Undeniable (25 page)

When we're born, none of these organisms are on board. Babies have no microbiome; there's no system of complex biological activity in their digestive tract. They get their microbiomes from their parents. All the snuggling, and kissy facing, and breast-feeding enables countless bacteria to make their way into an infant's tummy, where they live and reproduce for that new human's entire life. The ecosystem or microbiome in our digestive tract coexists with us. We depend on it. Much of the food we eat is broken down by these bacteria. When things go wrong with our intestinal microbiome, trouble starts.

I have a feeling (and it's not a good one) that everyone reading this book has been horribly sick at some point in his or her life. Many species of bacteria produce waste products that are toxic. Our bodies have systems set up to detect and expel the sickening toxins. We vomit—we expel—which usually, but by no means always, does the trick. Bacteria are here today because they were able to spread themselves around. The expectorated fluids from inside the body help spread bacterial material. This seems obvious now, but it is a fairly recent discovery. Even 150 years ago, back in Darwin's time, people weren't yet sure that microorganisms could make you sick or kill you. Biologists discovered the microbiome just over the past couple of decades. They are still puzzling out how the microbes in your body help keep you healthy and well nourished. A person's microbiome might even be an important factor in controlling his or her obesity.

The discoveries of immune responses and germs have changed the world. The discovery of the process by which all these germs have come to be has enabled us to embrace the good and fight the bad. Consider the following: We have developed dozens of antibacterial drugs. These are molecules that break down or pierce the cell walls and membranes of bacterial pathogens. But because bacteria are continually reproducing, they are also continually mutating and evolving new defenses. Through the filter of survival of the best suited, many of the bacteria in our environment today cannot be stopped by antibiotics that worked effectively just a few years ago. If we want to continue living healthy lives, we are going to have to come up with new ways to fight bacteria. That will take a deep understanding of what goes on in the bacterial world. You will not be shocked to learn that it has to do with evolution. More about that in the next chapter.

There are an absolutely astonishing number of bacteria on our planet. By most reasonable estimates, there are about a million-trillion-trillion, or 10
30
, of them (ten followed by 30 zeroes) here on this planet. There are more bacteria on Earth than there are stars in the observable universe. Like every other living thing, bacteria exploit the same chemicals for nourishment. And so, they compete. They compete like crazy. To that end, they fight each other. They fight not with spears and stones, but with poisons. Bacteria produce poisons to kill or severely inhibit other bacteria. By long word-coinage tradition, these toxins are called “bacteriocins.” They are able to “cut” bacteria. There's a bacteriocin specific to
E. coli
, which goes by “colicin.” Get it? Cut coli? Making up words like that is a popular business in biology.

In general, the known antibiotics are toxins or chemical inhibitors produced by other types of organisms. Penicillin, for example, comes from a fungus, which is quite a bit different from a bacterium. Somewhere along the way, the mold
Penicillium notatum
chanced upon a combination of chemicals that disrupts the cell walls of a great many bacteria, which enables the fungus to advance its hyphae (fungal tendrils) without getting attacked, at least not successfully attacked. Being an organism that is different from a bacterium, a fungus can carry an antibiotic—in this case cell-wall-disrupting chemicals. But if you are a single-celled bacterium producing a chemical within your cell membrane and wall that would split the membrane and wall wide open of another closely related bacterium, it gets complicated.

With billions upon billions of reproductions, bacteria have come upon chemicals, bacteriocins, that attack other bacteria with proteins that are specifically shaped or keyed to disrupt the cell wall of just one or a very few other types of bacteria. These proteins don't attack the cell wall of the bacterium producing it … That wouldn't work. A protein is a workhorse molecule produced by living things; the chemical properties of a protein derive in part from the molecule's shape. It's not just that a protein might carry a nitrogen atom that might bond with an oxygen atom. It's that the protein holds or presents those atoms in such a way that they react only with other molecules that can or do receive or interact with them; these proteins fit like keys in locks.

