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In the late nineteenth century, ecology began to grow into an independent science from its roots in natural history and plant geography. The emphasis of this new "community ecology" was on the composition and structure of communities consisting of different species. In the early twentieth century, the American ecologist Frederic Clements pointed out that a succession of plant communities would develop after a disturbance such as a volcanic eruption, heavy flood, or forest fire. An abandoned field, for instance, will be invaded successively by herbaceous plants (plants with little or no woody tissue), shrubs, and trees, eventually becoming a forest. Light-loving species are always among the first invaders, while shade-tolerant species appear later in the succession.

Clements and other early ecologists saw almost lawlike regularity in the order of succession, but that has not been substantiated. A general trend can be recognized, but the details are usually unpredictable. Succession is influenced by many factors: the nature of the soil, exposure to sun and wind, regularity of precipitation, chance colonizations, and many other random processes.

The final stage of a succession, called the climax by Clements and early ecologists, is likewise not predictable or of uniform composition. There is usually a good deal of turnover in species composition, even in a mature community. The nature of the climax is influenced by the same factors that influenced succession. Nevertheless, mature natural environments are usually in equilibrium. They change relatively little through time unless the environment itself changes.

For Clements, the climax was a "superorganism," an organic entity. Even some authors who accepted the climax concept rejected Clements' characterization of it as a superorganism, and it is indeed a misleading metaphor. An ant colony may be legitimately called a superorganism because its communication system is so highly organized that the colony always works as a whole and appropriately according to the circumstances. But there is no evidence for such an interacting communicative network in a climax plant formation. Many authors prefer the term "association" to the term "community" in order to stress the looseness of the interaction.

Even less fortunate was the extension of this type of thinking to include animals as well as plants. This resulted in the "biome," a combination of coexisting flora and fauna. Though it is true that many animals are strictly associated with certain plants, it is misleading to speak of a "spruce-moose biome," for example, because there is no internal cohesion to their association as in an organism. The spruce community is not substantially affected by either the presence or absence of moose. Indeed, there are vast areas of spruce forest without moose. The opposition to the Clementsian concept of plant ecology was initiated by Herbert Gleason, soon joined by various other ecologists. Their major point was that the distribution of a given species was controlled by the habitat requirements of that species and that therefore the vegetation types were a simple consequence of the ecologies of individual plant species.

With "climax," "biome," "superorganism," and various other technical terms for the association of animals and plants at a given locality being criticized, the term "ecosystem" was more and more widely adopted for the whole system of associated organisms together with the physical factors of their environment. Eventually, the energy-transforming role of such a system was emphasized. Ecosystems thus involve the circulation, transformation, and accumulation of energy and matter through the medium of living things and their activities. The ecologist is concerned primarily with the quantities of matter and energy that pass through a given ecosystem, and with the rates at which they do so.

Although the ecosystem concept was very popular in the 1950s and 1960s, it is no longer the dominant paradigm. Gleason's arguments against climax and biome are largely valid against ecosystems as well. Furthermore, the number of interactions is so great that they are difficult to analyze, even with the help of large computers. Finally, younger ecologists have found ecological problems involving behavior and life-history adaptations more attractive than measuring physical constants. Nevertheless, one still speaks of the ecosystem when referring to a local association of animals and plants, usually without paying much attention to the energy aspects.

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