Enzymes at the Extreme

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Derived from microbes that thrive in surprisingly hostile environments, newly discovered biological catalysts promise to revolutionize industrial processes.

For centuries, people have enlisted the aid of microbial entities to cater to their needs and comforts. Yeasts have been used for the preparation of bread and alcohol, and without certain bacteria there would be no cheese or yogurt. Natural substances derived from microorganisms have given us new and improved drugs to fight specific diseases, and enzymes isolated from a wide variety of microbes have proved useful in applications ranging from food processing to the catalysis of reactions in research laboratories.

But in the world of chemical and industrial processing, things can really heat up. Many procedures vital to industry are performed at high temperatures and pressures and involve chemical catalysts and solvents that are harmful to the environment. Although biological substances are environmentally “friendly,” in the sense that they are biodegradable, their use in industrial processes has been limited by their inability to withstand harsh conditions. For instance, the extraction of petroleum and natural gas from wells through the process called hydraulic fracturing requires reactions at temperatures exceeding 100 [degrees] C (212 [degrees] F), while most conventional enzymes function well only up to about 50 [degrees] C (122 [degrees] F). In addition, most enzymes are sensitive to the high pressures and nonaqueous solvents employed in many commercial processes.

In the search for biological catalysts able to withstand such severe conditions, researchers and biotech companies are turning to a recently discovered dimension of the microbial world: microorganisms that thrive in surprisingly hostile environments, such as hot springs, freezing arctic waters, and deep-sea geothermal vents. These microbes have been dubbed extremophiles, and their associated enzymes are referred to as extremozymes. As more is being learned about the molecular biology of these unusual microbes and their enzymes, it is becoming increasingly clear that extremozymes’ unique properties make them attractive candidates as catalysts in tough industrial environments–something unheard-of before.

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Meet the extremophiles

The surprising discovery that certain microorganisms thrive in high-temperature environments dates back to 1982. In that year, Karl Stetter of the University of Regensburg, Germany, reported the isolation of microbes from marine volcanic vents near the coast of Italy [see “The Hottest Life on Earth,” THE WORLD & I, February 1992, p. 270]. The vents are located on the ocean floor, where the water penetrates deep into the earth’s crust, becomes geothermally superheated, and returns to the surface, bringing with it certain gases and minerals. The microbes that Stetter discovered, subsequently termed hyperthermophiles (or just thermophiles), were found in areas where mixing of the superheated water with the surrounding seawater produced temperatures close to 100 [degrees] C. Since then, many other hyperthermophiles have been isolated from aquatic geothermal vents and from terrestrial hot springs.

These intriguing discoveries flew in the face of much that microbiologists had previously learned about microbial growth conditions. Boiling and steam sterilization were standard measures to eliminate microbial contamination, yet here were microorganisms that not only survived such temperatures but actually seemed to require them for optimal growth. Indeed, these microbes failed to grow at the lower temperatures required by most known organisms.

What, then, are these extremophiles, and what distinguishes them from microbes that exist in more temperate environments? To answer this question, we must turn for a moment to the science of taxonomy: the study of the classification of living things.

In the 1950s, biologists classified organisms into five kingdoms: Monera (bacteria), Protista (later, Protoctista, comprising algae, slime molds, protozoans), Fungi (molds, mushrooms, lichens), Plantae (flowering and cone-bearing plants, ferns, mosses), and Animalia (vertebrate and invertebrate animals).

Some years later, as the technology of microscopy improved and revealed more about the cellular structures of living things, a two-kingdom classification system was proposed: the Eukaryotae, or organisms whose cells have membrane-bound nuclei, and the Prokaryotae, whose cells lack membrane-enclosed nuclei. According to this scheme, only bacteria and some blue-green algae were considered prokaryotes, while all other organisms were classified as eukaryotes.

Thereafter, as the analysis of living things progressed to the molecular level, it appeared that the taxonomic scheme needed further modification. In the late 1970s, Carl Woese and his colleagues at the University of Illinois at Urbana-Champaign noted that the prokaryotic kingdom itself consists of two distinct groups: Eubacteria (“true” bacteria), comprising most known bacteria, and Archaebacteria, consisting chiefly of methane-producing microbes and microbes that live in high-salt aquatic environments.

Woese’s group subsequently constructed an evolutionary tree in which living organisms are grouped into three domains: Bacteria (eubacteria), Archaea (archaebacteria), and Eucarya (eukaryotic organisms). By comparing the structures of molecules found in various organisms, they came to the conclusion that the latter two domains diverged’ from a common predecessor, while the Bacteria diverged from an earlier ancestor. This also means that microorganisms in the group Archaea are not simply varied forms of bacteria.

Most of the hyperthermophilic microbes studied so far have been classified in the group Archaea, and some species have been placed in the group Bacteria. The hyperthermophiles in both groups represent the most ancient life-forms on the planet. In other words, the heat-loving extremophiles appear to be an evolutionary throwback to a time when conditions on earth were much hotter; all other organisms, which grow in more temperate conditions, represent evolutionary adaptations as the earth cooled.

