A little Sunday soil science

In Jewish tradition, or at least so I've heard, a butcher knife was purified by burying it in the ground for several weeks. This seemingly paradoxical use of dirt to clean is evidence that humans long ago recognized a mysterious transforming power in soil, "that element where," as a poet said, "life and death are exquisitely balanced." When we study the chemistry and biology of soil, we can see examples of the soil's transforming power.

The soil taken as a whole can be looked on as a catalytic system. This system has many interrelated subsystems, some biological, some abiotic. The abiotic catalysts are surfaces. Soil is a region where surfaces, or interfaces between phases, are dominant. The ocean is all wet. Rocks are merely solid. The atmosphere is fairly homogeneous. But in soil, the three phases are intimately commingled. The solid surfaces grow and dissolve, bind species from the liquid phase, and release them again, exchanging them for other ones. In these processes, electrons sometimes jump from one species to another. For example, certain organic molecules trade electrons fairly readily with iron and manganese ions. The organics can lose electrons to solid iron and manganese oxides, which become reduced to soluble Fe²⁺ and Mn²⁺. Thus, the oxides are gradually dissolved. If oxygen is present, it may be able to reoxidize the metal cations (even though it was unable to directly oxidize the original organic molecule). In this case, the oxides do not dissolve, but act strictly as catalysts for the oxidation of the organic compounds.

Life has elaborated on the theme of surface reactions. Cells are full of membranes, which are a kind of surface, although a liquid-liquid one, made possible by the immiscibility of polar and non-polar molecules. And enzymes are protein molecules that form a surface of just the right shape and charge distribution to catalyze a particular reaction. Many soil transformations depend on these biological catalysts. Nitrogen and oxygen are shy strangers going their separate ways in the well-lit atmosphere, but once they are pulled into the dark nightclub of the soil, they lose their inhibitions and are lured into an intricate dance of combination and recombination, fueled by the energy in reduced carbon and lubricated by enzymes of the soil bacteria Nitrosomonas and Nitrobacter. Nitrogen may lose as many as five of its electrons, but its innocence can be redeemed if oxygen becomes depleted and the denitrifying bacteria—like cops to the rescue, or priests dispensing absolution—arrive on the scene and restore what was lost. Nitrogen limps back to its home in the sky, but is no wiser for the experience, for the next day the whole thing happens again...and again...and again, in an endless cycle.

The surfaces in the soil are stages on which chemical and biochemical dramas are played out.

Confession of a soul searcher

I was raised in California by communists from Texas. Actually, my father was the one who railed against the opiate of the people. My mother tried, once or twice, to sneak my four sisters and me into the Methodist church, where she had grown up (my father was raised Episcopalian, and his grandfather was one of the early Jehovah's Witnesses), but my father stopped her. So I grew up without the concept of "the soul." It was just another one of those mysterious words, like "god" and "love," that other people made a lot of fuss about. I could see clearly right through myself, and I was sure that I didn't have a soul. Interestingly, my three youngest sisters were equally sure that they did have souls, and, who knows, maybe they did. They were all a lot louder than I was. Maybe their souls were the source of all that jabbering.

What I believed in, when I was a boy, were Science and Revolution. My father was a physician and scientist as well as a political activist. As children, my sisters and I were happy, both because it's the nature of children to be happy, and because we thought we were, somehow, at the vanguard of history. Let the other kids talk about what they'd seen on TV the night before...we didn't have a television because TV was bourgeois, and it, along with the rest of the establishment, was going to be swept away soon anyhow and be replaced by an idyllic new world of selfless love and selfless work. Or so we believed. But the solidarity of our family proved to be an illusion. As we children entered adolescence, the family dissolved into a chaos of betrayal and madness. My father left us. My oldest sister married, at 16, a much older man and moved away to the east coast. My next two sisters had mental breakdowns and were hospitalized. I started writing poetry and took a long detour from science (I had been doing pre-med at Berkeley). I did little but read for many years, supporting myself with various short-term laboring jobs. Finally I concluded that nature was wiser than man. My ideal was to live in such a way that doctors and lawyers, symbols of man's authority, were unnecessary. This I proposed to do by becoming a peasant, living within nature as much as I could. I worked on farms, met and married a woman, we had a child, and then my wife left me to go back to the comfort of her suburban family. I realized that my peasant life was too limiting. I was a happy animal, but I wasn't a man. I returned to school at the age of 39 and got bachelor's and master's degrees in agronomy. I found that I could get along with agronomy students, many of whom were from other countries. So now I travel the world, planting my seeds. A couple of years ago, not long after my oldest sister hung herself, I started praying every morning. I still don't have a church (the closest thing is Sunday morning yoga class), but I find that I have to do something to express my awe at the infinite power that is creating the universe.