Ken Krane, nuclear scientist and emeritus professor of physics, Oregon State University

The term “God particle” tends to rankle physicists. The flippant reference to the recently discovered particle believed to be the Higgs boson was coined by Leon Lederman, the former director of the Department of Energy’s Fermilab and Nobel Prize winning physicist. But, says Ken Krane, nuclear scientist and emeritus professor of physics at Oregon State University, had it not been for the name, the discovery might not have generated such headlines in July. It was good, he adds, to see physics in the news.

It’s no exaggeration to call the discovery momentous. In July, two teams working at the world’s largest atom smasher (the Large Hadron Collider at the European Center for Nuclear Research, known as CERN, near Geneva, Switzerland) announced independently that they had strong experimental evidence for the existence of the Higgs. In an interview shortly after the announcement, Krane explained what scientists found, what it means for their science and why it matters to the rest of us.

Krane chaired the Oregon State Department of Physics from 1984 to 1998 and has written or edited nearly 20 books and monographs, as well as dozens of research articles. The American Association of Physics Teachers recognized his exceptional teaching by awarding him its Millikan Medal in 2004.

Terra: What did the physicists at CERN find?

Krane: Every time we bang particles together like we do at CERN, we create dozens of new particles. These are not particles in the sense that we ordinarily think of them. They live for a definite but very brief time and then decay into a multitude of other particles. We don’t see the original particles that were produced, but what we see is all the decay products that must live long enough to make it into the detector where they generate signals that we can record. If you add up all those signals, you can get to the mass of the particle that was created. So you need to be fairly sure you’ve captured everything. And then you’ve got to be fairly sure of what the background (random fluctuations of energy) is in that region. And that’s what they’ve done.

In this record of a proton collision at CERN, muon tracks are red, and electron tracks and clusters in the LAr calorimeter are green.

The result is a particle with a mass that is nothing special in terms of particles we normally deal with. It has about half the mass of a uranium atom. Not insignificant, but it’s not a huge massive particle in a realm that’s not been explored before.

Scientists talk about “a five-sigma result.” That’s five standard deviations (five times the average distance between all data and the mean), and that’s pretty secure, strong confirmation that this is a real observation, not just some random event. In my experiments in a very different area, if I were to see a peak on a background that is five standard deviations above the background, that’s a peak (evidence of a particle), not a fluctuation of the background. By analogy, in a random distribution of men with an average height of 6 feet with a standard deviation of 2 inches, someone who is 6’10” would certainly stand out.

Terra: What does it mean for physics?

Krane: We know an elephant is more massive than a mouse, and we understand why. The mass of a body is basically the total mass of all the atoms of which the body is composed, and there are more atoms in an elephant’s body than in a mouse’s body. At a more fundamental level, we understand why a single atom of a heavy element such as lead is more massive than a single atom of the lightest element, hydrogen. The mass of an atom is essentially the total mass of all its constituent protons and neutrons, and the lead atom has about 200 protons and neutrons while the hydrogen atom has only one. So a common way of understanding the mass of an object is on the basis of the masses of its constituent parts.

Particles have their particular masses because of how they interact with the Higgs field.
— Ken Krane

Unfortunately this type of logical reasoning breaks down at the most fundamental level. The electrons in an atom are members of a family of three particles that are “elementary” in the sense that they have no internal structure and can’t be taken apart into still smaller entities. The electron is the lightest member of this family. The other two members are 200 and 3500 times as massive as the electron. Why do these three particles have different masses? Why these particular values? And where does their mass come from if it can’t be accounted for in terms of constituents? This is the question that particle physicists have been trying to answer by searching for the Higgs particle.

In 1964, British physicist Peter Higgs proposed that the universe is filled with a force field now known as the Higgs field and that particles get their masses by interacting with this field. Each different particle has a different strength of interaction with this field, which results in the different masses for the particles. According to this explanation, particles would otherwise be massless, but they get their apparent masses by interacting with this gooey field, much as an object that flies effortlessly through air is more sluggish in traveling through water.

In theoretical physics, each type of force (gravity, electromagnetic, nuclear, etc.) can be accounted for through a force carrier, which is a type of particle called a boson. The force carrier for the Higgs field is known as the Higgs boson, and its observation would amount to a verification of Higgs’ hypothesis and the first step for scientists to be able to study the origin of mass. Now instead of throwing up our hands and saying, “Particles have their particular masses just because they do,” we can now say, “Particles have their particular masses because of how they interact with the Higgs field.” The latter explanation gives scientists a basis for a deeper understanding of the way the universe works, and it enables new experiments to study this interaction and achieve a better understanding of how mass originates.

The standard kilogram is housed at the International Bureau of Weights and Standards near Paris. The National Institute for Standards and Technology in the United States maintains an official copy.

From a scientific point of view, the concept of mass is not terribly well understood, nor is the standard of mass well defined in terms of measurable quantities. A century ago, we replaced other unit standards in physics, the standard second and standard meter, with very precise atomic standards. Originally the meter was based on two scratches in a bar kept in a vault in Paris. Everybody else could take their bar and compare it to the standard bar. That’s how standards of weights and measures were done.

Now, we’ve replaced the standard for length with an atomic wavelength and the standard of the second with an atomic frequency, and if you look at the dozens and dozens of basic standards in physics, they’ve almost all been replaced with very precisely determined atomic standards, except for mass. The standard of mass is this kilogram sitting in a glass bell-jar in a vault in Paris. We don’t yet have a way of going from that standard mass to an atomic mass.

Terra: What did it take for physics to arrive at this point?

Krane: The Large Hadron Collider (the “hadron” family includes particles such as protons and neutrons that interact through the so-called “strong” force) is a circular racetrack 17 miles long buried in a tunnel more than 500 feet below the border between France and Switzerland. It was designed to smash together beams of protons traveling in opposite directions around the circle at speeds in excess of 99.999999% of the speed of light. The accelerator, which began operating in 2008, was designed to optimize the search for the Higgs particle. It was built at a cost of approximately $9 billion by an international consortium of nations, because such a large project is beyond the science resources of any one nation. The European Center for Nuclear Research (CERN), which operates the accelerator, includes several thousand scientists and engineers on its staff. Many more thousands of scientific visitors travel to CERN to participate in experiments.

The Large Hadron Collider was constructed by a consortium of nations to explore the fundamental nature of the universe at the subatomic level.

There are two detector systems at the LHC. Each reported results supporting the existence of the Higgs particle. The construction and operation of these detector systems involved in excess of 5,000 scientists from more than 30 countries and 200 universities and scientific institutes.

Terra: Why does it matter for society?

Krane: Science is a human endeavor, first of all. It is an indication of our desire, manifest for three millennia since the ancient Greeks first speculated about the existence of atoms, to achieve an understanding of the fundamental nature of matter. Our instincts as human beings push us toward a deeper understanding of nature. Just like small children, scientists are always asking “why?” and seeking answers.

The discovery of the Higgs field probably offers no cure for any disease. Nor will it solve the energy crisis or contribute to reversing global warming. But it does advance our understanding of the way the universe works at the most fundamental level.

In the 19th century, little was known about atoms or the ways that atoms combined to form chemical compounds. The development of the Periodic Table of the Elements showed that many thousands of chemical compounds could be understood on the basis of fewer than 100 basic building blocks, the chemical elements. And that understanding in turn led to successful theories of atomic structure and to the development of new chemical compounds and electronic devices that are now essential to our lives.

The situation was similar for particle physicists in the 20th century. Out of a complicated array of thousands of “elementary” particles came an underlying order called the Standard Model, which consisted of 6 “light” particles called leptons, 6 “heavy” particles called quarks, 4 field particles called bosons that are the carriers of the different forces by which the particles interact (electromagnetism, strong and weak nuclear forces), and the Higgs boson. All of these components of the Standard Model have been observed in laboratories except the Higgs boson. It is the last remaining “element” of the Standard Model that is needed to complete our understanding of the fundamental nature of matter.

Even though the outcome of the research may have no immediate practical applications, the research leads to technological developments that benefit society. Research in high-energy particle physics has produced advances in the technology of particle accelerators, which are used for medical diagnosis and treatment. The need for better imaging of the results of particle physics experiments led to the development of devices that are now widely used in digital cameras. Complex particle physics experiments require advanced computing hardware and software. Computing techniques developed for these experiments are now being used to map the human genome and to search for new molecular structures that could be used to develop new types of medicines. The need to share large data files among international teams of particle physicists led to the development of the World Wide Web. In support of accelerators such as the European facility where the Higgs was observed, industries that build components, including superconducting magnets, computer systems and particle detectors, develop more efficient manufacturing and testing techniques that result in improved consumer goods.

Completing the Standard Model isn’t the end of particle physics. It’s not like people won’t be interested in it any longer and the graduate students will be going to other projects. There are still lots of interesting things to be found out there.

Physicists have identified 12 building blocks that are the fundamental constituents of matter. Our everyday world is made of just three of these building blocks: the up quark, the down quark and the electron. This set of particles is all that's needed to make protons and neutrons and to form atoms and molecules. (Image courtesy of Fermilab)

There are some other wrinkles that have been thrown into the Standard Model recently. The model was originally based on particles called neutrinos (three of the “light” particles in the Standard Model) having zero mass. That’s not true any longer. In the last 10 or 20 years, we’ve learned that neutrinos have a very, very tiny mass, but definitely not zero. The basics of the Standard Model don’t include neutrinos with mass. So already we have to fix it up because we don’t understand neutrino mass (and it’s not yet clear if the Higgs mechanism could be applied to give mass to the neutrinos).

Another mystery concerns the nature of “dark matter” which comprises about 25% of the universe (in addition to 5% ordinary matter and 70% “dark energy,” which is even less understood). Dark matter has mass and is affected by gravity, but it’s not composed of anything like ordinary matter, so it’s not there in the Standard Model. If you put things together in the Standard Model, you get the protons and neutrons of ordinary matter, and dark matter isn’t composed of protons and neutrons.

Another puzzle is why the Higgs mass has the particular value that it does. The Higgs particle can explain the masses of the other particles, but calculations of the mass of the Higgs particle come up with values many orders of magnitude bigger than the actual value that it seems to have, based on this discovery. So again, the models have to be fixed up to bring the Higgs mass down to this actual value.

Terra: This discovery is one of many that have changed our understanding of the subatomic world in the past several decades. How has your view of physics changed over the course of your career?

Krane: The quark model was introduced in the 1960s when I was a graduate student. Previous to that, there was a list of hundreds and hundreds of particles. There was no way of categorizing them or understanding them. Now we can talk about the substructure and interactions that produce these particles. You can understand the way these particles form groups and families, like the way you can talk in chemistry about compounds of halogens because they have certain characteristics and certain valences, and they form compounds in certain ways.

The other thing that I get excited about in the time since I was a graduate student is the coming together of astrophysics and particle physics, which were very separate realms. Astrophysics has become a precise experimental science in the last couple of decades, where we can now measure things to two or three significant figures. We can pin down the age of the universe within 1 percent and other parameters as well, such as the temperature of the universe, in the same way.

I mentioned that there are three members of the electron family. Each of these is paired with a member of the neutrino family, and there are also three pairs of quarks. Why do they match up and why only three? Should we build a big accelerator to find out if there’s a fourth generation of electron-like particles? The answer to that is “no.” We know that because the evolution of the early universe would have been measurably different if there had been four members of the electron family and four pairs of quarks. The early temperature would have been different. The early composition would have been different.

And the present composition, determined by its early evolution, would be different. Today we can study such characteristics of the universe as the relative amounts of helium and hydrogen or the relative amounts of deuterium (“heavy hydrogen”) and ordinary hydrogen, from which it can be concluded that there almost certainly cannot be another generation of electron-like particles or neutrinos. So there is no point in building an accelerator to search for such particles.

There are now numerous university research programs known as “particle astrophysics.” The two separate fields, one dealing with the very small and the other with the very large, have been joined into a new research specialty. Somehow, the theory of elementary particles is at some point going to have to work in the neutrino masses, which is an astrophysics discovery, and they’re also somehow going to have to include dark matter, which is another.

Someday in some accelerator we’ll be able to smash things together and create dark matter, whatever it is. The particle physicists will have to go to work to do those experiments and interpret those experiments and put the results into the framework of the Standard Model. It’s remarkable to see how these two fields have come together and have common goals in understanding the universe.

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Learn more about Oregon State research in nanoelectronics, photovoltaic and magnetic materials, biophysics, and computational and theoretical physics.

Scientists confirmed and updated their findings in papers published on August 1, 2012.

Read the July 4 announcement from CERN about the particle believed to be the Higgs boson.

Watch a video produced by CERN to explain how physicists came up with the Standard Model.

On a light box, an OSU researcher observes protein gels used in biochemical experiments. (Photo: Jan Sonnenmair)

It’s not a huge stretch to say a story like this is unfolding at Oregon State University. Against legions of bacteria and other microbes that cause TB, cholera, malaria and other infectious diseases, a cadre of OSU scientists has taken up arms. Their light sabers are machines called chromatographs and mass spectrometers. Their droids are “high-throughput” plate readers and underwater robots. Their curative elixirs derive from weird and remote organisms like gelatinous “sea squirts” from Africa’s Cape of Good Hope and giant tubeworms from the Axial Volcano a mile beneath the Pacific Ocean.

The story’s ending has yet to be written. But so far, the odds are with the germs. As Earth’s first inhabitants, bacteria have a 3-billion-year evolutionary jump on Homo sapiens. Superbly adept at adaptation, they’ve found genetic avenues into every ecological and biological niche, from polar icecaps to the human gut. They divide like crazy (some can double their population in nine minutes) and use an astounding array of strategies to make themselves at home. Many bacterial species do good things, like recycle waste. But other species, the ones scientists call pathogens, can invade and quickly overwhelm their host organisms, whether animal or plant. Miracle drugs like penicillin, once seen as impregnable shields against deadly infection, are losing their power as the bacteria regroup and recalibrate.

For all its brainpower and glittering technology, modern science is struggling to stay ahead of these microscopic shape shifters. The microbes have outmaneuvered just about every drug medical science has thrown at them.