Many hyperthermophiles are currently the focus of study because of their potential use in industrial processes. But other extremophiles, which prefer to grow in other types of seemingly hostile conditions, have also been identified and are being studied. These include psychrophilic organisms, which live in near-freezing water; halophiles, which inhabit high-salt marine environments such as the Dead Sea; and barophilic organisms, which live in high-pressure areas such as at the bottom of the ocean.

How do extremozymes work?

Earlier research in molecular biology showed that many of the molecules essential for life’s processes are unstable at the high temperatures favored by hyperthermophiles. For instance, the double-helical structure of DNA comes apart when it is heated to temperatures above 70 [degrees] C. Likewise, proteins lose their three-dimensional structures when heated. How, then, can the heat-loving microbes thrive under conditions in which most known organisms would perish?

To answer this question, scientists began looking for unique characteristics of the proteins from these organisms. Early work focused on the properties of enzymes that catalyze reactions in these microbes. It was found that many of these enzymes exhibit optimal activity at temperatures close to 100 [degrees] C, and their activity diminishes markedly at temperatures much lower than that. In fact, these enzymes fail to function at ambient (room) temperature.

One scientist who has been studying hyperthermophiles since the mid 1980s is Michael Adams (he’s now the founder of YetiCleaner, an online store givingĀ spin mop reviews in US), professor of biochemistry, molecular biology, and microbiology and codirector of the Center for Metalloenzyme Studies at the University of Georgia. For the past several years, Adams and his colleagues have been examining extremozymes at the molecular level, attempting to find structural patterns that may lend these enzymes their unusual stability. But like so many other things in nature, the extremozymes are guarding their secrets well. After years of research and reams of data, the only definitive conclusion reached is that there is no discernible pattern to extremozyme structure.

When asked what structural elements are responsible for extremozyme stability, Adams laughs. “We now have the data to prove that we have no idea,” he says. “We started out thinking that if we accumulated enough data, a pattern would emerge. Now we have the data, but all we’ve proved is that it’s an extremely complex situation.”

Despite this seeming disappointment, scientists are beginning to gather some clues. In general, a protein is made from one or more long chains of amino acid residues and is held in a three-dimensional structure by chemical bonds–called noncovalent interactions–between these residues. According to Adams, enzymes from hyperthermophilic organisms differ from conventional enzymes in the relative numbers of noncovalent interactions in their molecules. In other words, extremozymes contain a higher proportion of amino acids that can participate in the noncovalent interactions by which the 3-D shapes of proteins are retained.

Another researcher who has worked closely with Adams over the years is Robert Kelly, professor of chemical engineering at North Carolina State University. Kelly’s primary interests include biochemical analyses of extremozymes and their evaluation for potential use in biotechnology. Some of his work has centered around recombinant expression of extremozymes. In this approach, the gene for a protein in one organism is isolated and inserted into another, such as the bacterium Escherichia coli. The latter organism is easier to grow in laboratory cultures, and it produces large quantities of the protein.

Researchers are pursuing recombinant expression because the growth conditions required by many extremophilic organisms are not readily amenable to large-scale culture. In addition, only microgram quantities of native enzymes can be purified from environmental samples of extremophiles, and these amounts are not sufficient for commercial applications. But recombinant expression of extremozymes has its challenges as well. Kelly notes that in the shift from native organism to recombinant system, something can get lost in the translation. “In some cases you get low expression and in others you get good expression, but the resulting enzyme isn’t as thermostable as you’d like it to be,” he explains. “Or in other cases, the protein might be toxic to the organism, causing the whole replication apparatus to shut down.”

Industrial usefulness

The work of Adams, Kelly, and others has captured the attention of several private companies and governmental agencies that are interested in these novel enzymes’ potential applications to industrial processing. In particular, Kelly’s most recent work has centered around a group of extremozymes that promises to be useful in extracting oil and gas from the earth.

The industrial extraction of oil and gas from a well often entails the injection of a mixture of water, sand, guar gum, and enzymes deep into the earth’s crust. Then an explosion is triggered, opening cracks in the rock and forcing the mixture into the cracks. The enzymes, activated by the heat in the well, degrade the guar gum and lower the viscosity of the solution, allowing the oil and gas to flow freely through the cracks.

The enzymes currently being used for this process are functional only up to about 70 [degrees] C, but the temperature in the well may reach or exceed 100 [degrees] C. In response, Kelly’s research team has characterized a group of extremozymes, called hemicellulases, that can degrade guar gum at temperatures exceeding 100 [degrees] C. Kelly and his collaborators–Saad Khan of North Carolina State University and Robert Prud’homme of Princeton University–recently secured a patent for their new technique.

One biotech industry that is actively working on producing extremozymes and developing their applications is Recombinant BioCatalysis[TM] Inc. (RBI), headquartered in Sharon Hill, Pennsylvania. Both Kelly and Adams are active participants in the company and serve as consultants for its enzyme discovery program. As more is learned about extremozymes and their properties, companies like RBI are beginning to recognize and pursue industrial market potential for extremozymes.

