Termites may be hard to love, but they should be easy to admire. Termite mounds are among the largest structures built by any nonhuman animal. They reach as high as thirty feet, which, proportional to the insects’ tiny size, is the equivalent of our building something twice as tall as the 2,722-foot Burj Khalifa, in Dubai. The mounds are also fantastically beautiful, Gaudíesque structures, with rippling, soaring towers, in browns and oranges and reds. The interior of a termite mound is an intricate structure of interweaving tunnels and passageways, radiating chambers, galleries, archways, and spiral staircases. To build a mound, termites move vast quantities of mud and water; in the course of a year, eleven pounds of termites can move about three hundred and sixty-four pounds of dirt (in the form of mud balls) and thirty-three hundred pounds of water (which they suck into their bodies). The point of all this construction is not to have a place to dwell—the colony lives in a nest a metre or two below the mound—but to be able to breathe. A termite colony, which may contain a million bugs, has about the same metabolic rate as a nine-hundred-pound cow, and, like cows (and humans), termites breathe in oxygen and expel carbon dioxide. The mound acts as a lung for the colony, managing the exchange of gases, leveraging small changes in wind speed to inhale and exhale. Also like lungs, a termite mound has a role as a secondary diffusion system, which carries oxygen to and carbon dioxide away from the far reaches of the underground termite nest. The mound functions as a humidifier, too, tightly regulating moisture levels across wet and dry seasons. Some termite species partly outsource their digestion through the practice of fungiculture—the farming of a grass-eating fungus, which they store, tend, and feed in an elaborate garden maze below the mound.

Termites appear to do all this without any centralized planning: there are no architects, engineers, or blueprints. Indeed, the termite mound is not so much a building as a body, a self-regulating organic process that continuously reacts to its changing environment, building and unbuilding itself. Its complex behavior emerges, as if by magic, from its simple constituents. It is generally agreed that individual termites are not particularly intelligent, lacking memory and the ability to learn. Put a few termites into a petri dish and they wander around aimlessly; put in forty and they start stampeding around the dish’s perimeter like a herd. But put enough termites together, in the right conditions, and they will build you a cathedral.

“Underbug” is more about humans who are preoccupied with termites than about termites themselves. Specifically, Margonelli is concerned with the sort of human whose interest in termites isn’t confined to wanting to kill them. (About half the scientific papers written about termites from 2000 to 2013 involve their extermination). These entomologists, geneticists, synthetic biologists, mathematical biologists, microbial ecologists, roboticists, computer scientists, and physicists are drawn to termites for a variety of reasons, not all of which are compatible. Some of these scientists, the minority, simply appear to be seduced by termites, and want to understand how they do what they do. One such is J. Scott Turner, a physiologist who, before turning to termites, placed alligators in wind tunnels in order to understand how they regulate their body temperature. By pumping propane gas down termite mounds, he was able to show that they function as lungs, not as chimneys that allow hot air to escape, which had been the previous assumption. (Putting things into a mound and seeing what happens is a favored mode of termite experimentation; Turner and his team have also experimented with plastic beads and molten aluminum. One convenience of working with termites is that there are few regulations concerning their treatment.)

Turner is a proponent of what he calls the “extended organism” thesis. (It’s meant as a variant of, and ultimately as an alternative to, Richard Dawkins’s “extended phenotype” model.) In Turner’s view, the physical termite mound—with its mud tunnels and walls, digested wood and grass and fungus—is part of the termite, rather than part of the environment on which the termite acts. The entire mound—insects plus structure—is thus a living thing: a self-regulating physiological and cognitive system, with a sense of its own boundaries, a memory, and a kind of collective intentionality.

The extended-organism hypothesis also recalls an older idea: that the termite, bee, or ant colony is a “superorganism.” This term was coined by William Wheeler in 1911, though the idea dates back to Darwin, who saw the superorganism as a solution to the “problem” of eusociality. The problem is this: if natural selection favors those organisms which are best at reproducing, then how do castes of nonreproductive insects ever evolve? One way to address the problem is to regard the colony as a whole as the unit of selection. The sterile worker should be thought of not as an individual organism but as a “well-flavored vegetable,” in Darwin’s phrase, produced by the queen.