This is the story of OSU’s heroic battle to outwit these cunning adversaries. From running high-speed experi- ments in Corvallis, to surveying patients at Portland’s Oregon Health & Science University (OHSU), to combing health-care data- bases for trends, the researchers are attacking infection and prevention from every conceivable angle. They search vast international databases for promising compounds. They decipher mechanisms for disease-promoting phenomena like bacterial sliming and swarming behaviors. They ponder unlikely-seeming disease pathways, such as those between pigs, fish and humans.

The eight professors in the colleges of Pharmacy, Science and Veterinary Medicine you will meet in these pages gather biweekly to trade insights and design collaborative investigations, ranging from microbes’ molecular structures to hospitals’ dosing protocols to urbanites’ risks for drug-resistant infections. Here we look in on their journey, from lab bench to sickbed to public square.

Deep Ocean Dive

Kerry McPhail reaches into a Styrofoam cooler and lifts out a jagged black rock the size of a cantaloupe. “We collected this from an active volcano on the bottom of the Pacific, a mile deep,” she says, her voice accented with the musical tones of southern Africa. Under her office’s fluorescent lights, the rock’s sharp facets shine like obsidian.

In their natural-products lab, Kerry McPhail (left) and Taifo Mahmud examine a flask containing an antibiotic-producing red marine cyanobacterium growing in modified seawater. The cyanobacterium produces different toxins depending on the composition of the seawater. (Photo: Jan Sonnenmair)

Her pride in this solidified chunk of deep-sea lava might suggest that McPhail is an Earth scientist. Why else would she join a 2009 NOAA expedition exploring the Axial Seamount 250 miles beyond Oregon’s shore? So it’s curious to learn that McPhail is neither a geologist nor an oceanographer, but a medicinal chemist in the OSU College of Pharmacy. Curious, too, is the fact that her research endeavors aboard the voyage were funded in part by the National Institutes of Health (NIH), along with Oregon Sea Grant.

What McPhail was seeking in those lightless depths, with the help of a diving robot named Jason II, was new sources of life-saving drugs. The black rock, grabbed by Jason II’s mechanical arm from inside the caldera, was coated with billions of protozoa that thrive on super-heated sulfurous waters at vent sites, where magma bubbles up from the subterranean. As unlikely as it seems, this bluish “microbial mat” may harbor healing chemical compounds never seen before. McPhail and her team have brought home other promising vent-dwelling extremophiles, as well, collected from giant tubeworms, “snow blowers” (white clouds of microorganisms spewing out in 200-degree plumes), orange-colored biofilms (slimy layers of swarming microbes). Some of her specimens were collected during the famous 2008 NOAA expedition when a never-before-witnessed eruption of the underwater volcano was caught on tape by OSU scientists.

“There’s an enormous diversity of microbes down there that people just had no idea about,” she says.

But the cold Pacific isn’t McPhail’s only odd-organism goldmine. Closer to Zimbabwe, where she spent her childhood on an agricultural research station and later in the capital city of Harare, she has been collecting and studying gelatinous creatures called tunicates. Known colloquially as “sea squirts,” these sac-like filter feeders are plentiful in the waters off South Africa. Having previously isolated potential anti-cancer compounds from tunicates, McPhail now has begun testing them for possible antibiotic properties. She also collaborates with OSU medicinal chemist Taifo Mahmud, who studies the curative powers of rare microbes living in the soils of “blackwater ecosystems” in the tangled jungles of Indonesia (see “Nature’s Medicine Chest,” Terra, Fall 2010).

Why are these strange and remote creatures so intriguing to McPhail? Why are deep-sea vent organisms significant enough for the NIH to award her one of its coveted “R21” grants for high-risk, exploratory projects? What makes tunicates worth the regular trips she makes to South Africa to collaborate with a fellow scientist at Rhodes University, where she got her Ph.D.?

It’s their very rarity that makes them promising in drug discovery.

“Unique organisms from unusual, diverse ecosystems have unusual chemistry,” says McPhail. “My lab is testing these organisms for unknown bioactive compounds — ones that target pathogens in unexpected ways. These compounds then can be used to design a new generation of drugs to fight infection.”

Tracing the chemical “fingerprints” of these novel compounds against known compounds catalogued in databases and examining microbial growth patterns in Petri dishes are the first steps in drug discovery. Next, McPhail will move on to studying disease progres- sion in animals. Once again, she’s eyeing a singular creature. This time, it’s the waxworm. Surprisingly, this caterpillar larva of the wax moth (a member of the “snout moth” family) has an immune system similar to that of mammals. That trait, along with being cheap and plentiful, makes the waxworm an excellent subject for drug discovery.

Nature of the Beast

In the global fight against infectious disease, new drugs are urgently needed. That’s because bacteria and other pathogens are evolving day-by-day, minute-by-minute, to withstand the onslaught of existing drugs. They survive by creating mutant versions of themselves or by swapping whole chunks of DNA with other microbes. Not only have pathogens learned to foil single drugs, they’re now fending off multiple drugs simultaneously. These multidrug-resistant germs have been dubbed “superbugs” in recognition of their ninja-like powers of intracellular infiltration and assassination.

A lab technician separates and analyzes DNA fragments isolated from a bacterium in an experiment to find natural-product biosynthetic genes. (Photo: Jan Sonnenmair)

“For every antibiotic that’s ever been used, resistance has developed,” says OSU researcher David Bearden.

“It’s a hard game to play, because the truth is, the more you use it, the less well it’s going to work. That’s just the nature of the beast.”

It’s that beast’s nature — elusive, mutable — that captures Bearden’s imagination as a clinician. Infectious agents, he says, are a lot like those moving targets in the carnival booth. By the time you get one in your sights, a new one has taken its place.

“It’s a foreign-invader scenario,“ explains Bearden, who chairs the Department of Pharmacy Practice. “You’re giving drugs to the person to kill the living organisms that are attacking them from inside. And all the while, the thing you’re fighting is changing.”

Just outside the window of his 12th-floor Portland office, the aerial tramcars connecting OHSU’s South Waterfront to Pill Hill creep up and down the forested slope like silver beetles. On the adjacent lot below, workers in hardhats are running cranes and positioning girders for the Collaborative Life Sciences Complex, a joint project of OHSU and the Oregon University System. Bearden and another dozen pharmacy researchers who work at the OSU Center for Health and Healing will join scientists and clinicians of OHSU and Portland State University in the new complex when it opens in 2014.

While McPhail and Mahmud are rummaging in some of nature’s most peculiar ecosystems for new drugs, Bearden is looking for better ways to use the drugs already available. Resistance gets a boost when too many people take too many antibiotics, he points out. Patients suffering from colds and flu may request — even demand — antibiotics from their doctors. But because those common ailments are caused not by bacteria but by viruses, taking antibacterial drugs is an exercise in futility. Adding to the problem, many patients take their prescriptions inappropriately or stockpile antibiotics for future use. Remnant germs may lurk in the organs or tissues of their human host, building strength for another assault.

To combat the misuse and overuse of antibiotics, Bearden is looking into optimizing dosages and calibrating them for special groups, such as the obese. “Substandard dosing — concentrations that fail to inhibit or kill all of the bacteria — can induce or enrich resistance,” says Bearden. “Say you have a population of 1 million bacteria, and maybe 1,000 of them are very resistant. If you kill off 999,000 of them, the rest of them have this nice, free niche to become the dominant population.”

From her office a few strides from Bearden’s, OSU epidemiologist Jessina McGregor elaborates: “Optimizing the choice of drug, the dosage, the duration of therapy and the route of therapy — whether oral, topical or intravenous — are the next steps in prudent antibiotic use after first cutting down on overuse. That’s the focus of a lot of pharmaceutical research on infectious disease.”

Bio-Bargain Hunter

When Aleksandra Sikora gets excited about a buy-one-get-one-free deal, it has nothing to do with the half- yearly sale at the mall. Rather, she does her bargain hunting in scientific supply catalogs, such as the dog- eared booklet from Greiner Bio-One that sits on her desk. By stretching dollars, the OSU microbiologist can run more experiments with the startup grants that currently fund her research on cholera (which sickens more than 300,000 yearly) and gonorrhea (the most prevalent infectious disease in the United States).

Aleksandra Sikora, along with her husband and research partner Ryszard Zielke, is investigating ways to combat the germs that cause cholera and gonorrhea. (Photo: Jan Sonnenmair)

Opening a cupboard in her level-2 bio-safety lab in OSU’s Pharmacy Building, Sikora takes out a crisp new package of clear-plastic trays, each about the size of a slice of bread.

“We use 20 to 30 of these sterile plates each time we run a screening for bioactivity,” says Sikora, who grew up in Gdansk, Poland, and has a Ph.D. from the University of Gdansk. “They’re expensive, about $3 to $4 each. If you buy them from Greiner Bio-One, you get one free for every two you order.”

What she’s after in those screenings are “hits” — that is, signs of bioactivity. A bioactive agent or compound is one that affects a living organism such as the gonorrhea-causing bacterium Neisseria gonorrhoaeae or the cholera-causing bacterium Vibrio cholerae, Sikora’s current subjects of study. A hit can show up as a faint glow (“bioluminescence”), which some microbes emit as they send chemical signals back and forth. It can also show up in patterns or rates of bacterial growth. Lack of growth, too, can tell a story.

If she gets a hit, she can see it almost instantly on a computer screen. Thanks to her pricey plastic trays and an even-pricier BioTek plate reader she ordered for her lab soon after arriving at OSU last fall after her post-doctoral training at the University of Michigan Medical School, the whole process is automated. She can run nearly 3,000 tests in just minutes using the high-speed robotic machine, which purrs with perfect precision. That’s because each plate contains 96 “wells” — little troughs that hold samples of bacteria inoculated with whatever compounds are being tested — and the plate reader holds up to 30 plates. Scientists call this type of ultra-fast screening “high-throughput” — in other words, putting samples through chemical and biological analyses at accelerated rates (compared to the old days, when researchers had to run them manually, one at a time).

The gleaming stainless-steel gear gracing Sikora’s lab will let OSU’s team of infectious-disease researchers create their own electronic “compound library.” To that end, Sikora is testing bioactive compounds from McPhail’s vent organisms and sea squirts and Mahmud’s blackwater bacteria, along with her own experiments.

Sikora’s target in the infectious-disease battle is the microbe’s cell wall — the point of contact between the pathogen and the host. It’s where virulence gets a toehold. Instead of targeting the whole cell with a drug designed to kill it outright, Sikora and Ryszard Zielke, her husband and research partner, hope to block “virulence factors,” the actions of bacteria that cause disease. Toxins and other proteins secreted from the cell wall, as well as the composition of the wall itself, are of particular interest.

Chatty Bacteria

In the pantheon of weird sea creatures, the Hawaiian bobtail squid ranks near the top. This 2-inch “stealth bomber of the ocean,” as Natural History magazine calls it, is worthy of Dr. Seuss’s imaginary bestiary. This tiny nocturnal squid even has a biological buddy, a bacterium called Vibrio fischeri that dwells inside a sort of built-in lampshade on the belly of the eight-legged cephalopod. The squid nourishes the dense bacterial populace, which repay the favor by glowing just enough to cancel out the squid’s silhouette as it swims, rendering it invisible to predators. “Interestingly,” OSU microbiologist Martin Schuster notes, “the bacteria don’t glow when they’re out in the open ocean by themselves.”

How do these one-celled wonders accomplish this stunning feat of variable bioluminescence? As biologists discovered in the 1970s, they do it by sending chemical signals back and forth. These bacteria essentially talk to each other in a process called “quorum sensing,” a stunning discovery that led to a paradigm-shift in microbiology: the realization that microbes aren’t loners but rather social creatures that communicate and cooperate with each other.

“Microbes talk,” says Schuster. “And we’re listening in.”

The discovery of quorum sensing in Vibrio fischeri, a microbe beneficial to its host, set off a flurry of new findings. Cell-to-cell communication, it turns out, is common in disease-causing bacteria, too. This includes Pseudomonas aeruginosa, the primary organism under study in Schuster’s laboratory. This notoriously antibiotic-resistant bacterium causes serious hospital-acquired infections and is the main cause of death among people suffering from cystic fibrosis.

Schuster is studying how germ-to-germ dialog fosters disease-causing actions among bacteria, such as secreting harmful toxins or enzymes that break down host tissue. Biofilm formation, a gabfest among millions of microbes, is another. These “cities of microbes” can be up to 1,000-fold more resistant to antibiotic treatment than free-floating bacteria and are the source of many chronic infections. They build a slimy coating that shields the germs deepest within the biofilm. They draw strength from their surrounding compatriots.

“Biofilms and nasty toxins that harm the host are produced by bacteria as a group,” Schuster says. “It’s a concerted effort.”

What Schuster hears as he eavesdrops on these secret chemical conversations constitutes a novel approach in antibiotic design: disarming rather than killing the pathogen with so-called anti-virulence drugs. “With traditional antibiotics, you basically wipe everybody out,” says Schuster. “Only the resistant clone remains and then just explodes.”

Scientists generally assume that if bacteria aren’t threatened with annihilation, they won’t work so hard to create new versions of themselves. Minus this “selective pressure” — evolution’s relentless push for genetic adaptation to environmental threats — resistance won’t develop. This assumption had never been tested experimentally, until now.

What would happen, Schuster wondered, if he shut off the bacterial chatter? Could he halt the behaviors that bolster the disease process? Could he slow the evolution of resistance, the looming problem with traditional antibiotics? The answer to both turned out to be yes. Graduate student Brett Mellbye ran a number of “evolution-in-a-test-tube” experiments, mingling drug-resistant bacteria with non-resistant bacteria. The non-resistant bacteria, Mellbye discovered, got ahead by “cheating” — that is, by exploiting the nutrients and other resources supplied by the resistant bacteria. The cheating put the brakes on resistance.

“The suppression of resistance is contingent on the targeting of cooperative behaviors,” Schuster cautions. The next step in verifying these findings is to move the experiments from test tubes to animal models.