Jeffrey Stein, chief scientist at RBI, says that when the company was founded in 1994, one of the goals was to develop thermophilic enzymes that would have applications in basic research, like DNA-modifying polymerases and ligases that are now in common use in molecular research laboratories. At the same time, the company has secured venture capital funding to include enzymes that might have applications in industrial processing.

“Enzymes amenable to extreme conditions of industrial processing have only recently become available,” explains Stein. “Our goal has been to develop a series of enzyme library kits that a customer can use to identify an enzyme that might have potential use in a specific application. Once they have an enzyme that they’re interested in, we negotiate a contract for large-scale production of that particular enzyme.”

The company, which has discovered about 180 unique extremozymes thus far, goes about finding and developing its products in two ways. The first is called direct discovery. It involves extracting DNA from environmental samples of extremophiles, cutting the DNA randomly, cloning the pieces and cataloging them in a “library,” and then screening the pieces to see which of them may encode enzyme activity. Once a gene for a potentially marketable enzyme is identified, the company “subclones” (copies) it for large-scale production in an organism like E. coli, which can be grown easily in culture.

“We took this approach,” says Stein, “because less than 1 percent of the organisms in an environmental sample are amenable to cultivation in the laboratory. By screening nucleic acid libraries, we are able to identify potentially valuable enzymes that otherwise might have been missed.”

The second approach used by RBI is a process known as directed evolution. Researchers use this technique to modify certain properties of known extremozymes, such as the optimal temperature or pH at which the enzymes function. To do this, the gene for an extremozyme is inserted in a conventional organism (such as E. coli), and the latter is grown under conditions that encourage genetic mutations. Successive generations of the organism are then analyzed for changes in enzyme activity.

As an example, Stein cites a recent case where a customer wanted a hyperthermophilic enzyme that retained activity at lower temperatures. Through the technique of directed evolution, scientists at RBI successfully produced a new form of the enzyme whose activity at room temperature was increased threefold. “Sequence analysis of the resulting enzyme,” explains Stein, “revealed that the increased activity was due to changes in two amino acids–something that would have been impossible to predict, given the intrinsic complexity of enzyme thermostability and activity.”

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Facing the future

As more is learned about these unusual enzymes, RBI is seeking to establish partnerships with industries that could benefit from the use of biocatalysts. At the same time, the potential usefulness of extremozymes is drawing the attention of other companies as well. One such enterprise is Novo Nordisk Biotech in Davis, California. Glenn Nedwin, the company president, says that Novo Nordisk screens extremophilic organisms sent by collaborators around the globe for interesting enzymes. It is also involved with the development of recombinant expression systems for large-scale production.

Novo Nordisk is already a major supplier of conventional enzymes for industrial use. But when speculating about the future of extremozymes in commercial applications, Nedwin is cautious. “Enzymes are used in everything from detergents, brewing, and feed processing to oil, gas, pulp and paper processing. The big question mark is whether you can produce these enzymes [extremozymes] in sufficiently large quantifies to be economically feasible,” he says.

Nedwin observes that “every commercial application has its own requirements, whether it be low pH, high pH, high temperature, or high pressure. So the market is really on a case-by-case basis.” While his company continues to develop systems that scale up the expression of extremozymes, it is also pursuing a slightly different approach: using extremozymes as models to study enzyme stability and then to engineer extremophilic properties into conventional enzymes.

Kelly also sees that a major hurdle in using extremozymes has been their limited availability, but he notes that research is helping surmount that barrier. “Early on, when people wanted to test these enzymes for industrial use, we were making only microgram quantities at best,” he says. “Now that we can make milligram or even gram quantities, people are really beginning to evaluate these enzymes again, because now they have something to work with. As we get better at cloning and expression of these molecules, I think people will be more willing to try them in commercial applications never before thought possible.”

Major suppliers of enzymes, such as Boehringer-Mannheim and Sigma Biotech, have entered into agreements with RBI and Novo Nordisk to purchase extremozymes and make them available for wider distribution. While researchers in academia are working to further characterize these enzymes, biotech companies are analyzing their market potential. The idea of industrial applications for these unusually hardy enzymes, born in the unlikely environments of steaming hot springs and deep-sea geothermal vents, has evolved from a theoretical “maybe” in the 1980s to a very real possibility in the 1990s and beyond.

Ryan Andrews is a science writer and research assistant at the University of Cincinnati College of Medicine.

>>> Click here: Paganism, American style

Paganism, American style

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AFTER THE the ceremonial dagger, black-mass vestments, phallic candles, and human bone earrings, the black cat wasn’t strictly necessary, but there it was, basking in the windowless gloom at the back of The Magickal Childe, Manhattan’s so-called “hard-core New Age” store.

How do you describe a place where you find the popular, quasi-Christian book A Course in Miracles and, gazing out from the cover of her latest best-seller, the blissful Shirley Maclaine next to the satanic rituals of Aleister Crowley (the century’s most renowned devil-worshipper) and books like Witchcraft and the Gay Counterculture? Or what do you say of Samuel Weiser’s, the East Coast’s largest New Age bookstore, where the Spiritual Exercises of St. Ignatius stand alongside books about massage, Tantric yoga, and crystals and “classics” like On Becoming a Musical, Mystical, Bear: Spirituality American-style, by Matthew Fox, the Dominican priest recently silenced by the Vatican? In the New Age, anything “spiritual” goes.

