Second-Generation Nanotechnology

Despite its versatility, protein has shortcomings as an engineering material. Protein machines quit when dried, freeze when chilled, and cook when heated. We do not build machines of flesh, hair, and gelatin; over the centuries, we have learned to use our hands of flesh and bone to build machines of wood, ceramic, steel, and plastic. We will do likewise in the future. We will use protein machines to build nanomachines of tougher stuff than protein.

As nanotechnology moves beyond reliance on proteins, it will grow more ordinary from an engineer's point of view. Molecules will be assembled like the components of an erector set, and well-bonded parts will stay put. Just as ordinary tools can build ordinary machines from parts, so molecular tools will bond molecules together to make tiny gears, motors, levers, and casings, and assemble them to make complex machines.

Parts containing only a few atoms will be lumpy, but engineers can work with lumpy parts if they have smooth bearings to support them. Conveniently enough, some bonds between atoms make fine bearings; a part can be mounted by means of a single chemical bond that will let it turn freely and smoothly. Since a bearing can be made using only two atoms (and since moving parts need have only a few atoms), nanomachines can indeed have mechanical components of molecular size.

How will these better machines be built? Over the years, engineers have used technology to improve technology. They have used metal tools to shape metal into better tools, and computers to design and program better computers. They will likewise use protein nanomachines to build better nanomachines. Enzymes show the way: they assemble large molecules by "grabbing" small molecules from the water around them, then holding them together so that a bond forms. Enzymes assemble DNA, RNA, proteins, fats, hormones, and chlorophyll in this way - indeed, virtually the whole range of molecules found in living things.

Biochemical engineers, then, will construct new enzymes to assemble new patterns of atoms. For example, they might make an enzyme-like machine which will add carbon atoms to a small spot, layer on layer. If bonded correctly, the atoms will build up to form a fine, flexible diamond fiber having over fifty times as much strength as the same weight of aluminum. Aerospace companies will line up to buy such fibers by the ton to make advanced composites. (This shows one small reason why military competition will drive molecular technology forward, as it has driven so many fields in the past.)

But the great advance will come when protein machines are able to make structures more complex than mere fibers. These programmable protein machines will resemble ribosomes programmed by RNA, or the older generation of automated machine tools programmed by punched tapes. They will open a new world of possibilities, letting engineers escape the limitations of proteins to build rugged, compact machines with straightforward designs.

Engineered proteins will split and join molecules as enzymes do. Existing proteins bind a variety of smaller molecules, using them as chemical tools; newly engineered proteins will use all these tools and more.

Further, organic chemists have shown that chemical reactions can produce remarkable results even without nanomachines to guide the molecules. Chemists have no direct control over the tumbling motions of molecules in a liquid, and so the molecules are free to react in any way they can, depending on how they bump together. Yet chemists nonetheless coax reacting molecules to form regular structures such as cubic and dodecahedral molecules, and to form unlikely-seeming structures such as molecular rings with highly strained bonds. Molecular machines will have still greater versatility in bondmaking, because they can use similar molecular motions to make bonds, but can guide these motions in ways that chemists cannot.

Indeed, because chemists cannot yet direct molecular motions, they can seldom assemble complex molecules according to specific plans. The largest molecules they can make with specific, complex patterns are all linear chains. Chemists form these patterns (as in gene machines) by adding molecules in sequence, one at a time, to a growing chain. With only one possible bonding site per chain, they can be sure to add the next piece in the right place.

But if a rounded, lumpy molecule has (say) a hundred hydrogen atoms on its surface, how can chemists split off just one particular atom (the one five up and three across from the bump on the front) to add something in its place? Stirring simple chemicals together will seldom do the job, because small molecules can seldom select specific places to react with a large molecule. But protein machines will be more choosy.

A flexible, programmable protein machine will grasp a large molecule (the workpiece) while bringing a small molecule up against it in just the right place. Like an enzyme, it will then bond the molecules together. By bonding molecule after molecule to the workpiece, the machine will assemble a larger and larger structure while keeping complete control of how its atoms are arranged. This is the key ability that chemists have lacked.

Like ribosomes, such nanomachines can work under the direction of molecular tapes. Unlike ribosomes, they will handle a wide variety of small molecules (not just amino acids) and will join them to the workpiece anywhere desired, not just to the end of a chain. Protein machines will thus combine the splitting and joining abilities of enzymes with the programmability of ribosomes. But whereas ribosomes can build only the loose folds of a protein, these protein machines will build small, solid objects of metal, ceramic, or diamond - invisibly small, but rugged.

Where our fingers of flesh are likely to bruise or burn, we turn to steel tongs. Where protein machines are likely to crush or disintegrate, we will turn to nanomachines made of tougher stuff.

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