Chapter 20
Taxonomy: Imposing Order on Diversity


1. Taxonomic Categories
Taxonomic Hierarchy

Approximately one and a half million species have been classified and there are estimates that over five million species remain to be discovered. For biologists to order this mass of information, a scientific system called taxonomy was introduced. We have attempted to simplify this system in our tree of life. This tree is not aimed at the Biology professor, but at informing the interested amateur.

The basic idea is to group species with similar characteristics together into families, and to group the families together into broader groupings. To this end, the taxonomic categories where devised, and they create the taxonomic hierarchy. The hierarchy goes (with an example):

Kingdom
Animalia
Phylum (Plural = Phyla)
In plants, this category is often called a Division
Cordata
Class
Mammalia
Order
Carnivora
Family
Canidae
Genus
Canis
Species
Lupus (the Wolf)
Species are often divided into sub-species, the latter differ only slightly from one another. Wolves are a good example.

When naming a species, it is customary to use the binomial system, introduced by Linnaeus in 1753. In this system, you use the generic name (Genus) followed by the specific name (species), possibly with a sub-species name after that. As this is a scientific name, it is written in italics - Sus scrofa is the Eurasian Wild Pig and Sus scrofa algira is its North African sub-species.

Many organisms have common names, but these are often confusing as the same organism can be known in different parts of the world by many various different common names. Likewise the same common name can be applied to different species, depending on the geographical area. For example: in parts of North America, the plant Primula veris is called a cowslip. In parts of Europe, the same name, cowslip, is given to Caltha palustris, a member of a completely different Genus!

There is an alternative system for catagorising organisms - cladistics. This system uses the idea of ancestry as it's basis for dividing organisms into clades.


Picture by LinneusA few links on Lineus and Taxonomy:

Carolus Linnaeus (1707-1778)

Carolus Linnaeus, or Carl Linné, 1707-1778, Swedish botanist.

Charles de LINNE: (good site, in French)

Botanical History - Department of Phanerogamic Botany
Swedish Museum of Natural History (S)







As another example, the position of humans within the taxonomy is as follows:

Class -- Mammalia
Subclass -- Theria
Infraclass -- Eutheria
Order -- Primates
Suborder -- Anthropoidea
Infraorder -- Catarrhini
Superfamily -- Hominoidea
Family -- Hominidae
Genus -- Homo
Species -- sapiens












2.The Origins of Taxonomy

Aristotle (384-322 B.C.E.)

Mine is the first step and therefore a small one, though worked out with much thought and hard labor. You, my readers or hearers of my lectures, if you think I have done as much as can fairly be expected of an initial start. . . will acknowledge what I have achieved and will pardon what I have left for others to accomplish.

Aristotle was born in Stagira in north Greece, the son of Nichomachus, the court physician to the Macedonian royal family. He was trained first in medicine, and then in 367 he was sent to Athens to study philosophy with Plato. He stayed at Plato's Academy until about 347 -- the picture at the top of this page, taken from Raphael's fresco The School of Athens, shows Aristotle and Plato (Aristotle is on the. right). Though a brilliant pupil, Aristotle opposed some of Plato's teachings, and when Plato died, Aristotle was not appointed head of the Academy. After leaving Athens, Aristotle spent some time traveling, and possibly studying biology, in Asia Minor (now Turkey) and its islands. He returned to Macedonia in 338 to tutor Alexander the Great; after Alexander conquered Athens, Aristotle returned to Athens and set up a school of his own, known as the Lyceum. After Alexander's death, Athens rebelled against Macedonian rule, and Aristotle's political situation became precarious. To avoid being put to death, he fled to the island of Euboea, where he died soon after.

Aristotle is said to have written 150 philosophical treatises. The 30 that survive touch on an enormous range of philosophical problems, from biology and physics to morals to aesthetics to politics. Many, however, are thought to be "lecture notes" instead of complete, polished treatises, and a few may not be the work of Aristotle but of members of his school.

A full description of Aristotle's contributons to science and philosophy is beyond the scope of this exhibit, but a brief summary can be made: Whereas Aristotle's teacher Plato had located ultimate reality in Ideas or eternal forms, knowable only through reflection and reason, Aristotle saw ultimate reality in physical objects, knowable through experience. Objects, including organisms, were composed of a potential, their matter, and of a reality, their form; thus, a block of marble -- matter -- has the potential to assume whatever form a sculptor gives it, and a seed or embryo has the potential to grow into a living plant or animal form. In living creatures, the form was identified with the soul; plants had the lowest kinds of souls, animals had higher souls which could feel, and humans alone had rational, reasoning souls. In turn, animals could be classified by their way of life, their actions, or, most importantly, by their parts.