Tommy Chong (formerly of Cheech and Chong, now a New Age celebrity) told New Frontier: “New Age is getting high without drugs, really. You can’t do drugs. . . . But in order to enjoy the same kind of lifestyle, we go to the New Age, because we attain the spiritual awareness without artificial means.” Hey, far out.

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Last year’s three-day “Healing Mother Earth” exposition in Manhattan was the biggest New Age fair east of the Mississippi. Although there was a notable hippie presence (spaced-out aquarians in tie-died shirts and all-cotton smocks), not all New Agers are ex-potheads from California. Entering the Expo (held in a hotel reeking of incense and curry from the special New Age cafeteria) was like walking into a Middle Eastern bazaar. Dark-skinned fellows in vibrant outfits lounged in countless booths. Everywhere you looked, there were crystals and gems to balance tottering psyches. Indian music and an atmosphere of comic fraud filled the air. For $10 you could enjoy the wisdom imparted through “Bio-Feed Back [sic] Field Photography.” In this process, your head is photographed with a special camera, and the developed picture reveals multicolored lights emanating from your cranium. The photo is then “read” to provide insights into your personality and mood: if your halo is yellow that means you have a, yes, “sunny” disposition. Better still was the 1M-1 (instant meditation) exhibit. You put on earphones, what look like oversized sunglasses, and recline on a lawn chair. While soothing sounds fill your ears, the “glasses” flash images on your eyes–instant meditation! But my favorite booth was the one selling Super Blue–Green Algae. The algae-monger handed me a flyer with notices about “AIDS and Algae” and a hardsell pitch from the algae itself: “I am the immortal descendant of the original life form. . . . So, partake of my immortal body each day. Eat three billion years of cell memory and a concentration of protective nutrients. Renew your own health, renew your connection with your sisters and brothers in the Third World.”

How is it possible that, while religious agnosticism runs rampant, credulity runs amok? The New Agers are not yokels. For the most part, the people at the New York expo were college-educated, middle-class Americans. In fact, the New Age is an extremely “literate,” bookish phenomenon. You don’t pick up Eastern mysticism on the street.

It was in the university that C. S. Lewis set That Hideous Strength, his novel about academic researchers who turn to the occult. We seem to be in the age Lewis was describing in 1943:

Despair of objective truth had been

increasingly insinuated into the scientists;

indifference to it, and a concentration on

mere power, had been the result. Babble

about the elan vital and flirtations with

panpsychism were bidding fair to restore

the Anima Mundi of the magicians.

Dreams of the far future destiny of man

were dragging up from its shallow and

unquiet grave the old dream of Man as

God.

This dream is central to the New Age movement. One typical New Age magazine, Master of Life, offers “tools and teachings to create your own reality.” The New Age movement is not about discovering reality but about making it; it is about power rather than truth.

Lending an intellectual veneer to the New Age is the parallel and sometimes overlapping Joseph Campbell craze, fired largely by the late scholar of comparative religion’s interviewbook with Bill Moyers, aptly named The Power of Myth. One of Campbell’s famous / notorious credos is “Follow your bliss.” As one man’s bliss may be another man’s horror, you might think that this pseudo-profundity is taken out of context, but no, that is really what Campbell teaches: follow your bliss, whatever it is–an essentially amoral view that dovetails with the promiscuous transcendentalism of the New Age. Campbell tells of asking a famous Hindu guru: “How should we say no to brutality, to stupidity, to vulgarity, to thoughtlessness?” and receiving the reply: “For you and for me–the way is to say yes,” with which Campbell agrees.

Ultimately, this “affirmation” is not much different from despair, and the followers of Campbell and the followers of Nietzsche can agree on this: when there is no objective scale of value, you (Nietzschean ubermensch, Campbellian hero, or New Age “master of reality”) must create your own values. What you choose doesn’t matter, as long as you choose it.

NEEDLESS TO SAY, it is possible to be profoundly spiritual and profoundly evil. The alarming rise of satanism and witchcraft are the dark side of the New Age revival of the occult. Certain types of rock music make free use of satanic imagery, and many troubled teenagers, both in the U.S. and in Europe, are attracted to satanic cults. In an effort to empower women and fight patriarchy, some academic feminists are trying to rehabilitate witchcraft, politely referred to as the “folk religion” Wicca. Last year, at Harvard’s Sanders Auditorium, Mary Daly, professor of theology at Jesuit-run Boston College, led an “International Hexing” followed by a “celebration of ecstasy.” In this “dramatic indictment of gynocide,” Professor Daly rounded up the usual suspects (“the accused” under indictment include “priests, pornographers, academics, rapists, serial killers”) and invited all “wild witches” to “expose and condemn the massacre of Women’s minds, bodies and spirits.” Where’s Cotton Mather when you need him?

