Science Matters (32 page)

Living things may consist of one cell only, or they may be multi-cellular. In a one-celled organism, the process of energy acquisition and the production of chemicals must all go on within each cell. In more complex organisms, like humans, cells specialize and the work is divided. The cells are organized into organs, and the organs into organ systems. Your digestive system, for example, contains a trillion cells, each its own complex chemical factory, each designed to do its bit in the system that takes in food and converts it into raw materials for use in the rest of your body. A combination of organ systems makes a complete organism.

Finding a way to order and catalog the wonderful diversity of living things was one of the main tasks of biology in the eighteenth and nineteenth centuries. The general scheme used today grows out of the classification first proposed by the great Swedish botanist Carl Linnaeus (1707–78). Think of every living thing as being situated somewhere on the branches of a great
tree. The Linnaean classification locates a specific organism by specifying the main branch, then the side branch, then a smaller side branch, and so on until we arrive at the final twig on which the organism is found.

Aside from occasional regroupings (particularly of fossils), the job of classifying living things is no longer considered to be a major research area in biology. Apart from medical research, neither is the study of complete organisms and their internal organs a major focus of modern biological sciences. For the most part, the study of cells, their constituents, and the molecules that compose them is where the action is today.

The classification of living things has undergone something of a revolution in the past quarter of a century. Many biologists (and biology textbooks) continue to adopt a taxonomy based on the physical appearances of organisms. This approach leads to a division of all life into five kingdoms, including plants, animals, fungi, single-celled organisms with a nucleus (or protista), and single-celled organisms without a nucleus (or monera).

Each kingdom is further divided into increasingly specialized branches called phylum, class, order, family, genus, and species. The human being, for example, is a member of the animal kingdom, phylum of chordates (animals with spinal cords), sub-phylum of vertebrates (chordates with backbones), class of mammals (vertebrates with hair who suckle their young), order of primates (mammals with opposable thumbs and big brains), and family of hominids (primates that walk erect and have other distinctive skeletal features). All members of this family except for genus
Homo
, species
sapiens
, are extinct. Human beings,
therefore, are referred to as
Homo sapiens
in the Linnaean scheme. The further we move back toward the main trunk in this scheme, the more inclusive the categories become—rabbits are mammals but not primates, fish are vertebrates but not mammals, and so on.

The end product of this classification scheme is the species, which biologists define to be a single interbreeding population. All human beings can interbreed, for example, so we are all members of the same species. Polar bears and black bears, on the other hand, both members of the genus
Ursus
, do not interbreed, and so are different species. We commonly describe organisms by two Latin words—like the dinosaur
Tyrannosaurus rex
or man’s best friend
Canis familiaris
—that represent the genus and species, and the entire classification scheme is implied by those names. Note that in this scheme two kingdoms are devoted to single-celled organisms. Here’s how several familiar one-celled creatures fit into this picture.

Bacteria
, a phylum of monera, are usually named according to their shape: cocci (spheres) or bacilli (rods). They cause a number of diseases, like syphilis, tuberculosis, and cholera, but also are instrumental in producing many antibiotics. Anaerobic bacteria get their energy from fermentation and can survive without oxygen. They decompose much of the world’s organic garbage.

Plankton include any small organism that floats on the surface of water. The most abundant plankton are bacteria, referred to loosely as blue-green algae, which produce much of the world’s oxygen supply.

The familiar amoeba is not just a free-form blob, but a single-celled organism with a nucleus and a complex internal structure. It moves around, engulfs its food, and is a favorite creature in high school biology labs.

The classic five-kingdom taxonomy, which relies principally on the physical appearance of organisms, is an eminently logical approach in a world where amoebas, mushrooms, maples, and humans appear so different from each other. However, as biologists discover more about the underlying chemistry of life, it appears that these disparate life-forms are remarkably similar to each other in terms of their biochemistry. By contrast, tiny cells without nuclei may appear relatively simple and similar to each other in a microscope, but their underlying chemistries often turn out to be wildly different from one another.

These biochemical discoveries have led to an alternate division of life based entirely on chemical differences among organisms. This new view of life was introduced by University of Illinois microbiologist Carl Woese, who employed the techniques of molecular genetics (see Chapter 16) to compare different cells. In the process he discovered a large group of simple one-celled organisms, collectively known as Archaea, that often thrive in such extreme environments as acidic hot springs, arctic ice, and in solid rock kilometers below the surface. These cells have remarkably distinctive and varied biochemical processes that set them apart from all other cellular life. These profound differences, which are reflected in the unique genetic makeup of Archaea, led Woese to propose that life can be divided into three distinct domains.

According to this new and now widely accepted view, the old kingdom of monera should be split into Archaea and Bacteria, which are chemically distinct domains of single-celled life without nuclei. The third domain in Woese’s new scheme, Eucarya, encompasses all life based on cells with nuclei, including the multicellular kingdoms of plants, animals, fungi, and the single-celled protista. This new three-domain classification scheme
reflects the fact that fungi, plants, animals, and amoebas are chemically and genetically extremely similar to each other, at least compared to Archaea and Bacteria.

Having introduced these two separate schemes of cataloguing living things, we have to add that there is no one “correct” classification scheme. How you want to classify living things depends on what you want to do. The traditional species-based system would be appropriate for someone studying the ecology of a forest, while the RNA-based scheme might be appropriate for someone studying microbes in a hot pool.