Though Aristotle's work in zoology was not without errors, it was the grandest biological synthesis of the time, and remained the ultimate authority for many centuries after his death. His observations on the anatomy of octopus, cuttlefish, crustaceans, and many other marine invertebrates are remarkably accurate, and could only have been made from first-hand experience with dissection. Aristotle described the embryological development of a chick; he distinguished whales and dolphins from fish; he described the chambered stomachs of ruminants and the social organization of bees; he noticed that some sharks give birth to live young -- his books on animals are filled with such observations, some of which were not confirmed until many centuries later.

Aristotle's classification of animals grouped together animals with similar characters into genera (used in a much broader sense than present-day biologists use the term) and then distinguished the species within the genera. He divided the animals into two types: those with blood, and those without blood (or at least without red blood). These distinctions correspond closely to our distinction between vertebrates and invertebrates. The blooded animals, corresponding to the vertebrates, included five genera: viviparous quadrupeds (mammals), birds, oviparous quadrupeds (reptiles and amphibians), fishes, and whales (which Aristotle did not realize were mammals). The bloodless animals were classified as cephalopods (such as the octopus); crustaceans; insects (which included the spiders, scorpions, and centipedes, in addition to what we now define as insects); shelled animals (such as most molluscs and echinoderms); and "zoophytes," or "plant-animals," which supposedly resembled plants in their form -- such as most cnidarians.

Aristotle's thoughts on earth sciences can be found in his treatise Meteorology -- the word today means the study of weather, but Aristotle used the word in a much broader sense, covering, as he put it, "all the affections we may call common to air and water, and the kinds and parts of the earth and the affections of its parts." Here he discusses the nature of the earth and the oceans. He worked out the hydrologic cycle: "Now the sun, moving as it does, sets up processes of change and becoming and decay, and by its agency the finest and sweetest water is every day carried up and is dissolved into vapour and rises to the upper region, where it is condensed again by the cold and so returns to the earth." He discusses winds, earthquakes (which he thought were caused by underground winds), thunder, lightning, rainbows, and meteors, comets, and the Milky Way (which he thought were atmospheric phenomena). His model of Earth history contains some remarkably modern-sounding ideas:

The same parts of the earth are not always moist or dry, but they change according as rivers come into existence and dry up. And so the relation of land to sea changes too and a place does not always remain land or sea throughout all time, but where there was dry land there comes to be sea, and where there is now sea, there one day comes to be dry land. But we must suppose these changes to follow some order and cycle. The principle and cause of these changes is that the interior of the earth grows and decays, like the bodies of plants and animals. . . .

But the whole vital process of the earth takes place so gradually and in periods of time which are so immense compared with the length of our life, that these changes are not observed, and before their course can be recorded from beginning to end whole nations perish and are destroyed.

Where Aristotle differed most sharply from medieval and modern thinkers was in his belief that the universe had never had a beginning and would never end; it was eternal. Change, to Aristotle, was cyclical: water, for instance, might evaporate from the sea and rain down again, and rivers might come into existence and then perish, but overall conditions would never change.

In the later Middle Ages, Aristotle's work was rediscovered and enthusiastically adopted by medieval scholars. His followers called him Ille Philosophus (The Philosopher), or "the master of them that know," and many accepted every word of his writings -- or at least every word that did not contradict the Bible -- as eternal truth. Fused and reconciled with Christian doctrine into a philosophical system known as Scholasticism, Aristotelian philosophy became the official philosophy of the Roman Catholic Church. As a result, some scientific discoveries in the Middle Ages and Renaissance were criticized simply because they were not found in Aristotle. It is one of the ironies of the history of science that Aristotle's writings, which in many cases were based on first-hand observation, were used to impede observational science.


The Tech Classics Archive at MIT has Aristotle's scientific writings available, including his History of Animals, On The Parts of Animals, and Meteorology. Aristotle's writings are also available on gopher from Virginia Tech.

For more general information, try this biography of Aristotle. Or visit "Aristotle et al." for texts dealing extensively with Scholasticism.






3. Modern Criteria for Classification


Taxonomy
Historically, classification has been by comparison of ANATOMY
more recently, use of molecular tools has allowed classification based on differences in DNA (and proteins). This commonly involves the use of gel electrophoresis. Another modern tool is Polymerase Chain Reaction (PCR), where small bits of DNA are amplified and then analysed by using gel electrophoresis.


