Friday, August 21, 2009

Unresolved Mysteries from the Deep Atlantic: The Secrets the Hagfish Hides

by Hiba Alhomoud, Cornell University

Three students aboard the J. B. Heiser stagger to reel in an endless length of water-drenched rope. The stationary boat rocks back and forth on the surface of the North Atlantic, seven miles off the coast of Maine. These budding scientists struggle to haul in a plastic barrel that has been buried in the mud four hundred feet below the water surface—a baited trap to catch the deep sea dwelling worm of the ocean, the enigmatic hagfish.

The rest of the students eagerly await the moment of unveiling; today is the day they will first set sight, smell and touch on the slimy marine creature. Their excitement at the retrieval of the barrel is brusquely broken by its gaping emptiness—an emptiness that is much like the puzzling evolutionary history of the hagfish. Dr. William Bemis, director of the Shoals Marine Lab on Appledore Island, tries to lighten the load of their disappointment: “Fishing is different from catching,” he jokes.

When you’re missing jaws, fins, scales, and a skeleton, you can’t blame someone for mistaking you for a worm—which is precisely the mistake scientist Carl von Linne had first made when he classified hagfishes as worms in 1758. Hagfish are often not considered to be true fish—and for good reason. These two-foot-long, cylindrical tubes lack all the major features that any ordinary fish would need to flaunt in order to earn its name. But hagfish are cold-blooded marine animals with gills, so they can’t not be fish. It’s not difficult to see why these rule-breakers have been the cause of many a debate between scientists, debates that won’t be finding their peaceful closure anytime soon.

Hagfish are special because they lie at the evolutionary crossroads of the origin of all vertebrates. Whether these slime hags could be the ancestors of all organisms with a backbone is one of the most problematic issues in the evolution of vertebrates. After more than one hundred and fifty years of studying the sixty species of hagfishes, the answer to this classic question remains as dark as the deep ocean in which they reside.

Hagfish lack many of the physical features that all vertebrates have, the most essential being a backbone. This means that hagfish branched off from the path along which vertebrates later evolved. So early scientists refereeing the game of evolution—the ones who group related organisms together, otherwise known as phylogeneticists—had to exclude hagfish from playing on the same team as their vertebrate cousins. But this wasn’t entirely the problem—the problem was that scientists were stumped as to which team hagfish actually belonged in. Ever since then, the blacklisted slime rods have been hanging around on the sidelines, waiting for the experts to make up their minds.

Part of the dilemma lies in the fossil record—or, in this case, the lack of one. Because hagfish don’t have bones, which are necessary for fossil formation, only one fossil has been uncovered—a single find that came from coastal rock deposited roughly 330 million years ago. Scientists uncovered this fossil in the form of a little nodule, about the size of your hand. But the split between hagfishes and vertebrates is predicted to have occurred around 530 million years ago, which leaves 200 million years of empty pages in the fossil record. And that’s not much to work with.

Even the fossils we do have aren’t particularly helpful—as Bemis flips through his presentation slides to one depicting the hazy image of a hagfish fossil, he remarks, “I want to impress upon you how crummy this fossil is.” According to Bemis, dealing with such old evolutionary splits is difficult because so much change can accumulate over such long periods of time. And if you don’t have the fossils to catalog the progression of these changes, there’s not much you can do to predict 200 million years’ worth of evolution.

Until relatively recently, biologists have mainly relied on common bodily features to group related animals together. For hagfishes, this meant being lumped together with lampreys, another family of sea-dwelling creatures that don’t bare much resemblance to fish. Much like hagfish, lampreys are missing fins, scales, and bones. On the other hand, lampreys boast the rudimentary material for a backbone; in this sense, lampreys were evolution’s beta software for vertebrae. But if lampreys are the most primitive living vertebrates, where does that leave hagfish? This is what Bemis refers to as “a perennial question in zoology.” And as with any story, there are two sides to this one.

Scientists on one side declared that hagfish and lampreys are distinct enough to not be thrown into one box with the same label. These scientists approached the enigma in the traditional fashion of comparing shared, specialized characteristics between different kinds of organisms in order to forge relationships between them. But because this outcome clashed with the earlier hagfish enthusiasts who had decided to lump the two animals together, a new group of scientists had to come to the rescue.

This group of scientists was unleashed with the recent wave of modern genomic studies, fully strapped with new and improved technologies that would crack the code once and for all. Scientists in this field are known as molecular systematists—they study the molecules of organisms, specifically their genes, to learn about their evolutionary origins. Genomes, unlike fossils, can carry a more intact and continuous historical record. The genome is essentially a blueprint that contains the assembly instructions for a living creature. Evolution is constantly and continuously re-drafting this blueprint, producing new species of living organisms.

With the modern tools available today, biologists who study genes can track these subtle changes in effectively the same way that fossils are used for this purpose. The difference is that genes don’t get buried, roughed up, or lost; for the most part, they’re preserved, like molecular fingerprints, in every cell of any given organism. In other words, genes are easily accessible. Guillermo Orti, Associate Professor at the School of Biological Sciences in the University of Nebraska, attests to this: “There is little doubt that molecular data are and will be most commonly used for phylogenetics. Part of the reason is the ease of collection.”

So when scientists like Orti set out to demystify the mystery of the hagfish using genetic data, the aim was to find clarity. As is often the case with scientific inquiry, however, the water only got murkier—findings from genetic studies raised more questions than they were able to answer. These budding researchers’ findings reverted right back to the claim that lampreys and hagfish are much too alike to be separable. The answer to the question of whether the hagfish is our Grandfather Backbone was buried way deeper than six feet under. And the more they kept digging, it seemed, the further down scientists were pushing it.

Orti acknowledges that the molecular data used for the genetic approach is not crystal clear. When molecular systematists use this technique, they don’t work with the entire genome to deliver results; only a few genes are taken into account. This makes for a pretty small sample, which in turn makes errors more likely. Dr. Thomas Near, Assistant Professor of Ecology and Evolutionary Biology at Yale University, doesn’t disagree: “I am a molecular systematist, but I do not think that molecules are giving us a robust answer to this question.”

Anatomy was making its point: that the hagfish is the singular origin of all vertebrates. But genes were making another point: that hagfish are too closely related to lampreys—in terms of their genetic codes—to belong in their own special group. The aim was to find two approaches that would back each other up, but scientists soon realized that they had unearthed a war waiting to be waged—age-old anatomy had been holding down the fort for centuries, but genetics was armed with new and improved weaponry and was ready to step up. So what’s a conflicted biologist to do?

According to Orti, the answer may lie in combining the two approaches: “We anticipate that in just a few years, efforts along these two fronts will converge.” The potential of a comparative approach, in which different ways of answering the same question are combined in a cooperative manner instead of being pit against each other, is eagerly endorsed by many scientists. “I'm not sure what it will support and that is the excitement of the chase!” expresses Dr. J. B. Heiser, Senior Lecturer in the Department of Ecology and Evolutionary Biology at Cornell University. The goal is to sweep the entire genome to create a large data set. With higher numbers of deciphered genes, this “phylogenomic” approach can assemble a larger fleet that is more resistant to inevitable attacks by systematic errors.

Bemis sees the genetic efforts to date as skimming the cream off the question: “Quickly done, not very thoughtful approaches seem to prevail; the hard work of actually understanding hagfishes as a group has yet to be done.” Perhaps two centuries’ worth of research is just the tip of a titanic and relentless iceberg. One thing is for sure: with a bottomless well of curiosity, these resolved scientists will keep hacking their way down to the clandestine secret of the hagfish until it is finally ready to tell its tale.

[Photo by Willy Bemis]

Thursday, August 20, 2009

Gulls: The Lion and the Lamb Within

by Olivia Tai, Cornell University

At first glance, gulls are not like humans at all. But one bird scientist thinks otherwise.

“I think that gulls are appealing in a lot of ways because they sort of remind us of ourselves. They have a lot of greedy behavior and selfish behavior, but they can also be extremely caring with nurturing qualities,” says Dr. Julie Ellis, a seabird ecologist at Tufts University. Some of the students and colleagues inspired by her passion for gulls know her as the “Gull Queen.”