Fishy Germ Swap

How could an Atlantic whitefish caught off Boston pass a germ to a pig on an Iowa hog farm that winds up infecting a teenager in Seattle? It hasn’t happened yet, as far as we know. The pathway from fish to hog to human is not a straight line; it zigs and it zags. But OSU veterinary microbiologist Dan Rockey says it’s just a matter of time before all the dots connect.

The reason: Antibiotic overuse isn’t limited to hospitals and doctors’ offices. Factory farms and feedlots, which routinely give antibiotics to healthy livestock to promote growth and prevent disease, can become breeding grounds for resistant germs. As a rule, pigs and cows don’t pass those dangerous germs to people. That’s because bacterial species rarely jump from animals to humans, or vice versa. For instance, chlamydia, the disease Rockey studies, is common across the animal kingdom, yet each animal has its own version of the germ. “A single chlamydia species generally dials in to a single animal species,” he explains. “The organisms that infect a koala bear or a horse or a lizard or a frog — those don’t cross over.”

But as we know, bacteria everywhere are hardwired to adapt — even on an Iowa pig farm. That’s where Rockey and some colleagues from Iowa State and the University of Washington recently discovered a strain of bacteria resistant to tetracycline, the most common antibiotic used to treat humans suffering from chlamydia (a range of diseases affecting eyes and sexual organs). The researchers traced the microbe to the pigs’ diet: fishmeal. It appears that a complex DNA switcheroo among fish pathogens created a genetic perfect storm for tetracycline resistance.

“One fish pathogen had all the right genes coded in the right sequence,” he says. “Lo and behold, crazy but true, this other fish pathogen, unrelated to the first pathogen, has a complimentary set of genes. Somehow, the two fish pathogens got together and then got into the chlamydia that infects pigs, which often are fed fish waste, especially in the Midwest. This story tells you how complicated it is for antibiotic resistance to spread between humans and animals.”

So far, chlamydia in humans remains treatable with tetracycline and other antibiotics. But Rockey’s research suggests that a day will come when the human chlamydia germs C. trachomatis and C. pneumoniae join the ranks of resistant germs. In his lab, Rockey was able to engineer a tetracycline-resistant human chlamydia strain using DNA from the resistant pig strain. If science can do it in the lab, nature can do it in the wild — and sooner or later, it will.

“If tet-resistance were to get into the human strain, it could spread around pretty quickly,” Rockey says. “Tetracycline is a primary drug of choice against chlamydia infections. This could really be a problem, especially in developing countries.”

Evidence is mounting that animal-human crossover can and does occur. Rockey cites a significant paper by the Phoenix-based nonprofit TGen (Translational Genomics Research Institute) describing how the creation of methicillin-resistant Staphylococcus aureus (MRSA) likely was generated by contacts among humans, pigs, bacteria and antibiotics. Here’s what the study found: Pigs acquired a strain of S. aureus from humans, a strain that initially was treatable by antibiotics. But because pig farms are awash in antibiotics, the strain quickly developed resistance inside the pigs. Today’s MRSA problem may well have originated with the next step in that chain of infection: the bacterium’s jump back to humans, this time in its resistant form.

Lance Price, the TGen study’s lead author, sounded a warning. “Our findings underscore the potential public health risks of widespread antibiotic use in food animal production,” he said in announcing the study results in February. “Staph thrives in crowded and unsanitary conditions. Add antibiotics to that, and you’re going to create a public health problem.”

Skin-to-Skin Contact

Factory farms and feedlots aren’t the only “crowded and unsanitary conditions” that promote staph infections. Gyms, dorms, barracks, playgrounds, day-care centers — close quarters where people have skin-to-skin contact — are a growing worry in health-care circles. In most cases, S. aureus, is usually a harmless hitchhiker on healthy human skin. But sometimes it invades its host, often through a cut or abrasion. The boils, carbuncles, pimples, yellow crusts and milky pus associated with staph infections, while unsavory, are usually treatable. However, adding MRSA strains to this mix leads to “more and more stubborn infections at which doctors throw more and more drugs,” Rockey says. Sometimes, patients fail to respond. Sometimes, they die.

This trend gives a sense of urgency to researchers like Jessina McGregor, an OSU microbiology graduate who came back to join the faculty after getting her Ph.D. from the University of Maryland School of Medicine. Like David Bearden, her colleague down the hall, McGregor is captivated by bacteria’s warp-speed knack for adaptation.

“You can actually observe evolution happening!” She leans forward in her chair, the energy in her voice rising as she contemplates the awesome power of microbial communities. “You can directly observe the bacteria’s response to evolutionary pressure. With larger organisms, you would have to watch for decades or millennia to witness evolutionary change.”

As an epidemiologist, McGregor scans, not populations of microbes in Petri dishes, but populations of humans in all sorts of settings — cities and states, hospitals and doctors’ offices, residential-care facilities and outpatient clinics. She studies long-term data and looks for trends. She plumbs the numbers to stem the threat of resistant disease.

One solution is outreach. Hand-in-hand with the Oregon Department of Health, she and OSU pharmacy students have spearheaded a local project under the national AWARE (Alliance Working for Antibiotic Resistance Education) umbrella, which fans out across the state with brochures, games, videos and face-to-face conversations for local communities. Other solutions may emerge from her current studies of urinary-tract infection patterns at Kaiser Permanente Northwest and OHSU, as well as infection rates among inpatient-versus-outpatient settings.

So far, McGregor says, Oregon and Portland have dodged the full force of resistance hammering other states and cities. “What’s happening in Oregon is very different than in other places in the U.S.,” she explains. “We have very different prescribing patterns here. Oregon is one of the lowest antibiotic utilizers per capita, behind only Alaska. That definitely helps us out.

“Having locally specific information to guide our policies is important. We don’t need to be reactionary ahead of the curve.”

Now More Than Ever

Ironically, the escalating demand for new drugs coincides with declining dollars for antibiotic research. That’s because pharmaceutical companies are concentrating on “blockbuster” medicines for patients with long-term conditions, like elevated cholesterol and high blood pressure. Antibiotics don’t pencil out on the balance sheet, say six sponsors of a bipartisan bill currently before Congress.

“The development of any new pharmaceutical costs hundreds of millions of dollars for basic and clinical research,” write the sponsors, three Democrats and three Republicans from six states. “For antibiotics, revenue is limited because they tend to be prescribed for short-course therapies that are completed in days or weeks.” If it passes, the GAIN Act (Generating Antibiotic Incentives Now) will create incentives to encourage R&D and speed up drug discovery.

The bill’s sponsors mince no scary words, spare no sobering statistics. “The antibiotic pipeline is dwindling, and a global crisis looms,” they write. “Each year, antibiotic-resistant infections are responsible for tens of thousands of deaths, hundreds of thousands of hospitalizations and up to $26 billion in extra costs to the U.S. health-care system. Just when we need innovation the most, the pipeline of drugs to replace ineffective antibiotics has dwindled to a trickle.”

To turn that trickle into a life-giving river, infectious-disease research at OSU and other universities is more urgent than ever. Taifo Mahmud sums it up simply: “We are running out of drugs. We have no other choice than to keep moving.”

After all, a hero perseveres, no matter the cost, no matter the odds.

Illustration by Teresa Hall

It’s one of life’s little ironies. The proteins in our bodies fight infection, carry messages, ferry oxygen and build tissue. But then, like double agents in a spy novel, they can betray us. They overreact to a virus and attack our own organs. They promote cancer, help clog arteries or set up roadblocks in the brain. We may never know until symptoms appear — a lump, chest pain, severe memory lapses — and irreversible damage is done.

Who wouldn’t like to get ahead of these heart-stopping scenarios? By detecting proteins gone awry or elevated in the earliest stages of disease, scientists are opening up the possibility of effective therapy before health is compromised. The standard checklist on the annual physical — temperature, blood pressure, reflexes, lung function, skin condition — is already backed up by blood tests for molecular markers such as cholesterol and other proteins. What researchers envision is an inexpensive (some aim for a “penny per protein”), accurate and rapid test that can be performed in a doctor’s office and provide unprecedented views of our biochemistry on the fly.

In medical research labs across the country, a race is on to identify new biomarkers and to develop highly sensitive technologies that can measure them. Talk about a needle in a haystack. A single blood sample can contain roughly 9,000 types of proteins, although different analytical techniques produce widely varying estimates. And on top of the sheer flood of proteins is the fact that they are shape shifters. Once released into the bloodstream, they may be altered before they reach their intended destination.

Oregon State University chemist Vince Remcho likens the search for proteins to fishing. “Ultimately you are searching for one particular protein or other molecule in a vast soup of molecules, so you have to choose the right bait. My group is in the bait business, bait and hook,” he says.

In Remcho’s lab in OSU’s new Linus Pauling Science Center, some of that bait consists of short relatives of DNA known as aptamers. If the team of students and other researchers has prepared their devices properly, they will attract big fish, proteins and other molecules that fit into the nooks and crannies of a particular aptamer and no other. Remcho and his international team (hailing from Indonesia, China, Nigeria, Thailand and the United States) develop new tools — lab-on-a-chip technologies, microfluidics and nanosensors — for scientific, medical and precision manufacturing purposes. But their goals can’t be achieved by chemistry alone, so at OSU, they rely on the expertise of physicists, engineers and molecular biologists to advance sensing science.

Marked Molecules

Knowing how to catch proteins is one thing. Knowing which proteins to catch is another. The U.S. Food and Drug Administration now recognizes nine biomarkers for use in clinical diagnosis of cancer, and researchers have identified others that serve as markers for kidney and liver disease, Alzheimer’s, rheumatoid arthritis, tuberculosis and other illnesses. “There are new markers coming out everyday from different labs,” says Arup Indra in the OSU College of Pharmacy.

The Indra lab is one of them. In 2009, he, Gitali Indra and collaborators at OSU and in France reported a new biomarker for head and neck cancers. With funding from the National Institutes of Health, they conclusively linked a protein known as CTIP2 to squamous cell carcinoma. Squamous cells are flat, plate-like cells in the skin and the lining of internal organs. When it occurs in the head and neck, squamous cell carcinoma is the sixth most common form of cancer worldwide — promoted by exposure to tobacco, alcohol and human papillomavirus.

It is aggressive and hard to treat. Despite advances in chemotherapy and surgery, five-year survival rates have not improved over the past 20 years. And until the CTIP2 discovery, researchers had had limited success in identifying biomarkers for use in clinical oncology.

In December 2011, the Indras and their colleagues Mark Leid of OSU and French biochemist Joseph Abecassis received a United States patent for the use of CTIP2 in cancer diagnostic tests. “Cells that are dividing rapidly express more CTIP2,” says Arup Indra. “It is a marker of cell proliferation. We don’t know for sure if it is a cause of cancer, but we suspect strongly that it is.” The protein has also been called a “master regulator” because it influences cell development in skin, teeth, the brain and immune system.

In storage tanks cooled by liquid nitrogen, the Indras maintain some human oral-cancer cell lines that overproduce CTIP2. With partners at OSU and the Oregon Health & Science University in Portland, Gitali Indra leads studies on its role in the development of normal tissues as well as cancer. “CTIP2 is expressed in normal cells but at much lower levels,” she says.

Personal Proteomics

“A higher-than-normal level (of CTIP2) indicates that an individual could be at risk,” adds Arup. “If you are getting more than a normal detectable level, you could determine that she requires monitoring.”

The Indras’ work with cell lines is just the beginning. Before CTIP2 becomes useful in the doctor’s office, its function needs to be studied in animals and then human subjects. “We need to understand how disease progresses in animal models, how levels of a given biomarker are changing,” says Arup.

Moreover, no protein acts alone. Each operates in a network. So the ideal biosensor will be capable of monitoring many proteins at once. The hope is that such devices will enable every person to have a composite protein profile, a biochemical fingerprint, for evaluating health as we age.

Researchers will need better technology to reach that goal. While the Indras can analyze CTIP2 and other proteins through existing laboratory techniques, their efforts bump up against detection limits. A better way to fish for proteins would enable them to pick out one molecule among thousands and to see small but possibly significant trends. Just as the Indras identify biomarkers and the Remcho lab develops ways to catch them, Ethan Minot is working on a new type of fishing line for CTIP2 — a more sensitive detection system made of carbon nanotubes.

Planting Nanotubes

These slender threads of pure carbon are hollow and so tiny that they are invisible to the naked eye, even under the most powerful light microscope. And they bring a valuable benefit to protein detection: They conduct electricity with such sensitivity that physicists can measure the tiny change in electric current that occurs when a single molecule lands on their surface. That makes them good candidates for the kind of detection system needed by the Indras and other molecular biologists. However, despite their size, making and developing a nanotube-based detection system is no small matter.

Ethan Minot and his team use light to analyze the structure of carbon nanotubes grown in the lab. (Photo: Jan Sonnenmair)

With support from the Oregon Nanoscience and Microtechnologies Institute (ONAMI) and OSU start-up funds, Minot has established a lab in the OSU Department of Physics for studying nanotubes and graphene (one-atom thick carbon sheets). He and his team sow nanotube “seeds” — catalysts that sequester carbon atoms from gases such as methane and ethylene — onto a silicon chip. At about 900 degrees Centigrade, carbon nanotubes grow in only a few minutes.

But it can take hours of painstaking work to determine exactly what kind of tubes the researchers have made. “When you bind carbon atoms together into the nanotube structure, there are at least 100 different ways to do it. So the diameter can be different and every one has slightly different properties,” says Minot. Carbon bonds also take a variety of angles as they grow. These so-called chiral angles affect the way a nanotube conducts electricity and binds to other molecules.

Fortunately, physicists have more than a few tricks up their sleeves. After they remove the chip from the furnace, they load it into a machine that has become standard in labs that manipulate matter at this scale: the atomic force microscope. The device can “see” structures smaller than the wavelength of visible light. Its fine-tipped needle creeps slowly across a surface and deflects ever so slightly when it comes close to a nanotube. The resulting map — mountains, valleys and objects on the molecular landscape — reveals the location and length of every nanotube on the surface.

