Shadows of Forgotten Ancestors

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