The key to understanding how protein molecules (enzymes) perform their chemical tasks lies in their complex three-dimensional shapes. The bumps and valleys on an enzyme’s surface serve to attract and then connect other chemical components. Each enzyme is thus a precise arrangement of thousands of atoms—primarily carbon, oxygen, nitrogen, and hydrogen. Protein crystallographers devote their research lives to unraveling the locations of all those atoms, in the hope of understanding the chemical basis of life. Deducing a protein structure is no easy task. It can take years of research to unravel the structure of a single modest-sized protein molecule.

We now know the structures of such important molecules as hemoglobin, chlorophyll, and insulin, but there are thousands of other complex proteins in living things. Protein crystallography, coupled with advances in computer modeling of protein folding, will remain an important research discipline for many decades to come.

The nervous system of an animal is not a simple electrical circuit. When a signal gets to one end of a nerve cell, the cell sprays various molecules out for the next cell to pick up. Thus the transmission of a nerve impulse is a complex chemical, as well as electrical, phenomenon. An enormous research effort is under way to understand nervous systems and how single nerves and their connections lead to larger-scale phenomena like behavior and learning. Ultimately, the goal is to discover the working of the human brain, but in the meantime scientists are content to work on single nerve cells (like the axon of the giant squid) and on small, relatively uncomplicated creatures like worms and cockroaches.

Like all other vertebrates, you possess an immune system designed to defend you against foreign cells and molecules. The main components of your immune system are five different types of white blood cells, each of which has a specialized role to play. One type (the so-called B cells) produces antibodies, which are Y-shaped molecules in which two ends of the Y fit specific kinds of foreign molecules. Antibodies thus lock onto the unwanted object. The third leg of the Y-shaped antibody then stimulates other parts of the immune system to destroy the entire antibody-plus-foreign-molecule package. This part of the immune system protects against small invaders like toxins and some bacteria.

Other white blood cells (called T cells) contain receptors that recognize molecules on the surface of foreign cells. The T cells then bind to the foreign cells and destroy them. In this way, your body eliminates parasites and cells altered by cancer or viruses.
Other kinds of T cells regulate the actions of the immune system. Some cause antibodies to be produced after the first exposure to a new invader; this is how we acquire immunity to diseases like measles. Still others suppress the action of the immune system.

The immune system is being studied intensely today, primarily because of its importance in medical research and treatment. The AIDS virus, for example, destroys T cells that regulate the immune system, which then loses its ability to respond to new diseases or eliminate cancer. In organ transplants, the immune system may attack the new organ as “foreign” unless physicians can find ways to suppress the response. And many scientists suspect that regulating and stimulating immune system molecules like interferon provides the best hope for developing cures for cancer.

W
HEN JIM’S CHILDREN
Dominique, Flora, and Tomas return to a café in their summer home in Red Lodge, Montana, they have no trouble picking out members of the town’s long-established families, even if they’ve never met them before. “You must be Joki,” they’ll say to a blond, Finnish-looking boy. They’re not great detectives, but living in a small town can be an exercise in practical genetics. Members of families do tend to look like one another, and with a little experience anybody can pick out resemblances.

But the genetic code is more than skin deep and it bears upon much more than casual questions of physical appearance. When Margee Hindle and Bob Hazen got married they knew that their children would have a fifty-fifty chance of suffering from Lynch’s syndrome, a genetic disease that invariably leads to colorectal cancer. Is Margee carrying the gene that afflicted her father and grandmother? Was that gene passed on, like a ticking bomb, to Bob and Margee’s children?

We pretty much take for granted one of life’s miracles: like
always begets like. Bacteria beget bacteria, birds beget birds, bananas beget bananas. Offspring display many traits—both good and bad—of their parents. Each new organism begins with a single cell, yet within that microcosm lies all the information needed to create the whole organism in all its complexity. In every form of life a few different atoms and molecules, in cells with the same kinds of architecture, adopt very different designs. How are such complex and varied blueprints passed from one generation to the next? How are they read? Scientists now realize that every living thing on Earth uses the same strategy:

Genetics, the branch of science devoted to studying how traits are passed from parents to their offspring, didn’t begin in a high-tech lab with fancy machines and technicians in white coats. Gregor Mendel (1822–84), an Austrian monk whose work was largely ignored in his own lifetime, performed the first comprehensive and systematic genetic experiments in a secluded monastery garden where he cultivated peas.

Mendel noticed that certain strains of peas bred true: tall plants, if bred together, gave rise to tall offspring, while short parents always yielded short offspring. When he produced a hybrid by fertilizing short plants with pollen from tall ones, the offspring were all tall, but if he then bred those hybrid offspring with one another, three-quarters of their offspring came out tall and a quarter came out short. Crossbreeding tall and short plants always resulted in tall and short plants—never medium-sized ones, as one might at first expect.

To explain many years’ worth of data of this type, Mendel introduced the concept of a basic unit of heredity, something we call the gene. His idea was that each adult possessed two sets of genes, one contributed by each parent. The interplay between these genes then determined the offspring’s characteristics. In this game, however, no compromise was possible—one gene or the other won.

To express this kind of competition, Mendel characterized genes as either dominant or recessive. A dominant gene is one that wins the competition if paired with a different gene. For example, in Mendel’s pea plants the gene for tallness is dominant. In the first generation of hybrids, where each offspring has one tall and one short parent, each offspring gets one gene for tallness, one for shortness. The fact that all offspring are tall says that in this situation tallness wins, so this gene must be dominant.

The role of recessive genes becomes obvious only in the second generation. All of the tall first-generation plants carry one gene for shortness, even though this gene is not expressed (to use the biologist’s term). Nevertheless, the gene is there and can be passed on to the next generation. Each parent, in fact, has a fifty-fifty chance of passing on the recessive gene for shortness, and an equal chance of passing on the dominant gene for tallness.