary substance less characteristic of and more general than the species; for example, man is an animal. Not all animals are men. It is clear that a genus contains species. There is no limit to the number of Aristotelian genera that might be found to contain the species. Aristotle does not structure the genera into phylum, class, etc., as does Linnaean classification.
The secondary substance that distinguishes one species from another within a genus is the specific difference. Man can thus be comprehended as the sum of specific differences (the "differentiae" of biology) in less and less general categories. This sum is the definition; for example, man is an animate, sensate, rational substance. The most characteristic definition contains the species and the next most general genus: man is a rational animal. Definition is thus based on the unity problem: the species is one yet has many differentiae.
The very top genera are the categories. There are ten: one of substance and nine of "accidents", universals that must be "in" a substance. Substances exist by themselves; accidents are only in them: quantity, quality, etc. There is no higher category, "being", because of the following problem, which was only solved in the Middle Ages by Thomas Aquinas: a specific difference is not characteristic of its genus. If man is a rational animal, then rationality is not a property of animals. Substance therefore cannot be kind of being because it can have no specific difference, which would have to be non-being.
The problem of being occupied the attention of scholastics during the time of the Middle Ages. The solution of St. Thomas, termed the analogy of being, established the field of ontology, which received the better part of the publicity and also drew the line between philosophy and experimental science. The latter rose in the Renaissance from practical technique. The greatest scientific classifier, Linnaeus, a brilliant classical scholar, combined the two on the threshold of that great neo-classicist revival now called the Age of Enlightenment.
The exploration of parts of the New World produced large numbers of new plants and animals that needed descriptions and classification. The old systems made it difficult to study and locate all these new specimens within a collection and often the same plants or animals were given different names because the number of specimens were too large to memorize. A system was needed that could group these specimens together so they could be found; the binomial system was developed based on morphology with groups having similar appearances. In the latter part of the 16th century and the beginning of the 17th, careful study of animals commenced, which, directed first to familiar kinds, was gradually extended until it formed a sufficient body of knowledge to serve as an anatomical basis for classification. Advances in using this knowledge to classify living beings bear a debt to the research of medical anatomists, such as Fabricius (1537–1619), Petrus Severinus (1580–1656), William Harvey (1578–1657), and Edward Tyson (1649–1708). Advances in classification due to the work of entomologists and the first microscopists is due to the research of people like Marcello Malpighi (1628–1694), Jan Swammerdam (1637–1680), and Robert Hooke (1635–1702). Lord Monboddo (1714-1799) was one of the early abstract thinkers whose works illustrate knowledge of species relationships and who foreshadowed the theory of evolution. Successive developments in the history of insect classification may be followed on the website by clicking on succeeding works in chronological order.
Andrea Caesalpino (1519–1603) in his De plantis libri XVI (1583) proposed the first methodical arrangement of plants. On the basis of the structure of trunk and fructification he divided plants into fifteen "higher genera".
John Ray (1627–1705) was an English naturalist who published important works on plants, animals, and natural theology. The approach he took to the classification of plants in his Historia Plantarum was an important step towards modern taxonomy. Ray rejected the system of dichotomous division by which species were classified according to a pre-conceived, either/or type system, and instead classified plants according to similarities and differences that emerged from observation.
Both Caesalpino and Ray used traditional plant names and thus, the name of a plant did not reflect its taxonomic position (e.g. even though the apple and the peach belonged to different "higher genera" of John Ray's methodus, both retained their traditional names Malus and Malus Persica respectively). A further step was taken by Rivinus and Pitton de Tournefort who made genus a distinct rank within taxonomic hierarchy and introduced the practice of naming the plants according to their genera.
