By Boyce Rensberger

SOMEWHERE NEAR THE border between life and non-life lie some of the strangest objects in the natural world -- viruses. These paradoxical entities, though not themselves alive, know how to invade living cells and commandeer the processes of life.

Unlike bacteria, which are living organisms that can take up residence in the body and feed upon human tissues, viruses are much smaller and simpler. Viruses cannot feed or grow. They cannot even reproduce by themselves. Viruses must invade living cells and take over the cell's internal machinery, directing it to manufacture exact replicas of the virus.

This, in fact, is all a virus is -- a microscopic machine for causing the cells of truly living organisms to make lots more viruses. The newly minted viruses break out of the exhausted, and often killed, cell and drift lifelessly toward fresh targets to repeat the cycle.

In doing so, most viruses cause only minor infections -- a cold or the flu -- but some can be far more devastating, causing cancer or AIDS. Or the result could be something in between: Herpes, hepatitis, mumps and measles are virus diseases. Many, like rabies, infect mostly animals. One, smallpox, was strictly a human infection. (Smallpox will probably be the only one ever eradicated because all the others can lurk in wild animals if humans are immune.)

The science of virology, which began with William Jenner's vaccine against smallpox in 1796, only to lapse until the mid-20th century, has surged to a breakneck pace in recent years with the rise of molecular biology.

As scientists have come to understand viruses in intimate detail, down to the last molecule, in some cases, they have also begun to understand something about the nature of life. It is not some mystical force but a highly predictable set of chemcal reactions that occur automatically when certain substances are combined.

So mechanistic are the processes of life that, like a car that runs no matter what presses the gas pedal, the chemical reactions that make for life can be controlled by the ingenious molecular structure of a nonliving object called a virus. But, as when a brick is on a gas pedal, the mechanisms of life can also be subverted to deadly ends.

It was just such a subversion that happened to David, the Texas "bubble boy" who died last year after spending almost all of his 12 years in a sterile isolation unit, protected by a plastic capsule from the ordinary bacteria and viruses that usually pose only minor threats to most people.

In an attempt to transplant into David the cells from his sister that could give him a working immune system, doctors inadvertently placed into his body a virus that killed him. David's death has given scientists one of the most frightening pictures they have ever seen of what an ordinary virus can do.

Shortly after David was born doctors discovered that his body was unable to produce the special blood cells that attack invading viruses and bacteria. Knowing that an ordinary infection could kill him, doctors put David in a germ-free isolation chamber to await discovery of a cure.

Over the years David lived in a series of increasingly elaborate sterile "bubbles" at the hospital, at home and even in a mobile unit in a van.

The cells David lacked are normally produced in the bone marrow and transplants of healthy marrow from closely related donors might have helped but David had no relative with compatible cells. Though David's body, lacking an immune system, could not have rejected the marrow, the marrow could have rejected David.

By the time David was 12, researchers developed a way to treat marrow from his sister to remove the cells most likely to attack her brother's body. David received a transplant, but after 80 days he turned sick for the first time in his life. He lost weight, developed a fever, abdominal pain, diarrhea and vomited blood. As doctors and family watched helplessly, David's condition worsened steadily until, four months after the transplant, he died.

The autopsy stunned doctors. David was killed not by an ordinary infection or by an attack of the transplanted marrow on his body. David died of cancer. Scores of bean-sized tumors riddled his body and every one contained a very common virus that is better known as the cause of mononucleosis, a severe but transient infection primarily of children and young adults.

David's sister had had mononucleosis years earlier. Apparently, doctors concluded, the virus had invaded her marrow cells and been suppressed by her immune system. Only when released from this suppression, in David's body, did the virus spring back into action. David's early symptoms were those of mononucleosis but, as the infection continued, the deadlier effect took over. The virus that killed David is called the Epstein-Barr virus, for its two discoverers. It is a member of the herpes family of viruses, closely related to ones that cause genital herpes, cold sores in the mouth, cancer of the thymus gland and another cancer called Burkitt's lymphoma. Though the effect of the Epstein- Barr virus is limited in people with good immune systems, the experience with David shows that in the absence of active opposition by the immune system, a virus can turn cells cancerous in a matter of months.

There are thousands of different kinds of viruses, but all have the same two main parts. The combination can be thought of as a Trojan horse -- an outer protein coat that tricks the cell into absorbing the virus or, in some cases, into allowing the protein coat to partially penetrate the cell's outer membrane. Once the virus has breached the cell membrane, the protein coat disgorges the second part hidden inside -- a strand of nuclei acid, either DNA or RNA, that carries the virus' genetic instructions.

Viral genetic instructions consist of genes that work exactly like those encoded into the native genes of all cells. Viral messages are special but they are written in the same code that the cell is already equipped to read and carry out.