Whether gulls draw out affection from us, or annoy us to no end, they deserve a chance to be understood as a highly social bird.

Nowhere is gull social behavior on more vivid display than on Appledore Island, a rocky oasis six miles off the coast of New Hampshire and home to Shoals Marine Laboratory. The island houses one of the largest colonies for two gull species: Greater Black-Backed Gulls and Herring Gulls. Last year in June, I observed gulls up close when I joined an Animal Social Behavior class at the lab. The course introduced me to field research in the behavioral sciences, which is what I study as an undergraduate at Cornell University. We focused exclusively on Appledore’s gull community, learning gull behavior by spending innumerable hours at their nests. At some point during all of that observation, I was able to overcome my stereotypes about the bird and see why they’ve enthralled researchers.

People think of gulls as flying rats. You may know them as food-stealing, trash-eating nuisances that hang out in the parking lot at McDonald’s. But the excessive population of gulls that causes these annoyances is the same reason why researchers are fascinated by these coastal birds. In Here’s How We’ll Do It, a published account of the lab’s origin, the founders chose Appledore Island partially because of an extraordinary abundance of Herring gulls. Since then, the island’s gull colony and convenient lab facilities have lured interested researchers and students to the field station.

Learning the gull communication signals is crucial to understanding gull behavior. A signal can be seen or heard, but it always contains a message meant to create a response. To understand the hidden message in a signal, an observer must spend a long period of time watching the animals. At first, the observer will find a lot of confusing sounds and movements. But soon, an observer finds an action that seems interesting, and waits patiently for the gulls to repeat it over and over again. The more you see the action, the more details you will notice—such as what usually happens before or after, where does it happen, and who responds to the secret message.

“It is the ability to notice and interpret these small changes that separates the best field scientists from the rest, and there is no better place to hone these skills than Shoals Marine Lab,” says Dr. William Bemis, the current director of the lab. There are so many gulls living near each other on Appledore Island that an inexperienced observer will see a lot of repetitive action even after a few hours.

In a community of gulls, each couple would choose a patch of land that they mark as their territory. To warn intruders, gulls emit short bursts of shrill calls followed by intimidating gestures. Great Black-backs may stretch their wings out like a Batman cape, ready to take flight and descend upon you. Herring gulls may rip out grass ferociously to let you know that they’re strong and infuriated. But if they don’t see you back away soon enough, they read your presence as a willingness to fight. Negotiations to back off only last so long before the gulls resort to violence.

Fights do erupt often when neighboring gulls attempt to expand their real estate. But gulls don’t discriminate; they constantly defend their homes against predators and anyone else that walks through—including biologists.

Although Bill Clark has no formal training in gull biology, he became fond of Appledore’s gulls when he volunteered at Shoal’s four years ago. As a retiree, Clark responded to Ellis’s call for volunteers and remained involved with her research ever since. One of his most memorable experiences at Shoals Marine Lab involved a male Herring gull nicknamed “Angel of Death.”

Clark explains the bird’s reputation: “He tends to sit up on the porch and dive down on people. Some years it seems to be just about everyone that comes past. Other years, he seems to develop a fondness for diving at several people. They’re on his list, apparently.” Clark suspects that the male remembers a past experiment, in which his eggs were taped with thermostats at the bottom to measure nest humidity and temperature. Not only did he develop a grudge toward humans from then on, but he also eluded experimenters who wanted to tag him with an identification band.

During one fateful day, Clark was ambling through the island with a heavy net in hand. “I was just going somewhere and I had no intention of catching him. But he came up and started to attack me. What was I going to do? So I just dropped the net on him and we banded him. He never forgave me apparently,” Clark recalls. Two weeks later, the Angel of Death sought his bloody revenge by attacking Clark from behind and cutting his head.

Ellis swears that the notorious bird recognizes Clark. Gulls might not only recognize people, but they may build resentment towards those who endanger their chicks. The Angel of Death seems capable of doing both, but gulls are generally protective of their young.

“You know, I’ve heard this from a lot of people that haven’t been to a gull colony. They always say, ‘I haven’t ever seen a baby gull. Where do all the baby gulls grow up? You know what, what are the gulls like as parents?’” Ellis says.

Gulls give lot of attention to their chicks. Parents hunt and leave fish undigested in their throats, so that they can retch it back up when they return home. If the food is too big for the little ones, parents may break the food into smaller pieces. They regurgitate nearly on command whenever the chicks peck at the red spot on the tip of their beaks. Sometimes, feeding the chicks becomes an overwhelming burden on the parents to hunt more often for food. Yet gull parents almost give in to the chicks’ every whim.

Now that I’m revisiting Appledore Island at a different time of the year, I see the stark contrast in how gull parents act at various ages of their offspring. While chicks were still fuzzy and clumsy during early summer months, their parents need to guard them at all times. Towards the end of summer, gulls barely squawk at me as I pass by on the way to the dorms. The chicks are almost as big as their parents, but still require a little more flight training before they gain their independence. Gulls only become über-aggressive when they have vulnerable chicks to defend.

Like gulls, we humans can be extraordinarily kind to family and act against our selfish tendencies. But when we sense danger directed towards our loved ones or our country, we rage wars for decades.

Gulls do have reason to fend hard for their chicks. Every year, a female gull lays an average of three eggs. According to a documentary that was recently filmed on Appledore Island’s gulls, entitled “Signals for Survival,” most gulls will raise one chick to independence, or none at all. If a chick gets killed, its parents just lost a huge portion of their annual production. That’s why their hostile behavior seems to contrast the tender care their chicks receive.

“If we’re going to co-exist with these birds, we need to learn about how they live and what their needs are,” says Dr. Thomas Seeley in “Signals for Survival.” Seeley is an expert on animal social behavior, and chairman of the Department of Neurobiology and Behavior at Cornell University. The idea of gull overpopulation is a clear example of how we misunderstand the gulls. Ellis believes that the way we dump our waste allows the gulls to easily eat the trash and grow in greater numbers. Instead, people tend to vilify gulls for wanting to eat the trash. If our garbage is affecting the gulls’ existence by haphazardly increasing their population, then we need to know more about these creatures instead of ignoring them.

“If you want to get to know the gulls, then come up to the Shoals and just watch them for a day,” Ellis says.

But research on gulls is not for the faint of heart. Clark gives a disclaimer to all aspiring gull researchers: they’d better give the animal a test-run before they commit. “Because they’re mean, they’re nasty, they’re ugly, and they’re going to poop all over you. These are not little koala bears that you can cuddle and hug. They’re tough characters and very, very neat to work with.”


3-D Animation, Lasers, and Robots: The Future Through Fish Skeletons

by Caroline Rusk

Nick Gidmark has x-ray vision. He’s no superhero, but he can see what’s happening under skin and muscle.

Scientists have studied how animals move from watching them on the outside. But they have never been able to see how the bones move in 3-D motion on the inside – until now. They can do this using a new technology called XROMM, or X-Ray Reconstruction of Moving Morphology. It combines x-ray video, laser scans, and 3-D animation to show how skeletons move. And someday, it might be a tool in doctors’ offices, just like a stethoscope.

Nick Gidmark, a graduate student at Brown University, wants to know more about how a certain group of fish moves. This group, called Teleosts, includes many familiar bony fish, such as herring, minnows, and trout. These fish have very movable skulls. Humans only have two major bones in their heads, the skull and the jaw. This makes chewing very simple, because the jaw can only move in so many directions. Teleost fish, however, have many bones in their heads, so that they can move more flexibly. For these fish, chewing is a little more complicated.

One fish Gidmark studies is the carp. A carp has more than 40 bones, just in its head. When a carp eats, it extends its mouth out towards its food, almost like us puckering our lips to drink from a straw. But instead of just the carp’s lips moving, its bones move too, pushing its entire mouth out to grab its next meal. With all of the bones moving, some of them deep in the fish’s head, it’s hard to tell what is going on.

