Book Review: Tim Friend, The Third Domain: The Untold Story of Archaea and the Future of Biotechnology (Washington, D.C.: Joseph Henry 2007). 296 pp.

by Kenneth W. Krause.

Kenneth W. Krause is a contributing editor and “Science Watch” columnist for the Skeptical Inquirer.  Formerly a contributing editor and books columnist for the Humanist, Kenneth contributes regularly to Skeptic as well.  He may be contacted at

Every termite’s hindgut is home to between 100 and 250 distinct microbial species.  Cooperative communities of anaerobic archaea and anaerobic and aerobic bacteria spawn fierce enzymes, allowing their symbiotic hosts to digest wood into sugar in about twenty-four hours.

Revolting?  Perhaps.  No big deal?  Think again.  First, the sugar can be readily converted into a great volume of ethanol, given that termites inhabit nearly seventy percent of the Earth’s surface.  Second, both methane, which can be used as feedstock for natural gas refineries, and hydrogen, two liters of which the insects can ferment from a single sheet of paper in one day, are generated through microbial metabolism.

In April 2003, long-time science and medical journalist, Tim Friend, received and accepted an invitation from Diversa Corporation—a private bioprospecting firm co-founded, at least on paper, by Craig Venter, the notorious “bad boy” of science who sequenced his own DNA and, more recently, built the first man-made genome—to accompany its scientists on a “bug hunt” through the lush jungles of Costa Rica.  The field team would collect insects, sediments, and water samples from various rainforest ecosystems for shipment back to the lab where microbial DNA would be examined for gene expression and sequencing.  It would then be catalogued and, when appropriate, manipulated through a process involving the “directed evolution” of amino acid sequences into new enzymes—in this case, with a specific pH, elevated temperature resistance, and the ability to bleach wood pulp more proficiently than was ever possible using a variety of industrial chemicals.  Diversa’s ambitions more generally were to mass-produce novel, genetically engineered enzymes for sale to several manufacturers seeking cheaper and more efficient means of production.

A luxurious abundance of raw materials awaits extraordinary companies like Diversa that base their businesses in microbial research.  Although fewer than 6000 species, including 90 archaea, have been identified and fully characterized through culturing so far, scientists estimate the existence of at least a billion Earthly microbial species.  Together they power the cycle of life, maintaining our atmosphere and climate and generating at least half of our breathable oxygen.  Small wonder for Friend, then, that both the Department of Energy and the biotechnology industry believe that “harnessing the genes of archaea and bacteria, especially the stranger ones, will rescue the habitable zone of Earth from the mess humans have made of it in a brief 200 years.”

Curiously, The Third Domain emphasizes bacteria as often as it does archaea, and at times the author remains annoyingly vague as to which domain is being discussed.  Nevertheless, Friend offers an engaging and effective chronicle of molecular biologist Carl Woese’s “discovery” of archaea in 1975, and the revolutionary consequences it had for the study of life’s origins, terrestrial ecology, and the search for creatures beyond our world.  Not surprisingly, the established scientific community received the discovery, along with Woese’s ensuing proposal to classify archaea as a new super-kingdom, with less than open arms.  As Woese himself put it in his 2003 Crafoord Prize acceptance speech, “The Archaea were unexpected to begin with, and having arrived, they were unwelcome.”

During the last three centuries, life forms (and other natural things) have been differentiated consistent with three major paradigms.  Carolus Linneaus’s 1735 Systemae Naturae divided everything into three kingdoms—Animalia, Vegetabilia, and Mineralia—relegating microbes to one of the first two categories depending on their motility or lack thereof.  In 1866, Ernst Haeckel advanced the classification game by grouping microorganisms into their own kingdom, Protista.  By the middle of the twentieth century, however, all forms of life had been branded as either prokaryotes (the cells of which lack a nucleus) or eukaryotes (the cells of which contain a nucleus) and, according to Friend, such remains the dominant scheme among many contemporary biologists, “much to the frustration of Woese and his closest disciple [biologist] Norman Pace.”