But researchers aren’t done. It takes another step — analysis of each nanotube by lasers tuned to precise frequencies — to determine the angle of the carbon bonds, which is key to the nanotube’s electrical properties. Working with the Remcho and Indra labs, Minot and his team are developing ways to bind small molecules — the bait — to nanotubes and then detect biomarkers such as CTIP2 — the fish — in a simple saline solution.

Something that has so far eluded the Minot lab’s grasp is the successful detection of a protein in a blood sample. “If you have a mixture that you’re sensing, like real blood, there are thousands of different types of proteins. Most of them you want to bounce right off the sensor. One out of a thousand (proteins) has the right chemical structure to stick to it. That’s the ideal situation,” he adds. “Sensors will pick up anything unless you treat the surface correctly.”

Out of the Lab

Members of Minot’s and Remcho’s labs and a colleague at UC Santa Barbara reported in January 2012 that they had succeeded in nearly tripling the speed of a prototype detection system. Their advance stemmed from preventing proteins from sticking to other surfaces in the system.

“To increase detection speed, we relied a lot on surface treatments that can stop proteins from sticking where they shouldn’t,” says Minot. “Our next step is to make specific proteins stick to the nanotube. There’s an element on the nanotube that will click onto an element on the aptamers (the bait for catching proteins). We prepare the nanotube in a reactive state and the aptamers with reactive ‘handles’ and wait for them to find each other.”

While refining biosensor chemistry is hard enough, the electronics present another major hurdle. “If anything stops this from being commercialized from the electronics point of view,” Minot adds, “it’s the fact that if you wait a half hour, there are slow changes in baseline resistance. When we do an experiment, it might last five minutes, and we bind proteins onto the surface in that amount of time. We see a very clear signal over that period of time.

“But commercial devices don’t have the same luxury as a research experiment. They don’t have a grad student, who knows exactly what’s going on, watching over it. Can this thing be automated, take the human interpretation out of it? That’s a big challenge.”

Meanwhile, Oregon businesses are expressing interest in OSU’s developing technologies. Minot is working with Voxtel in Beaverton on methods for controlling nanotube properties in manufacturing. And a company known as mAbDx Inc., a spinoff from the University of Oregon, has taken an option on an antibody to CTIP2 based on work by the Indras and Leid.

Not Just Nanotubes

Nanotubes are just one of the technologies in development. Other approaches at OSU include magnetized “nanobeads,” the focus in Pallavi Dhagat’s lab in the School of Electrical Engineering and Computer Science. Working with Remcho’s group, Dhagat has developed a way to turn ferromagnetic iron oxide nanoparticles, extraordinarily tiny pieces of rust, into sensors. Such particles not only can detect chemicals with sensitivity and selectivity, but they can be incorporated into a system of integrated circuits to instantly display the findings. The applications could extend to homeland security and environmental monitoring as well as to medical diagnostics.

Meanwhile, the search for faster, affordable, sensitive and accurate diagnostic tools is ongoing. At Caltech researchers have proposed a multi-protein testing method in which a blood sample is washed across a chip. They generate a mosaic of colors, each one associated with a different protein. A Boston University group is measuring changes in light waves propagating across a metallic surface designed to bind proteins.

“It doesn’t have to be nanotubes,” says Minot. “Maybe somebody else is going to get it. But there’s a lot of excitement that we’re moving this way. Someone is going to nail it.” And when they do, the proteins that betray us will have nowhere to hide.

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Feb. 22, 2013, scientists at the University of Pennsylvania report a nanotube-based technique for early detection of prostate cancer.

Illustration by Mary Susan Weldon

One sunny spring afternoon, friends sat together in the backyard of a Corvallis home sipping wine, bemoaning the recent hike in gas prices to $3.50 per gallon. Among them were a former product-development specialist for Hewlett-Packard and an Oregon State University chemist. Perhaps inspired by the bioethanol in their glasses, what might happen, they wondered, if they could turn local agricultural by-products — grass and wheat straw, fruit and vegetable processing wastes — into fuel? Thus was born the idea for a new company, Trillium FiberFuels.

They didn’t intend to compete against the rapidly expanding corn-ethanol industry. As of 2010, more than 200 facilities, mostly in the Midwest, were churning out about 13.5 billion gallons of corn ethanol a year. The Trillium co-founders’ hope was that they would develop a more environmentally sustainable product (lower greenhouse-gas emissions, less water pollution), provide another revenue source for rural Oregon land-owners and contribute to the national energy goal of producing 36 billion gallons of biofuel annually by 2022. Trillium had entered the cellulosic-ethanol business.

Priority No. 1 for any new company is to stay alive. So Trillium succeeded in competing for federal and state grants and spun off another small business along the way (Cascade Analytical Reagents and Biochemicals). In a small wood-frame building just off Highway 99 north of Corvallis, the company has developed a method (known as xylose isomerization) to ferment the 20 percent to 40 percent of plant biomass that resists being turned into ethanol by yeast. Trillium president Chris Beatty credits research by OSU Distinguished Professor Stephen Giovannoni, who isolated and sequenced the genome of a microorganism used in the company’s experiments.

The goal is to produce cellulosic ethanol at a competitive price and ramp up production quickly. “If you’re going to make a dent in this business, it’s either grow big or stay home,” says Vince Remcho, Trillium co-founder, OSU professor of chemistry and affiliate scientist with the Pacific Northwest National Laboratory. Other co-founders include Beatty, Steve Potochnik and Grant Pease, all with former or current ties to HP.

Priming the Pump

Trillium isn’t the only business collaborating with OSU to have grand ambitions. Spun directly out of research or boosted by patented OSU technology, others are aiming to grab significant shares of business and consumer markets. Some of their products are already coming off farm fields and manufacturing lines.

Through their relationships with OSU, these and other companies create jobs, diversify the Oregon economy and respond to market demands for more sustainable, consumer-driven technologies. And in turn, OSU benefits. Students gain experience through internships. Faculty stay up-to-date on industry practice. And licensing revenues provide new research funds. “The purpose of our efforts is impact,” says Ron Adams, executive associate vice president for research. “It relates to our land grant mission, so we’re furthering economic development and social progress. We’re partnering in R&D that will result in new products and business opportunities.”

Still, working with businesses isn’t like serving students or competing for research grants. Adams and others are mindful that entrepreneurs and business managers face rapidly changing risks and protect their interests accordingly. “The people who are investing their lives and money in those enterprises are not depending totally on us to get it done,” Adams says. “If you’re an entrepreneur running one of these companies, you want 100 percent control.”

While companies do look to universities for innovation and skilled, well-educated employees, “we’re not an economic development organization,” adds Brian Wall, director of the Office of Commercialization and Corporate Development. “We are an economic driver through our graduates, research partnerships and licensing. We’re always on the lookout for discoveries that offer opportunities for commercialization and new business investment. This is an important area of growth and impact.”

The rules that define that process — agreements on copyright, licensing, royalties and other steps — are based on policies created by the Oregon State Board of Higher Education.

Show Me the Money

Private-sector partnerships show up as support for problem-oriented research. Nationally, according to the National Science Foundation, industry funded nearly 6 percent of the roughly $55 billion in research performed in institutions of higher education in 2009. At Oregon State in 2011, studies funded directly by industry totaled about $5.4 million, or 2 percent of the university’s $261.7 million in grants and contracts. However, that doesn’t include contributions from research gifts, agricultural commodity groups, the forest-products industry and testing services, which bring the total close to $13 million, or about 5 percent.

What about return on investment? Perhaps the most dramatic comes from the agricultural sciences, which helped Oregon farmers and ranchers to earn a record $5.2 billion in farm-gate sales in 2011. Oregon beef topped the list as the state’s most valuable agricultural commodity. Ranchers have a long history of working with OSU researchers through Agricultural Experiment Stations in animal and rangeland science on feed, herd health and cattle management.

Impact also comes from fledgling startup companies like Trillium. Over the past eight years, new OSU-assisted companies have raised $160 million in private investment and created 350 jobs, says Rick Spinrad, vice president for research. New businesses proceed through stages, he adds, from research-inspired startup to venture-funded, revenue-producing and growth-focused.

At every step is a major hurdle: money to pay for product development, market analysis and management expertise. Among the sources of funding that help young companies transition from one stage to another are the Oregon Nanoscience and Microtechnologies Institute (ONAMI), the Oregon Built Environment and Sustainable Technologies Center (BEST) and the OSU University Venture Development Fund. The latter leverages tax-deductible contributions from private citizens. The OSU Foundation conducts fundraising, and the OSU Research Office manages investments. Recent examples include:

• Ultra-high-temperature water pasteurization for another startup, Home Dialysis Plus ($182,700)
• Market analysis of a landmark new LCD display by Inpria Corporation ($100,000)
• Development of a thermal energy storage system by a new company, Applied Exergy ($148,514)
• Proof-of-concept display for a new type of diode that could replace silicon and reduce energy, leading to a new company, Amorphyx ($150,000)

Trillium FiberFuels, meanwhile, announced in April 2012 that it received a $150,000 Small Business Technology Transfer grant from the U.S. Department of Energy (DOE) to develop a commercial-scale enzyme production process for the cellulosic biofuels industry. Based on manganese peroxidase, which is found naturally in white-rot fungi, the new process emerged from the lab of OSU researchers Christine Kelly and Curtis Lajoie. The company has also received funding from sources such as the U.S. Environmental Protection Agency, the National Science Foundation, U.S. Department of Agriculture, ONAMI and Oregon BEST.

“There is a reason to invest in research in biofuels,” says Remcho. “It will play a role in U.S. and worldwide energy needs in the future. So it’s coming. We just need to do it intelligently.”

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The Oregon State College of Engineering partners with businesses from HP to Azuray Technologies to deliver solutions for product development.

Ancient Blood Brothers

Like the “sloth moth,” which lives only in the fur of the ambling two-toed and three-toed mammals, the “bat fly” exists only in the fur of the winged, cave-dwelling mammals. Now scientists know that the flea-like, blood-sucking fly has been hanging around with bats for at least 20 million years. That’s because an unfortunate bat fly became entombed in a sticky glob of tree sap eons ago and has been there ever since, preserved in the solidified amber. Bat flies coevolved with bats, explains one of the world’s leading amber experts, OSU zoologist George Poinar Jr., who discovered the fossilized fly in the semi-precious stone from the Dominican Republic.

Reported in this week’s issue of the journal Science, the findings could lead to new understandings about the molecules that drive processes in biology, medical diagnostics, nanotechnology and other fields.

X-ray reflections between the black and green lines hold useful information but are typically discarded. (Image courtesy of Andy Karplus)

Like dentists who use X-rays to find tooth decay, scientists use X-rays to reveal the shape and structure of DNA, proteins, minerals and other molecules. As X-rays pass through the lattice of atoms, they reflect distinctive patterns, and scientists use those patterns to determine what atoms are present and how atoms are bonded to each other. However, some data are typically discarded because of concerns over quality. In particular, data derived from edge regions of the pattern — although very important for understanding the details of structure — are often overwhelmed by the random errors associated with measuring a weak signal in the midst of a lot of background noise.

Oregon State University biophysicist Andy Karplus and his colleague Kay Diederichs at the University of Konstanz in Germany have now proven that useful information can be gleaned from data that have up to about five times the noise levels that have previously been considered acceptable. “The criteria that have been used in the past are way too conservative,” said Karplus. “These data that people have been throwing out are actually good.”

The bottom line for crystallographers is the accuracy of their molecular models, those physical representations of the arrangement of atoms. The better the model, the better it will predict the pattern created by X-rays passing through a molecule, and the better it will be for guiding the development of new drugs and nanotechnologies that operate at the molecular scale. Although the first X-ray diffraction pattern was recorded 100 years ago and the first protein structures were determined 50 years ago, scientists have struggled to find statistical methods to connect data quality and the accuracy of their models.

This chart offers proof that data at the edges of X-ray reflection patterns contribute to model accuracy. (Image courtesy of Andy Karplus)

The new method may be the most important conceptual advance in the past 20 years in how these data are used in modeling, the scientists said. In 1992, statistics were developed to ensure that models were not biased by randomness or “noise.” The new method carries that further by showing how data from parts of the measurement where noise becomes stronger can still provide information that makes the model more accurate. It also allows scientists to see directly where the model is limited by noise in the data and where the model is a better estimate of molecular structure than experimental data.

“The question is, ‘Where do we cut it off?’” said Karplus, whose research focuses on protein structure and stability. By adding data at incremental steps and showing how the model improved, Karplus and Diederichs showed that scientists had been cutting off their analyses too soon and discarding data that could sharpen their view of molecular structure.

“The big impact on the field will be that every structure determined from here on out will be a little more accurate because people won’t throw away data that are OK. If you have a crummy image of the protein, it will get a little sharper. If you have a good image of the protein, it will also get a little sharper,” added Karplus.

For example, he noted, some enzymes work in concert with water molecules embedded within their structure. However, it takes data at a certain level of detail (about 2.6 angstroms) to discern exactly where water molecules are suspended between the atoms of an enzyme. If X-ray data at that scale were being discarded, it could mean that the scientists are not able to conclusively demonstrate the presence of water and thus cannot properly understand how the enzyme works.

While the method will be an important step for X-ray crystallographers, Karplus and Diederichs think that other physical sciences may also find ways to benefit from this type of data quality analysis. They also discovered that one branch of science has been using this type of statistical analysis for many years. The field of psychometrics — the analysis of data from psychological tests — has used a similar technique called the “Spearman-Brown prophecy formula” to determine the minimum length of such tests.

Andy Karplus

Kay Diederichs

Karplus and Diederichs have worked together off and on since 1985 when Karplus was an Alexander von Humboldt post-doctoral fellow in Germany. In 1997, they published a paper demonstrating that certain statistics used in analyzing X-ray crystallography data were misleading, but few crystallographers have adjusted their practices since that time. In 2011 during a sabbatical leave, Karplus visited with Diederichs in Germany to develop the new method. “Now that we know that very noisy data are useful, this will presumably enable still further improvements as it stimulates new software development to do a better job of handling such weak data,” said Karplus.