All that is visible when the carp eats and swims is a smooth covering of scales. It is easier to see what bones are moving by dissecting the head. Then the bones, joints, and muscles are visible, but not in motion. Another way to see the bones is to watch them move in an x-ray screen. But x-rays can give fuzzy or unclear images, and sometimes bones are hidden behind others. These two options are not always enough to understand the movement of the skeleton, simply because neither gives a clear picture of all of the bones in motion.

Nick Gidmark studies one particular bone in the carp’s head. Neither x-rays nor dissections can help him to understand the bone because the tiny bone sits deep in the middle of the carp’s head. And it isn’t attached to any other bones or muscles – it is woven into a basket of ligaments. This makes it hard to see and to understand. It is called a kinethmoid. Nobody is quite sure what it does, and that’s exactly what Gidmark wants to figure out. “I think fish are cool,” he says, “I want to learn how this works. I’m curious.”

From observing the fish normally, anatomists think that the kinethmoid rotates as the carp sticks its mouth out. But Gidmark wants to know more. If it does rotate, he wants to know what makes it do so and how that is related to the carp stretching its mouth out to eat. XROMM is just the tool to show him the answers.

To use XROMM, Gidmark puts 3 metal beads in each of the four bones he wants to watch. Then he takes x-ray videos of the carp eating from two different angles. In the x-ray, the images of the metal beads appear dark and sharp against the gray transparent bones, which is exactly what he wants. He also gets the exact shape of the bone using laser scans of the carp. Gidmark brings all of these elements together in an animation program called Maya, the same one that Pixar used to bring Woody and Buzz to life in Toy Story. The finished product looks, as Gidmark says, “as if you had x-ray vision and you were watching some bones move while the fish was eating.” The video is in 3-D and looks like a fish head skeleton from a museum brought to life. And what excites Gidmark is that it clearly shows the kinethmoid rotate as the carp extends its mouth. The 3-D nature of the image makes the bone visible among the others.

Gidmark has concluded that there is a very close connection between the kinethmoid rotating and the fish extending it mouth to eat. This means it probably plays some sort of cause-and-effect role in the chain reaction to move the mouth. But its exact function is still unclear. Gidmark explains that he plans to put off learning more for the moment and use XROMM to study other things. But he will probably return to the kinethmoid in the future.

Carp aren’t the only animals whose moving skeletons XROMM has revealed. Researchers have also made 3-D x-ray videos of a pig foot, a pig head, a duck head, an iguana’s ribcage, a frog’s ankle, and the wings of pigeons and chukar partridges. But beyond just watching animals move, this technology has some other practical applications.

Brooke Flammang-Lockyer, a teaching fellow and Ph.D. candidate at Harvard, studies how fish move when they swim. For her post-doctoral research next year, she plans to build a robotic pectoral fin. Pectoral fins are the arm-like fins on the fish’s sides. XROMM is going to help build the robot.

The Navy is interested in Flammang-Lockyer’s robotic fin because it wants to invent underwater vehicles that are easier to control and turn than the submarines they have now. A robotic fin may just be the answer. The Navy is in luck, because there are already hundreds of fin designs for them to choose from – someone just has to figure out how to get them off of the fish and onto a vehicle. That is Flammang-Lockyer’s job.

“Bio-inspired design is becoming a very large field now,” she says. It makes sense: nature usually equips animals for their environment better than we can equip ourselves. The plan is to build a fin that a submarine can use the same way a fish uses its own fins. Flammang-Lockyer explains that many researchers have studied the pectoral fin, but there has been no work done on the shoulder bones underneath the fish’s skin that control the fin. She needs to understand how they work to design the best robotic fin.

This is where XROMM comes in. Flammang-Lockyer has long been aware of the x-ray video system because her lab at Harvard often works with the Gidmark’s lab at Brown. She hopes to create a 3-D animated video of the movement of the fish’s shoulder bones so that she can replicate the natural fin movement.

Besides propelling Navy submarines, Flammang-Lockyer sees a future for a robotic fin in research. The robot would provide a more reliable test subject than a live fish. Flammang-Lockyer says, “Fish are often hard to get to repeat things when you want them to, but if you have a good robotic model, then you can use that to do different tests.”

Even though Nick Gidmark is mainly interested in fish, he thinks that XROMM is going to contribute to human medicine. He explains that stemming from his lab’s interest in the way animals move, “we get these totally unexpected applications that are really useful for human anatomy and clinical science that nobody really thought of until a couple years ago.”

Gidmark thinks XROMM has the potential to change human orthopedics. He imagines a day when people with knee problems will be able to walk into the doctor’s office, get a CT scan of their knee, and walk on a treadmill next to a video camera. Then the doctor will make an XROMM video and tell what the problem with the joint is. It will work for any joint: shoulder, jaw, hip. A surgeon could look at the 3-D video and see exactly how to fix the problem: shave a little bone here, stick a little cartilage there, and voilà, that joint that used to bother you when you ran or played basketball wouldn’t hurt anymore.

But before any of this can happen, there needs to be a less invasive way to track movement than inserting metal markers into the bone. Right now, Gidmark explains, computer programmers are developing a way for a computer to make the bone’s digital image follow its motion exactly. But until the program is finished, researchers would have to spend months to create a full XROMM video without markers. Gidmark predicts that the computer-run technique will be available for use in about five years.

Brooke Flammang-Lockyer has faith that humans will soon have access to XROMM for their own use. “Coming up with the technology was the hard part, but adapting it for use in humans is much easier in comparison.”

And that may just translate into taking the pain out of people’s everyday lives. Who says scientists can’t be superheroes?


by Shelley Stuart

Of all the scientific disciplines, archaeology depends most on the generosity of others. Not everyone would allow a team of academics onto their property, some wearing shirts declaring “archaeologists will date any old thing.” Not everyone would consent to a dozen strangers searching for bones and bits of pottery on their little island paradise.

Smuttynose Island, a shrub-crowned island in the Gulf of Maine, doesn’t look like your typical island paradise. It’s a scrawny, windswept place, an island that braves the wild winters through sheer obstinacy. The two equally stubborn buildings that still exist on the west side of the island are simple cottages from bygone days. Owned by Stephanie and Nathan Hubbard, these buildings house a rotating roster of Smuttynose Stewards. These volunteers act as docents, and regale the occasional visitor with the island’s juicy history of axe murders, pirate treasure, mysterious graves and ghosts.

The island’s more mundane history lured Nathan Hamilton, an archaeologist from the University of Southern Maine, to Smuttynose for his research. Hamilton wants to know more about the fishing industry that was active during the Colonial years. The Hubbards have a deep interest in the natural history, past ecology and use of Smuttynose so they graciously allowed Hamilton and the nearby Shoals Marine Lab to set up a field school there. In 2009, Hamilton and his team of students began looking for artifacts.

Using six-inch trowels, they carefully excavated a pit the size of a beach towel. Centimeter by centimeter they peeled away layers of earth. Sifting the dirt through fine mesh screens, the team members hunted for artifacts smaller than a green pea. Hamilton obsessively bagged and cataloged hundreds of cod fish bones, fish hooks, pottery pieces and pipe stems.

Hamilton’s artifacts look like Puritan trash at first glance, but to an archaeologist they all hide precious nuggets of information. If Hamilton were like most scientists, he would have hoarded his findings until found the time to analyze and publish his results. But Hamilton is a philanthropist in his own right – he gives knowledge.

As Hamilton puts it, most scientists play things pretty close to the vest. There’s an emphasis of my paper, my data, my artifacts. The result: I have a backlog of work, and you remain in the dark. Hamilton takes a completely different approach. He is as open and sharing with his data as the Hubbards are of their land.

Hamilton took “his” fish bones to Beverly Johnson, an organic geochemist at Bates College. She will analyze the bones to measure how much carbon dioxide was dissolved in the Gulf of Maine in the 17th and 18th centuries. Comparing carbon dioxide levels in old cod bones to the amounts in present-day fish will shed more light on the ongoing question of climate change.

It will take several more years of digging before Hamilton fully understands what Smuttynose looked like in the 1600’s. But the Hubbard’s willingness to grant access to the archaeological treasures beneath their land, and Hamilton’s openness with those same artifacts, will allow scientists from different areas to better understand a small piece of our world.

