The history of life and the biological processes responsible for this history are extraordinarily complex. To understand these processes, scientists apply a variety of standard tested and proven methods for understanding the natural world. The most important and commonly known of these is the scientific method. This way of approaching problems underlies much scientific research, and is one of the ways science is distinguished from other means (philosophical or religious) of understanding the universe. Science begins with the process of observation. This observation can be as simple as noticing that the sun always sets in the west. Scientists then create hypotheses to explain these observations. In this case, scientists in the past argued over whether the western setting of the sun was due to the motion of the sun or the motion of the Earth. Often more than one explanation is possible.

At this point an experimental scientist will take the most important step, testing the different hypotheses. These tests are designed so that each hypothesis has the opportunity to pass or fail. This is especially important because it allows scientists to exclude explanations that fail to pass certain tests. (A hypothesis may fail a statistical test, or it may fail to explain another important but independent observation.) If a particular hypothesis survives repeated testing, it may become generally accepted by the scientific community. Such hypotheses are called theories. (Although commonly you may hear the phrase “it’s just a theory,” scientists use the term much differently.) Theories are “predictive.” They generally encompass groups of hypotheses that link together many observations and provide a means to make statements about the way the world works (though rather than predicting the specifics of what will happen, theories generally predict how things will happen, the underlying “rules.”) Rarely, some theories (such as the theory of gravity) may be so universal that they are termed laws.

There also is a vast body of science that is “comparative” rather than “experimental.” This includes most of paleontology. Comparative science makes observations and poses explanations for those observations. Unlike scientists who work with experimental systems, however, scientists working with comparative approaches to understanding the world cannot physically manipulate the world through designed experiments. Rather, they bring together their observations, develop hypotheses to explain patterns, and make predictions of what they are likely to find next, based on what they already know. Then, as further research and discovery proceeds, new findings must remain consistent with existing hypotheses, in effect serving as tests of these hypotheses. New findings help refine these explanatory tools. Evolutionary theory is largely based on comparative biology rather than experimental biology, although it clearly includes both kinds of approaches.

Scientists also have developed specialized sets of words to describe the organisms that are the products of millions of years of evolution. Perhaps the most familiar is taxonomy—the system used to give names to different species. Taxonomy gives every organism two names, or a binomen, with one name for the genus and another for the species. The name Tyrannosaurus rex, for example, refers to a dinosaur with the genus name Tyrannosaurus and the species name rex. The names are usually formed from Latin or Greek roots, but other languages are frequently used today. The binomen is always italicized to make it stand out as a proper name, with the genus name capitalized and the species name in lowercase.

Taxonomy allows every scientist to use the exact same name when referring to the same organism, whether the scientists speaks English, Italian, or Chinese. But taxonomy alone is merely a list of names, similar to a phone book. A separate system places all these names into context. This system is called classification, and it lets scientists put species together into groups depending on how they are related to one another. Smaller groups are placed into larger groups, and they are all tied together through their evolutionary histories.

The original system of biological classification—the Systema Natura—was developed by the Swedish scientist Carolus Linnaeus in 1735. The Linnaean system organized all species into a hierarchy, from the smallest units (species) to the largest (kingdom). In between were different levels, each given a name. Thus kingdoms were composed of phyla (sing. phylum), phyla were composed of classes, classes of orders, orders of families, families of genera (sing. genus), and genera of species. Tyrannosaurus rex is a species in the genus Tyrannosaurus. The genus Tyrannosaurus is a member of the family Tyrannosauridae, and that family is part of the order Saurischia. Saurischia is an order within the class Reptilia, and Reptilia forms part of the phylum Vertebrata within the kingdom Animalia.

More recently, some scientists have begun to develop a new system of classification. This phylogenetic system dispenses with particular levels such as orders. Instead, species are classified according to the pattern of descent as revealed by study of evolutionary relationships. In this system, species still exist but they are not lumped into a series of fixed groups in a rigid hierarchy. Scientists called systematists try to piece together these bits of data into a single coherent picture—a “tree” of the history of life on Earth.

This tree is more properly called a phylogeny, and it represents the branching pattern of lineages resulting from the evolution of life over time. Let us imagine a single species—the ancestor—that represents the trunk of the tree. As that species evolves, some of the individuals become distinct from the rest. These individuals eventually become isolated from the original group, so that they no longer can breed with them. This marks the formation of a new species. At this point we would indicate a split in the trunk of the tree, with two main branches representing the two species now present. As this process is repeated over billions of years, countless new branches are created on the tree of life.

How is it possible to diagram this tree when we can see only some of the branches? In fact, we see only the tips of the branches—we cannot see directly how they are connected to one another. Systematists use the principles of inheritance and similarity to reconstruct the tree of life. They examine many different species and look for patterns of homology. They may notice that two species both have horns, or wings, for example, and must determine if these structures are homologous or analogous. The most easily interpreted homologies are those that are shared by a few species but absent in most others, clearly linking the species that shared them. By tallying up as many of these similarities as possible, systematists can calculate which species are most closely related to which others. Once many species have been studied, part of the tree of life can be reconstructed.

In recent decades, molecular biologists have learned a great deal about the genetic structure of organisms. In particular, it is now clear that the genetic code resides in a few key molecules such as DNA and RNA. These molecules carry the genetic identity of each individual in their molecular pattern, but they also carry information about the species and genus of each individual as well. Molecular systematists now use this information to try to reconstruct the phylogenetic relationships or organisms, just as traditional systematists use the physical features of those same organisms. Often the two forms of data can be combined to produce a more accurate picture of the tree of life.

The genetic code also allows scientists to determine how fast evolution occurs by examining the rate of change in DNA between one generation and the next. In the 1960s, geneticist Motoo Kimura proposed the neutral theory of molecular evolution. This theory suggests that many genetic changes are adaptively neutral and have little or no effect on the function of the molecule for which the genes code. By having no effect on molecular function, the mutations can survive—they are invisible to natural selection. The neutral theory holds that changes within a species (polymorphism) and changes between species (divergence) are really two phases of the same process. Later, Linus Pauling and Emile Zuckerkandl proposed that, if this theory is correct, molecular evolution should occur at a constant rate and it should be possible to calculate a molecular “clock.” In other words, the degree of genetic difference between two species can be used as a measure of the time elapsed since their evolutionary divergence.

The neutral theory and the molecular clock hypothesis remain controversial. It has become clear that molecular evolution does not always occur at a constant rate. As a result, it is necessary to develop different “clocks” for different groups of organisms. A recent advance has been the use of paleontological data to calibrate these “clocks.” Because certain divergence times (for example, the split between humans and chimpanzees) can be estimated from the fossil record, the rate of genetic change between certain species can be calibrated to these times before the “clock” is used for other studies.