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Founder, The Whole Earth Catalog; Co-founder, The Well; Co-Founder, The Long Now Foundation; Author, Whole Earth Discipline

Microbes Run the World

That opening sentence of The New Science of Metagenomics sounds reveille for a new way of understanding biology, and maybe of understanding society as well.

The breakthrough was shotgun sequencing of DNA, the same technology that gave us the human genome years ahead of schedule. Starting in 2003, Craig Venter and others began sequencing large populations of bacteria. The thousands of new genes they found (double the total previously discovered) showed what proteins the genes would generate and therefore what function they had, and that began to reveal what the teeming bacteria were really up to. This "meta"-genomics revolutionized microbiology, and that revolution will reverberate through the rest of biology for decades.

Microbes make up 80 percent of all biomass, says Carl Woese. In one fifth of a teaspoon of seawater there's a million bacteria (and 10 million viruses), Craig Venter says, adding, "If you don't like bacteria, you're on the wrong planet. This is the planet of the bacteria." That means most of the planet's living metabolism is microbial. When James Lovelock was trying to figure out where the gases come from that make the Earth's atmosphere such an artifact of life (the Gaia Hypothesis), it was microbiologist Lynn Margulis who had the answer for him. Microbes run our atmosphere. They also run much of our body. The human microbiome in our gut, mouth, skin, and elsewhere, harbors 3,000 kinds of bacteria with 3 million distinct genes. (Our own cells struggle by on only 18,000 genes or so.) New research is showing that our microbes-on-board drive our immune systems and important portions of our digestion.

Microbial evolution, which has been going on for over 3.6 billion years, is profoundly different from what we think of as standard Darwinian evolution, where genes have to pass down generations to work slowly through the selection filter. Bacteria swap genes promiscuously within generations. They have three different mechanisms for this "horizontal gene transfer" among wildly different kinds of bacteria, and thus they evolve constantly and rapidly. Since they pass on the opportunistically acquired genes to their offspring, what they do on an hourly basis looks suspiciously Lamarckian — the inheritance of acquired characteristics.

Such routinely transgenic microbes show that there's nothing new, special, or dangerous about engineered GM crops. Field biologists are realizing that the the biosphere is looking like what some are calling a pangenome,  an interconnected network of continuously circulated genes that is a superset of all the genes in all the strains of a species that form. Bioengineers in the new field of synthetic biology are working directly with the conveniently fungible genes of microbes.

This biotech century will be microbe enhanced and maybe microbe inspired. "Social Darwinism" turned out to be a bankrupt idea. The term "cultural evolution" never meant much, because the fluidity of memes and influences in society bears no relation to the turgid conservatism of standard Darwinian evolution. But "social microbialism" might mean something as we continue to explore the fluidity of traits and vast ingenuity of mechanisms among microbes — quorum sensing, biofilms, metabolic bucket brigades, "lifestyle genes," and the like.

Confronting a difficult problem we might fruitfully ask, "What would a microbe do?"