Sometimes science begins with the heart, not the head.

[Image of Smuttynose by Robin Hadlock Seeley]

A Visit to the Intertidal Zone

by Lauren Klappenbach

A small, rocky island in the Gulf of Maine is the perfect place to explore the delicate, dynamic habitats that thrive where land meets sea. These brine-soaked borderlands known as intertidal zones are home to a rugged assortment of organisms, all armed to deal with battering waves, parching sun, and salty inundation.

On Appledore Island off the coast of Maine, a group of students from Shoals Marine Laboratory walked along a narrow path that wound its way to the island's western edge. They were accompanied by a trio of biologists, Lauren Quevillon of Cornell University, Kipp Quinby, a Lab Preparator from Shoals Marine Laboratory, and Helen Hess, a Professor from College of the Atlantic. The three women, all experts in marine biology, led the group on a modest expedition of discovery and learning. Their destination was the intertidal zone.

The path wove through a succession of grassy clearings before stepping down onto a wide beach of rocks and pebbles. Smooth stones formed a jumbled mix with organic debris that had been churned up by surf and wind--decaying seaweed, wave-warn bits of wood, broken snail shells.

At the edge of the rocky beach, about a fifty yards from the sea, the terrain turned rough and gave way to hefty slabs of granite that bulged from the surrounding land at precarious angles. The students progress slowed as they struggled to find their footing. Finally, they arrived at the uppermost edge of the intertidal, the furthest reach of the high tide's waves.

Helen Hess moved to the front of the group. She stood facing the students who had gathered around her in a semi-circle. The sea served as backdrop, it rolled in gentle waves that slapped and gurgled as they hit the rocks. "How many of you have explored the intertidal before?" she asked. Several students nodded, others shook their head.

Professor Hess told the students to look at the landscape that surrounded them. She described things through the eyes of a biologist. She spoke of natural gradients in the intertidal, of habitat pockets shaped by the animals that were adapted to live in them. People tend to look for patterns and edges in everything and try to draw lines between one habitat and the next. In reality, nature is a continuous blend of one patch to the next. Gradients, not grids, are the stuff of nature.

Each creature has its own set of "physiological tricks" that enables it to cope with the harsh conditions in a particular plot of the intertidal. "Barnacles are the classic example of tough customers," Hess said, pointing to the clusters of cup-like shells that stuck stubbornly to the rocks.

The intertidal zone is a habitat driven by the rhythms of the tides. The creatures that inhabit the intertidal zone--sea urchins, snails, mussels--spread out along its depth to occupy only the patches to which they are ideally suited. As you move from one location to the next in the intertidal zone, creatures face different physical demands. Different demands at each level mean different inhabitants at each level.

Periwinkles graze on seaweed at the high end of the intertidal. Filter feeders like barnacles and mussels nestle amongst the rocks at the middle of the intertidal, wetter areas that remain soaked for longer periods of time than the high reaches of the intertidal. At the lowest layers of the intertidal, closest to the water, an assortment of strange sea creatures such as tunicates, hydroids and sponges take up residence.

Rocky seashores like those on Appledore are most common along the coast of New England north of Cape Cod. During the last ice age, glaciers scrubbed and scoured the shorelines in this region, leaving them clean of sediments. All that remained was exposed bedrock. The habitats that sprouted up on the barren surface are unlike any other. Algae and diatoms form the base of the food chain.

Helen Hess, Kip Quinby, and Lauren Quevillon guided the students closer to the water, deeper into the intertidal zone. There, the rocks were draped with thick mats of the leathery, brown algae Ascopyllum, also known as “knotted wrack”. Other seaweeds such as Fucus or “rockweed” adhered to small patches where clumps of Ascophyllum had been torn away by the crashing waves.

Lauren Quevillon stepped to the front of the group. From a dry vantage at the edge of the high tide mark, she pointed across a continuous mat of seaweed. Four small cages, each six inches tall and fifteen inches square, sat atop olive brown ribbons of seaweed, "These cages take a beating. We set up several others but a storm came through and tore them away, even though they were bolted into the granite." she says. Life in these rocky tidal waters is wrought with challenge--both for the creatures that live there and for the scientific equipment deployed to study them.

Quevillon studies an invisible creature in the intertidal--a parasite. The cages each hold a single healthy crab, one of the parasite's host species. Closer to the water where deep pools of saltwater are left behind at low tide, there are more cages housing healthy crabs. Quevillon hopes to find out where in the intertidal zone crabs are most likely to become infected with the parasites.

A dark storm that had been gathering on the horizon snapped a bright strand of lightening across the sky to the south of the island. "We better get going," a student said, looking at the slippery rocks that they had to cross on their return. The wind picked up and the light began to fade as the thick clouds rolled in off the sea. A misty rain started to fall. Even the rocks far from the intertidal start to glisten and grow slick with moisture.

The group decided to end their intertidal visit and return later in the evening. In the meantime they headed back to the lecture hall to talk more about the intertidal zone.

The rain was falling in thick sheets by the time the students made their way back to the center of Appledore Island. The journey ended at Leighton Hall, a small shingle-sided building that sits tall on a bed of granite. Inside, they shed their wet raincoats and soggy backpacks as they made their way into the lecture room. There, Quevillon explained the things they've just seen, and more importantly, the things they didn't see.

Quevillon's research focuses on a tiny parasite that lives in the intertidal zone. It's a species of flatworm with a peculiar life history. To get from one stage of its life to the next, it relies not on a single host but on a greedy succession of three: a bird, a snail, and a crab.

The parasite begins its life cycle as a tiny worm deep in the small intestine of a host bird. There it produces eggs in vast quantities.

"It's really a game of numbers with parasites," Lauren said. It is crucial for the worm to manufacture a surplus of eggs to sustain its numbers. The bird, not harmed by the parasite, excretes the eggs in its droppings that litter the seaweed. "Many of the eggs get washed away, but some adhere to the seaweed."

The eggs, left to chance, only survive if ingested by a snail that grazes on egg-laden seaweed. Despite slim odds, some eggs do succeed and are eaten by the snails. Once inside the snail, the parasite makes its way deep inside the snail's shell. The parasite feeds on the snail's internal organs. As it does, it reduces the feeding efficiency of the snail and the snail eats less seaweed. This in turn affects the balance of algae in the intertidal zone.

"These parasites, things you cannot see with the naked eye, are structuring communities--that's huge," Lauren said.

That evening, the students return to the intertidal zone again with Quevillon.

Quevillon picked a snail from beneath a rubbery frond of knotted wrack. It retreated into its shell. Infected snails are easy to identify. The parasite damages the snail's liver, causing discoloration of the snail's foot. "The vast majority of snails out here have parasites, you turn them over and they have bright carrot-orange feet," Lauren explained. "There's an eighty percent chance this one's infected," she said as she watched it, waiting for it to expand its foot from its shell. The snail remained stubbornly entrenched in its shell. "This one's not going to come out for a while," Lauren said. She placed the back in the bed of seaweed.

The sky began to lose its luminosity as the sun sank beneath the horizon. The tidal pools grew grey and colorless in the dimming light. The students gathered and began their journey back, stumbling across slippery rocks and knotted strands of seaweed. The animals and algae of these rocky shores are not the only creatures that know where they belong when facing the harsh intertidal environment--humans know too.

A Bird in the Hand

by Dale Quinby, College of the Atlantic

A young American Redstart on its first migration, following the Atlantic coastline south, is likely to find itself out over the Gulf of Maine some miles from shore. The bird is tired and has used up most of its fat reserves. Then, down below, it sees a small patch of green amid the blue. The exhausted bird heads down, landing in the shrubbery on the island. Its first impulse is to feed on the berries in the bushes. But as it flutters around, it finds itself suddenly caught and held by some invisible force. Disoriented and frightened, the redstart flaps its wings and thrashes about trying to free itself but is only held tighter.