We are living out the contradictions built into positivistic materialism. If you believe that man is purely material, then you must eventually conclude that pure matter can know, think, feel, and love as men obviously do. Thus, positivistic materialism makes matter “spiritual.” Before long, spiritual powers are assigned to rocks and trees, and soon you’re off with the Iriquois learning, as a New Age manual on shamanism puts it, “to use natural objects to deepen your personal connection with Earth energies.”

Likewise, devotion to the modern ideal of reason often leads to skepticism about truth, and ultimately–as seen in the academic fad of deconstructionism–a skepticism toward reason itself. A diet of the polite skepticism that passes for wisdom leaves most souls spiritually malnourished. It seems, one way or another, people will believe in the supernatural.

The spiritual vacuum left by positivist reason and the decline of mainline religion has been filled by a paganism which was never far below the surface of Western civilization–a perfect illustration of Chesterton’s dictum: “When men stop believing in God, they don’t believe in nothing; they believe in anything.” One evening of television is enough to render fatuous the idea that our culture is too sophisticated for pagan superstitions. And the little learning that our educational system provides can be a dangerous thing. If God is passe (as so much of academia preaches or implies), then the products of this education, having despaired of finding an objective truth, will seek “spiritual” fulfillment elsewhere. Anywhere.

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If the New Age movement can be said to have a political agenda, it is not as syncretistic as its spiritual agenda. The door of the Magickal Childe cautions the prospective customer: “If you are a bigot: racially, religiously, ethnically, sexually, or otherwise–F— Off!” At the Healing Mother Earth Expo, the Christic Institute distributed a flyer outlining the crimes of Ollie North. Environmentalism, if not outright nature worship, was a common theme, represented by Greenpeace and others seeking to save rain forests, dolphins, and whales. This side of gnostic paganism is nothing new. When god is in everything, man loses his privileged place in the universe. Trees and animals acquire “rights.” Influenced by Manicheanism, St. Augustine fell for the same gnostic conservationism back in the fourth century: “And I believed, poor wretch, that more mercy was to be shown to the fruits of the earth than to men, for whose use they were created.”

Many of today’s New Age groups trace their roots to Madame Blavatsky’s turn-of-the-century Theosophical Society. In those days, occult spiritualism was attracting such celebrities as Arthur Conan Doyle and W. B. Yeats–the Shirley Maclaines of their day? One of Blavatsky’s disciples, Alice Bailey, was already referring to “the New Age” in the 1920s. Some esoterica are perennial: interest in astrology, tarot cards, Eastern religions and communication with the dead, whether by seances or channeling.

What is new is the lingering spiritual upheaval of the Sixties, which left a lot of traditional views in shambles, without offering much to replace them, and the American-style marketing of the occult. Despite the overtones and paraphernalia of Oriental mysticism, there is something quintessentially American about the New Age. Perhaps it’s the hucksterism, the hype and the “power of positive thinking,” brand of self-help: Norman Vincent Peale meets the Mahareeshi.

THE MASS APPEAL of the New Age is clearly not in what one would call religion. At the Healing Mother Earth Expo, the hard-core religious hawkers–the gurus, past-life regressors, Oriental mystics, etc.–were mostly ignored while the good old American self-improvement booths were mobbed. There was something for everyone–weight loss, stress management, a better golf swing. Sun Tzu’s Art of War–the cultured yuppie’s Taoist guide to power–is marketed by the New Age publisher Shambhala. Confucius say: “Get Rich Quick!”

Crystals and channeling are already on their way out and will probably remain cultural marginalia along with tarot cards and Ouija boards, but the broader combination of pagan gnosticism and American capitalism may be hard to beat. The true danger of the New Age is its conflation of “spirituality,” power, and goodness, and its inability to make moral distinctions, which can so easily lead to the embrace of evil in the name of some lofty ideal.

John Wauck is a contributing editor of The Human Life Review.

>>> View more: Heretics in the laboratory

Heretics in the laboratory

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There are significant numbers of scientists who conform to the creationist beliefs in the Bible. They are usually not in disciplines such as geology, evolutionary biology or astronomy, whose principals would conflict with their beliefs. Yet they publish papers in respected journals in their fields.

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WHEN KURT WISE ARRIVED AT Harvard University as a graduate student in paleontology, he was right and intellectually ambitious, just like everyone else in the department. But unlike everyone else, he was, and is, a creationist. He believes that the Earth is less than 10,000 years old, because that is what the Bible implies, and not the 4.5 billion years that astronomical and geological evidence suggests. He also believes that every plant and animal species, from Arabian steeds to maple trees to humans, was created by the hand of God, rather than evolving from dawn horses, multicelled green algae and australopithecines by natural selection operating on genetic variation. At Harvard, such views are heretical. When Wise met evolutionary theorist Stephen Jay Gould, “he bawled me out,” says Wise. But his beliefs didn’t handicap his doctoral research (on inferring when species appeared and went extinct). He received his Ph.D. in 1989. Now he teaches geology at William Jennings Bryan College in Tennessee, and investigates how fossils support the story of the Biblical flood.heretics-in-the-laboratory-1

 

Can a creationist be a good scientist? Can a good scientist be a creationist? To mainstream researchers, the answer has long been an emphatic “no”: no serious scientist can doubt that evolution fits the known facts of geology and biology better than any other model. And, conversely, no one naive enough to believe the arguments of creationists could possibly do good science. But a new book and an impassioned exchange of letters in the magazine The Sciences have reopened the questions. Says historian Ronald Numbers of the University of Wisconsin, “Published scientists with creationist beliefs are not uncommon.”