The paper is also the subject of a Perspectives piece in the same issue of Science by Phil Evans of the MRC Laboratory of Molecular Biology in Cambridge, England. The research was supported by grants from the National Institutes of Health and the Alexander von Humboldt Foundation.

That is about to change.

Joseph Spatafora, a botanist at Oregon State University, sits in front of a computer system that will store the data that he and an international team generate as they sequence the full set of chromosomes for 1,000 fungus species. (Photo: Lynn Ketchum)

A new study headed by Joseph Spatafora, an Oregon State University professor of botany and plant pathology, will use powerful new tools of genomics to learn more about fungi. Spatafora and an international team of scientists will sequence the full set of chromosomes for 1,000 fungus species, creating at least two reference genomes for each recognized family within the fungal kingdom.

This project builds on the knowledge created by a previous 10-year study called Assembling the Fungal Tree of Life, also led by Spatafora. That study helped to develop a classification system of fungi from around the world and paved the way for creating a reference encyclopedia of what fungi exist, how they are related, what they do and how they do it.

“With this genome encyclopedia we’ll have access to the playbook of fungi,” Spatafora said, adding that the playbook is important to carbon cycling, food science, environmental cleanup, human health and more.

Species Unknown

There are an estimated 1.5 million species of fungi, yet only about 100,000 species have been described. Spatafora credits recent advances in gene sequencing technology that will make it possible to unravel genetic details with speed and accuracy.

“We’ve used fungi for so many services to society for centuries without much knowledge about how they are assembled at a genomic level. Think about what we can discover with this powerful knowledge,” he said.

The 1000 Fungal Genomes project is one of 41 projects funded through the U.S. Department of Energy’s Joint Genome Institute whose purpose is to enable scientists from universities and national laboratories around the world to explore the hidden world of microbes and plants for solutions to major challenges in energy, climate and environment. Spatafora leads an international team of researchers, including Jason Stajich at University of California at Riverside and Igor Gregorlev of the DOE Joint Genome Institute.

Masters of Life

Fungi have an enormous impact on life and ecosystem functioning, as decomposers, pathogens, and essential components of the global carbon cycle. They are capable of degrading almost any biological material as well as many synthetic compounds. Therefore, fungi are useful in the development of alternative fuels, carbon sequestration and bioremediation of contaminated sites.

In order to harness this potential, the 1000 Fungal Genomes project will build a reference library as a foundation for accurate analyses of the enormous volumes of data that will be created through genomic research.

Tricholoma cf. terreum grows on a forest floor in Oregon’s Coast Range. (Photo: Lynn Ketchum)

Fungal species to be analyzed will come from at least five science centers around the world, including University of Missouri at Kansas City; University of Arizona; USDA Center for Forest Mycology Research; USDA Northern Regional Research Laboratory; and the Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre, the Netherlands.

The first year of the five-year project focuses on some of the most diverse classes of fungi that have been studied so far in these culture collections. As the project matures and as knowledge grows, the research will expand to include questions of sampling strategy, curation of data, research and analytical protocols, training and publications.

See more information on the 1000 Fungal Genomes project.

OSU undergraduate Sam Bartlett, right, used the tools of organic chemistry — reflux condenser, thin-layer chromotography, nuclear magnetic resonance — to develop a new synthetic chemistry method. He works with Assistant Professor Chris Beaudry in the new Linus Pauling Science Center. (Photo: Karl Maasdam)

With guidance from Chris Beaudry, assistant professor of chemistry, he developed the most efficient and productive method yet reported for a fundamental step commonly used to synthesize new molecules.

Bartlett and Beaudry published their findings in October in the Journal of Organic Chemistry. The research has already drawn the attention of pharmaceutical scientists and has potential in fields from nanotechnology to biochemistry.

“If you’re a synthetic chemist and you want to build complicated molecular architectures – a pharmaceutical, a new material for nanotechnology, a new probe for a biological system – you need to make new chemical bonds,” Beaudry said. “This oxidation is convenient to do, very mild, operationally simple and high yielding. It is the solution to this problem.”

Bartlett’s discovery started with a chance meeting. The student from Corvallis, Oregon, was taking an advanced chemistry course from Beaudry and happened to meet the professor in the Interzone, an off-campus coffee shop. “I asked him if he had any research opportunities in his lab,” Bartlett said.

“I suggested that Sam look into this problem,” Beaudry recalled. “There was some indication that we had a lead hit on how to solve it. Sam took it and ran with it.”

The problem was to convert one commonly used compound (beta-hydroxyketone) to another (beta-diketone). Both are fundamental starting points in the synthesis of more complex organic molecules. Previous methods produced unwanted byproducts and only 30 to 35 percent of the desirable molecule, says Beaudry.

Bartlett found that an oxidant called IBX (o-iodoxybenzoic acid) converts nearly 100 percent of the beta-hydroxyketone to the beta-diketone, thus saving chemists time – and simplifying the synthesis process.

Bartlett, who graduated from Crescent Valley High School, is applying for graduate school, where he intends to focus on synthetic organic chemistry.

“I just like the search for new knowledge,” said Bartlett. “There’s a lot we still don’t know. There are problems out there we still need to solve. Even if I don’t find a solution, I’m contributing to the scientific community.”

Bartlett had support for his research from two programs: the Undergraduate Research, Innovation, Scholarship & Creativity program sponsored by the OSU Research Office, and a Howard Hughes Medical Institute fellowship. He is continuing to work in Beaudry’s lab in the new Linus Pauling Science Center on steps to make a natural plant compound that has potential anti-fungal and anti-inflammatory properties.

The first lesson the elephants taught Ursula Bechert was that they had a sense of humor.

On her first day at the Wildlife Safari in Winston, Oregon, Bechert got soaked as she gave the animals their daily shower. The next day, she came to work wearing rubber boots, hoping to at least keep her feet dry. Noticing Bechert’s change in apparel, an elephant named Alice quietly drew water into her trunk while Bechert washed another elephant, slipped it into one of Bechert’s boots, and filled it with water.

Ursula Bechert, left, worked with elephants at the Oregon Zoo in 2000 (photo courtesy of Ursula Bechert)

“I swear she had the biggest grin on her face,” Bechert says, remembering Alice’s mischievous nature.

Bechert, director of Off-Campus Programs in Oregon State University’s College of Science, has spent much of her life in the company of animals. After fulfilling her childhood dream of becoming a veterinarian and working in small animal practice, she returned to school to earn a doctorate in reproductive endocrinology and completed her thesis while working with elephants at the Wildlife Safari, a nonprofit zoological park.

Driven by a passion for conservation, Bechert has worked with elephants and other species to manage animal populations and find effective solutions for conflicts that arise between humans and animals. Recently, she has been studying the effects of a new form of an immunocontraceptive vaccine known as porcine zona pellucida (pZP) in elephants and wild horses. The vaccine may help reduce conflicts by keeping animal populations in check. Her early results suggest that this new vaccine formulation may be an important tool to alleviate tensions caused by other controversial methods of population management.

“Originally, I wanted to help individual animals as a veterinarian,” Bechert says. “Through research, I realized I could impact entire populations. By working on population management tools like contraception, I now hope to help sustain animal populations in the wild. I don’t believe that we will have succeeded in saving a species if those animals only survive in captivity; we need diversity of species for healthy ecosystems.”

One Shot, 10 Years

To prevent conception in animals, pZP vaccines produce antibodies that block sperm from attaching to unfertilized eggs. While pZP vaccines have been used in the past to manage elephant and horse populations, the vaccine Bechert is working with is a unique formulation called SpayVac®.

In northern Botswana in 2003, Bechert and a team of researchers applied tracking collars to elephants. Scientists observed that after landmines were removed in Angola, elephants resumed migration through areas they had avoided during the civil war. Understanding elephant movements and habitat use can help minimize human-elephant conflict. (Photo: David Rogers)

Produced by Canada-based ImmunoVaccine Technologies Inc., SpayVac® has the potential to act as a multi-year contraceptive. Other pZP vaccinations require a booster four weeks after the initial injection and must be administered annually to remain effective, which Bechert says is more expensive and stressful for handlers and animals. A single shot of SpayVac®, however, has been demonstrated to be effective in other animal species for up to 10 years.

Bechert began working with SpayVac six years ago when she studied the vaccine’s effect on captive elephants in North America. As viable habitat and resources become more limited in many African and Asian countries, Bechert says, the incidence of human-elephant conflict increases, necessitating elephant population control.

“They’re competing over common resources like water,” Bechert says. “Some villages try to keep elephants out by creating biological barriers with chili peppers elephants don’t like.”

Managing elephant populations with a multi-year contraceptive could help reduce the number of confrontations and the need to cull elephants to control their populations, Bechert says. So far, SpayVac® has shown promise because pZP antibody concentrations have remained high in the elephants that were vaccinated, indicating that the vaccine is still active.

Through her research on SpayVac®, Bechert is working to find a solution to human-animal conflicts in the United States as well.

Wild Horses

In a recent study funded by the United States Geological Survey (USGS), Bechert led a team of OSU researchers in assessing the safety of SpayVac® for use in horses. Like elephants, wild horse populations are exceeding the carrying capacity of the land they inhabit. Horses roam freely in the western U.S. and have generated controversy as cattle ranchers feel they must compete with wild horses for land and forage for their cattle. Addressing the problem has been difficult because land managers, cattle ranchers and horse lovers disagree about how growing horse populations should be managed.

Wild horses on Bureau of Land Management range near Burns in southeastern Oregon (Photo courtesy of the Bureau of Land Management)

The federal Bureau of Land Management (BLM) oversees management of horse populations and is struggling to find solutions that are effective and humane, Bechert says. Other methods of managing the wild horse population, which exceeded the BLM’s optimum management level by nearly 12,000 horses as of February 2011, include BLM roundups that capture and maintain horses in captivity or adopt them to individuals. Such activities, Bechert says, are an expensive and temporary solution to the horse overpopulation problem.

Just as Bechert believes SpayVac® could ease the tension between humans and elephants on the other side of the globe, she says the vaccine may be the best way to alleviate the competition between ranchers and horses over land resources in the U.S.

Starting in the spring of 2010, Bechert and a team of OSU researchers conducted a trial to determine whether SpayVac® could be effectively and safely used in horses. The study was completed last fall. While Bechert is currently in the process of publishing the results, she says their preliminary findings demonstrate no adverse effects to the general health of horses that received the vaccine, and results were promising.

In response to Bechert’s findings, the USGS began a five-year study of 90 mares in the spring of 2011 to observe the long-term effects of the contraceptive vaccine. While this study progresses, Bechert plans to publish the results of her work and apply for funding to support additional research on how the vaccine affects the horses’ ovaries and determine whether it is reversible. Understanding how the vaccine works and whether it can be reversed, she says, is important to effectively incorporating it as an effective management tool. If the USGS study goes well, Bechert says the BLM will likely begin to administer the vaccine in wild horse populations within the next five years.

Wild horses in a trap at the Warm Springs Herd Management Area near Burns in southeastern Oregon. (Photo courtesy of the Bureau of Land Management)

“I think this vaccine will do a lot to reduce human-animal conflict,” Bechert says. “Administration is easy and the vaccine is much more cost effective compared to other methods or products being used. I’m passionate about it for the animals, because from their perspective, getting one shot is much less stressful and easier than being rounded up and adopted or maintained by the BLM. I think SpayVac® will make a wonderful population management tool, and that really motivates me.”

Light spectra by artist Stephen Knapp illuminate a wall in the new Linus Pauling Science Center. In their research, scientists use spectra to detect and measure the abundance of chemical elements. (Photo: Theresa Hogue)

In 2011, the first Baby Boomer turned 65 — the leading edge of a wave that is going to change the country. By 2030 one in every five Americans will be older than that. People are already living longer, taking time to travel and to enjoy their families. Think gourmet cooking classes, fishing trips and art museums.

But they will increasingly face the diseases that now kill most people in the developed world: heart disease, cancer, stroke, diabetes and neurodegenerative diseases such as Alzheimer’s and Parkinson’s.

They want answers and solutions. And in the future, many of those answers will come from a new research facility at Oregon State University, the Linus Pauling Science Center.

This new $62.5 million, 105,000-square-foot research and educational structure, just completed this fall, has arrived at an opportune time in American history. But its foundations were laid 94 years ago, in the fall of 1917, when a young student arrived at Oregon Agricultural College and enrolled in a chemistry course. Linus Pauling, OSU’s most accomplished alumnus, went on to win two Nobel Prizes.

“Linus Pauling revolutionized the fields of chemistry and molecular medicine, and this facility will be a working memorial to him, a great tribute,” says Balz Frei, director of the Linus Pauling Institute. “It will help further establish LPI as a national leader in the study of diet, optimal nutrition and micronutrients.

“Chronic disease prevention through diet and lifestyle is the future of medicine,” Frei adds. “And it’s for everyone, not just the elderly.”

Advances in health will come from better understanding of phytochemicals such as sulforaphane, a cancer-fighting compound in broccoli and other cruciferous vegetables. Other research focuses on vitamin D in enhancing immune function and fish oil in preventing fatty liver disease. New types of antioxidants and “anti-inflammatories” are also being investigated, such as lipoic acid, which may be key to getting the most out of life as we age.

Chemical Collaboration

The institute will share the new facility with the OSU Department of Chemistry. Specialists in analytical, materials and organic chemistry will work in close proximity to their peers in the health sciences and develop new strategies for disease diagnosis and treatment. “These new facilities house approximately $10 million in state-of-the-art transmission- and scanning-electron microscopes and nuclear magnetic resonance spectrometers that will serve the entire campus,” says Vince Remcho, chemist and associate dean in the College of Science.

The new instruments were made possible by grants from the M.J. Murdock Charitable Trust, the National Science Foundation (NSF) and partnerships between several of OSU’s colleges, the OSU Research Office and the Oregon Nanoscience and Microtechnologies Institute (ONAMI).

Chemists in the new facility bring with them “an astonishing research track record, as measured by publication count, impact, external funding and intellectual property development,” Remcho adds.