"Well hi, squirtums," says David Holmes as he carefully unwraps the strands of thin plastic mesh tightly tangled around the bird’s feet, neck, and wings. Many of the all but invisible threads are hidden under the feathers and have to be coaxed out by touch, in a painstaking process. Once he frees it from the net strung along the path, Holmes carefully puts the bird in a paper bag. Back at the Appledore Island Migratory Station (AIMS), Holmes and his team of volunteers will weigh, measure, and band the bird before releasing it. The tiny metal band on its ankle bears an identification number and instructions in the event that the bird is recaptured at another location. The volunteers at the station will handle between 3,500 and 4,000 birds every year.

Holmes started the bird banding station on Appledore in 1981 as a hobby project. Since then, many more volunteer banders and helpers, jokingly referred to among themselves band-aides, have joined the effort. Research for doctors’ theses has been done at the station as well, including that of Sara Morris. Morris, an associate professor of biology at Canisius College, took over running AIMS in 1990. Because most of the birds caught on Appledore are migrant visitors heading to other countries, most of the research projects at AIMS focuses on migration movements and how the birds use places like Appledore where they stop to refuel for the rest of their trip.

Conservationists have been very interested in how birds use these pit-stops recently because of the plight of the red knot, a small shore bird which migrates over 9,300 miles from the Arctic to Tierra del Fuego every year. The red knot stops at Delaware Bay on its journey to feed on the horseshoe crab eggs there. Due to overfishing, there weren’t enough horseshoe crabs laying eggs to support the red knots, leading to a population crash that started in the late 1980’s and continues today. Though state officials are working to correct the problem by limiting horseshoe crab harvesting, the situation raised public awareness about the importance of these stop-over spots.

Appledore is an ideal place to study the needs of migrating birds because of its isolated position out in the Gulf of Maine. Islands are perfect for research because they are contained, so researchers can tell exactly what plants and animals are there. When they know exactly what is there for birds to eat, it is easier to tell what is being eaten. Conservationists can then apply results from small scenarios like this to other places. As Holmes puts it, "If people decide these birds are worth protecting, how do we do it?"

Part of learning how to protect birds is learning how they behave. That way humans can change how they act to avoid conflicts since birds are unlikely to change their habits for our convenience. Recently at AIMS Kristen Covino, as part of her doctorate thesis, looked at how birds decide when to travel. Covino captured birds of half a dozen species that migrated at night and were also hardy enough to endure the experiment without sustaining any harm. These birds were then held in cages for the day with unlimited food to keep them in good shape before they were released at dusk. Covino attached capsules filled with glow-stick liquid to the birds’ rumps so that she could see where they flew after being released. If they flew off Northeast, she knew they were resuming their migration. If they settled into the bushes, then they were staying the night on the island. Covino used this information to look for patterns in how birds decide to migrate.

The purpose of Covino’s yet-unpublished study was to understand what factors go into making the bird’s decision, like the bird’s physical condition, weather, wind patterns, and season. Knowing when birds are more likely to migrate and where they might go can help humans avoid interfering with the migration by changing our habits, like where we choose to route airplanes. Flocks of birds can cause airplane crashes, so those involved in air traffic control are very interested in research like Kristen’s to help make airplane flights safer. "Some of the best studies have been funded by the US Department of Defense," says Holmes.

Airplanes aren’t the only dangers birds encounter on their migrations. "It’s all the standard stuff," says Holmes. "Habitat destruction; chemical issues with food supplies; hazards like cell towers; windows, which are the number one non-natural killer of birds; and cats, which are the second." Wind turbines are an increasing worry for the researchers at AIMS as more and more people look to wind power to solve the energy crisis. The state of Maine is now looking to supplement the oil it uses with wind power in the near future, using large off-shore wind farms.

AIMS has been part of the effort to test the effects of wind turbines on migrating birds since a turbine was installed on Appledore Island in 2007. The banders check the area around the turbine twice a day for any birds that hit it. So far they haven’t found any casualties, but Holmes warns against attaching too much significance to these results. "You can’t extrapolate about a little kind of thing like this." The programs proposed by wind-power advocates are on a much larger scale and would need a great deal more study to understand the impacts. "We hope the state of Maine will be environmentally conscious about this," says Holmes.

The Appledore Island Migration Station is the site of a great deal research that helps us understand what birds need and how to give it to them, but perhaps one of the most important services it provides is simply the opportunity for volunteers and visitors to see birds up close and personal, to hold one in hand and feel its heart beating. A cedar waxwing, a beautiful bronze bird the size of a cardinal, sitting on a child’s hand makes that child think about birds and what they are doing more than any number of class-room discussions ever could.

"We do have an impact on people," says Holmes. "At least one of our banders became a bander because she experienced the Appledore banding station, and that happens with some frequency." Holmes also tries to educate visitors at the station about conservation, explaining how to handle the birds safely and encouraging people to keep their cats indoors, as they are the second-most non-natural killer of birds. "We at least try to plant small seeds," says Holmes.

[Photo by Colleen Cassidy]

The Search for A Patch of Green: Appledore Island and Bird Migration

by Andrew Powers, Dalhousie University

It is 7:00 AM and it is time to "walk the line" for netted birds. Stella Walsh walks ahead and a certain amount of excitement starts to build up in the visitors. The nets wind through the forest, ending just out of view. A person’s heart could almost stop at the electrifying moment when a fluttering bird is in the net. This causes the net, which formerly ebbed and flowed like the sea, to jump and quiver instead. Walsh carefully extracts the bird feet first, then the wings, and finally the head. She explains that in removing the bird there is no strict set of rules. The bander will often also softly speak to the bird to try and calm the squawking beast, while expert fingers work to release it from the net. However, these birds are not being caught just for fun. They are often passing though on their way to tropical climates and back again. It is hard to imagine an animal that weighs a couple of ounces traveling for thousands of miles on delicate wings every year. The migration patterns of these birds force the banders to have some of the longest working days, often from sunrise to well past sunset.

The banders are working hard here because it’s an island six miles off the coast of Maine, which is very different than most other banding stations. Although Appledore Island is far away from the mainland, birds are still plentiful here. This fact goes against what popular opinion might believe about animal populations in a small area, that they are small in number. This fact begs the question, why are so many birds stopping here?

Three banders are working this August to further explore this mystery. During the two major migrations, to and from the tropics, birds use Appledore Island as a stopover spot in the Gulf of Maine. They follow a specific path using a magnetic bearing, much like a compass that takes them on the same route every year.

These birds are not only here for a quick stopover though. The island is also home to several species of nesting birds, some of which do not migrate at all. The non-migratory birds need to be tough enough to survive the harsh winters, which is a different strategy of survival than that of the birds which are able to migrate, which need to be able to store enough energy for the long flight. Of the nesting birds, both the migratory and non-migratory birds lay eggs on the island in the spring. The younger birds that hatch stumble into the nets more often than the adults, and can be more easily banded.

Banding is not a perfect science, but it is cheaper than satellite tracking. Bands cannot always be recovered, as compared to more expensive means. However many bands can be added to many birds so that there is a greater chance of viewing a trend in the information, such as life span. Through this banding, researchers on Appledore have discovered that birds use the island as a stopover on migration. Every year some of the same birds have been found in the nets, showing that the animals are using the island as a rest stop while traveling the highway of the sky.

David Holmes, a master bander on Appledore, states that in the springtime, it is common to "see birds fall out of the sky, at least in the old days, until 10 in the morning." The vast number of these migrating birds stopping on Appledore can be visually seen by scanning the skies for birds quickly dropping down from high in the air. Holmes knows this fact from experience as he has been on the banding staff for thirty-three out of the thirty-five years that the Shoals Marine Lab’s banding station has existed.

Holmes, when off-season, spends the year as a piano and flute instructor. Another bander, Stella Walsh spends the off-season as a healthcare worker, filling out paperwork. Holmes describes bird banding as one of the few fields that "citizen science" can make a real difference. Even though the banders do not pursue their summer passion at home, they are still have to be well trained to be able to band correctly. It is rare for a citizen to pursue such a difficult science that can take five to ten years to master. These citizen scientists must also have more drive than their university scientist counterparts as they are paid little or no money for their skills

The banding and measuring process is both challenging and extensive. After the bird is netted, the magic begins. It is then brought back to the lab to take measurements. These include leg length, stored fat, feather patterns, and the weight of bird. An unbanded bird will also have a band added to the leg. The band assigns a "serial number" to identify each bird for its whole life. Individual banders carefully work to reveal these facts and are luckily at the Shoals Marine Lab station, working hard on the opening morning of the season.