From the virus' point of view, the goal of the instructions is to force the cell to manufacture new viruses exactly like the virus. Viruses have none of the machinery to carry out genetic instructions. Without such machinery, viruses simply exist as nonliving assemblages of molecules. Cells do have this machinery -- it exists to carry out the cell's own genetic instructions -- and for this reason viruses must invade cells to proliferate. The virus' few genes tell the cell to make many copies of the virus' nucleic acid, to make all the special protein molecules needed for the virus' coats and to package the newly made viral genes in the protein coats.

A single virus that invades a cell can cause it to manufacture hundreds of duplicate viruses that eventually break out of the cell and drift on to invade new cells. Some viruses can make cells obey their instructions without abandoning the cell's normal function and no disease results. Other viruses drive the cell so ruthlessly that the cell abandons its normal function or dies; as the infection spreads, the number of failed or killed cells becomes great enough to cause symptoms of disease. The herpes virus that causes cold sores, for example, simply kills so many cells in the skin of the lip that it causes a pit of dead and rotting cells, an ulcer. Polio virus invades nerve cells and as they are destroyed, the functions they once controlled are stopped, causing paralysis.

Often the disease symptoms are a result of the body's response to the cell destruction. When cells are destroyed, infection-fighting white blood cells and fluids accumulate at the site, causing inflammation and swelling. Viral infections in the nose, such as colds, bring so much fluid to aid the healing process that the result is a runny nose.

Depending on the type of virus, the timing of these steps can vary greatly -- killing cells within minutes or leaving them intact and functioning for years as the viral nucleic acid lurks silently until triggered by some change in the cell's internal environment. Something like this apparently happened to the EB virus lurking in the cells from David's sister. Some researchers suspect that these so-called slow viruses may cause a variety of otherwise mysterious diseases such as multiple sclerosis, Alzheimer's disease, some forms of cancer and some kinds of arthritis. Because a slow virus' disease-causing ability takes so long to go into action, it is difficult to demonstrate their transmission from one animal to another in the laboratory.

Viruses come in two basic types, those with genes made of DNA, the same kind of long-chain, double helix molecule of which human genes are made, and those with genes made of RNA, a similar molecule that human cells use to transmit genetic information to the cells' protein-making machinery.

Once inside the cell, the coded instruction of the DNA virus is read and carried out as if the DNA were the cell's own. The cell treats the viral DNA exactly as if it were the cell's own, housed in the cell nucleus.

DNA's instructions -- which consists of segments called genes, each specifying the structure of a given type of protein molecule -- are copied into segments of RNA that exit the nucleus and travel to the protein-making machines, called ribosomes. Ribosomes read the RNA's instructions and assemble the specified protein.

When the DNA is from a virus, it does much the same thing, causing the invaded cell to transcribe its genes into RNA, which then direct the manufacture of new viruses. Some RNA viruses, such as the AIDS virus, skip this step and directly command the ribosomes to assemble new virus components. Other RNA viruses are more devious. Some of their genes direct the assembly of special proteins, called enzymes, that cause the manufacture of DNA copies of the RNA and that then carry the DNA into the nucleus and splice it into the cell's DNA.

These viruses, called retroviruses, do not kill the invaded cell. Instead they convert the cell into one that not only makes new viruses but that, when it reproduces itself by dividing, endows both daughter cells with the same virus-making DNA. Retroviruses thus become permanent residents of cells and all their progeny.

Among the retroviruses are ones known to cause cancer. Some of the viral genes that they splice into the cell's DNA give the cell the ability to divide more frequently than normal. The result of one cell suddenly proliferating faster than the others around it is a tumor.

The viral genes that do this were long ago named oncogenes, from the Greek onc for cancer. When molecular biologists learned how to read the genetic message of normal cellular genes, they were astonished to find that a few were almost identical to viral oncogenes. The slightest change in one of these genes -- a mutation that, in effect, changed one letter in a genetic sentence, would convert them into cancer-causing oncogenes. These normal cellular genes were named proto-oncogenes.

These discoveries show that human cancer can start in two ways -- by the invasion of retroviruses that splice oncogenes into the cell's DNA and by a random mutation that happens to make the tiny change that turns an innocuous proto-oncogene -- caused by radiation or toxic chemicals -- into a deadly oncogene. While the virus' genes determine its effect on a cell, it is the protein coat that determines which cells the virus can invade. It is also the protein coat that determines whether the body can recognize a virus and destroy it before too much damage is done.

Protein coats are made of a wide variety of protein molecules but most tend to fall within three architectural classes -- cylindrical tubes, regular polyhedrons and combinations of the two, sometimes with added filaments sticking out.