Primary support for the center, which was designed to the U.S. Green Building Council’s LEED silver standards, came from the Wayne and Gladys Valley Foundation – a $20 million gift – and another $10.6 million from Pat and Al Reser. Most of the research in the facility will be supported by grants from the National Institutes of Health and NSF.

Carabids

But first, a few more details. And no, I wasn’t exploring some sort of bizarre insect cemetery. I was visiting the Oregon State Arthropod Collection (OSAC), a misleadingly commonplace room on the fourth floor of Cordley Hall on OSU’s main campus. Though minimally advertised, this organismal library is comprised of cabinets with boxes full of arthropods, carefully preserved and delicately pinned into place. Remove the lids to those boxes, and the collection flashes to life with bright colors: metallic glimmerings of beetle exoskeletons, satiny blue shimmers of butterfly wings.

The collection ranges from breath-taking to bizarre, like the eye-catching tarantula. While intimidating, the giant spider is much less of a threat when perfectly preserved and floating in a glass jar. OSAC hosts the largest collection of Pacific Northwest insects in the world, while also including many other arthropods such as spiders and scorpions.

So why doesn’t everyone know about OSAC? First of all, it serves the scientific community by providing a resource to researchers in the Pacific Northwest and beyond. In a monumental effort to make the collection more accessible online, staff members are digitizing the entire collection. In addition to these services, OSAC occasionally collects its own specimens when time and funding allows, adding material to its holdings yearly.

Open Access

The museum is open to the public by appointment but focuses on meeting the needs of visitors with research-related questions. And unlike a giant exhibition museum, there is no admission charge.

pentatomidae

“There’s a strength that comes from being a small, regional collection with a really great legacy and history,” says Chris Marshall, curator and manager for the collection. “While we’re not currently out collecting samples , we’re seeking to help other groups who are doing work like that, and they can reciprocate by depositing material.”

This function highlights the importance of regional collections. OSAC allows researchers to go beyond the limitations of field guides. For example, when conservationists with the Xerces Society for Invertebrate Conservation needed to acquaint themselves with a specific butterfly before surveying it in the wild, they came to OSAC for help. By directly observing the butterflies in OSAC’s collection, the conservationists learned how to recognize the species they were going to study. Further enriching the resource, labels on the specimens told them when and where to look for the butterfly.

“For these conservationists, one of the first steps toward understanding how to preserve them is learning how to recognize them,” Marshall points out. “A photograph in a field guide is just not the same as seeing twenty preserved butterflies in a drawer.”

In the future, researchers can look back at these records and see how butterfly populations have changed. In much the same way, OSAC’s collection of arthropods, which includes specimens at least a century old, is a physical representation of past conditions. Scientists can look at an insect and its label and know where it was at a certain time.

What We’ve Lost

Collections are the historical records of science, playing an especially vital role in conservation. If we don’t know how things once were, how can we know that anything is different? Robert Pyle, founder of the Xerces Society, correlates the loss of species with the impoverishment of human knowledge, what he calls the “extinction of experience.” It’s an unconscious lowering of standards.

Ornithoptera

This is a concept that Randy Olson, a scientist and filmmaker, features in his project, Shifting Baselines. “Shifting baselines” is “the failure to notice change,” says Olson. His project focuses on marine conservation, but the general idea can be applied to any environment. Olson describes the beautiful, vibrant nature of Jamaican coral reefs in the 1970s. He cites Jeremy Jackson of the Scripps Institution of Oceanography, who says that coral bleaching and overfishing have now reduced these corals to algae-covered messes.

That’s where shifting baselines come into play. If Jackson hadn’t kept records, if that colorful coral reef were not his baseline, who would know it had ever existed? Our present day baseline would be a lack of corals, and slowly, our concept of the world before human interference would grow unclear.

Baseline of Bugs

With its stockpile of preserved arthropods, OSAC is creating a baseline of its own. Many species are in decline, and should extinction happen, OSAC provides the means to see what we have lost. Its role in arthropod surveys also contributes to record-keeping.

“We don’t have the arrogance to say we’re the best collection in the country by any means,” Marshall adds. This may be true in terms of numbers; the Smithsonian has over 35 million specimens. But for the Pacific Northwest, there couldn’t be a more important arthropod collection.

Oregon may seem to be brimming with insects today, but how does that compare to fifty years ago? Think how it will compare to fifty years from now.

As I walked out of OSU’s impressive arthropod collection, I imagined a hypothetical day when Oregon’s great insect biodiversity might be limited to the confines of that room. Despite my youthful aversion to “bugs,” I would hate to see them gone for good.

In a Paradigms class, OSU physicist Janet Tate works with students investigating the properties of oscillations. (Photo: Karl Maasdam)

At Oregon State University, advanced physics instruction has already made the transition. Ten years ago, Corinne Manogue and colleagues in the OSU Department of Physics overhauled their whole approach to teaching. They turned the focus from lecture to action, from professor to student, from rote learning to problem solving. They redesigned a classroom where students collaborate around tables and sketch and share ideas on small white boards. They concentrate on topics that are central to the understanding of subdisciplines (such as classical mechanics, optics or electromagnetism) normally treated in separate courses. They can shift from presentation to group discussion to lab in seconds. No lecture-style seating or time to rest for these physicists-to-be.

“Learning this way was extremely exciting,” wrote OSU graduate Ethan Bernard in 2003. “And I remember toying with the application of basis functions, vector fields and canonical ensembles to diverse things like taste, color, economics and evolution. I learned faster in Paradigms that at any other time in college.”

“To my knowledge, OSU is the only university in the country to do this overhaul in the upper division,” says Manogue. Begun in 1997 as a modest effort to accommodate students enrolled in engineering physics internships, the OSU reform initiative has received more than $1 million in National Science Foundation support, including a 2007 grant to write two new textbooks, to create a detailed Web site and to adapt abstract mathematical tools to specific circumstances in physics.

Since 1999, Manogue has presented the program, known as Paradigms in Physics, to educational conferences and to more than a dozen of the nation’s 760 degree-granting physics departments. Elements of the curriculum are being adapted at other universities such as Texas A&M and the University of Colorado.

Paradigms strives to give students a rich understanding of the many approaches that physicists take to problem solving. Power, says Manogue, comes with mastery of the tools that physicists have developed in concert with mathematicians and software engineers. So the Paradigms courses — three-week intensive classes that meet daily — revolve around ten fundmental topics (oscillations, central forces, one-dimensional waves, and periodic potentials, for example) and the equations, graphs, computer visualizations and narratives that define those topics.

“Typically, students get exposed to a topic once in an advanced course,” says Manogue. “They either get it or they don’t. But that’s not the way a lot of people learn. They learn by doing things over and over again in different contexts.”

In a typical junior-level class, Manogue poses a problem and asks students to discuss it, to define it in mathematical terms and to describe the solution in words. As students talk, she stops to listen at each table and asks leading questions, challenging students on their choices of words or equations. Whether dealing with the oscillations of a string, an electromagnetic charge in space or the forces that affect planets as they revolve around the sun, students are encouraged to think like physicists.

In the senior year, students use many of the same tools to explore more advanced topics in subjects such as quantum me-chanics or electromagnetism. By building on what they learned in the previous year, they reinforce their knowledge and gain confidence.

“About mid-year, they start saying things like, ’I’m starting to understand what it means to be a physicist,’” says Manogue. “Or what it means to solve physics problems. It’s almost like they were undergoing a phase transition, where they just start thinking differently.”

Manogue suspects that the changes in learning stem from the philosophy of active engagement, but pinpointing which methods are critical takes systematic assessment. In 2007, the department hired Assistant Professor Dedra Demaree to lead physics education research and bring these active engagement ideas to the large-enrollment introductory courses.

And the department’s home in Weniger Hall is scheduled to receive an upgrade in its classroom facilities in the near future. In rooms now equipped with standard lecture-style seating, the department is working with Peter Saunders in OSU’s Center for Teaching and Learning and the Classroom Renovation Committee to incorporate designs that can accommodate more active learning approaches.

Learn more about OSU’s Paradigms in Physics program at physics.oregonstate.edu/paradigms

“Many oceanographic processes — and the natural history of microbial plankton is no exception — are veiled by the vastness and complexity of the oceans,” Stephen Giovannoni says. (Photo: Karl Maasdam)

Microbes are masters of adaptation.

In some of Earth’s most extreme environments — Antarc- tica’s frigid ice fields, Yellowstone’s sulfuric hot springs, Crater Lake’s lightless depths, the oceans’ deep-sea basalts — Stephen Giovannoni has discovered thriving communities of bacteria. As the holder of the Emile F. Pernot Distinguished Professorship in Microbiology, he has discovered some of the most abundant life forms on the planet.

About two decades ago, the Oregon State University micro- biologist went looking for microscopic master-adapters in yet another place thought to be inhospitable to life: the clear, still waters of the Sargasso Sea south of Bermuda. There, he made a remarkable find. Not only do bacterioplankton (ocean-drifting bacteria) live in this sea once considered a desert, they’re everywhere. It turns out that this newly found branch of bacteria, named SAR for the Sargasso, is among the most plentiful — and thus evolutionarily successful — life forms on the planet.

“SAR11 is ridiculously abundant,” Giovannoni says, referring to the first SAR strain identified. In fact, the species came to be called Pelagibacter ubique (“ubiquitous ocean bacterium”) when it started turning up in seawater samples worldwide. “They have been present in more than 50 studies from around the globe and account for 25 percent of all the genes found in these studies.”

It had eluded detection mainly because of its diminutive size — small even for a microbe. “SAR11 was basically invisible before,” Giovannoni says, explaining that the key to its success was
simplicity and efficiency. “SAR11 is just better than any other organism at capturing the traces of organic matter dissolved in the oceans.”

After this astounding discovery in 2002, Giovannoni’s lab devised novel technologies for growing these kinds of extra-tiny organisms without Petri dishes. Using gene cloning and DNA sequencing, he and his colleagues have so far sequenced 27 hard-to-grow microorganisms never before described. They have shipped samples to scientists all over the world.

“Our research has led to a general appreciation of how impor- tant these previously unknown organisms are to global ecology,” says Giovannoni. Support from the Emile F. Pernot fund, the National Science Foundation and the Gordon and Betty Moore Foundation have been key. (Emile Pernot helped to establish OSU’s Department of Microbiology. The professorship created by his daughter Mabel Pernot is awarded on a rotating basis and will next be held by Theo Dreher, department chair.)

To figure out how marine microbes compete for and adapt to spatial, temporal and seasonal niches and how they contribute to the cycling of carbon in the oceans, Giovannoni is looking at every- thing from marine snow (carbon-carrying particles that sink into deeper ocean layers) to spring upwelling and summer stratification to species richness (total species in a sample) and surface warming.

“Dynamic interactions between these marine microorganisms lie at the heart of the carbon cycle,” the researcher says. “But progress toward understanding these interactions has been slow to emerge because of the complexity of microbial community ecology.”

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For information about supporting research and teaching through faculty endowments, contact the Oregon State University Foundation, 1-800-354-7281 or visit CampaignforOSU.org.

(Illustration: Santiago Uceda)

Lionfish memo to coral reefs in the Bahamas: There’s a new predator in town. Native to the South Pacific, the invasive lionfish is reducing the abundance of native fishes on coral reefs in the Bahamas (see “Deep Ecology,” in Terra, spring 2008). OSU zoologist Mark Hixon leads a team of graduate students and other collaborators working to understand the impacts as well as the factors that naturally control this voracious predator in its native habitat.

In lab and field studies conducted in 2010, they are comparing Bahamian reef systems with and without lionfish and have demonstrated that lionfish outcompete Nassau grouper, which are native to the Bahamas, for access to reef shelters. Lionfish do not eat small grouper, and grouper do not affect lionfish as either a predator or a habitat competitor.

Ongoing studies include lionfish behavior and ecology in the invaded and the native ranges and daily activity observations, as well as patterns of growth and survival.

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See Mark Hixon’s 2010 “Oceans of Life” presentation, including videos of lionfish feeding.

For information about supporting research and teaching through faculty endowments, contact the Oregon State University Foundation, 1-800-354-7281 or visit CampaignforOSU.org.

A school of yellow tang in Hawaii (photo by Bill Walsh)

The findings add credibility to what scientists have believed for some time, but until now been unable to directly document. The study also provides a significant demonstration of the ability of marine reserves to rebuild fishery stocks in areas outside the reserves.

The research was published this week in PLoS One, a scientific journal.

“We already know that marine reserves will grow larger fish and some of them will leave that specific area, what we call spillover,” said Mark Hixon, a professor of marine biology at OSU. “Now we’ve clearly shown that fish larvae that were spawned inside marine reserves can drift with currents and replenish fished areas long distances away.

“This is a direct observation, not just a model, that successful marine reserves can sustain fisheries beyond their borders,” he said. “That’s an important result that should help resolve some skepticism about reserves. And the life cycle of our study fish is very similar to many species of marine fish, including rockfishes and other species off Oregon. The results are highly relevant to other regions.”

The findings were based on the creation in 1999 of nine marine protected areas on the west coast of the “big island” of Hawaii. They were set up in the face of serious declines of a beautiful tropical fish called yellow tang, which formed the basis for an important trade in the aquarium industry.

“This fishery was facing collapse about 10 years ago,” Hixon said. “Now, after the creation of marine reserves, the fishery is doing well.”

The yellow tang was an ideal fish to help answer the question of larval dispersal because once its larvae settle onto a reef and begin to grow, they are not migratory, and live in a home range about half a mile in diameter. If the fish are going to move any significant distance from where they are born, it would have to be as a larva – a young life form about the size of a grain of rice – drifting with the currents for up to two months before settling back to adult habitats.

Mark Christie, an OSU postdoctoral research associate and lead author of the study, developed some new

Yellow tang larvae drift for miles on ocean currents before settling to live in coral reefs (Photo: Sarah Mctee)

approaches to the use of DNA fingerprinting and sophisticated statistical analysis that were able to match juvenile fish with their parents, wherever they may have been from. In field research from 2006, the scientists performed genetic and statistical analyses on 1,073 juvenile and adult fish, and found evidence that many healthy juvenile fish had spawned from parents long distances away, up to 114 miles, including some from marine protected areas.