The small reddish-brown bird that has been captured is slowly being removed from the net, while fluttering its wings and chirping.
It is important to keep the birds calm during this procedure so that no injury will occur. "The first concern is the welfare of the bird," Walsh instructs. The smallest injury, such as a broken leg or damaged wings, could eventually cause death.

Walsh places the bird in a bag and carries it back to the station, where the other banders are patiently waiting after their data work. Holmes then steps forward to meet the bag. Walsh removes the bird from the bag, to have Holmes point to the bird and ask the visitors, what they might guess as the species of bird. He draws attention to some certain details of the body such as the slightly curved bill and the held up tail. Holmes identifies it as a young Carolina Wren, which has an unusual life on the island.

Maine is at the northern end of the Carolina Wren’s breeding range. These birds have traveled to Appledore and are non-migratory. In the mid-1990’s the population was literally wiped off of the island due to an extraordinarily harsh winter and the bird’s sensitivity to cold. It then took five years for the wrens to return and breed again. This is a prime example of the dangers a non-migratory bird will face on Appledore island or even elsewhere.

An island’s climate is unique compared to the mainland because it has less snow, due to the warmth of the ocean. However in addition to this, it often has more wind, which cannot be blocked by large trees. There are no tall trees on Appledore Island because the soil is not deep enough for them to take root because after a relatively thin layer of soil, the roots hit thick bedrock.

Despite the lack of these trees the island can still provide a refuge to the migrating birds through the smaller shrubbery. Fruit-eaters, such as Cedar Waxwings arrive here to take advantage of the fruiting plants such as cherries. However, cherries are not always as abundant as the birds might hope. During the summer an insect called a webworm, will cover cherry trees in thick webs and feed on the tree. These trees then produce less food for these birds that then cannot get the energy they need. "Birds have flown over all this water to a patch that’s supposed to be green" Holmes sadly states. This change can reduce the chance of the birds surviving to the next stopover and can be tough on a population.

Appledore migrating birds have been recorded as far North as Newfoundland and as far south as Venezuela, but this journey can only be possible by the maintenance of these stopover sites. If the food and shelter are good enough there, then a bird can make it from stop to stop, all the way to its best breeding and feeding grounds. Banding has shown that in addition to the migration stopover, some birds also find it to be more successful to use the island as a breeding spot or even to spend their whole lives on. However, no matter the reasons for birds to be on Appledore, it is vital that this unique area be preserved so that we may still have as many feathered wonders as we do today. This island is not the only place in the world that birds migrate through. There are many other stopover spots in the world, each for an individual type of bird, such as large bodies of water with lots of plants for ducks, and dense woodland filled with insects for warblers. These areas need protection to save birds and ensure avian survival into the future.

[Photo by Colleen Cassidy]

Life in the Intertidal Zone: A True Feat

by Gavriel Wolf, Cornell University

To most, the intertidal zone, or what amateurs like myself would call the shore line, is a rocky beach with little more danger than some slippery algae and a whole lot of falling bird poop Through the eyes of scientists who study the intertidal, however, it is a war zone. The algae are armored competitors, and the bird poop is filled with parasites that can puree the insides of a snail.

Lauren Quevillon, who is doing research on a parasite called Cryptocotyle lingua on Appledore Island, one of the Isles of Shoals, guided our group to the intertidal on to get a closer look at her work. As a storm was brewing in the distance, she pointed out a set of shoebox-sized cages holding crabs. As bolts of lighting began to connect the sky and ocean, Lauren hastily explained that the cages were set in the water at different heights, to determine the regions where the parasite was most likely to invade the crab.

The cages that Quevillon originally set are now gone. Lauren spent half an hour drilling two three-inch screws into limestone to hold each cage. She thought, "These things are going nowhere." But soon, a storm came and ripped the bolts out, pulling the cages out to sea. "Now think of what the storm can do to the organisms," Quevillon pointed out. At this point we were not only thinking about the strength of the storm, but we were scared of experiencing it, we ran back for shelter.

Slow and stationary organisms are completely exposed to the elements on the wave battered rocks of the Atlantic shores. On the boulder-strewn shores, there is no sand or loose rock for crabs and snails to find refuge. The tide moves in and out twice a day. While the tide is out, plants and crustaceans must be able to withstand the hot, dry rock, where birds dive-bomb crabs, and snails drill through mussel shells. As the water rushes back in, they must be prepared for an ocean filled with insatiable fish, and the dehydration of salt water.

In addition to the summer waves that tear snails and algae from the rocks, sliding winter ice sheets strip everything except the most robust creatures from surviving on these rocky shores.

The ice sheets are a small reminder of the historical glaciers that gouged out the intertidal shores, between 10,000 and 20,000 years ago. During the last ice age, the sand and pebble beaches were dragged away by glaciers, leaving large rocks in their wake. Only the most daring organisms were left to recolonize the uninhabited shores from New York to Canada.

While the exposed shoreline poses a laundry list of dangers, it also offers a buffet of perks. The constantly undulating ocean delivers food particles to barnacles and other organisms that feed by filtering water. The sweeping water helps algae inhale carbon dioxide and exhale oxygen. Finally, algae sunbathe in the large amounts of energy that shines down uninterrupted by trees or bushes, and reflects off the ocean water.

The variety of opportunities for both danger and growth divides the Appledore shore into zones. The very top of the intertidal only gets a spraying of water, while the lowest regions are almost always submerged. The area in between is a slowly changing continuum of different environments. "The way we tend to describe the intertidal is by the most dominant creatures ", explained Kipp Quinby, a lab preparator on the island.

On one outing Quinby painted a picture of precisely what is happening on the frontlines, where ocean meets land.

The brown line marking the very top of the intertidal, known as the splash zone, is tattooed into the rock by a plant like bacteria. With so little water reaching this region the bacteria are the only sea creatures that can survive

Just a foot or two below the bacteria lays a flattened forest of algae. The long linguini-like plant is about as tough as they come. A waxy surface provides protection against predators, while a death grip to the rock protects it from being swept away by the waves. As we walked along the algae during low tide we heard it crunching underfoot. I was sure it was dead. Quinby explained, however, that the algae does not die, but dries out almost completely as the water recedes, and comes back to life when the water returns.

Underneath the blanket of algae, slightly lower down on the intertidal, the rock is littered with small white mounds of limestone. Barnacles create these bone-like structures. "As a larvae they basically glue their head to the rock," Quinby explained, and build calcium up around themselves for protection.

Barnacles inhabit the middle region of the intertidal where they can out survive the mussel, their biggest competitors for food. As we moved into the depths of the intertidal we could see the mussels amongst a moss-like algae. Mussels stay lower on the intertidal where they will be submerged for a greater portion of the day, to protect themselves from drying out. In order to take control of the zone, mussels will literally sit on top of barnacles, essentially starving them to death.

The intertidal also teems with skittering and creeping crustaceans. Crabs and snails move between zones intensifying the ongoing battle. The snails set up camp in the upper and middle regions of the intertidal, while the crabs reign supreme in the lower and middle regions. It is in this overlap where the true carnage lies. Snails make mincemeat of barnacles and mussels, crabs turn snails into crunchy snacks, and giant Blackback seagulls swoop in and impale the crabs. A littering of snail shells and crab legs are all that is left.

On the battlefield lie Quevillon’s cages. The cages appear to protect the crabs from any ocean dwelling creatures, however the metal wire does little to keep out the microscopic parasites.

The parasite makes seagulls, snails, crabs, and fish the hosts for its lifecycle of growth and reproduction. The process begins and ends in the gulls. The parasite grows to its adult stage in the intestines of the gull and begins a constant production of tens of thousands of eggs. The eggs set up shop in the bird’s poop and wait for deployment. The original parasite dies in the gull’s stomach, while its progeny are launched indiscriminately into the world. With any luck, the parasite-filled feces will land on some seaweed. An unsuspecting snail, just trying to grab a bite to eat, will then ingest a few privileged parasites.

