Because evolution is conservative and reluctant to tamper with instructions that work, the DNA code incorporates documents—job orders and blueprints—dating back to remote biological antiquity. Many passages have faded. In some places there are palimpsests, where remains of ancient messages can be seen peeking out from under newer ones. Here and there a sequence can be found that is transposed from a different part of the message, taking on a different shade of meaning in its new surrounds; words, paragraphs, pages, whole volumes have been moved and reshuffled. Contexts have changed. The common sequences have been inherited from remote times. The more distinct the corresponding sequences are in two different organisms, the more distantly related they must be.
These are not only the surviving annals of the history of life, but also handbooks of the mechanisms of evolutionary change. The field of molecular evolution—only a few decades old—permits us to decode the record at the heart of life on Earth. Pedigrees are written in these sequences, carrying us back not a few generations, but most of the way to the origin of life. Molecular biologists have learned to read them and to calibrate the profound kinship of all life on Earth.5 The recesses of the nucleic acids are thick with ancestral shadows.
We can now almost follow the itinerary of the naturalist Loren Eiseley:Go down the dark stairway out of which the race has ascended. Find yourself at last on the bottommost steps of time, slipping, sliding, and wallowing by scale and fin down into the muck and ooze out of which you arose. Pass by grunts and voiceless hissings below the last tree ferns. Eyeless and earless, float in the primal waters, sense sunlight you cannot see and stretch absorbing tentacles toward vague tastes that float in water.6
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A particular sequence of As, Cs, Gs, and Ts is in charge of making fibrinogen, central to the clotting of human blood. Lampreys look something like eels (although they are far more distant relations of ours than eels are); blood circulates in their veins too; and their genes also contain instructions for the manufacture of the protein fibrinogen. Lampreys and people had their last common ancestor about 450 million years ago. Nevertheless, most of the instructions for making human fibrinogen and for making lamprey fibrinogen are identical. Life doesn’t much fix what isn’t broken. Some of the differences that do exist are in charge of making parts of the molecular machine tools that hardly matter—something like the handles on two drill presses being made of different materials with different brand names, while the guts of the two are identical.
Or here, to take another example, are three versions of the same message,7 taken from the same part of the DNA of a moth, a fruit fly, and a crustacean:
Moth:GTC GGG CGC GGT CAG TAC TTG GAT GGG TGA CCA CCT GGG AAC ACC GCG TGC CGT TGG …
Fruit fly:GTC GGG CGC GGT TAG TAC TTA GAT GGG GGA CCG CTT GGG AAC ACC GCG TGT TGT TGG …
Crustacean:GTC GGG CCC GGT CAG TAC TTG GAT GGG TGA CCG CCT GGG AAC ACC GGG TGC TGT TGG …
Compare these sequences and recall how different a moth is from a lobster. But these are not the job orders for mandibles or feet—which could hardly be closely similar in moths and lobsters. These DNA sequences specify the construction of the molecular jigs on which newly forming molecules are laid out under the ministrations of the molecular machine tools. Down at this level, it’s not absurd that moths and lobsters might have closer affinities than moths and fruit flies. The comparison of moth and lobster suggests how slow to change, how conservative the genetic instructions can be. It’s a long time ago that the last common ancestor of moths and lobsters scudded across the floor of the primeval abyss.
We know what every one of those three-letter ACGT words means—not just which amino acids they code for, but also the grammatical and lexigraphical conventions employed by life on Earth. We have learned to read the instructions for making ourselves—and everybody else on Earth. Take another look at “START” and “STOP.” In organisms other than bacteria, there’s a particular set of nucleotides that determine when DNA should start making molecular machine tools, which machine tool instructions should be transcribed, and how fast the transcription should go. Such regulatory sequences are called “promoters” and “enhancers.” The particular sequence TATA, for example, occurs just before the place where transcription is to occur. Other promoters are CAAT and GGGCGG. Still other sequences tell the cell where to stop transcribing.8
You can see that the substitution of one nucleotide for another might have only minor consequences—you could, for example, substitute one structural amino acid for another (in the “handle” of the machine tool) and in no way change what the resulting protein does. But it could also have a catastrophic effect: A single nucleotide substitution might convert the instructions for making a particular amino acid into the signal to stop the transcription; then, only a fragment of the molecular machine in question will be manufactured, and the cell might be in trouble. Organisms with such altered instructions will probably leave fewer offspring.
The subtlety and nuance of the genetic language is stunning. Sometimes there seem to be overlapping messages using the same letters in the same sequence, but with different functional import depending on how it’s read: two texts for the price of one. Nothing this clever occurs in any human language. It’s as if a long passage in English had two completely different meanings,9 something like
ROMAN CEMENT TOGETHER NOWHERE …
and
ROMANCEMENT TO GET HER NOW HERE …
but much better—on and on for pages, perfectly lucid and grammatical in both modes, and, we think, beyond the skill of any human writer. The reader is invited to try.
In “higher” organisms, many long sequences seem to be nonfunctional genetic nonsense. They lie after a “STOP” and before the next “START” and generally remain ignored, forlorn, untranscribed. Maybe some of these sequences are garbled remnants of instructions that, long ago, in our distant ancestors, were important or even keys to survival, but that today are obsolete and useless.* Being useless, these sequences evolve quickly: Mutations in them do no harm and are not selected against. Maybe a few of them are still useful, but elicited only under extraordinary circumstances. In humans some 97% of the ACGT sequence is apparently good for nothing. It’s the remaining 3% that, as far as genetics goes, makes us who we are.
Startling similarities among the functional sequences of As, Cs, Gs, and Ts are seen throughout the biological world, similarities that could not have come about unless—beneath the apparent diversity of life on Earth—there was an underlying and fundamental unity. That unity exists, it seems clear, because every living thing on Earth is descended from the same ancestor 4 billion years ago; because we are all kin.
But how could machines of such elegance, subtlety, and complexity ever arise? The key to the answer is that these molecules are able to evolve. When one strand is making a copy of the other, sometimes a mistake occurs and the wrong nucleotide—an A, say, instead of a G—will be inserted into the newly assembled sequence. Some of them are honest replication errors—good as it is, the machinery isn’t perfect. Some are induced by a cosmic ray or another kind of radiation, or by chemicals in the environment. A rise in temperature might slightly increase the rate at which molecules fall to pieces, and this could lead to mistakes. It even happens that the nucleic acid generates a substance that alters itself—perhaps thousands or millions of nucleotides away.