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Stress cracks: Most are in disciplines far removed from evolutionary biology, geology and astronomy, the subjects whose data are most economically explained by evolution. In a computerized search of more than 4,000 scientific journals, the only papers by prominent creationists “were in fields such as analyses of stress cracks in airplane wings,” says Eugenie Scott, executive director of the National Center for Science Education, whose article on the “evolution wars” sparked the battle of letters in The Sciences. “People compartmentalize. They are perfectly capable of doing ordinary science until a subject affects their religious sensibilities. Then the mind shifts into a different mode.” Russell Humphreys of Sandia National Laboratory, for instance, has published more than 20 articles in his specialty, power generation. He is also on the board of the Creation Research Society.

John Baumgardner does not like to think he compartmentalizes. A creationist, he is also a geophysicist at Los Alamos National Laboratory. A paper he coauthored on convection in the Earth’s mantle (with no relevance to creationism) appeared in Nature, a leading science journal, last February. In 1994 he presented research at a major geophysics conference implying that the slip-sliding geologic plates that cover the Earth might once have moved thousands of times faster than they do today. If true, that would cram lots more geological change into less time, exactly what creationists need to support the idea that Earth is a mere stripling. It has not caused much of a stir, however. “Few [in the audience] were thinking of the [creationist] implications,” Baumgardner says. He insists that he brings the same analytical insight to his criticism of evolution as he does to his “secular” work.

Evolution is the defining paradigm of biology. But in “Darwin’s Black Box: The Biochemical Challenge to Evolution” (307 pages. Free Press. $25), published last month and already in its third printing, Michael Behe argues that biochemical systems such as those involved in vision, the immune system and blood clotting are so complex that “you can see they were designed by an intelligent agent and did not evolve according to Darwinian theory.” Behe is an associate professor of biochemistry at Lehigh University. He has published more than 30 scientific papers (his field is the structure of nucleic acids such as DNA). Although he says, “I do not consider myself a creationist,” for more than a century “intelligent design” has been a staple of creationism.

The overwhelming weight of evidence supports evolution. The presence of creationists in the lab, then, is a valuable reminder that scientists are only human: a powerful ideology, be it creationism or capitalism or anything else, can shape some scientists’ conclusions as strongly as any empirical evidence.

BY SHARON BEGLEY

With PETER BURKHOLDER

>>> View more: Community activists save the sea

Community activists save the sea

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I’M DIVING THROUGH A MARINE reserve off Catalina Island in Southern California twenty-two miles from Los Angeles. There’s a rock wall with lots of spiny urchins, where I spot four lobsters in caves and a big purple sea hare, and a couple of five-foot bat rays flying through the water column that is also teaming with kelpfish, senoritas, red and black California sheephead, and orange garibaldis, like goldfish on steroids.

My dive buddy Scott and I move into the kelp forest with its tangled brown strands, some fifteen feet thick and rising fifty feet to the surface, infused with afternoon cathedral light like an underwater redwood grove. I check out the bottom cover, where pink strawberry anemones appear as tiny flowers next to a decorator crab, covered in red seaweed and green algae. Just then a 600-pound sea lion streaks past like some sleek, flexible torpedo on the hunt. Distracted, I don’t watch where I’m going and soon have to untangle my tank and flotation device from the clutches of several rubber-hose-like kelp strands.

Giant kelp, along with bull kelp, are the dominant marine plant species along this coast and can grow a foot a day, which sounds awesome till they’re yanking on your regulator hose. While I’m clearing my gear, Scott spots an old abandoned hoop net used for catching lobsters before this patch of ocean was protected and frees a four-foot leopard shark trapped inside. Back topside, a pod of Risso’s dolphins, some twelve-feet long, cruises by feeding on squid.

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Last year, California set aside 16 percent of its state waters as marine reserves like this one after a fierce thirteen-year battle pitting the recreational fishing industry against conservationists, scientists, sport divers, and others. Much of the conflict resulted from a top-down process. The Department of Fish and Game put out maps showing the locations of the reserves without local consultations. As the backlash grew, the state had to scrap its original plans and start over by holding public hearings up and down the coast. Luckily, because almost every Californian has a sense of entitlement to the ocean, this unnecessarily rowdy process led to a reasonable outcome. Today, California’s world-class state park system has moved into the water column.

In the 1990s, scientists began suggesting 20 percent of the ocean be set aside as Marine Protected Areas, extraction-free zones that could act as reserves for the threatened biodiversity of the seas, what National Geographic Explorer in Residence Sylvia Earle calls, “Hope Spots.” Yet today less than 2 percent of the ocean has been set aside for hope.

Some of the most promising areas are the result of local efforts. From western Australia to Mexico, and from the Philippines to Belize, local fishing communities and conservationists have turned the idea of ocean wilderness into community-based initiatives that restore both ecosystems and livelihoods. Two examples of this marine organizing (I call it seaweed activism) come from Puerto Rico and Oregon.