The parasite then moves into the snail’s internal organs where it begins to wreak havoc. After going through a series of life stages, and reproducing asexually several thousand times, the parasite replaces the tissue of the snail’s reproductive organs, effectively castrating the snail. The parasite attack also slows down the snail’s daily activity, in effect stunting its growth and thinning its shell. The snail essentially becomes a robot for the parasite’s reproduction factory.

After going through a complete metamorphosis inside the snail, the parasite pops out as a Cercaria, a two-eyed head with a nutrient filled tail. It must find a host quickly; the tail is like "a boxed lunch, and it only lasts so long", Quinby joked.

Cercaria, too small to see with the naked eye, must find a fish or a crab in an infinitely large ocean. Their odds of survival are next to none. The parasite epitomizes the volatile existence of living in the intertidal. In just one life cycle, they alternate between exponential growth and population crushing destruction a total of five times.

The cercaria that do find a host, form a cyst on a fish or inside of a crab, where it waits for the gull to take the bait. Once inside the gull’s gut, the process starts all over again.

The parasites life cycle may seem like it is only affecting the host organisms. With an aerial view, however, the parasite’s immense impact on the intertidal becomes clear. When parasite populations get out of control large numbers of snails are castrated and crippled, causing snail numbers to drop. The barnacle population, in turn, grows unchecked by one of their primary predators. The expanding barnacle population takes over rock space leaving less room for other organisms such as algae. The ripple effect goes on, possibly changing the framework of the intertidal.

Quevillon’s research focuses on one small part of the parasite’s involved life cycle. She sees her work as helping to paint a more accurate picture of the large implications that this parasite may have on the Atlantic intertidal. Each scientific discovery adds another piece to this complicated intertidal puzzle.

The intertidal is a complex system, where a creature’s daily life is a struggle for survival. This twenty foot wide strip of land is a place that scientists have been studying for hundreds of years, each generation getting a little closer to a complete understanding of the intertidal.

In the last 150 years, with Louis Pasteur’s discovery of life on a microscopic scale, new players have been added to the struggle. At times, scientist seem to have a good grasp of the who, why, and how of the intertidal. With a keen eye and maybe an island full of research equipment, however, the unknown seems to continually assert its dominance.

Wednesday, August 19, 2009

No Bones About It: New Imaging Technology Lets Scientists See Right Through You

By Celia Smith, Cornell University

The image on the projector screen is eerie and a bit shocking. The ghostly form of a fish swims into view, its body completely transparent except for the pale bones of its skeleton: a moving, breathing x-ray. The graceful interlocking of the carp’s bones pushes it toward some scraps of food. Suddenly, its snout springs forward until the bones in its mouth form a hollow tube. Like a vacuum cleaner attachment, the carp’s extended mouthparts powerfully suck up the scraps, which then float lazily back into its shadowy stomach.

What looks like a marine take on a zombie movie is called XROMM, which stands for X-Ray Reconstruction of Moving Morphology. That’s just a fancy way of describing the creation of three-dimensional x-ray videos to study the symphony of muscle, tendon, and bone that is animal movement.

Until now, there have been many ways scientists have studied how body parts work together to produce all the movements we see in the animal kingdom. Previous research has included examining animal anatomy, and building models. XROMM is unique because it allows scientists to see the individual movements of bones while they are still inside a living, breathing animal.

With this ability to observe natural motion in such detail, scientists have re-created the workings of animal bodies with greater precision than ever before. The carp x-ray video is an example of XROMM’s uncanny ability to capture and display animal movements. It was taken by Nicholas Gidmark, a PhD student in the department of Ecology and Evolutionary Biology at Brown University, who is using XROMM to study the movements of fish jaws.

Jaws evolved in the animal kingdom after an evolutionary split left behind the jawless fish, such as lampreys and hagfish, around 500 million years ago. Since then, most other fish as well as humans have evolved strong jaws with wide ranges of motion. But despite their long history of development, human jaws are built quite simply. "Basically, there are two elements to chewing: the skull and the lower jaw," Gidmark says, "and at the end of the day, there are only so many ways the jaw can move."

Gidmark is interested in a group of animals with much more complex and evolved jaws than ours: the ray-finned fishes. This group of fish, which includes sturgeon, salmon, goldfish, and the carp from the x-ray video, is equipped with heavy-duty mouth machinery that can grasp, bite, and suck with astonishing power. Their many jaw bones and range of motion make them much more difficult to study than humans, and scientists have often had to rely on guesswork to determine which bones do what. Gidmark is now using XROMM technology to look at the movements of individual bones in these fish during the catching and chewing of food.

To create an XROMM image, researchers first take an x-ray ‘video’ of a subject from two different angles. The videos are similar to the x-rays you get on either side of your head at the dentist, only these are recorded as two sets of moving images at the same time. The x-rays capture the images of small metal markers, which have been implanted into specific areas in the bones.

Once the x-rays have been taken, a computer program combines information about the animal’s movements with a three-dimensional scan of its bones. The software uses the metal markers from the video as reference points to match precisely each bone-scan image with its ghostly x-ray outline. The end result is a lifelike image of a real bone, moving around in three-dimensional space.

Scientists can then use computer animation to make the images move around, either to examine how they behave in nature, or to experiment with other possible motions. This ability to play with the images on the computer is important for the scientists, who often find it difficult to get live animals to move the way they want in order to study them. "We use the same computer program Pixar used for Toy Story," says Gidmark proudly. He explains how the program also allows him to view the bone images from any angle, just as though he were a cameraman filming a scene.

To demonstrate, Gidmark shows a clip of a finished XROMM representation. In addition to the x-ray motion shown by the carp, this image displays the bones’ precise shape and pitted texture from the bone scan. The result looks just like a bunch of disembodied bones hanging in space, calmly opening and closing in an unmistakable chewing motion.

Gidmark isn’t the only one who sees how useful three-dimensional x-ray images can be for the study of animals. Henry Astley, also a Brown University researcher, is focusing on frogs. Any casual observer can see that frogs can jump very far for their size; up to six feet for an American bullfrog. Scientists always assumed that the frogs’ leg muscles were responsible for sending it over such impressive distances. But that didn’t always add up, since some frog jumps were estimated to generate up to eight times the amount of power one would expect from muscles alone.

Using XROMM, Astley has been able to show that, in fact, tendons should get the credit for these lengthy leaps. "Think of it like a bow and arrow," says Astley. "If you just throw an arrow, it doesn't go very far. But if you use a bow, you can slowly load energy into the bow and release it all at once. Like the bow, the tendon stores the energy produced by the muscle, then suddenly releases it all at once."

In addition to fish and frogs, XROMM can be used to explore the motion of animals we have never seen move before…like dinosaurs. Even though there are none alive today, artists and scientists can collaborate to re-create their movements, using what we know about their anatomy.

"How does a T. rex run? We can make some good guesses," says Gidmark, who adds that there is high demand from movie makers for this type of imaging. For example, the makers of Jurassic Park and other film producers have developed characters using "motion capture;" a cousin of XROMM technology in which markers are placed on the surface of a subject (such as a model or actor) for tracking movements.

Since motion capture markers are not actually implanted within muscle or bone, copying movements this way is less accurate than using XROMM. However, as entertainment technology becomes more and more sophisticated, XROMM may be introduced to create more lifelike characters.

The precision of XROMM may find its greatest use in human health and medicine. "There are applications for medical and clinical science no one ever though of until about twenty years ago," says Gidmark. The ability to look at exactly how bones and other body parts are working together could be a tremendous help to doctors in diagnosing their patients. For example, x-ray videos of someone walking on a treadmill combined with a bone scan of their leg could help pinpoint the cause of knee pain.