Now when I say that bacteria couldn't do this one thing so they do that other thing, I should clarify. It's not a choice as such. Bacteria produce proteins, all kinds of proteins. These are the molecules that give things like your bones, skin, and hair their shape and structure. If a bacterium happened to produce a protein that split its own wall open, well, that organism would die. But by having billions upon billions of proteins reproducing for millions upon millions of years, proteins get produced that serve as bacteriocins; they destroy or kill other bacteria, albeit only bacteria of a very specific type.

With the discovery of this remarkable property of many bacteria, scientists have sought to produce antibiotic-style bacteriocin drugs that attack just one specific type of bacterium. Suppose you got sick with some miserable staphylococcus infection, and the particular strain of staph you got has been around a long time. Its bacterial ancestors have encountered the human-made antibiotic drugs for decades, and the descendant strain that your body is fighting is resistant, or largely unaffected by the cell-wall-disruptive qualities of our penicillin, or erythromicin, or what have you.

You might start to lose. The bacterium might start to produce so much toxin that you can't fight it. But then scientists take samples of the particular strain of staph from your mouth, for example. Next they breed a particular type of bacterium that happens to produce a particular type of bacteriocin that happens to kill the staph bacterium that's infecting you. An agency like the Centers for Disease Control and Prevention (the CDC) could in turn breed a group of closely related bacteriocin-producing bacteria, or administer the isolated bacteriocin protein on its own, which you could drink like a glass of orange juice. The bacteriocins produced inside you either by the special strain of anti-staphylococcus bacteria or by the bacteriocin itself, and you'd recover in no time.

This line of evolutionary attack sounds seductive, but it works only if we can identify the specific bacterium and its cell-wall-disrupting bacteriocin. Researchers in southern Russia have been doing it for years. Along with attacking infectious diseases with bacteriocins, their research has involved attacking skin infections. By identifying just what bacterium is infecting a patient, these researchers have managed to come up with the right bacteriocin-producing bacteria that can produce enough of the bacteriocin protein to destroy the infecting strain.

A future that makes this technology available to all of us would be a bright one indeed. It would be a life-affirming result of our understanding of evolution, and the many historical steps that got us to this point. First scientists including Anton van Leeuwenhoek, the seventeenth-century Dutch microscopist, discovered the microscopic world. Then other scientists discovered that our immune system could be trained or induced to fight specific diseases that it's exposed to. Then scientists identified specific bacteria and specific viruses. Then scientists discovered chemicals or molecules that disrupt cell walls and membranes of certain bacteria. Then scientists discovered that bacteria fight each other. For example, way down in your intestines, there are generally three different types of
Escherichia coli
fighting each other with specialized bacteriocins all the time. This is what researchers mean when they talk about “standing on the shoulders of giants.” Science is a beautifully cumulative process.

For about two hundred years, humans have used other animals to test the effects of medicines and medical procedures. You may have heard of the Rh factor in blood. The term comes from rhesus monkeys, in whom it was discovered and studied. You may have been troubled or grateful for procedures in which eye makeup is tested on rabbits before its release to market. You may know about mice that are given certain doses of certain food additives or cigarette smoke to test for ill effects. You've probably used the term
guinea pig
to describe someone who goes first in a procedure in which the outcome is unknown.

All of these test animals can be used to see what would happen to us if were placed in the same situation for a simple reason: At the cellular level, humans and monkeys and pigs and mice are very much alike in construction or design. We share almost all of our biochemistry. We all have DNA, and it's nearly the same. In rhesus monkeys, we're close to 93 percent the same. In mice, it's closer to 90 percent overall. Just think about the potential consequences of these numbers. If you're a germ, you might be able to move from species to species. That's why we worry about, for instance, avian flu and swine flu. Or alternatively, 10 percent may be enough to invalidate any conclusions about infections that you might draw. In either case, human researchers can use our understanding of mutations and natural selection to determine how much of what we observe in these animal models applies to us.