4. The Five Kingdoms of Life


Five Kingdoms


Link to Five Kingdoms page



Link to Five Kingdoms Web pageLink to a book about the Five Kingdoms




5. Taxonomy: An Inexact Science

TAXONOMIC LEVELS:

the orderly categorizing of species


Types? Kinds? Classes? Species?
Largemouth bass, a fish, a vertebrate, a centrachid, Micropterus salmoides
What's in a name?


The disciplines in biology known as SYSTEMATICS and TAXONOMY are concerned with making some order out of the chaos that comes from there being somewhere between 2 million and perhaps 15-30 million different kinds of organisms (SPECIES) on the Earth. No one knows how many species there actually are, but nearly 2 million (mostly insects) have already been given a formal name! And some biologists estimate that as many as 20-30 million more species of plants, animals, fungi, protistans and monerans have yet to be discovered, perhaps most of them living in obscure or poorly explored areas such as tropical rain forests and the deep sea.

Hierarchy in Biology

Biologists like order in their world. Even non-biologists, such as primitive tribes in Amazonian jungles, have local names for most of the important plants and animals that they interact with. In other words, organization is important for thinking about or discussing different kinds of organisms in any rational way.

The first order of business is to apply a formal name to each unique type of organism. Biology owes a debt of gratitude to the great Swedish botanist, Carl von Linné (who became better known by his Latinized name, Carolus Linnaeus) who devised the system of Binomial Nomenclature that is the standard way to designate the formal scientific name for each newly discovered species. This system uses two words (hence, binomial) to name each species, and these words are a generic term (the Genus) and a word that is basically an adjective, the so-called specific epithet! For example, Micropterus salmoides, Littoraria irrorata and Homo sapiens, are formal scientific names, with salmoides meaning "resembling a salmon", irrorata describing a particular coloration (in this case, of a snail), and sapiens referring to 'being wise, or sagacious' - - a reference to human intelligence!

Once species have been named, they are grouped into sets, a series of categories, each of which is referred to as a TAXON (thus, the notion of Taxonomy). Biologists have (almost!) agreed upon a common system for such groupings that::

1. Assigns a formal scientific name to each species

2. Groups species together that are (evolutionarily) more closely related to one another

3. Employs a hierarchical system such that the largest category (a Kingdom) includes unique categories (each called a Phylum) that define each major type of organism (for example, chordates, echinoderms, molluscs, arthropods and annelids) and that in turn include smaller and smaller sets (Classes, Orders, Families) down to individual species.

When biologists group organisms into these kinds of categories, they utilize what is referred to as a CLASSIFICATION. One such hierarchical classification looks like this:

Phylum Mollusca

Each of the categories in bold type is a TAXON. Each taxon that is above another in this series (e.g., Order being above Family) is more inclusive than the taxon below it. This results in the PHYLUM being the largest, most inclusive taxon for that particular group or kind of organisms, and an individual species being the single unit around which all this grouping is focused.

Some classifications have more subdivisions than the one illustrated here. The number of subdivisions also is related to the number of species in a particular group. For example, in the most recently described Phylum of animals (the Phylum Cycliophora) (which, incidentally, was just described in 1995), there is only a single species known! That species is Symbion pandorina. It is rather pointless to construct a whole series of subdivisions to CLASSIFY a single species.


What about our fish example at the beginning of this exercise? Well, one classification for fish goes like this:

Phylum Chordata

So what's in a name? Well it depends on the 'name' that we use. We could refer to largemouth bass by their common name (largemouth bass) or by their scientific name (Micropterus salmoides) or refer to them as an example of a 'centrachid' fish -- a term derived from the name of the Family taxon to which this species is assigned. When we refer to any animal as a 'vertebrate', we are from a taxonomist's perspective, referring to the fact that the animal belongs to one of the three Subphyla of the phylum Chordata. (The other two are the Cephalochordata and the Urochordata).

We use the word 'fish' rather casually, but from a taxonomic point of view the word really refers to members of the vertebrate Class Actinopterygii (or in older schemes, the Class Pisces or Osteichthyes). When we consider sharks, we are actually referring to members of an entirely different class of vertebrates, namely the Class Chondrichthyes.

Since these animals are all vertebrates, they also must be Chordates -- members of the Phylum Chordata. Humans (Homo sapiens) also are both chordates and vertebrates, but they belong to the Class Mammalia (as do the whales). So, humans are as different 'taxonomically' from largemouth bass as are sharks!

