Science is so exciting! Why? Because it is aweinspiring, fun, and creative. Most scientists would not do anything else—they are truly dedicated to what they do. You can hardly get them to be quiet once they start talking about their work. Unlike most people, they usually love their jobs! However, this is not the common view presented of most scientists. They are commonly thought of as nerds, freaks, weirdoes, or evildoers as portrayed in movies or television. These are fantasies where, with a few exceptions, scientists are shown negatively because it fits dramatic needs (Crichton, 1999). It's just not true in real life.

In 1950, the great vertebrate paleontologist George Gaylord Simpson published a book titled “The Meaning of Evolution.” Simpson divided his work into three parts: (a) the Course of Evolution, (b) Interpretation of Evolution, and (c) Evolution, Humanity, and Ethics. I will take a different approach. Rather than detailing the course of evolution (topics of which are covered elsewhere in this volume), or interpreting patterns seen in the history of life, or trying to construct an ethical program, I will just consider three aspects: (1) what we mean by evolution, (2) the status of the theory of evolution, and (3) what evolution means to understanding the natural world. Some ideas about the importance of human existence and its implications do emerge, however, from the third topic, and several of my points do parallel some of Simpson's conclusions.

One of my favorite places to collect fossils is a steep, high railway cut in a rural part of southern Kentucky, where a ridge made of limestone sat right across the most efficient route the railway could take. When that cut was first made, professional paleontologists and amateur fossil collectors came by to have a look at the newly exposed rock; but although the fossils could be seen, we could get hardly anything out because they were almost all too firmly locked within the rock. Within just a couple of years, weathering had caused some of the weaker, clay-rich layers to break down a little, yielding loads of fossils. The rock around the fossils broke apart into small grains, and the fossils themselves, skeletal remains of marine animals, could be picked up by the hundreds of thousands: crinoids, blastoids, brachiopods, screw-shaped parts of bryozoans, trilobites, individual cone-shaped corals, strange conical snails, even rare starfish.

The term “fossil record” is used in two ways: to mean either the totality of fossils preserved in all rocks or the sum of human knowledge of those fossils. In both cases, the term carries the connotation also of the geologic context of the fossils—their distribution in time and space and their relationship to the enclosing rock. One of the primary scientific interests of the fossil record is what it can teach us about the history of life and the processes of large-scale transformation, or evolution, in the forms, diversities, and biological interactions of living things.

This is a personal guided tour of biological classification, not a quick-and-dirty manual, nor a comprehensive account of the history of systematic biology. This is a reflection on why and how we classify extinct and extant organisms. I wish to explore alternative views of hierarchy, permanence and delineation of categories, and the use of data. I hope to convince you that biological classifications are necessary tools, but also strong ideological statements. The prevailing approach to classification at any time reflects distinct views on nature, how it is organized, and how you use information.

The biological process of evolution—descent with modification—generates and structures the remarkable diversity of life on Earth today and in the geological past. Take a moment to consider the vast number of different kinds of living things: mushrooms, koalas, sunflowers, whales, mosquitoes, kelp, bacteria, tapeworms, lichens, clams, redwoods,…the list could go on and on, seemingly forever. Without some understanding of how the diversity of life was generated, the scope of the diversity may seem overwhelming, perhaps even unknowable. Fortunately the structure of this extraordinary diversity, generated by the process of evolution, can be discovered using the methods of systematics. Evolution can be thought of as “an axiom from which systematic methods and concepts are deduced” (de Queiroz, 1988). Systematics, therefore, provides a way to organize the diversity surrounding us, and make sense of it in an evolutionary framework. Patterns of similarity and difference in morphology, genetics, and development—the evidence of evolution—can only be explained in an evolutionary context by means of systematics. No other method seeks to identify patterns that are evolutionary in origin, generated by the process of common descent.

Ever since Darwin proposed his theory of evolution (or more correctly, theories; see Mayr, 1991) it has been assumed that intermediates now extinct once existed between living species. For some, the hunt for these so-called missing links in the fossil record became an obsession, a search for evidence thought needed to establish the veracity of evolutionary theory. Few modern paleontologists, however, search explicitly for ancestors in the fossil record because we now know that fossils can be used to chart the order of evolution regardless of whether they are directly ancestral either to extinct organisms or to those living today.

The Belgian inventor and scientist Joseph Antoine Ferdinand Plateau (1801–1883) pioneered one of the first devices aimed at making pictures that seemed to move. Plateau studied various optical illusions that seemed to result from the persistence of the image on the retina of the eye after the image had passed from view. In 1832, he built an apparatus consisting of a flat wheel on which were sequential images of a dancer dancing. When the wheel was turned, the dancer was “seen” to execute the dance. Plateau chose a revealing name for his invention. He called it a “phenakistiscope,” meaning “deceitful view” (Fig. 1). The images did not move, but they looked like they did.

Microfossils are of prime importance in documenting patterns of evolution due to their great abundance (often tens of thousands to millions of specimens in a hand sample) and widespread distribution (in both time and space) in the fossil record. The term “microfossil” is often used for paleontological material that requires a microscope for its study, no matter what its biological affinities. For the purposes of this article we will be looking at the remains of protists (single-celled organisms). The several examples I discuss in this chapter are of three groups of planktonic (floating) protists: the calcareous nannoplankton (tiny plant-like protists whose single cell is covered in minute calcitic scales), the radiolaria (animal-like protists with siliceous shells), and the planktonic foraminifera (animal-like protists with calcitic shells). These organisms have been the subject of extensive study because the material from which they are often extracted, cores of deep-sea sediments, are usually comprised of a more complete sedimentological record (i.e., have fewer breaks) than shallow shelf deposits. Hypotheses of evolutionary history have been constructed for many groups (lineages) of microfossils using specimens from deep-sea cores. Ancestor-descendent relationships have been recognized by tracking shape and form (morphologic) changes through time. This approach to reconstruction of evolutionary history provides an empirical record of morphologic evolution; that is, a record based on observations.