Patients in need of a diagnosis would not be able to wait for metal markers to be drilled into their bones; but without the markers, it is very difficult for scientists to properly match the three-dimensional bone scan images with the x-ray videos. Computer software may become sophisticated enough to efficiently match the images in a "markerless" version of XROMM, but seeing this technology in a doctor’s office is probably still a few years down the road. However, Gidmark believes it has the potential to drastically improve health and medicine, removing a lot of the guesswork from the process of figuring out where it hurts.

Other human uses for XROMM include creating what Gidmark calls a "gold standard" in medicine, meaning that the program could be used to show scientists exactly how a body part should ideally work. For example, if doctors have a standard model for the proper anatomy and motion of human limbs, building comfortable, functional prosthetics could become much easier.
"When we try to build something, XROMM can say: ‘yes, that’s how it moves,’ or ‘no, that’s not how it moves,’" explains Gidmark. In the case of prosthetics, XROMM can help create a standardized computer image of normal human arm movement; flexing, extending, making a fist, and so on. That image can then be used as the template for building a man-made arm that will work exactly like a natural one.

"What I like about this type of science is, it’s more concrete than, say, chemical analysis," says Gidmark. "There’s a bone, and I can see it, but I don’t know what it does." With a bit of luck, and some cutting-edge three-dimensional imaging technology, he soon will.

[Image of carp skeleton courtesy Nick Gidmark]

Two in the Net: How Birders Are Changing The World, One Bird at a Time

by Colleen Cassidy, a recent graduate of Cornell

David Holmes wears his binoculars on a pair of suspenders, speaks in acronyms, and can spot a leaf-colored bird in a tree ten feet away. Holmes holds the rank of Master Bander and works at the Migratory Bird Banding Station on Appledore Island in the Gulf of Maine. His day starts at dawn, when birds are most active. "They wake up and they need to put fuel in the tank," he explains.

He and his team of volunteers catch the birds in mist-nets, which resemble saggy volleyball nets. The nets’ filmy weave, combined with the low dawn light, make them almost invisible to birds, and to people. "Catching yourself is counterproductive," says Lindsay Herlihy, a bander-in-training, "but not always unavoidable."

The first catch of the day is an American redstart, a member of the warbler family. This individual is young, with yellow side spots and a gray back, instead of the adults’ bold black and orange patterning. Holmes gently untangles the bird from the net and brings it back to the lab in a small paper bag.

He rattles off a four-letter acronym and a string of numbers, which represent the bird’s species, and which net it came from. "The first thing we do is to put a band on, so if he escapes and we catch him again, we can get the rest of his information." Tipping the bird upside down, he deftly maneuvers a pair of pliers around the bird’s leg and attaches an aluminum band. The bird cheeps and flutters at the humiliation of his belly-up position, but Holmes has a firm grip. He reads off the band’s number to Herlihy – another string of numbers, each one unique. "It’s like giving the bird a name," Herlihy explains.

Holmes and Herlihy are unlikely to encounter this bird again once they release it. Banded birds, even small ones like this redstart, contain a wealth of useful information. Using the data collected by Holmes and his team, as well as new information obtained by tracking individual birds wearing data recorders, scientists are building a clearer picture of the routes migratory birds use to travel. This picture will have consequences for everyone from airline pilots to wind farmers.

Using the island as a refueling station, migrating birds gorge on the abundant insects and late-summer fruits. The birds store fat that they will call upon as they journey south to their wintering grounds. "With a good fat load, these birds can fly one hundred hours non-stop," says Holmes. "They can cover incredible distances."

Millions of other songbirds will join the redstart on his journey, streaming toward the southern hemisphere in a cloud of feathers and flutters. But exactly how the birds get from Maine to Managua is a puzzle scientists are just beginning to crack.

Using dime-sized "bird backpacks," scientists have recently been able to follow individual birds from the beginning to the end of their migration. Bridget J. M. Stutchbury, a biologist at York University in Toronto, fitted 34 songbirds with the backpacks – packages of equipment designed to detect where the bird was in relation to the sun. Once Stutchbury retrieves the backpacks from the birds, she will use this information to determine how fast the bird was flying, where it stopped to rest and for how long, and exactly what route an individual bird took. This is the kind of information the bird banders had hoped to get by recapturing banded birds "but we almost never catch the other station’s banded birds." David Holmes says.

Holmes is enthusiastic about using Stutchbury’s data to learn about the fate of migrating birds. "The elephant in the room, when you talk birds, is collisions." Collisions between birds and planes happen thousands of times each year – twenty will occur in the time it takes to read this sentence.

According the Bird Strike Committee USA, in 2007 alone over 12,000 bird strikes caused $650 million in damages to aircraft. These numbers were gruesomely brought to life in January 2009, when U.S Airways Flight 1549 made an emergency landing in the Hudson River after two birds struck the engines shortly after take-off. The United States Department of Defense is responsible for mapping airline routes, and knowing the exact routes that migrating birds use will allow pilots to avoid those routes, and prevent similar incidents from occurring.

Migrating birds also face hazards from the green energy movement. More and more countries have been turning to wind power as an alternative to gas and oil for producing electricity. As a result, giant banks of wind turbines have been sprouting off coastlines. Placing the turbines over water puts them in the path of the strongest winds, and also in the path of many migrating birds.

The State of Maine is hoping to install a large bank of turbines just off its coast, but wants to know how those turbines would affect migrating birds. Appledore Island, six miles off the Maine coast, recently acquired a wind turbine in the hopes of reducing the island’s reliance on costly generator power. The State of Maine asked Holmes and his banding team to monitor the turbine for bird collisions, so every morning Holmes walks around the turbine, checking for the bodies of songbirds. "In five seasons of doing this, we have not found a single dead bird," Holmes reports. "except the ones put there on purpose."

Holmes cautions against placing too much weight on their results. "We’re looking at a small turbine that’s on a small island, so you have to be careful applying what we see here to a situation with many, large turbines over water."

Nevertheless, Holmes remains upbeat about the future of wind farming. "There’s an experiment in Mexico right now, looking at the migrating raptors." Each year, thousands of birds of prey fly down the western side of Mexico and cross over to the Gulf of Mexico. "They were seeing 300,000 birds in one day," he says, "it’s been called, ‘the river of raptors.’" The World Bank would like to provide funding to put large banks of wind turbines along the birds’ migration route, "but they have one requirement: whoever ends up running the turbines will have to shut them down completely during migration season."

Holmes is thrilled that non-birders have taken an interest in birds. "We’re finding out pieces of how the world works," he says. And those pieces are rerouting plane and shaping the clean energy movement. Holmes has finished banding and measuring the redstart, and carries it outside for release. The bird leaves his hand, its duty to science finished, its own small piece of the puzzle now recorded and available for future use.

Tuesday, August 18, 2009

The Island of Science Writing: An Introduction

Appledore Island, located off the coast of Maine, is home to the Shoals Marine Laboratory. The lab is both a school and a research center. Students come by boat to island to spend anywhere from a week to a month taking classes on subjects ranging from shark biology to underwater archaeology. Meanwhile, researchers use the lab as their base of operations for field work and experiments. Students and scientists together work under the watchful eye and the all-day squawking of the island's colonies of gulls.

In August 2009 I came to Appledore to teach a course on science writing. The class was made up of undergraduates, just-graduated students wondering what they were going to do with their lives, and a couple full-time writers considering making a shift of career.

Over the course of the week the students were introduced to the island's intertidal zone, went hunting for hagfish, and visited an archaeological site on neighboring Smuttynose Island, where thousands of years of history is preserved just below the grass. The students then had to write a 500-word piece about each subject.

The students then dove into their final project, a 1500-word story. They could expand one of their 500-word pieces, or take advantage of other stories-in-waiting on Appledore. Some students decided to talk to two teaching assistants who are at the cutting edge of visualizing animals in motion by making 3-D X-ray films. Others chose the bird banders of Appledore, who have banded over 100,000 birds during the migration seasons since 1981. Others struck out on their own, finding stories I didn't even know were waiting to be told.

Science on Shoals is a record of their work. It allows them to complete the journey from research to publication. And it also allows people off the island to enjoy the work of these students and to learn about a remarkable place.

[Update 8/19 8 pm: Changed Appledore to Smuttynose. Thanks, Jim.]