Modern biologists try very hard to construct classification schemes (or PHYLOGENIES) that are based on the best current understanding of evolutionary relationships among organisms [mostly using a process called CLADISTICS - which you can learn about by clicking on the SYSTEMATICS button on the Five Kingdoms page]. Therefore by understanding taxonomy or systematics, one gains an appreciation for who is most closely related to whom.


Some Rules

No system of any kind can be a 'system' unless there are some agreed-upon rules that make it uniform and practical. Trouble is, not all biologists agree about all the 'rules'! But you can see the results of a few of the more common rules by reviewing the phylogenies depicted above.

1. First and foremost, ALL scientific names include a generic term and the specific epithet. Both of these terms are italicized (or underlined) and ONLY the genus is capitalized, and it is always capitalized.

Occasionally a scientific name is partially derived from a person's name. For example, Unionicola dimocki is a species of water mite and includes a specific epithet derived from someone named Dimock. Even though the person's name is a proper noun, in a scientific name, it is not capitalized -- unless the genus happens to be derived from a person's name, but that's pretty rare.

2. The word SPECIES is spelled the same in both the singular and the plural. [The word specie has an entirely different meaning. Look it up!]

3. The proper plural of genus is GENERA, not genuses, geni, etc.

4. Among zoologists, the taxon known as a FAMILY always ends in -idae. (Littorinidae, Centrachidae, Hominidae). When spelled that way, the taxon should be capitalized (which is true for all taxa when they are spelled out in full). Often however taxa are used as adjectives. For example, the centrachid fishes include sunfishes, largemouth bass, etc. In that case, centrachid is not capitalized.

5. One variation is that botanists use the ending 'acea' to designate the Family level taxon instead of 'idae'. Thus, roses belong to the Family Rosacea.

6. Botanists also use the term Division synonymously with the zoological term Phylum. Thus the seed-producing plants are in the Division Spermatophyta, which includes the two Classes Gymnospermae (pines and cycads) and Angiospermae (the flowering plants).

7. The plural of Phylum is Phyla.

As a final note, when a scientist gives a previously unamed species a formal scientific name, that scientist's name becomes an add-on to the species' name. Since Linnaeus himself described a large number of species with his system of binomial nomenclature, his name is associated with a lot of species. In fact, his role is so prominent that he often is designated only by the letter L. For example, the complete scientific name of a commercially important species of sea mussel is Mytilus edulis Linnaeus. The name often is abbreviated as Mytilus edulis L., and the 'el' stands for none other than Linnaeus himself!


6. Exploring Biodiversity:
How Many Species Exist?


Link to Biodiversity page


Link to Biodiversity in Brazil


Fire damage in Brazil - NYT 980322
Link to article in yesterday's New York Times about fires in Brazil (22-March-98)
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7. Evolutionary Connections: Classification Conundrums, or Where Shall We Put the Algae?

Link to First Millenial Foundation

FMF Glossary

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Blue-green algae

Blue-green algaeBlue-green algae such as Spirulina are very peculiar organisms. For some 250 years after Carolus Linnaeus first proposed what came to be called the "Linnean" classification system, scientists classified all living organisms into two great kingdoms, as either plants or animals. However, some organisms, when studied closely, do not appear to fit well into either category. Bacteria, for example, are too simple to be animals, yet they are not like plants either since they do not have chlorophyll or a cellulose covering. And there are some organisms that crawl or swim around and capture food like animals, yet they contain chlorophyll or are covered with cellulose like plants. Over the past 20 years most biologists have come to accept the five-kingdom classification system. In addition to plants and animals, there are protista, fungi, and monorans. The monorans are divided into two broad sub-kingdoms, the bacteria and the blue-green algae. Blue-green algae, such as Spirulina, perform a remarkable array of biochemical syntheses. They have chlorophyll and thus can capture the energy of sunlight through photosynthesis. They can also bind nitrogen into organic compounds; in fact, they can synthesis all of the amino acids that humans need but cannot synthesize for themselves. Spirulina even make most of the vitamins that humans need in the diet. Spirulina provide, nutritionally, an ideal food for humans. Couple that with the fact that Spirulina can readily be grown in the nutrient-rich waters around an OTEC facility, and the importance of Spirulina to the Millennial Project, especially to Aquarius Rising, becomes clear (see mariculture).



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Last updated on 9 September, 1999 by David Ussery