Every one of us in the developed world has benefited directly from the medical tests performed with these animals. It's yet one more scientific achievement based on evolution.

In many ways, we have barely begun learning how to fight back against disease. Just think what else we don't know about bacteria and their interactions. With each step in the process, we used the method of science: Observe. Hypothesize. Predict. Experiment. Compare what you expected with what really happened. This rigorous form of the scientific method—one in which very disciplined experiments are conducted under carefully controlled conditions—really is a result of medicine. In order to observe and isolate the effects of germs, for example, you have to look very carefully, because you just can't see them without isolating them carefully and peering diligently through a microscope. Evolutionary theory benefited from medicine, and now medicine benefits from evolutionary theory.

As I look back on this particular human endeavor, I'm astonished at how careful these scientists were to isolate smallpox, rabies, mumps, measles, whooping cough, and rubella. We might say that we are a lucky bunch to be alive right now. But it wasn't luck. It was a strategy; it was science. You are here because a large number of people worked together around the world and across the centuries to understand how the natural world really works.

 

26

ANTIBIOTIC DRUG RESISTANCE—EVOLUTION STRIKES BACK

Do you get a flu shot every year? You should, because influenza (flu) viruses are evolving right under your vulnerable-to-infection nose, and you need to keep up. Viruses make their living by infecting living cells and inducing them to make copies of the virus. Those replicas pour out and encounter nearby cells, which results in more infection and yet more copies of the virus. If you think that sounds like war, you're not far off. In the winter of 1918–1919, the Spanish Flu killed about 50 million people—more than all of the combat in World War I, which had only just ended. Keep in mind that there is no evidence that viruses are malicious. They are just following their evolutionary path, multiplying wherever they encounter a survival advantage. The frightening thing is that the mindless, relentless drive of natural selection is now overwhelming our best defenses, making once-tamed diseases dangerous all over again.

Humans come to the battle equipped with their own defense, also shaped by evolution: the immune system. It's a complicated set of chemicals and processes that your body carries with it to fight diseases brought on by viruses, germs, and multicellular parasites. It learns from experience, developing targeted defenses against every infection as it occurs. So, let me pose this question: If our immune systems were working at a normal pace or performance level, wouldn't we have overcome every infectious entity our bodies have ever come across, or have come across us? Wouldn't we have defeated every germ and parasite in nature? As I'm sure you're aware, we have not. Nature doesn't work that way. It's one of the least pleasant consequences of evolution.

Over the course of your life, you've undoubtedly been infected by colds, flus, stomach viruses, food poisoning bacteria, and nature only knows what all else. Yet, neither you nor anyone else has overcome all these threats. You may even be in the good habit of washing your hands frequently to keep from getting sick again. You know intuitively that there are more germs out there that your immune system has never seen, and there will be the rest of your life.

So, let's pose the next logical question. Where do all these new never-before-encountered germs come from? There is no reason to look for a biowarfare factory in some undisclosed location that produces new germ designs and unleashes them on the world. Instead there are as many germ factories as there are people. Each of us serves as an incubator for new strains or varieties of germs.

Because of their complete lack of nerves or brains, germs are not mean-spirited or ornery. They just are what they are. Since the beginning of bacteria here on Earth, at least 3.5 billion years ago, there must have been configurations of molecules that caused those bacteria trouble. Like every living thing we have ever found on Earth, viruses have long-stranded molecules that carry the genetic information a virus needs to force or induce bacterial cells to produce more of these same viruses. Since they're made of the same molecular stuff, and they are so very much alike on the molecular level, it is reasonable to infer that bacteria and their viral enemies, the bacteriophages (the viruses that attack bacteria), came into existence about the same time. Hence my inclusion of the Vira as a domain of life. Each organism has vied for the same chemical resources since Earth cooled off enough to have liquid water extant on its surface.