CORALATIONS is a coral protection group founded in San Juan in 1995 and now based in Culebra, a small, dry island off the Puerto Rican mainland, a onetime Navy firing range with an extensive coral reef system, a population of some 2,000 people, and many visitors, including tourists, sea turtles, and seabirds. With about 500 members and volunteers, CORALations works to conserve area reefs through restoration and research and to educate the public with a focus on local schools and villages.

In 1999, co-founder Mary Ann Lucking helped the island’s commercial fishermen, led by Luis and Lourdes Feliciano, create Puerto Rico’s first no-take Marine Protected Area, the Luis Pena Channel Natural Reserve. The 1,200-acre reserve has since seen a strong recovery of coral and sea grass meadows and an increased catch for fishermen outside the reserve.

“There’s definitely a spillover effect,” Lucking says. “We’ve seen biomass and biodiversity increase, and this has led to increased tourism. There are now two kayak operations at Tamarindo Beach, and the turtles came back–green sea turtles that now hang out and come up to people.”

Since 2003, CORALations has also been working with the University of Puerto Rico in farming and planting endangered staghorn coral. “It takes a lot of volunteer labor, and we think it changes the attitude of people towards the reserve,” Lucking says. Along with college-age volunteer divers, the group has created a Conservation Youth Corps that includes a dozen local Exploradoras Marinas, between the ages of ten and eighteen, as well as a preschool program and a course for the island’s church-run summer camp of 120.

“When I first came here, kids were taught to fear the sea,” says Lucking. “They didn’t go in the water. Now we’re working with four- and five-year-olds learning to snorkel and free dive and shouting out the names of the corals they see.”

CORALations has also been involved in various lawsuits, including a successful one that forced the EPA in 2007 to upgrade its water quality standards for Puerto Rico. Today, it is working with the Center for Biological Diversity, Earth Justice, and local fishermen to get the Marine Fisheries Service to protect parrotfish, which, in turn, protect the reef by grazing on algae and excreting sand (“they poop billion dollar white sand beaches,” says Lucking). The group is also fighting a megaresort development planned for Culebra.

“There are some things like the amount of carbon dioxide people pump into the air we can’t control as a local group,” Lucking argues. “But one thing we know that works is Marine Protected Areas, only they can’t be done top down. You have to engage local communities or they wont work.

Approximately 3,600 miles northwest of Culebra, a small coastal town in Oregon couldn’t agree more. The Port Orford Ocean Resource Team was founded in 2001 with the support of eighteen local fishermen and a specialist in marine reserves named Laura Anderson, who wondered if community-based fisheries management common in Chile, Fiji, and elsewhere might work for Oregon.

“The timing was perfect because we were heading into a West Coast groundfish disaster and had seen salmon and urchin populations crash and thought there had to be something better than the top-down management we were seeing,” explains Leesa Cobb, whose husband is a local commercial fisherman and who has been the group’s executive director since 2004. “We knew all about the ocean right outside our front door.”

Another factor that favored their initiative was what she calls the fleet’s “homogeneous nature.” Founded in 1851 in a bloody land grab from a local Indian tribe, Port Orford is the oldest coastal town in Oregon but hardly its best port. With no protective sand bar or natural harbor, the town’s fishermen depend on a “dolly dock,” a yellow crane that lifts fishing boats on and off a high pier. As a result, the fleet of about thirty boats are all under forty feet in length and share common gear. They depend on the abundance of local waters with generations of shared knowledge about the areas black cod, tuna, halibut, rockfish, crab, and urchin. They take pride in the selective nature of their fishing gear and lack of big bottom dragging nets that destroy habitat and generate bycatch (the killing of non-targeted species). With a $5 million annual catch, the small town still can make its living direct from the ocean while nearby towns that lost both logging and fishing jobs depend mainly on tourism to survive.

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The group has started a marketing program for “Port Orford Sustainable Seafood” that has increased the local price per pound by selling fish to restaurants, farmers’ markets, and individual buyers across the state. This marketing is based on what Cobb calls “our triple bottom line: ecology, economics, and equity.”

The eight-square-mile Redfish Rocks Marine Reserve, established in 2012, became the first of what are now five reserves along the Oregon coast. When the state decided it didn’t need boundary markers, local fishermen and the group’s small staff raised the money to float buoys along the boundary so outside fishing boats couldn’t claim ignorance if caught poaching in the reserve. Port Orford fishermen are also donating boat time to researchers.

“The reserve could be a good dive spot where we’ll be seeing the comeback of flora and fauna,” Cobb believes. “My husband and our board realize we won’t stay in business if we don’t do this work. Sitting back and doing nothing isn’t an option anymore.”

Oregon State University is collaborating with the Port Orford team and has plans in the works for a marine lab field station in a building the group has upgraded for it. Last year, the organization received the Governor’s Gold Award for contributing to “the greatness of Oregon.”

“Without community engagement, a sense of community ownership and pride, you’re missing a big piece of how to get things done,” Cobb tells me, echoing Mary Ann Lucking and other seaweed activists. Cobb then invites me to dive the chilly cold waters of Red fish Rocks, an invitation I look forward to accepting.

