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seawater come from dead cells, and nitrate-respiring bacteria inexorably remove biologically usable nitrogen from the environment. What, then, fuels the biological nitrogen cycle and keeps it from running down?The answer is that some organisms are able to convert atmospheric nitrogen to ammonium, using the cell’s store of energy. No eukaryotic organism can fix nitrogen in this way, but many prokaryotes can. (Farmers commonly include soy or other beans in their crop rotation because these plants restore nitrogen to the soil. The task of nitrogen fixation, however, is accomplished by bacteria that live in small nodules on the roots of bean plants, not by the beans themselves.) A small amount of nitrogen is fixed by lightning as it cuts through the atmosphere, but biology’s thirst for nitrogen is quenched mainly by bacteria.
    The cycles of carbon, nitrogen, sulfur, and other elements are linked together into a complex system that controls the biological pulse of the planet. Because organisms need nitrogen for proteins and other molecules, there could be no carbon cycle without nitrogen fixation. Nitrogen metabolism itself depends on enzymes that contain iron; thus, without biologically available iron, there could be no nitrogen cycle … and, hence, no carbon cycle. Biology on another planet may or may not include organisms that are large or intelligent, but wherever it persists for long periods of time, life will feature complementary metabolisms that cycle biologically important elements through the biosphere.
    By now it should be apparent why I insisted earlier that plants and animals evolved to fit into a prokaryotic world rather than the reverse. It is a prokaryotic world, and not only in the trivial sense that there are a lot of bacterial cells. Prokaryotic metabolisms form the fundamental ecological circuitry of life. Bacteria, not mammals, underpin the efficient and long-term functioning of the biosphere.
    How can this astonishing diversity of prokaryotic cells be ordered and assembled along with that of eukaryotes into a phylogeny that encompasses all of biology? Size and shape fail us, and so does physiology; organisms as disparate as fungi and elephants, or E. coli and redwoods, are simply too different from one another to assemble into a believable tree based on form and function alone. The solution requires that we return to the unity of life, the molecular attributes shared by all known organisms. In a groundbreaking paper published in 1965, Emile Zuckerkandl and Nobel laureate Linus Pauling proposed that molecules can be read as documents of evolutionary history. Just as the anatomicalstructures of limbs or skulls reflect descent with modification, so too do the chemical structures of DNA and proteins. The long chain of amino acids that makes up, say, the respiratory protein cytochrome c differs slightly between humans and chimps and more so between humans/chimps and horses. The sequences of nucleotides in the genes that code for these proteins differ correspondingly.
    Carl Woese of the University of Illinois built decisively on this conceptual foundation. Woese spent his formative years in science investigating ribosomes, the sites within cells where proteins are manufactured. He knew that all organisms contain ribosomes, that all ribosomes contain functional complexes made of RNA and proteins, and that these complexes all contain several subunits. By comparing among organisms the sequences of nucleotides that make up the RNA molecules found in the small subunit of ribosomes, Woese made the great leap that brought phylogeny to the microbial world, sowing the seeds for a Tree of Life worthy of the name.
    Figure 2.1 shows the Tree of Life, a depiction of the genealogical relationships of all living organisms, based on comparisons of molecular sequence in the genes that code for small subunit ribosomal RNA. Experts argue about its details, but all biologists agree that our ability to draw Darwin’s great Tree of