One of the defining features of life is the modification of organisms through adaptation and genetic mutation. Evolution has shaped millions of years of variation, from the original single-cell structures to the enormous diversity of life we see today. Today we can observe the process at work today in many species, and we can manipulate the process in the lab.

LUCA. The spectacular expansion of life forms makes it hard to believe that all life on Earth is related. But in fact all life seems to have originated with just one type of cell that emerged about 3.5 billion years ago: the Last Universal Common Ancestor ( LUCA). It is generally thought that original cell was much simpler than anything in existence today. LUCA was preceded by rudimentary molecular arrangements that hardly met the criteria for a cell, and it has been assumed that ancient LUCA contained just enough moving parts to function as a cell. The discovery in all microbes of a very primitive internal structure called an organelle (for storage of a polyphosphate) has raised the possibility that LUCA was more complex than scientists had thought.

Charles Darwin, one of the greatest minds in the history of science, was so fearful of the antagonism his theory of evolution was certain to provoke that he delayed publication for more than a decade. Only when another great naturalist, Alfred Wallace, shared his very similar findings with Darwin, did Darwin finally publish Origin of Species in 1859. And indeed, the theory met with bitter rejection. This was a period still governed by the notion that the Earth and all life was the work of a divine Creator, and that the creation had taken place over six days. Even today when the evidence for evolution is undeniable, there is still resistance among some religious groups. In the United States, which is probably the most conservative of the world's developed nations, between 40-50 percent of the adult population questions evolution.

In the mid-1800s when Darwin and other scientists were trying to understand the reasons for the physical changes that could be seen in generations of creatures and the obvious relationship between some species, the means for doing so were very limited. Darwin and others experimented with mutations on birds and other animals, but they knew nothing about DNA and almost nothing about the cell. Even the methods for collecting and analyzing fossils were very limited.

Evolutionary biology has come a long way since Darwin. It has partnered with geology (geobiology), chemistry (biochemistry, biogeochemistry) and genetics. Such cross-disciplinary research has increased the understanding of the interdependence of the organic and inorganic worlds. The history of evolution is really a co-evolution of organisms, minerals, geology and atmosphere.

Principles of Evolution. Evolution involves several important processes, all of them dynamic:

heredity. genetic makeup of the parent(s) is passed on to the offspring. At the level of single cells, heredity can also occur horizontally: genes can be passed between different types of bacteria. Such crossing may account for the confusing history of the earliest cell variations. Eukaryotes share genetic material with both bacteria and archaea, for example.

variation. small differences between individuals in a species always (even clones) that, over generations can become more significant. A genetic change in response to environmental conditions may occur initially in isolated individuals, but eventually spread to an entire species. Darwin noted this variation among the beaks of different finch species in the Galapagos Islands, where the availability of particular foods on the different islands influenced the shape of finch beaks. Significant variation can develop rapidly, and has been observed in many species, including insects, birds and even humans.

natural selection. The evolution of wings, fur, eyes, teeth and brains present many examples of natural selection, whereby specific genetic alterations improved the survival rate of a species.

Phylogeny: species classification. Evolutionary biologists distinguish the relationships between organisms by creating phylogenetic groupings based on both physical characteristics and on genetic information. Comparisons of fossils and extant creatures reveal the evolutionary history of organisms. For example, vestigial structures in modern animals, such as feet in whales and tailbones in apes, prove that modern whales are descended from an extinct wolf-like animal and that apes descended from monkey ancestors. A second way to reconstruct evolutionary history is by genetic analysis. This has some advantages, but there are two problems: first, the amount and quality of DNA preserved in fossil bones is problematic; and second, genetic analysis of ancient DNA can be ambiguous about the relationships between organisms, especially at the level of single cell organisms.

The broadest categorization is the domain and the most narrow is the species. There are three domains --the parent single cell groups from which all multicellular organisms descended-- to the most narrow: the species. As scientists refine the fossil and genetic data, the original "tree of life" taxonomy has become much more complicated. This is reflected in several different representations of the relationship between organisms today; they are all more elaborate than the traditional tree graphic shown in biology books less than a generation ago. Here, the classification is described briefly and several graphics are presented.

