Shadows of Forgotten Ancestors (15 page)

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DNA polymerase is an enzyme. Its job is to assist a DNA strand in copying itself. It itself is a protein, configured out of amino acids and manufactured on the instructions of the DNA. So here’s DNA controlling its own replication. DNA polymerase is now on sale at your local biochemical supply house. There’s a laboratory technique, polymerase chain reaction, which unzips a DNA molecule by changing its temperature; the polymerase then helps each strand to reproduce. Each of the copies is in turn unzipped and replicates itself.
¹⁶
At every step in this repetitive process, the number of DNA molecules doubles.
In forty steps there are a trillion copies of the original molecule. Of course, any mutation happening along the way is also reproduced. So polymerase chain reactions can be used to simulate evolution in the test tube.
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Something similar can be done for other nucleic acids:

In the test tube before you is another kind of nucleic acid—this one single-stranded. It’s called RNA (ribonucleic acid). It’s not a double helix and does not have to be unzipped to make a copy of itself. The strand of nucleotides may loop around to join itself, tail in mouth, a molecular circle. Or it may have hairpin or other shapes. In this experiment it’s sitting mixed with its fellow RNA molecules in water. There are other molecules added to help it along, including nucleotide building blocks for making more RNA. The RNA is coddled, jollied, handled with kid gloves. It’s extremely finicky and will do its magic only under very specific conditions. But magic it does. In the test tube not only does it make identical copies of itself, but it also moonlights as a marriage broker for other molecules. Indeed, it performs even more intimate services, providing a kind of platform or marital bed for oddly shaped molecules to join together, to fit into one another. It’s a jig for molecular engineering. The process is called catalysis.

This RNA molecule is a self-replicating catalyst. To control the chemistry of the cell, DNA has to oversee the construction of factotums—a different class of molecules, proteins, which are the catalytic machine tools we’ve been discussing above. DNA makes proteins because it can’t catalyze on its own. Certain kinds of RNA, though, can themselves serve as catalytic machine tools.
¹⁷
Making a catalyst or
being
a catalyst gives you the biggest return for the smallest investment: Catalysts can control the production of millions of other molecules. If you make a catalyst, or if you
are
a catalyst—the right kind of catalyst—you have a long lever arm on your destiny.

Now in these laboratory experiments, which are being carried out in our time, imagine many generations of RNA molecules more or less identically replicating in the test tube. Mutations inevitably occur, and much more often than in DNA. Most of the mutated RNA sequences will leave no, or fewer, copies, again because random changes in the instructions are rarely helpful. But occasionally a molecule comes into existence that aids its own replication. Such a newly mutated RNA might replicate faster than its fellows or with greater fidelity. If we were uncaring about the fates of individual RNA molecules—and while they may arouse feelings of wonder, they seldom elicit sympathy—and wished only for the advancement of the RNA clan, this is just the kind of experiment we would perform. Most lines would perish. A few would be better adapted and leave many copies. These molecules will slowly evolve. A self-replicating, catalytic RNA molecule may have been the first living thing in the ancient oceans about 4 billion years ago, its close relative DNA being a later evolutionary refinement.

In an experiment with synthetic organic molecules that are
not
nucleic acids, two closely related species of molecules are found to make copies of themselves out of molecular building blocks provided by the experimenter. These two kinds of molecules both cooperate and compete: They may aid each other’s replication, but they are also after the same limited pool of building blocks. When ordinary visible light is made to shine on this submicroscopic drama, one of the molecules is observed to mutate: It changes into a somewhat different molecule that breeds true—it makes identical copies of itself, and not its pre-mutation ancestor. This new variety, it turns out, is much more adept at replicating itself than the other two hereditary lines. The mutant line rapidly out-competes the others, whose numbers precipitously fall.
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We have here, in the test tube, replication, mutation, replication of mutations, adaptation, and—we do not think it is too much to say—evolution. These are not the molecules that make us up. They are probably not the molecules involved in the origin of life. There may well be many other molecules which reproduce and mutate better. But what prevents us from calling this molecular system alive?

Nature has been performing similar experiments, and building on its successes, for 4 billion years.