At a time when the popular perception of paleontology is dominated by images of dinosaurs and other spectacular vertebrates, or the mysteries surrounding the Cambrian “explosion” of animal life, it is perhaps not surprising that the rich and informative fossil record of plants has scarcely made an impact on the public consciousness. In reality, as one would expect from those organisms that comprise the bulk of the biological material in terrestrial ecosystems, the fossil record of plants is extensive (Stewart and Rothwell, 1993). Leaves, wood fragments, pollen grains, spores, fruits, seeds, and other plant parts are the most common fossils in rocks deposited in ancient flood plains, lakes, and many other environments—and they are often exquisitely preserved. This excellent fossil record provides important information about the ecology of ancient terrestrial ecosystems. The quality of the plant fossil record also makes paleobotanical data highly informative about the historical pattern of plant evolution. It is this pattern, and its congruence with patterns in the characters of living and fossil plants—as summarized in a classification—that is the focus of this chapter.

The problem with using fossils as evidence for evolution is that they are dead. You cannot experiment on them or watch them do anything. However, fossils more than make up for this shortcoming and provide compelling evidence for evolutionary change, because of their unique temporal dimension. Fossils give us information not just about the form of organisms, but also about their form through time. “Reading” this information from the fossil record, however, requires that we understand a central concept about how all science (and especially historical science) works, namely that processes produce patterns and, therefore, process can be reconstructed or inferred from those patterns. This is true even in the “hard” or “experimental” sciences. You do not have to see a process occur to have confidence that it did. When we look at the fossil record and ask, “How did it come to be this way?”, we answer by inferring continuity among the patterns resulting from a process of change that took place millions of years ago. We call that inferred process of continuity with change evolution.

The fossil record of vertebrates provides abundant evidence for both the fact and the theory of evolution (Carroll, 1997; Prothero and Schoch, 1994). In support of the fact that evolution has indeed occurred, the vertebrate fossil record clearly documents evolutionary change along lineages, that is, along direct lines of ancestors and descendents. The fossil record also shows step-wise evolutionary changes resulting in the emergence of new kinds of vertebrates from pre-existing kinds—for example, the origin of mammals from the “mammal-like” reptiles. In support of the theory that natural selection, in particular, has been largely responsible for evolutionary change, the fossil record shows that the numerous “transitional” forms that lived in the past—far from being nonviable “monsters”—were functionally integrated organisms that were well adapted to their ecological roles. Finally, the vertebrate fossil record preserves certain large-scale phenomena, such as radiations and trends, which show that evolutionary forces can act over very large time scales.

Movies are the myths of late-20th century western culture. Because of the power of films like ET to capture our imagination, we are more likely than past generations to accept the possibility that life exists elsewhere in our galaxy. Such a myth can be used to sketch the main themes of this chapter, which concern the origin of life on the Earth.

Paleontologists learn and tell the history of life; it is our job. You might suspect that paleontologists spend most of their time studying fossils. While fossils are an important source of information for the paleontologist, other types of evidence can also tell us about biological history. For instance, the rocks themselves provide important information, especially about past climates. It makes perfect sense that organisms are more easily understood if you know the environment in which they lived. A third important source of information is all around us.

Charles Darwin's (1859) case for the fact of evolution was as crucial to his theory as was the mechanism he proposed. The idea of natural selection becomes interesting and compelling only in the context of all the great facts of natural history that it explains. Life on earth has changed. New forms have appeared, replacing forms that have ceased to exist. Origination and extinction are two of the great facts of natural history. They underlie the patterning of biological diversity. Case by case, these facts are explained more consistently, more simply, and more compellingly by the mechanisms of evolution than by any set of ad hoc explanations.

The realization that the continents are mobile and not fixed in position, and the discovery of the processes driving that mobility, is one of the great scientific achievements of the 20th Century. From the outset, fossil evidence has been important in reconstructing past continental positions, usually by providing data on ancient similarities and differences that appear at odds with present-day geographies. However, the fossil record does much more than provide evidence on ancient continental positions: it also shows the diverse evolutionary effects that the dynamics of the Earth's crust have had on the passengers inhabiting those mobile continents.

In modern biology, natural selection is widely treated as the central mechanism of evolution. Darwin built his greatest book on it; largely ignored for the latter part of the 19th Century, its centrality was restored during the Modern Synthesis of the 1930s. Since then, its importance has sometimes been exaggerated into claims that selection drives adaptation toward optimality. Its effects have been studied in captive and wild populations of all sorts of organisms, and in past as well as present biotas. But it has also been downplayed as only one of many factors of evolutionary change, an editor with no creative force, incapable of guiding any real change in lineages. Natural selection is as intrinsic to ecological theory as to evolutionary theory, and links the two fields as few other concepts do. But like nearly all population processes, its effects on evolution in the long run remain an open question, difficult to test directly.

Change has been the rule in the history of life. Mammals today dominate the terrestrial habitats where dinosaurs once held sway. In modern oceans, ecologists can study many species of arthropods, but trilobites are long gone. Using data from the fossil record, David Raup estimated that only about one in a thousand species that ever lived on this planet is still alive today (Raup, 1991). On the other hand, the number of species and higher taxa has increased steadily over geologic time. Thus the history of life is essentially a history of turnover of species, lineages, and higher taxa over time.