|Life||History of Taxonomy|
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Life on Earth
Botanicus.org, via From Wikipedia, Creative Commons Attribution-Noncommercial 2.5 license.
In order to make sense of the natural world, science creates categories and classification systems. In the case of living organisms, which include millions of species that evolved through several billions of years of Earth history, and whose characteristics (especially in the case of fossil species) and evolutionary relationships are often imperfectly understood, classification often becomes arbitrary. Add to this the fact that specilaists working in different fields may have different approaches or preferences, and it is easy to see how the subject can become confusing, and ideas and methodologies have changed radically over time.
Aristotle was the first to give the first detailed classification of living things. His classification of animals was:
However, he had made no effort to classify plants or fungi. His ideas were essentially based on the idea of the scala naturae, the "Natural Ladder" according to which the entire natural world could be arranged in a single continuum. During the medieval period this become incorporated into the idea of the Great Chain of Being.
Classical and medieval thinkers used logical and philosphical categories, but these were based on the most general principles, and while perhaps useful for abstract philosophy, were not much use in understanding the natural world. In the theocratic Middle Ages this didn't matter much, but with the progressive advance of knowledge during the Renaissance, the Age of Reason, and the Enlightenment, there developed an interest in the secular world for its own sake. Botanists especially were fascinated by exoteric new plants discovered during the voyages of exploration. It is not coincidental then that the father of modern biological classification was a botanist, Carl Linne, better known by his Latin name Linnaeus. Linnaeus's simple yet brilliant idea was to distinguish nomenclature - the science of naming - from description. He therefore rejected the long-winded descriptive names of plants used by his predecessors and contemporaries, and replaced them with a simple two name system, a generic and a specific (think surname and given name, e.g. Smith, John). These where then grouped in hierarchies such as class, order, and so on. With only slight refinements, the Linnaean system is the scientific, biological classification system still used today.
Scientists and naturalists like Linnaeus in Sweden, and later the anatomist and naturalist Georges Cuvier in France, and Owen in England, and their collegues and co-workers, established in the 18th and early 19th century the science of what we now know as Taxonomy. Taxonomy is concerned with discovering, identifying, describing and naming organisms. For this to work it requires institutions to hold collections of these organisms, with relevant data, carefully curated: such institutes include Natural History Museums, Herbaria and Botanical Gardens. Richard Owen for example established the British Museum of Natural History in London, where his statue still resides.
Linnaeus, like his 18th century contemporaries, had a static, biblical view of the world. All the species that exist and that he described were the same as those originally created by God, and every species that ever lived was still alive today. This simple worldview was undermined in the late 18th and early 19th century by the discovery of fossil species totally different to anything alive. This led to birth of paleontology, under men like Cuvier and Owen. Cuvier, the father of paleontology, who was the first to name and correctly identify many fossil animals (e.g.: Pterodactylus, Mosasaurus, Didelphys, Palaeotherium) was still a creationist, but explained the existence strange armoured fish, ichthyosaurii, tertiary mammals, mastodons, and the rest in terms of repeated catastrophies, after which God would recreate the world. The biblical flood was considered the most recent of these catastrophes. Owen, who named the order (now superorder) Dinosauria, instead adopted a Goethean concept of evolving archetypes (but not of physical evolution; Owen was strongly opposed to Darwin's theory when it came out). By these sort of mechanisms, Cuvier and Owen could explain the existence of antediluvial (before the flood) monsters. All this changed with Darwin's discovery of the principle of evolution. Darwin, Huxley, and Haeckel established the evolutionary paradigm, and, like Cuvier and Owen, had no problem identifying prehistoric life with Linnaean categories. What evolution did was to make the Linnaean system more dynamic. Thus, Huxley was able to show that Archaeopteryx, the first bird (Class Aves) was also a transitional form between reptiles (Class Reptilia) and modern birds. This synthesis of Darwinian science and Linnaean taxonomy was further elaborated on in the mid 20th century by vertebrate paleontolgists Romer and Simpson, and came to be later known as Evolutionary Systematics
In the 1980s, an alternative to Evolutionary Systematics, called Phylogenetic Systematics, or Cladistics became popular, especially among vertebrate paleontologists. Cladistics is more properly considered under the next Unit, Phylogeny. The central difference between the Linnaean and Cladistic systems is that one is a taxonomic, classification system, the other a means of constructing phylogenetic hypotheses; or in less jargonesque language, deciding which of a number of possible evolutionary trees is likely to be the more correct one (which doesn't mean it is the right one, as new discoveries can always overturn the current hypotheses) . Over the past few years, an attempt is being made to develop a formal, cladistic system of taxonomy and nomenclature to replace the linnaean system, called the Phylo Code, but this is yet to catch on at a wider level in biology.
One might suppose that classification should reflect phylogeny, and that phylogeny would automatically result in a superior classification system, but this is not necessarily the case. Taxonomiess may involve organisms that appear to be closely related but are not, phylogenies can result in unweildly systems, or phylogenetic definitions can be totally overturned by new discoveries and hypothesis Taxonomies can be overturned as well, but are generally more robust (Benton 2007).. The most reasonable approach therefore is to acknowledge the usefulness of both descriptive classification and phylogenetic hypotheses as two equally partial and complementary means of understanding the natural world. MAK120229
 Contrary to popular belief, cladistics does not describe the actual evolutionary path of life. That is, it is not concerned with or describe the evolution of later organisms from common ancestors in the way that, say, Darwin or more recently Richard Dawkins do, and what the Evolutionary systematics of Romer and Simpson also describes. It simply provides a way of generating hypotheses regarding the way living organisms are related to each other. Cladograms, in other words, are not evolutionary trees. What cladistics does do is provide a more precise and verifiable method of creating hypotheses regarding the evolutionary relationships of past and current organisms (Phylogeny, a word invented in the late 19th century by Haeke), but used here ina somewhat different context).
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