The parent of each domain is a particular cell type with features sufficiently distinct to qualify as a true ancestor for a long line of subsequent species. By one type of categorization, these groups are the archaea, bacteria and eukaryotes. By another, older but still used categorization, archaea, prokaryotes and eukaryotes. The issue behind the two categorizations is whether eukaryotes, which are structurally much more elaborate, evolved from prokaryotes or not. Another concern is how closely related each domain is to the other two. It is difficult to reconstruct the history of the oldest cells on Earth.

Different types of bacteria form symbiotic relationships, and sometimes one type captures another. Through gradual capture of symbiotic bacteria and possibly archaea, eukaryotes developed a much more complex structure. The captive bacteria became the mitochondria and other organelles within the eukaryote cytoplasm, creating an elaborate division of labor and many ecological advantages. Although the mitochondria has preserved its own genetic makeup, it is fully dependent on the eukaryote it serves; it is a dynamo involved in almost all cellular tasks. This absorption pattern is the source of chloroplasts in the cells of plants and algae, which process convert light into energy.

Extinctions. Although life is amazingly resilient, in the long history of the planet, almost all life forms have become extinct -95 percent or more at some time. Fortunately, life always seems to rebound, and so far each rebound has brought significant increase in biological complexity and diversity. For example, the Cambrian era starting some 500 million years ago, followed what was possibly the greatest extinction in the history of the Earth. But the Cambrian introduced a huge variety of creatures, and most important the basic body structures that shaped the morphology of all living creatures today. We trace the complex eye, teeth, the bilateral body (eventually with limbs) and many other physical structures to this period.

Some 65 million years ago the extinction of the dinosaurs presented an evolutionary opportunity to the tiny mammals that co-existed with the giant creatures. The mammals, previously insignificant, developed from a relatively few groups to a huge variety of species that filled the many niches that were suddenly —in geological terms—available: animals that could live in trees, on grassland, in water.

Major causes of extinctions

loss of food source. After massive fires, floods, droughts, and other events, organisms may lose their food source. Organisms that are unable to move or to change their diets, or to obtain adequate nourishment are likely to perish.

loss of habitat. Climate change and natural disasters can destroy habitat. But one of the leading causes today is human population. The intrusion on natural habitats by agricultural expansion, together with human diversion and pollution of water and increasing urbanization, all put tremendous pressure on organisms. Many large animals, including elephants, buffalo and the predator cats, cannot adapt to their shrinking territories. Some species are able to move to new territories, but many are perishing.

ecosystem imbalance. All organisms live within an system of interdependent relationships with other species. The loss of one key species within the system can bring about a disastrous elimination of others. For example, the loss of top predators such as sharks (killed for their fins) causes an imbalance that leads to the elimination of one or more species within their particular ecosystem.

catastrophe. All sorts of catastrophic events can cause extinctions. Massive volcanic eruptions have, at times in Earth's history, made the atmosphere so toxic and hot that many organisms could not survive. The great meteor that struck Earth 65 million years ago destroyed much of the life on the planet at that time. Some scientists have even argued that gamma rays from a few supernova explosions around 41,000 years ago may have penetrated Earth's atmosphere (information based on radioactive potassium in tusks and human artifacts from between 34,000 and 13,000 years ago, a period of massive extinctions.

climate or atmospheric change. Periodic natural climate changes have sometimes occurred too rapidly for some organisms, bringing death to those that have not been able to move or adapt. A great many species became extinct in the last great ice age, and in many cold-adapted creatures were unable to adapt to extreme warming. Atmospheric changes such as the increase in oxygen when plants began their rapid evolution led to the extinction of almost all other life, for which oxygen was toxic. Similarly, the sudden increase in methane in the deep past wiped out a great deal of life. And today, we are in the midst of another great extinction, this one due in part to the sudden increase in CO2 and in part to toxins introduced by human industry.

extermination. The abrupt demise of one or more species may come about from predation —either from other animals or from humans. Some massive animals such as the mastodons in North America may have been eliminated by stone age humans. In the past two centuries, humans have exterminated many species of mammals, birds, fish and plants by hunting or deliberate elimination.

disease. Many types of diseases —from fungi, viruses, bacteria—spread and kill faster than the antibodies and other defenses can adapt. The Tasmanian wolf is a modern example: a fungus is spreading rapidly in this isolated population of animals, and the prospects of species survival are poor.