“This is similar to the type of forensic technology you might see on television, but more advanced,” Christie said. “We’re optimistic it will help us learn a great deal more about fish movements, fishery stocks, and the genetic effects of fishing, including work with steelhead, salmon, rockfish and other species here in the Pacific Northwest.”

This study should help answer some of the questions about the ability of marine reserves to help rebuild fisheries, the scientists said. It should also add scientific precision to the siting of reserves for that purpose, which is just one of many roles that a marine reserve can play. Many states are establishing marine reserves off their coasts, and Oregon is in the process of developing a limited network of marine reserves to test their effectiveness. The methods used in this study could also become a powerful new tool to improve fisheries management, Hixon said.

“Tracking the movement of fish larvae in the open ocean isn’t the easiest thing in the world to do,” Hixon said. “It’s not like putting a radio collar on a deer. This approach will provide valuable information to help optimize the placement of reserves, identify the boundaries of fishery stocks, and other applications.”

The issue of larval dispersal is also important, the researchers say, because past studies at OSU have shown that large, fat female fish produce massive amounts of eggs and sometimes healthier larvae than smaller fish. For example, a single two-foot vermillion rockfish produces more eggs than 17 females that are 14 inches long.

But these same large fish, which have now been shown to play key roles in larval production and fish population replenishment, are also among those most commonly sought in fisheries.

The study was done in collaboration with the University of Hawaii, Washington State University, National Marine Fisheries Services and the Hawaii Department of Natural Resources. It was funded by Conservation International.

“The identification of connectivity between distant reef fish populations on the island of Hawaii demonstrates that human coastal communities are also linked,” the researchers wrote in their conclusion. “Management in one part of the ocean affects people who use another part of the ocean.”

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See Mark Hixon’s 2010 “Oceans of Life” presentation, including videos and images of seafloor trawling.

“Bug Poop Grows Trees” (BPGT)

In Andrew Moldenke’s forest ecology course, students get the BPGT acronym drilled into their heads from Day One. Oregon’s fabled old-growth forests owe their existence to insect digestion, and the professor wants to make sure nobody forgets it.
More…

Chris Marshall had collected insects in a lot of unusual places. But scrounging for a rare species of moth in the fur of a three-toed sloth had to be the weirdest.

It happened one black, sweltering night in the unexplored rainforests of northern Guyana in 2006. The OSU entomologist, rousted from his hammock by a commotion in camp, switched on his headlamp. He found himself looking into the frightened eyes of a docile, moon-faced mammal captured by the native guides assisting the scientific expedition.

The two-foot tall creature, whose coarse, shaggy hair glistened with a green patina of algae, sat quietly as Marshall gently searched its back for specimens of the Bradipodicola hahneli (“sloth moth”), which lives exclusively in this hairy habitat. Then, without warning, the sloth turned to face the researcher. Before Marshall could react, the animal wrapped its powerful, apelike arms around him. With the sloth’s hot breath on his neck, Marshall felt a rush of adrenaline as he visualized its peg-like teeth and its four-inch hooked claws.

“I had a furry, wild animal clinging tightly to my body with its face inches from mine,” Marshall recounts. “I couldn’t have pried it off without great effort. It was then that I realized I didn’t really know whether these animals are friendly or aggressive.”

No blood was spilled that night. The guides disengaged the sloth and sent it slouching up the nearest tree. Marshall, meanwhile, sealed his hard-won specimens into tiny plastic vials. Before the journey was over, the zoology faculty member would fill thousands of such vials, as well as glassine envelopes and zip-locked, ethanol-filled polyethylene bags, with bugs destined for arthropod collections in Corvallis and the Guyanese capital of Georgetown. Among the specimens shipped out of the jungle were several beetles never seen by scientists. To identify his discoveries would require months of meticulous lab work and tedious database searching.

“It’s always exciting to identify a new species, but there’s no automatic definition of how that’s done,” Marshall explains. “Some scientists are turning toward using a certain percentage of difference in DNA, but there’s still skepticism about that approach. More traditionally, we look at things like shape, body structure, male genitalia, ability to interbreed and other attributes of an organism. Integrating all of this information into a coherent notion of a ‘species’ can take months or years. That’s the main reason it takes so long to identify everything from a trip like this.”

The expedition’s finds — which in addition to the beetles included new species of katydids, butterflies, catfish and frogs — will contribute to scientific understanding of the Guyana Shield and other tropical rainforests at risk from extraction industries such as drilling, mining and logging, as well as deforestation for agriculture. Conservation International, one of the expedition’s sponsors, has designated “biodiversity hotspots” like the Guyana Shield as “the richest and most threatened reservoirs of plant and animal life on earth.”

“The air was calm, full of the eternal hum of insects, a tropical chorus of many octaves, from the deep drone of the bee to the high, keen pipe of the mosquito.”
Sir Arthur Conan Doyle, The Lost World, 1912

Marshall and a team of researchers from Venezuela, Colombia and the United States had joined Guyanese scientists in this South American wilderness to seek insects, birds, reptiles, amphibians and fish that are unique to this place, a land so otherworldly, so untouched, that it inspired Sir Arthur Conan Doyle’s 1912 tale of remnant dinosaurs. In this “lost world” known as the Guyana Shield, vast plateaus of ancient granite rise 3,000 feet above a jungle canopy whose shadows hide jaguars as elusive as ghosts and snakes as thick as tree trunks. Mazes of rivers breed electric eels, stingrays and caimans (cousins of the crocodile). Also swimming in the teeming waters is one of the world’s largest freshwater fish, the arapaima, which can grow to 10 feet in length and weigh more than 400 pounds.

“Ironically,” Marshall notes, “the arapaima is related to the minnow.”

But it’s the bugs, millions and millions of them, that dominate the landscape. Like the “sloth moth,” which subsists on blue-green algae growing on the slow-motion mammal, each species exists in perfect adaptation to a precise niche in the biosphere. Scarabs scour the forest floor for dead things and manure. Mantises disguise themselves as sticks or leaves. Butterflies “puddle” on moist soil, resembling seas of pale-green petals as they ingest salts and minerals. Katydids clutch smaller bugs in their spiny legs and crunch them with their powerful jaws. Lightning bugs glow like sparks from campfires. Ants use their shovel-shaped heads to plug their burrows against predators. Other ants spy their prey with giant, high-resolution eyes.

Guyana’s butterflies, dragonflies, scorpions and spiders were intriguing to Marshall, who curates and manages the Oregon State Arthropod Collection (see sidebar). But his scientific investigations were focused elsewhere. While his fellow entomologists concentrated on ants and katydids, he attended to his specialty: beetles. The jungle boasts beetles that shine like obsidian and others that shimmer with rainbow iridescence. Even though he’s an expert on the glossy black beetles of the family Passalidae, Marshall admits to having a soft spot for the drabber members of the world’s vast and varied beetle species, estimated at 5 million. “I like the small, humble brown beetles better than the big, showy ones,” he says. “I find it more interesting to sift through the unobtrusive, obscure groups. Fewer collectors care about them, so they’re much less studied.”

Some of the bugs he encountered, however, were not so appealing. The ubiquitous ticks, for instance, forced him to soak his clothes in pyrethrins (pesticides made from chrysanthemum flowers). Malaria-bearing mosquitoes made sleeping nets mandatory. To foil swarms of sticky, persistent black flies, which can carry river-blindness disease in their painful bite, Marshall worked in long sleeves despite the oppressive heat. “The horsefly was everyone’s bane,” he says. “We couldn’t get away from them. One day we were hiking through a swamp of spiny palms. It was hard to walk, and it was real wet, very humid and muggy. That’s where the horseflies were the worst they could possibly be.”

Another perilous pest was the sandfly. Smaller than an ordinary mosquito, this insect transmits a disease called Leishmaniasis. The protozoan, a microscopic single-celled organism, can cause devastating wounds that destroy skin and mucous membranes, causing massive scars. Worse, some victims have lost ears and noses.

Why would Marshall and his fellow researchers risk life, limb and nose in this inhospitable place? Beyond the basic motives of science (delving into mysteries, uncovering clues, connecting dots) and beyond the more prosaic goal of beefing up the bug collections at Georgetown and at OSU, they were driven by the urgency of an endangered ecosystem. The expedition was part of an ongoing movement to protect the shield’s extraordinary biodiversity from human exploitation. In cooperation with a small group of Amerindians indigenous to the Guyana Shield, the Guyanese government has set aside a 1.5 million-acre swath of the rainforest as a preserve. Funded by the Smithsonian Institution, National Geographic and Conservation International, the expedition carried out a “rapid biodiversity assessment” — in essence, a marathon collecting binge for zoologists — to help document the scope of Guyana’s species diversity. One set of specimens would go to the Center for the Study of Biological Diversity at the University of Georgetown.

The mission had a cultural component, as well. The native guides and porters were naturalists-in-training. Members of the Wai Wai tribe have been tasked with managing the preserve, protecting the animals and plants living along the mighty Essequibo River and its tributary, the Sipu, against poachers, loggers and miners. Investigating their ecosystem along with the university-trained scientists, the Wai Wai were preparing to become para-biologists and rangers, formalized roles for the people who have been Guyana’s unofficial “forest keepers” for generations.

Expedition to the Edge

“Once some bandy-legged, lurching creature, an ant-eater or a bear, scuttled clumsily amid the shadows.”
A.C. Doyle

Marshall first met his guides after the expedition embarked in early October 2006 from a small airfield on the outskirts of Georgetown. A reluctant flyer, he felt the color drain from his sweat-beaded face as the twin-prop plane lifted off and rose above a patchwork of small farms and scattered houses. Soon, from the window of the droning aircraft the entomologist saw nothing but the rainforest’s emerald canopy stitched to the sky in every direction.

The flight, it turned out, was just the first of Marshall’s many white-knuckle experiences in Guyana. The plane touched down near the banks of the Essequibo, where the Wai Wai guides, “druggers” (equipment porters) and “line cutters” (machete-wielding trailblazers) were waiting to take the team upriver. In this trackless forest, modes of travel are two: foot and canoe. Several dugouts, hand-carved of dark purple heartwood in the ancestral Wai Wai tradition, sat on the riverbank. But in a jarring clash of cultures, each primitive boat sported a shiny outboard motor. The 750-horsepower Evinrudes, lent to the expedition by Conservation International, have obvious advantages over paddles for transporting several entomologists, an ornithologist, an ichthyologist, a herpetologist, a mammalogist and a water-quality expert — as well as hundreds of pounds of food and gear — deep into the lost world.

The boats pushed off. The tangled green understory, lush and luminous in the filtered sunlight, closed around the travelers. It wasn’t long before Marshall noticed water pooling around his feet, apparently seeping through a crack in the heart-wood hidden under bulging bags of gear. During the two-day journey, whenever the canoe struck a submerged log with a loud crack! (as it did every now and then), he halfway expected the vessel to split in two “like a peapod” and dump the researchers into waters as brown and opaque as chocolate milk. But the craft, which the Wai Wai patched each night with sticky, resinous bark scrapings, was sound and sturdy in its ancient design. It never foundered.

After the researchers disembarked, they spent another day hiking into the forest to reach their first survey site.

It’s Marshall’s expertise as a coleopterist (beetle specialist) that made him vital to the expedition. That’s because beetles, particularly dung beetles, are important components of tropical rainforest systems. “Dung beetles are important decomposer organisms, involved in nutrient recycling, seed dispersal and the control of vertebrate parasites,” British researcher Andrew Davis and colleagues wrote in the Journal of Applied Ecology in 2001. “Consequently, dung beetles are a useful indicator group because they reflect structural differences between biotope types.”

The lowly dung beetle or scarab (family Scarabaeidae), largely ignored after its heyday as a deity in ancient Egyptian mythology, has recently reclaimed some of its lost stature, this time as an indicator organism. All over the planet, from Australia to Southeast Asia, ecologists and entomologists study scarabs as gauges of ecosystem well-being and harbingers of stress.

“There is a lot of interest in dung beetles globally because of their ability to reflect changes in ecosystem health and land usage,” says Marshall. “Each species has specific soil and forest ecological needs, and some of them are linked to very specific vertebrate fauna – mammals and birds. As mammal and bird diversity declines, so does the scarab beetle associated with that habitat.”

Collectors lure scarabs with baited traps. However, packing in buckets of hog manure, the usual bait, would be impractical in Guyana. And because scarabs are fast and efficient manure removers, finding it in the rainforest can be difficult. So Marshall and other dung beetle experts are sometimes forced to resort to human excrement.

“It’s not the ideal bait,” Marshall hastens to explain. “There is an ongoing effort to create a synthetic lure. But scarabs’ sense of smell is extremely sensitive, and designing an imitation for manure is actually more complex than it might at first appear.”

Distasteful as dung beetle baiting might be, the strategy brings speed and efficiency to ecological research. “With passive traps,” the entomologist explains, “you can do a survey of the dung beetle in 24 to 48 hours that can serve as a surrogate for the months of work necessary to survey birds or mammals.”

“…during the hot hours of the day only the full drone of insects, like the beat of a distant surf, filled the ear…”
A.C. Doyle

When he wasn’t baiting traps and collecting captive scarabs, Marshall was chopping open rotting logs in search of his other Guyana get-list priority: patent-leather beetles. As shiny and black as Sunday-school shoes, these showy bugs have intrigued him since the 1990s when he was a Ph.D. student at Cornell, not so much for themselves but for their symbiotic bond with another species of bug, the mite (see sidebar, “Born To Love Bugs”).

One late afternoon near dusk, alone and far from camp, he was hurrying to collect his captive scarabs before the light failed. His excitement about finding a rare specimen in his trap dissolved instantly when he heard a sound in the brush. He froze, his senses on hyper-alert as the crunch-crunch-crunch of large feet on leaf litter got louder and louder. He weighed his options: Stick around and take pictures or back away slowly. Both hoping and fearing that the unseen creature was a jaguar, the researcher sucked in his breath and decided to stand his ground, focusing his video camera on the rustling shadows. When the beast emerged into the dappled light, it was standing just feet in front of him: a giant South American anteater, Myrmecophaga tridactyla, its funnel-like nose snuffling the earth in search of termites. The gangly, bushy-tailed animal stood up on its hind legs, looked curiously at the researcher and then lumbered away, snout to the ground.