Today, most evolutionary theorists favor the “inclusive fitness” explanation of eusociality, a theory developed by W. D. Hamilton in the early nineteen-sixties. Hamilton showed mathematically that altruism can be a beneficial reproductive strategy for an organism, so long as the altruistic act benefits another organism to which it is sufficiently genetically similar. As a human being, the obvious way for me to reproduce my genes is to have biological children, who will inherit half of my genes. But I can also reproduce my genes by helping my sister, who shares on average half of my genetic material, nurture and protect her own children, who will share a quarter. If sacrificing my life will enable my sister to have more than twice as many children as I would have had, my sacrifice is “worth it,” from the perspective of my selfish genes. E. O. Wilson, though an early evangelist for Hamilton’s theory, has recently argued for a return to the superorganism as a solution to Darwin’s problem. In this, Wilson is very much in the minority; Richard Dawkins has called his criticisms of inclusive fitness “downright perverse.”

Most of the other scientists Margonelli follows are interested in termites as a means to human ends, and aim at simplifying their complexity to something replicable. Consider termites’ ability to convert dead plant matter into energy. They do this with the help of the hundreds, sometimes thousands, of species of microbes—bacteria and protists—that live in their guts, ninety per cent of which are found nowhere else on earth. Some of these microbes are themselves, like the termite superorganism, composite animals. The protist Trichonympha, found in some termite guts, is itself host to colonies of symbiotic bacteria. Termites and their gut microbes are thought to have coevolved between two hundred and fifty million and a hundred and fifty-five million years ago, when some cockroaches ingested wood-eating microbes, and then began sharing what entomologists politely call “woodshake”—a mixture of feces, microbes, and plant matter—among themselves, mouth to mouth, and mouth to anus. This practice, known as “trophallaxis” (another of William Wheeler’s coinages), allows a communal pooling of digestive capacity, which can then be handed down from one generation to the next. (With the rise of fecal transplants to cure C. difficile infection and other gastrointestinal disorders, trophallaxis is gaining popularity among humans; the F.D.A. has, since 2013, officially classified human feces as a drug.) The Department of Energy says that the U.S. can produce 1.3 billion tons of dry biomass—from harvested trees, cornstalks, high-energy grasses, and the like—without taking anything away from regular agricultural uses. If humans can crack the code to termite digestion, the U.S. could turn the stuff into nearly a hundred billion gallons of biofuel a year—what’s sometimes called “grassoline”—and thereby reduce automobile emissions by eighty-six per cent.

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The search for a termite-inspired grassoline is a major goal of the emerging field of synthetic biology, in which biological systems—metabolic pathways, cells, organisms—are reëngineered to produce things humans want, including biofuels and precursors of drugs. One of the field’s leaders is Jay Keasling, who runs the Department of Energy’s Joint BioEnergy Institute, or J.B.E.I. Keasling imagines a fully modular system of synthetic biology, with different companies producing different off-the-shelf parts—empty cell “bags,” the chromosomes with which to program them, the molecules to “boot” them up—that can readily be assembled to produce the desired chemical output. Manufacturing a termite biofuel would require identifying the genes for wood eating from the termite’s microbe colony and inserting them into a cellular bag. The first challenge is overcoming the fickleness of microbes: less than one per cent of them can be isolated and grown in a petri dish. This used to mean that it was nearly impossible to map the genomes of the termite’s wood-eating microbes. But in 2004 a team led by the Berkeley earth scientist Jill Banfield came up with “metagenomics,” a process of sequencing the genes of an entire microbial community at once. In 2007, Nature published a metagenomic analysis of gut microbes from a Costa Rican termite; puzzle-piecing together fifty-four million base pairs of DNA, researchers identified more than a thousand genes that might be for digesting wood. A termite biofuel seemed not far off.

Yet the synthetic biologists at J.B.E.I. still have not produced a grassoline that can compete with ordinary fossil fuels. (They have turned their attention to the production of other biofuels, including those in demand by the military.) Margonelli suggests two reasons for this failure. First, the termite’s gut turned out to be too complex to understand, let alone imitate. Phil Hugenholtz, one of the researchers who helped sequence the gut microbes of the Costa Rican termite, jokes that “you might as well go and hook your car to a bunch of termites.” Second, the biology itself seems to resist being reëngineered in the way that synthetic biologists would like. “What we’re doing,” Héctor García Martín, a physicist who works with Keasling, says, “is taking a bug”—like E. coli—“with no interest in producing biofuels and forcing it to produce them.” García Martín goes on to cite the microbiologist Carl Woese, who observed that, unlike electrons, cells have a history—something like memories of what they have metabolized in the past. These “memories” are encoded not in the cells’ DNA but somewhere else in their chemistry, so it may be misguided to think in terms of swapping genetic programs in and out of cell “bags.” The willingness, on the part of a physicist like García Martín, to talk about the “memories” and “interests” of biological systems is surprising. But it reflects a larger shift among synthetic biologists away from a belief in the fundamentally mechanical nature of life.