Augustus Quirinus Rivinus (1652–1723), in his classification of plants based on the characters of the flower, introduced the category of order (corresponding to the "higher" genera of John Ray and Andrea Caesalpino). He was the first to abolish the ancient division of plants into herbs and trees and insisted that the true method of division should be based on the parts of the fructification alone. Rivinus extensively used dichotomous keys to define both orders and genera. His method of naming plant species resembled that of Joseph Pitton de Tournefort. The names of all plants belonging to the same genus should begin with the same word (generic name). In the genera containing more than one species the first species was named with generic name only, while the second, etc were named with a combination of the generic name and a modifier (differentia specifica).
Joseph Pitton de Tournefort (1656–1708) introduced an even more sophisticated hierarchy of class, section, genus, and species. He was the first to use consistently the uniformly composed species names which consisted of a generic name and a many-worded diagnostic phrase differentia specifica. Unlike Rivinus, he used differentiae with all species of polytypic genera.
He abandoned long descriptive names of classes and orders and two-word generic names (e. g. Bursa pastoris) still used by his immediate predecessors (Rivinus and Pitton de Tournefort) and replaced them with single-word names, provided genera with detailed diagnoses (characteres naturales), and reduced numerous varieties to their species, thus saving botany from the chaos of new forms produced by horticulturalists.
Linnaeus is best known for his introduction of the method still used to formulate the scientific name of every species. Before Linnaeus, long many-worded names (composed of a generic name and a differentia specifica) had been used, but as these names gave a description of the species, they were not fixed. In his Philosophia Botanica (1751) Linnaeus took every effort to improve the composition and reduce the length of the many-worded names by abolishing unnecessary rhetorics, introducing new descriptive terms and defining their meaning with an unprecedented precision. In the late 1740s Linnaeus began to use a parallel system of naming species with nomina trivialia. Nomen triviale, a trivial name, was a single- or two-word epithet placed on the margin of the page next to the many-worded "scientific" name. The only rules Linnaeus applied to them was that the trivial names should be short, unique within a given genus, and that they should not be changed. Linnaeus consistently applied nomina trivialia to the species of plants in Species Plantarum (1st edn. 1753) and to the species of animals in the 10th edition of Systema Naturae (1758).
By consistently using these specific epithets, Linnaeus separated nomenclature from taxonomy. Even though the parallel use of nomina trivialia and many-worded descriptive names continued until late in the eighteenth century, it was gradually replaced by the practice of using shorter proper names combined of the generic name and the trivial name of the species. In the nineteenth century, this new practice was codified in the first Rules and Laws of Nomenclature, and the 1st edn. of Species Plantarum and the 10th edn. of Systema Naturae were chosen as starting points for the Botanical and Zoological Nomenclature respectively. This convention for naming species is referred to as binomial nomenclature.
There are 8 main taxonomic ranks: domain, kingdom, phylum, class, order, family, genus, species.
There are slightly different ranks for zoology and for botany.
Since the 1960s a trend called cladistic taxonomy (or cladistics or cladism) has emerged, arranging taxa in an evolutionary tree. If a taxon includes all the descendants of some ancestral form, it is called monophyletic, as opposed to paraphyletic. Other groups are called polyphyletic.
A new formal code of nomenclature, the PhyloCode, to be renamed "International Code of Phylogenetic Nomenclature" (ICPN), is currently under development, intended to deal with clades, which do not have set ranks, unlike conventional Linnaean taxonomy. It is unclear, should this be implemented, how the different codes will coexist.
Domains are a relatively new grouping. The three-domain system was first invented in 1990, but not generally accepted until later. Now, the majority of biologists accept the domain system, but a large minority use the five-kingdom method. One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera). Consequently, the three domains of life are conceptualized as Archaea, Bacteria, and Eukaryota (comprising the nuclei-bearing eukaryotes). A small minority of scientists add Archaea as a sixth kingdom, but do not accept the domain method.
Thomas Cavalier-Smith, who has published extensively on the classification of protists, has recently proposed that the Neomura, the clade which groups together the Archaea and Eukarya, would have evolved from Bacteria, more precisely from Actinobacteria.