Just another bug collector.

Sharing Guyana’s rainforests with the sloth and the anteater are arthropod species in the hundreds of thousands. Only a few thousand have been identified and cataloged. That ratio is reflected worldwide: Just 2 million of Earth’s total number of animal and insect species — estimated as high as 30 million — have been described, according to the World Conservation Union’s Species Survival Commission. Faster than scientists like Marshall can find and identify unknown life forms, others are disappearing forever. More than 15,000 species are at high risk for extinction, and the rate is speeding up as the Earth warms and habitats shrink.

For Marshall, knowing what’s at stake dwarfs the danger and discomfort of rainforest exploration.

“The knowledge gained far outweighs the risks,” he says. “It’s only through these types of expeditions that biologists discover new species and work toward our ultimate goal of documenting the Earth’s insect diversity.”

The global race to understand patterns of biodiversity and ecology is in full-tilt, Marshall says. “When a species goes extinct, we lose a piece of the puzzle forever,” he stresses. “To complete the whole picture, we need to do two things: halt or reverse the trends that are driving extinctions and share specimens with the world’s natural history museums.”

“We need to preserve as many pieces of the puzzle as possible. And we need to do it quickly.“

This lionfish (Pterois volitans) swam to within six inches of the camera as the shot was taken. “We think that he saw his reflection in the glass and was trying to scare off his ‘rival,’” says Robbie Wisdom. (Photo: Daniel Wisdom)

When talk turns to the mud-dwelling creatures of the deep seafloor, Mark Hixon jumps up from his swivel chair, strides to a cabinet in his office and swings open the door. Taking out a long cardboard box, he gently lays it on his desk.

“This,” he says, reaching inside, “is a sponge from just off the Oregon coast. Isn’t it cool?”

He holds up the dried organism, an 18-inch-long spire the color of raw pinewood, delicately honeycombed. Its tousle of roots tells you why scientists long classified sponges, mistakenly, as plants. In your hand it is nearly weightless.

“There’s a whole host of things that live down there,” says Professor Hixon, an internationally known marine ecologist in OSU’s Department of Zoology.

The astounding array of seafloor organisms — brittlestars and bivalves, marine worms and sea pens, cold-water corals and sponge species by the score — plays a vital role in ocean systems by providing food and shelter for finfish and shellfish. Before manned submersibles and remotely operated vehicles (ROVs) gave scientists direct, deep-water access, Hixon says, many viewed the teeming ocean mud as empty ooze. Now they know the seafloor is the “nursery” for many of the finned species humans eat.

Hixon’s research on fish population dynamics has taken him to most of the planet’s oceans, both temperate and tropical. One of the world’s leading authorities on coral reefs, he has been cited in scientific journals more often than any other coral-reef ecologist in the Western Hemisphere over the past decade, according to the Thomson Institute for Science Research. He was ranked third worldwide behind two scientists who live adjacent to coral reefs year-round.

One big mystery relevant to both fisheries management and marine conservation is whether and how isolated populations of adult fish are linked. Understanding these links will help answer questions such as, Can protecting fish in one location compensate for overfishing in another location? Hanging in the balance are decisions about marine reserves that, while designed to sustain fisheries, have raised fishing industry concerns.

In two ongoing studies — one in Hawaii, the other in the Bahamas — Hixon and his graduate students are investigating connections among isolated populations of coral-reef fishes. They are studying the demographics of the yellow tang on Hawaii’s Big Island and the bicolor damselfish in Exuma Sound off the Bahamas. They are sampling DNA from adult and juvenile fish at multiple reefs. Their goal is to understand the drift patterns of fertilized eggs and larvae that travel with tides and currents in a process known as “larval dispersal.” And they are testing whether a high level of larval connectivity is also reflected in the population dynamics of adult fish.

Ultimately, the answers will guide conservation and management, not only of fish, but of the reefs themselves. These complex ecosystems brim with more species than anyplace on the planet, even tropical rainforests. And many are dying. Pollution, global warming and overfishing have degraded about 20 percent of Earth’s coral reefs so far. Another 50 percent are at risk. In Hawaii, the yellow tang, coveted by the aquarium trade for its brilliant color, was depleted until the state created marine reserves along the Kohala-Kona coast to protect them. Preliminary data from Hixon and his colleagues suggest the reserves are working. “Long-term policy about marine reserves must be based on data rather than hearsay,” he says. The yellow tang genetics, still being analyzed in Hixon’s lab, will reveal which of Hawaii’s reefs need replenishment from spawn drifting in from highly productive “source” reefs and where those respective reefs are located.

Ocean Views

In his three decades as a fish ecologist, Hixon has dived in oceans from the Pacific to the Atlantic, the Caribbean to the Coral Sea. Studying marine science at UC Santa Barbara was, for him, just a natural extension of a sea-centered boyhood as a surfer and the son of a naval officer. As the family moved from one coastline to another, young Mark – a fan of Sea Hunt and ocean explorer Jacques Cousteau – had a recurring dream: He would be standing on the beach trying to imagine what lived beneath the heaving seas when, suddenly, the water would disappear, revealing fishes “swimming around in the air.”

As a doctoral student in the 1970s, he shivered through dozens of bone-chilling dives in cold-water kelp forests. These days, he relies on small research submarines in the frigid northern waters as he studies the ecology of coastal marine fishes, focusing on what naturally regulates populations and sustains biodiversity. His scuba gear gets used mostly in warm-water ecosystems.

The tropical reef research, part of OSU’s top-ranked efforts in conservation biology, has relevance here in Oregon. “Off Oregon, it’s impossible to gather the enormous amount of data we can extract from warm, clear tropical waters,” Hixon says. “However, once our methods are developed and tested in the tropics, we can bring them home to Oregon.”

Such research is timely. Governor Ted Kulongoski is leading an initiative to create marine reserves in the Oregon Territorial Sea to replenish and preserve the state’s marine ecosystems and fisheries. Hixon’s work will help test the effectiveness of Oregon’s reserves. For example, in the 1990s, Hixon, who chairs the Marine Protected Areas Federal Advisory Committee, witnessed a post-trawl patch on Oregon’s continental shelf from the portal of a research sub named Delta. He and his team were surveying fish populations on the rocky reefs between Bandon and Cape Blanco, a fish-rich outcrop called Coquille Bank, when they stumbled upon a muddy area deeply scarred by groundfish trawl nets. An adjacent area unmarred by trawl tracks provided a readymade control site. The researchers decided to conduct a comparative study, the first-ever documentation of trawling impacts on the deep mud seafloor off North America’s West Coast.

The contrast was stark. About half as many groundfish species were living in the trawled area as in the untrawled area. Numbers of individuals, too, were significantly lower in the trawled site. Most striking, though, was the disparity in sea pens and other invertebrates. Members of the jellyfish phylum, the fragile, soft-bodied sea pens stood out brightly in Delta’s spotlight as it scanned the sediment in the lightless depths. Forests of the flowerlike stalks of yellow-and-orange polyps were anchored in the untrawled mud. But where the nets had passed, sea pens were virtually absent, Hixon and Brian Tissot of Washington State University reported in the Journal of Experimental Marine Biology and Ecology last year.

Sea pens and other such invertebrates can’t swim away when their habitat is disturbed. Nor can they quickly rebound. These “sessile, slow-growing, long-lived species,” Hixon notes, “are likely to recover slowly” from the effects of bottom dragging.

“What we saw off Coquille Bank,” Hixon concludes, “was completely consistent with studies conducted all over the world showing that bottom trawling has severe impacts on seafloor habitat.” Unfortunately, Hixon and Tissot’s findings were dismissed by the Oregon trawl industry, which questioned their validity, despite appearing in a peer-reviewed scientific journal.

“My greatest frustration as a scientist happens when any special interests reject peer-reviewed science,” says Hixon. As Chair of the Ocean Sciences Advisory Committee for the National Science Foundation, Hixon notes that rejection of scientific findings about climate change and ocean acidification stem from the same attitude. Hixon likes to quote Aldous Huxley, author of Brave New World: “Facts do not cease to exist because they are ignored.”

For Hixon, biology and conservation have become inseparable as threats to the oceans continue to grow. “The challenge,” he says, “is to successfully walk the fine line between scientific objectivity and personal advocacy. Some scientists refuse to walk that line, but I did not abdicate my citizenship when I became a scientist.” Discovering how to connect science (left-brained and analytical) with public engagement (right-brained and passionate) is as urgent to Hixon as tracking fish movements across reefs. Data alone won’t save our oceans. “People must feel it here,” he says, placing his hand over his heart, “to value not only themselves and the present, but also to value others and the future.”

To that end, he and Professor of Philosophy Kathleen Dean Moore, director of OSU’s Spring Creek Project for Ideas, Nature and the Written Word, are investigating the psychology of conservation communications: how to craft messages that effectively change minds and behaviors.

Mark Hixon wants our progeny to inherit a world still relatively intact. He wants tomorrow’s children to have a chance to dive into the pulsating rainbow of biodiversity that is the tropical reef. “You feel as if you’ve fallen into a universe of stars,” he says. “It really, truly is amazing.”

Meet the photographers, Daniel and Robbie Wisdom

Protecting tropical reefs is a passion for these two graduate students in OSU’s College of Oceanic and Atmospheric Sciences. The Idaho natives plan to live in Australia where they can pursue scuba and underwater photography. Both are enrolled in OSU’s Marine Resource Management program. Daniel works with Assistant Professor Kelly Benoit-Bird analyzing fish-school movements with high-frequency sonar. Robbie is studying cooperative marketing programs for small seafood micro-canners in the Pacific Northwest with Gil Sylvia, superintendent of the Coastal Oregon Marine Experiment Station in Newport.

See Mark Hixon’s 2010 “Oceans of Life” presentation for the F.A. Gilfillan Memorial Award

• Mark Hixon’s Web site
• Department of Zoology
• College of Science
• National Science Foundation
• National Undersea Research Program
• OSU Foundation

OSU news releases

• OSU Recognized for Coral Reef Research (9-24-07)
• ‘Ten Commandments’ Could Improve Fisheries Management (2-19-07)
• OSU Marine Biologist to Chair Federal Advisory Committee (10-19-06)
• Experts Propose Major Mapping Program on Oregon Coast (3-22-06)

The spread of American beach grass could raise risks for structures along the Northwest coast, such as these new houses at Ocean Shores, Washington. (Photo: Phoebe Zarnetske)

Unnoticed by most beach–goers, a showdown is under way in Oregon’s coastal dunes, and the winner could pack increased risks for coastal property, especially during winter storms.

OSU scientists have documented a slow but steady takeover by American beach grass (Ammophila breviligulata), an invasive species from the East Coast and Great Lakes. They have found that protective “foredunes” covered by the new species are only about half as high as those created by the European species of grass (Ammophila arenaria), another non–native that was dominant. And they are initiating research to understand what gives the American variety the edge and what that might mean for coastal property owners and native plant restoration.

The takeover has already occurred from Ocean Shores, Washington, to Pacific City, Oregon, and it’s continuing. “This decrease in dune height may translate into a significant decrease in coastal protection from storms and tsunamis,” says Eric Seabloom, an OSU assistant professor of zoology. Historically, the dunes were more open than they are today, hosting plants such as wild rye and relatives of morning glory, buckwheat and other wildflowers. The European grass has stabilized Oregon dunes since it was first introduced for this purpose around 1900. “It did its job extremely well,” says Sally Hacker, OSU associate professor of zoology and an expert on estuaries. “Without it, the sand would cover towns and roads.”

It was so successful that by the 1930s it had spread along the entire Oregon coast and created an extensive “foredune” system, large protective sand hills in front of almost every sandy beach. These dunes can provide significant protection for homes, roads, towns and other infrastructure, and serve as a barrier against flooding during storm surges.

The second invasion, by American beach grass, went practically undetected for 50 years. Introduced near the mouth of the Columbia River in the mid–1930s, also to stabilize beaches, it out–competes its European cousin. It wasn’t until a survey in the late 1980s by Seabloom and a colleague at Evergreen State College that scientists realized how far it had spread, south to Tillamook Head and north to the Olympic Peninsula.

Coastal surveys have now determined that from Pacific City north, American beach
grass has nearly replaced the European variety. “Lower dune heights, increasing
wave heights that have been observed over the last 50 years and global climate change
could create a scenario in which the dunes no longer serve a coastal protection function,”
Hacker says.

With funding from Oregon Sea Grant, zoology Ph.D. student Phoebe Zarnetske of
Storrs, Connecticut, is teasing out the story behind these trends. In experiments at the
Hatfield Marine Science Center in Newport and at the O.H. Hinsdale Wave Research
Laboratory on the OSU campus, she is subjecting the two grasses to varying rates
of sand deposition to see which one thrives. She has visited practically every sandy
beach in Oregon and Washington to survey beach grass conditions. And as a student in OSU’s Ecosystem Informatics IGERT program, she will develop a mathematical model to explain how this dynamic system is changing.

Beyond the protection concerns, there are other ecological issues in play as well. While
the foredune system created by European beach grass is good for coastal landowners, it is not so good for endangered native plant species and the federally threatened
Western snowy plover. As more sand accumulated in growing stands of the European
grass, the land behind the dune tended to get turned into wetlands and forest habitats.
“The willows and other trees and larger shrubs you often see behind the dunes
are an indication that wetlands are being formed in the mini–valley behind the
dunes,” says Hacker.

As European grass advanced, beach habitat disappeared, taking with it the
plovers’ critical nesting grounds. The southward march of the American beach
grass could reverse the trend. Hacker and Seabloom are also working
with Peter Ruggiero, a coastal geomorphologist in the OSU Department of Geosciences,
to understand how coastal sediment supply and nearshore oceanographic
conditions influence beach grass competition and the coastal protection capabilities
of dunes. The researchers plan to meet with coastal property owners in 2008 to
discuss the results of their work.