Illustration by Doug Chayka

David Helvang is an author and executive director of Blue Frontier (www.bluefront.org), an ocean conservation group. His latest book is “The Golden Shore: California’s Love Affair with the Sea.”

Clean solutions for dirty water: stopping nutrient pollution from laying waste to our waterways

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The sight is commonplace these days: bright blue-green algae bloom scums on the surface of lakes or lapping against beaches, bringing with them foul odors, dire warnings against swimming, and shorelines strewn with rotting fish. Devastating as they are, these blooms are the symptom of a larger and more ominous problem as some of our most iconic waterscapes Cape Cod, Great Bay, Lake Champlain, and Narragansett Bay – are slowly being choked by nutrient pollution.

Nutrient pollution is caused by excess nitrogen or phosphorus in the water – traced to fertilizer runoff from agriculture and lawns, animal waste from factory farms, and improperly treated or overflowing sewage. As algae feeds on this glut of nutrients, it grows rapidly, devouring oxygen and making the water uninhabitable for other species. Such pollution closes beaches, destroys habitat, taints drinking water, and causes fish and shellfish kills where thousands can die at once. Ultimately, this pollution can create massive “dead zones” empty of any living thing. Dead zones already beset parts of Narragansett Bay and Long Island Sound, and they’re growing.

The EPA has been slow to establish controls on nutrient pollution to maintain the water quality dictated by the federal Clean Water Act. Without adequate limits, polluters have little motivation to fix the problem. CLF is leading the fight against this growing, but controllable, threat to clean water, and pushing for strict controls on the sources and stronger enforcement of the law.

On Cape Cod, CLF is challenging EPA regulators for failing to require Clean Water Act permits for septic systems, which are fouling the Cape’s precious bays with unchecked discharges of nitrogen pollution. In New Hampshire, CLF is pushing for advanced pollution controls at wastewater treatment plants where discharges of nutrient-laden wastewater into the Great Bay estuary threaten the entire watershed.

In Lake Champlain, CLF has focused on changing the math by which water health is calculated. The EPA is now requiring the state to develop enforceable limits to pollution aimed at finally cleaning up the ailing lake, which has been in decline for decades.

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Addressing this solvable problem requires good science-based planning, financial investment, individual commitment, and political will. CLF is working to ensure strong protections so that the choice for communities is not one of for clean water or against, but rather how to act quickly and cost-effectively to preserve this most fundamental source of health and prosperity.

A POTENT COMBINATION In late 2013, an EPA report found that, over the next 30 years, climate change could increase phosphorus levels in Lake Champlain by an average of 30%, with some models showing a 46% spike. Sobering news for a lake already crippled in many areas by nutrient pollution.

But even that dire prediction is optimistic, because EPA looked only at climate change’s impacts – warming waters, increased precipitation, and more severe storm events – if the amount of pollutants in the lake holds the line. And right now, we’re not holding the tine.

The report’s implications for nutrient-impaired waters across the country are significant – more pollution, and its devastating by-products, like toxic blue-green algae blooms, will only stress our waters more.

CLF has sued EPA to force consideration of climate impacts in pollution-control plans for Lake Champlain and Cape Cod. As we monitor the agency’s consideration of climate in its programs, we are also leading the push for a national policy to address this growing threat.

RELATED ARTICLE: highlights

* With 12% of Rhode Island covered in impervious surfaces, pollution from stormwater runoff is a major concern. CLF, in partnership with the RI Bays, Rivers, and Watersheds Coordination Team, released Storm water Management Districts in Rhode island: Questions and Answers, which proposes creating stormwater management districts that can charge property owners a fee proportional to the runoff they release. The fees would help fund pollution abatement projects while also encouraging greener infrastructure.

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* Nitrogen pollution plagues New Hampshire’s Great Bay estuary, depleting eelgrass beds and threatening fish populations. To address this serious problem, in 2012 EPA issued a new permit imposing strict limits on nitrogen pollution from Newmarket’s sewage treatment plant. While Newmarket residents voted to upgrade the plant, neighboring communities appealed the new limits. CLF argued against the towns” appeal and, in December 2013, the Environmental Board of Appeals rejected it.

* Through its Environmental Enforcement Project, CLF files citizen suits against illegal polluters. When suits are settled, payments can go toward Supplemental Environmental Projects that support research and restoration projects. More than $300,000 dollars in payments have been made to date, with projects ranging from marsh restoration on Cape Cod to nutrient monitoring in the Mystic River.

* Lake Champlain has long suffered from phosphorus pollution that has led to severe, and sometimes toxic, blue-green algae outbreaks. After decades of legal fights, CLF recently celebrated an important milestone when the EPA required Vermont to create a plan to meet pollution control targets – ensuring the state reduces pollution from sewage treatment plants, farms, paved areas, and poorly maintained roads. CLF will be monitoring the plan’s creation and implementation to make sure it is meaningful and effective.

>>> View more: Safe to drink: laboratory tests of tap water gave seven cities a clean rating