The reason for these relatively simple shapes is that viruses, minimalist entities that they are, do not contain enough genetic information to specify more complex designs. In most cases protein coats are made of many identical molecules of one or a few different proteins whose inherent chemical properties cause them to link up automatically to form sheets or tubes of fixed sizes. The invaded cell does not have to assemble the protein coat; the coat's protein molecules -- once synthesized by the cell -- come together, much like the atoms within a crystal, in patterns dictated by the chemical properties of the individual protein molecules.

Perhaps the strangest protein coat is that of a class of viruses that attack only bacteria. (Even bacteria get virus infections.) Called bacteriophages, these viruses combine a tube with a polyhedron on one end and some filaments on the other. The combination is reminiscent of the Apollo lunar module and the virus approaches its target, a bacterium, in much the same way.

The legs are made of a protein that binds specifically with the proteins on the surface of certain bacteria. The virus lands on the bacterium, flexes its legs to bring the tube into contact with the cell wall. The tube penetrates the wall and the polyhedron injects its DNA into the bacterium.

Different viruses with simpler coats, usually polyhedrons alone or polyhedrons encased in a membrane, infect human cells. Instead of leaving the empty coat on the outside, these viruses have coat proteins of a kind that tricks the cell membrane into thinking the virus is a molecule of nutrient or other substance normally absorbed into cells. The membrane, "thinking" it is about to take in something desirable, forms a pit into which the virus nestles. The pit deepens and closes over the top of the virus, producing a kind of bubble in the cell with the virus inside. Once inside, the coat is broken down by the cell's normal enzymes and the alien genetic message released.

The protein coat is the key to immunity against viruses. If the viruses are circulating in the blood stream, as they commonly do to travel in the body, the immune system can attack the virus. The body is able to tell the difference between its own proteins and foreign proteins. When a foreign protein is detected, antibodies are manufactured with just the right structure to bind to the protein. If enough antibodies cover the virus, it is unable to invade cells.

Because it takes time for the immune system to respond to a new foreign protein, some viruses may escape long enough to invade cells and cause disease. Once inside cells, viruses are safe from antibody attack. But, once the supply of circulating antibodies is large enough, they will neutralize newly manufactured viruses that are released back into the bloodstream, stopping the course of the disease. Antibodies tailored to a given virus remain in the bloodstream, usually for several years, sometimes for life. Any new infection by the same virus will thus be blocked before the viruses can invade cells and reproduce. Vaccines work by exposing the immune system to viruses that have been damaged in the laboratory so that they cannot produce disease but that still possess some of the same proteins on their surface to stimulate antibody production.

In theory a conventional vaccine can be made against any virus but researchers often have trouble growing enough virus in the laboratory because they cannot provide the virus with the right animal cells or other special conditions required to reproduce.

To overcome this barrier, scientists are working on artificial vaccines made not from whole viruses but from copies of individual protein molecules in the virus coat. Once these proteins are identified, the genes for them can be extracted from the virus and spliced into bacterial cells using the methods of genetic engineering. The bacteria make quantities of the virus protein which is then harvested and purified into a vaccine.

One perennial problem, however, may continue for some time. The influenza virus enjoys the ability to evolve rapidly, changing its protein coat every few years. As a result, people who gain immunity to one form of the flu are powerless against a new variant of its protein coat. This is why, when a new flu virus appears, it causes epidemics; no one has antibodies against it. A year later, however, many people have become immune and the epidemics wane until the virus' coat genes mutate.

Another problem is the common cold. It is caused not by one virus but by hundreds of different kinds that all happen to invade similar cells to produce much the same symptoms. Small children are vulnerable to all, but with each infection they gain a new immunity. By adulthood, they are resistant to many and their incidence of colds declines.

One of the great mysteries that still confronts virologists is where viruses originally came from. Nobody knows for sure but there are two theories.

One is that viruses are degenerate forms of living one-celled parasites that existed millions of years ago. Many currently living parasites that inhabit animal bodies have lost structures needed for independent life but not for life inside another organism. It is conceivable, biologists say, that certain prehistoric parasites progressively lost all their cellular apparatus and the corresponding genes until nothing was left but the few viral genes.

Another possibility is that viruses are escaped animal genes, renegade bits of an animal cell's DNA that included enough genes to encode their own protein coats. Cancer viruses may be examples of these. The oncogenes they contain have genetically coded messages almost identical to those of certain normal genes in animal cells, the ones known as proto-oncogenes. Virologists cannot imagine how the similarity could have arisen except through escape of animal genes, which then may have undergone the minor modifications that distinguish them.

As molecular biologists learn more about the molecules of the lifeless entities called viruses, their findings suggest new ways to combat some of the most serious diseases afflicting humanity. It is this promise that fuels the research with growing tax dollars. But as the research progresses, it yields a byproduct of profound new insights to the nature of life at its most fundamental level.