Obsessed with the biggest of big pictures—the genesis of all life—Woese passionately explored the minute world of microbes beginning in the 1960s, convinced that bacteria were yet ill-defined and ill-classified.  Bucking the perceived complacency or perhaps even obstinacy of biology’s most monumental figures, James Watson and Francis Crick in particular, Woese argued that, in order to understand the evolution of early life, scientists had to learn more about RNA, which mutates very slowly, ribosomes, which are basic to the genetic coding process for virtually all species, and of course microbes, which in one form or another represent the most ancient form of Earthly life.  He focused on the so-called 16s rRNA gene—known to be highly conserved among all bacteria—and inferred that species with similar sequences were more closely related than species with relatively divergent ones.  A new tree of life sprouted and eventually took shape in Woese’s laboratory.

Salt, sulfur, and heat adoring microorganisms had been familiar to the scientific community for some time.  But most biologists had considered them nothing other than exotic bacteria uniquely adapted to extreme environments.  Preeminent evolutionary biologist, Ernst Mayr, for one, refused to accept an archaean domain until his unfortunate death in 2005.  Over the years, however, Woese discovered significant differences between the two as he meticulously catalogued hundreds of microbial species.  Salt marsh halophiles contained unique ribosomal sequences, and a variety of extreme species possessed unusual lipids with ether as opposed to ester bonds linked into branched rather than straight chains.  In Germany, Otto Kandler independently confirmed that these oddball microbes were using unknown RNA polymerases when transcribing DNA code into messenger RNA.

Woese published his demand for a new classification scheme featuring archaean, bacterial, and eukaryotic super-kindoms in the November 1977 Proceedings of the National Academy of Sciences.  Norman Pace fleshed out the field of microbial ecology, which, in turn, inspired DOE funded projects, including a joint grant to Venter and Woese to sequence a sexy, high-temperature, deep-sea methanogen.  At last, the editors of Science magazine held a press conference in August 1996 to declare the new archaean domain.  “In decoding the genetic structure of archaea,” Venter announced, “we were astounded to find that two-thirds of the genes do not look like anything we’ve ever seen in biology before.”

In 1984, Woese received a “genius” research award from the MacArthur Foundation.  In 1988, he was elected to the exclusive National Academy of Sciences, and four years later he became the twelfth recipient of the Leeuwenhock Medal, microbiology’s highest honor.  Woese now believes that we might never know whether archaea is actually the most ancient form of Earthly life.  Ever the independent thinker, he challenges the doctrine of common descent, postulating communal evolution instead.  In the beginning, he argues, at least three simple, loosely structured cells evolved together as they bathed in a fertile pool of genes, swapping and filching DNA as necessary.  Under Woese’s non-Darwinian theory of “horizontal gene transfer,” writes Friend, primitive life “can seize whatever energy is available under a wide variety of temperatures and chemical conditions.”

Indeed, it is precisely archaea’s and bacteria’s evolved versatility that leads many to reason that, if life exists elsewhere in the universe, it is probably microbial.  Metabolism, after all, does not require heat and, as far as we know, most terrestrial archaea dwell in especially cold environments—including ocean floors, deep caves, and our thin, radioactive upper atmosphere.  Life on Jupiter’s moons, Io and Europa, could very well resemble microorganisms inhabiting the Valley of Geysers or Yellowstone Lake, where Friend assisted with much important field work.  And the frigid methane seeps in the Gulf of Mexico could provide valuable insights into potential life on Mars.  “Every expedition into an extreme environment,” the author believes, “is a surrogate for what might exist beyond Earth.”

There is, however, a dark side to archaea.  Soaring global carbon dioxide and methane levels suggest that humans may have inadvertently established an ill-fated foundation for a second Archaean Empire.  Then again, if we can manage to actually exploit these bizarre creatures to our collective advantage, we might reverse a few threatening trends, mend much of the damage we’ve already caused, and save billions of dollars each year in the process.  The most crucial fact is that only microbial life can extract nutrients and energy directly from insanely hazardous inorganic matter.  In other words, with the help of sufficiently motivated companies like Diversa and talented, freethinking scientists like Carl Woese, microscopic extremophiles might someday save the world, and us along with it.


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