Once even crude replication becomes possible, an engine of enormous powers has been let loose into the world. For example, consider that primitive organic-rich ocean of the Earth. Suppose we were to drop a single organism (or a single self-replicating molecule) into it, considerably smaller than a contemporary bacterium. This tiny being divides in two, as do its offspring. In the absence of any predators and with inexhaustible food supplies, their numbers would increase exponentially. The being and its descendants would take only about one hundred generations to eat up all the organic molecules on Earth. A contemporary bacterium under ideal conditions can reproduce once every fifteen minutes. Suppose that on the early Earth the first organism could reproduce only once a year. Then in only a century or so, all the free organic matter in the whole ocean would have been used up.

Of course, long before that, natural selection would be brought to bear. The genre of selection might be competition with others of your kind—for example, for foodstuffs in an ocean with dwindling stocks of preformed molecular building blocks. Or it might be predation—if you don’t look out, some other being will mug you, strip you down, pull you to pieces, and use your molecular parts for its own ghastly purpose

Major evolutionary advance might take considerably more than one hundred generations. But the devastating power of exponential replication becomes clear: When the numbers are small, organisms may only infrequently come into competition; but after exponential replication, enormous populations are produced, stringent competition occurs, and a ruthless selection comes into play. A high population density generates circumstances and elicits responses different from the more friendly and cheerful lifestyles that pertain when the world is sparsely populated.

The external environment is continuously changing—in part because of the enormous population growth when conditions are favorable, in part because of the evolution of other organisms, and in part because of the ticking geological and astronomical clockwork. So there’s never such a thing as a permanent or final or optimum adaptation of a lifeform to “the” environment. Except in the most protected
and static surrounds, there must be an endless chain of adaptations. However it feels on the inside, it might very well be described from the outside as a struggle for existence and a competition between adults to ensure the success of their offspring.

You can see that the process tends to be adventitious, opportunistic—not foresighted, not with any future end in view. The evolving molecules do not plan ahead. They simply produce a steady stream of varieties, and sometimes one of the varieties turns out to be a slightly improved model. No one—not the organism, not the environment, not the planet, not “Nature”—is mulling the matter over.

This evolutionary shortsightedness can lead to difficulties. It might, for example, cast aside an adaptation that is perfectly suited for the next environmental crisis a thousand years from now (about which, of course, no one has a glimmering). But you have to get from here to there. One crisis at a time is life’s motto.

US AND THEM

W
hether there were many instances of the origin of life on Earth or only one is a deep and perhaps impenetrable mystery. For all we know, there may have been millions of dead ends and false starts, unmourned ancient genealogies snuffed out as new ones arose. But it seems very clear that there’s only one hereditary line leading to all life
now
on Earth. Every organism is a relative, a distant cousin, of every other. This is manifest when we compare how all the organisms on Earth do business, how they’re built, what they’re made of, what genetic language they speak, and especially how similar their blueprints and molecular job orders are. All life is kin.

In our imagination, let’s cast our eyes back to the earliest organisms. They could not have been so purebred and pampered a line of self-replicating molecules as contemporary DNA or RNA—superbly efficient in the replication and proofreading of their messages, but reproducing only under the meticulously controlled conditions upon which modern organisms insist. The first living things must have been rough-and-ready, slow, careless, inefficient—just barely good enough to make crude copies of themselves. Good enough to get started.

At some point, probably extremely early on, organisms had to be more than a single molecule, no matter how talented that molecule might be. For very precise instructions to be followed to the letter, for reproduction to occur with high fidelity, other molecules were needed—to scour building blocks from the adjacent waters and bend them to your purpose; or, like DNA polymerase, to be midwife in the replication process; or to proofread a newly minted set of genetic instructions. But it did you no good if such accessory molecules kept drifting out to sea. What you needed was a kind of trap to keep useful molecules captive. If only you could surround yourself with a membrane that, like a one-way valve, lets in the molecules you need and doesn’t let them out … There are molecules that do that—that, for example, are attracted to water on one side of them, but are repelled,
absolutely revolted by water on the other. They’re common in Nature. They tend to make little spheres. And they’re the basis of cell membranes today.