The translation Ressler worked on is a one-for-one, simple substitution. My arbitrary string, pressed through the table, maps to a single protein: arginine-glycine-proline-threonine___Transliteration to aminos alone seems to move me no nearer the evolution of heart, chest, hands, eyes — those devices against the caprice of environment. Slavish substitution appears no more helpful in finishing my triple bridge than those primitive DOD translators Ressler once tapped us into. One night, taking us on a tour through the vast MOL on-line network, he tapped into a machine translation program. He selected "French" for target language and typed in the string "I am left behind." We shouldn't have been playing with the restricted program at all, but that didn't keep Todd and me from hanging on his every keystroke. The algorithm churned away on a mighty effort of pattern matching and produced "Je suis gauche derrière." He hooked up two of these software Berlitz's back to back, feeding English-to-French back into its reciprocal. "Out of sight, out of mind" returned to source language as "blind lunatic."
All I've done with codon translation is rename the elements I started with. ACG becomes threonine; I've just swapped chemical terms. And yet, the map is never quite the place, nor the place as navigable as its image. It has taken me months to see that the coding problem is just the start of the cryptography. If that were the extent of inheritance, the lookup table would produce only tautological definitions. The hundreds of base pairs in a gene, broken into triplet codons and fed through the decoder, would produce the telegram "Please refer to original dots and dashes."
All these ciphers mean nothing until I find the difference created in translation. The table only softens the inscrutable script, shapes the clay into executable words. Cracking the code is just the tip of the Goldberg. The lookup list of simple equivalences requires me to learn how to interpret, implement the text that comes out of it. For data to grow, respond, rise up and walk I must look at the secondary structures locked in the life molecule. I want a deeper definition from the string — its isomorphs of hope, ache, posted desire.
The bouillabaisse is richer than I've guessed. The punched tape running along the inner seam of the helix is much more than a repository of enzyme stencils. It packs itself with regulators, suppressors, promoters, case-statements, if-thens. Genes coding for messengers, readers, and decoders of genes. Genes to copy and build the genes' copiers and builders. Genes that may speed, slow, or reverse their own mutation. The automated factory imbeds a blueprint for its own translation machinery — a glimpse of real invention that knocks me for a loop.
How, from simple substitution, can this absurd surplus emerge? A gene and its enzyme, while code-equivalent, are worlds apart in function. The decoded string contains more than its original. My mistake has been in thinking of enzymes as simple ropes of twenty-colored beads. Even though this model provides more necklaces than the most scrupulous socialite could wear in an eternity of nights out, my metaphor misses a key point. Each color pattern corresponds to a specific necklace twist. And shape, in stereochemistry, is behavior by another name.
Protein necklaces are actually closer to wildly tangled wool fuzz. They are strings, but coiled as erratically as Norwegian hair run through a home permanent. (Wool, hair — two prime analogies.) Only, the twists that the fiber balls up into are rigid, fixed by the sequence of the aminos. I feel my first spark: the growing poly-peptide — arginine, glycine, proline — folds up in a manner determined by the amino sequence coded for in the synthesizing gene. The resulting three-dimensional globule carries spatial information; a landscape of grottos, peaks, and plains gives the enzyme catalytic ability — the power to bring about reactions that otherwise might not have taken place.
Even if the strand is stretched, it will spontaneously reform to the coiled arrangement unique to its linear sequence. This complex but ordained shape turns the enzyme into a cookie cutter, machine tool, a shoehorn introducing big foot into recalcitrant slipper. Smaller molecules align with spots on the enzyme landscape where they precisely fit. Held in place, they are brought together to react with another similar squatter. Each uniquely shaped enzyme is expert at bringing about a particular reaction. The human genome codes for countless enzymes, each a chemical command, a potential engine capable of producing a specific chemical event.
DNA carries just part of the instructions for these purposive, molecular machines. The actual welding — go straight a fraction of a micron; make a hard turn, 137 degrees in plane X, north-by-northwest — depends on physics. The shape an enzyme takes, and therefore its function, results from the laws governing atoms in space. To manufacture breathing, searching, speaking, rule-defying life from out of constrained matter requires no transcendence. Every level of the hierarchy arises from the previous, without any need to change the rules or call in outside assistance. Yes, some sleight of hand: a knit sock is just a series of knots, a computer just switches, a haunting tune just the intervals that walk it down the scale. But what other way to grasp a thing except as the emergent interplay of parts, themselves emergent from combined performances at lower levels?
The emergence of function from codon assignments is like that child's toy: two intermeshed gears with an asymmetrically affixed pen that produces unpredictable designs. The surprise, recursive flowers the toy makes aren't hinted at in any part of the assembly— not gear, not pen, not the cranking hand. Each of these parts does only what is allowed. The flower lies latent in the aggregate rules of geometry, which know nothing about flowers. In the same way, my most inexplicable high-order ability — understanding things through metaphor, applying the light of likeness to probe the layers of the pyramid — already lies infolded, hidden in the craggy terrain, the hintless indifference of my crumpled-up polypeptides.
Solving the lookup table — itself arbitrary — is prerequisite for my locating the particle of purpose, the smallest programmed machine in that regress of programmable machines making up living tissue. In grounding Mendel's invariant inheritance squarely in molecules, Ressler hoped to position science for a theory of molecular evolution. Protein synthesis would reveal how the destructive anarchy of chance, capable only of wearing the rock away, can carve Chartres. The production of enzymes, each shaping an urge to bring about reactions that would not occur spontaneously, is the first rung up form's ladder toward free will.
The catalyzing shape of enzymes is the seam between predetermined atomic interactions and the self-ordering living library. Enzymes are the machines DNA creates and sends out into the cellular factory. They are the factory. The coding problem was, to Ressler's generation, nothing less than a matter of locating the fundamental message unit behind the biosphere. Just as the innermost in a set of nested Chinese dolls anticipates the shape of the outermost, the way the array of living things bends itself to the environment depends on the ability of chains of amino acids to fold into specific, reaction-promoting molds. Or a step before that: on the way nucleic acid hides the enzyme shape in a helical archive.