2014 Thesis Excerpts

Lindsay Brownell One Fish, Two Fish, Lungfish, Youfish: Embracing Traditional Taxonomy in a Molecular World

Julia Duke The Beast Within: Measuring the Minds of Zoo Animals

Suzanne Jacobs The Ruins of Science

Alexandra Morris Preying on the Predator: The Shark Fin Controversy

Abi Nighthill Taking Nature’s Pulse

Jennifer Rood Succulent and Spiny: The Bahamas’ Quest for a Sustainable Lobster Fishery

Emma Sconyers I Carry You in My Heart: Facing an Incurable Prenatal Diagnosis

Sam Wotipka Seizing a Species: The Story of the Great Salt Lake Brine Shrimp Harvest


One Fish, Two Fish, Lungfish, Youfish: Embracing Traditional Taxonomy in a Molecular World
Lindsay Brownell

In the basement of Harvard University’s Museum of Natural History there is a fish. Actually, there are over a million preserved fish in the museum’s Ichthyology collection, but there is one particular specimen of blue parrotfish, Scarus coeruleus, that is older than the museum itself. It arrived at Harvard in 1869 from Cuba wrapped in newspaper, was filed away in a drawer and sat there unopened for 144 years. I happened to be exploring the collection in search of an idea for an article from Harvard’s archives, and found the parrotfish still sealed in its newspaper cocoon. Intrigued, and with the somewhat bemused consent of the collection’s curator, I carefully began to unwrap it.

The newspaper had turned tobacco-brown with time and crumbled in my fingers like dead leaves. Diario de la Marina was printed across the top in bold, black letters, and below that, “El periódico oficial del apostadero de la Habana” – “the official newspaper of the colony of Havana.” This particular issue was dated Tuesday, the 31st of August, 1869. The news briefs on the left side of the front page included a London Evening Post report that Spain had firmly refused the United States’ most recent propositions with respect to Cuba’s independence. The backside of the front page detailed the most recent military offenses against Spanish forces. All had clearly not been quiet on this fish’s home front.

As I was sorting through the pages of Diario de la Marina, I discovered that along with the parrotfish’s skeleton was a packet of its scales, contained in what looked like a folded letter. I opened that, too. Beautiful cursive writing stretched across the crinkled, time-stained page, dated July 13th. “My dear father,” it began in Spanish, “The other day I sent you a barrel; inside were fifteen and a half yards of cloth for wrapping fish…” It was signed “Your daughter, Amelia.” All my other article ideas were forgotten. I wanted to know more about this father was whose hands had so lovingly wrapped this fish with his daughter’s words, preserving a slice of history and his own life along with its bones.

The man, it turns out, was Felipe Poey, Cuba’s most celebrated naturalist and one of the most prolific zoologists of the nineteenth century. Why is such a prolific scientist so little known today? The field of taxonomy was in an uproar. Darwin’s recent publication of On the Origin of Species had completely upended the way that taxonomists understood their field and their work. There was raging debate over how classifying and naming creatures should be done.

Today, taxonomy is at another crossroads. The debate now is not between evolutionists and creationists, but between those supporting DNA evidence as the ultimate determinant of species relationships and those who champion the traditional method of comparing samples’ physical traits to organize them into the neat evolutionary trees that pepper our textbooks. Those trees’ straight, black lines between species seem to promise that this, finally, is the truth about how they came to be, but taxonomists are far from consensus about what arrangement is correct.

Full thesis here: http://dspace.mit.edu/handle/1721.1/92629


The Beast Within: Measuring the Minds of Zoo Animals
Julia Duke

The case of Central Park Zoo’s infamously “depressed” polar bear, Gus, is an extreme example of a common yet controversial human practice; we readily see human-like emotions in animals. Scientists call this anthropomorphism. It is difficult to view a large, furry mammal playing with a red ball, slouching with its head on its paws, or staring straight at you, without musing on the being’s inner state. When a dog pursues its own tail for hours, or a zebra bounds excitedly around its exhibit, we can’t help but wonder; what are they thinking? The connection felt between New Yorkers and Gus, the care and consideration afforded an Ursus maritimus, illustrates a common concern we have with the mental experiences of animals.

While watching Gus pace back and forth across his pool, lingering by the viewing window, or peering back at the humans peering in, people at Gus’s exhibit pondered the bear’s deepest emotions, ailments, and desires. Though Gus spent his entire life in captivity, both keepers and visitors likely wondered, did Gus yearn for thousands of acres of ice and snow? Did he dream of snagging a fresh seal dinner as it popped out of the open water? Was he as tormented by his manmade confinement in the center of New York City as his perpetual pacing seemed to suggest?

Zoos—the good ones at least—have always taken care of their charges’ physical health: providing food, shelter, and medicine for their illnesses. These physical provisions are the parameters by which good welfare has traditionally been defined. Keepers and vets keep checklists and routines to ensure animals’ bodies are in good condition, that fur is shiny, eyes are clear, appetite is healthy, and excrement looks normal. But if an animal has all of its physical needs seemingly taken care of, yet still shows signs of discontent, how do you fix a problem that you can’t be sure is there? Zoo goers don’t hesitate to declare an animal “unhappy,” but zoo keepers and researchers shy from such words. The animals may be expressing poor welfare, but “unhappy”? That’s not a word they are comfortable with.

A growing frustration with this quandary is rising within the zoo world. Popular, expressive individuals like Gus prompt public awareness and media attention. As zoos are confronted by visitors’ and investors’ concern for their animals’ mental health, there is a growing willingness to tackle the unknown: the inner feelings, emotions, and even thoughts of the furry, scaled, and winged creatures in their care. While visitors watch seals clap and gibbons swing from branch to branch, speculating on which ones look happy, sad, pensive, or grumpy, some zoos are taking steps to perform objective scientific tests that can confirm those impressions.

The question is: How do you set up a rigorous, controlled experiment to enter an animal’s mind? And how do you ensure that, in the process of probing parrot, penguin, and puma feelings, that you do more than just bestow them with your own emotions?

Full thesis here: http://dspace.mit.edu/handle/1721.1/92631


The Ruins of Science
Suzanne Jacobs

Nearly 11 acres of preserved prairie nestled in the Illinois suburbs, Fermilab is a bizarre blend of the natural world and some of humanity’s most advanced scientific instruments. Grassy fields, lakes and forest fill the wide gaps between buildings where scientists study the inconceivably small particles that make up everything in the universe, even the seemingly empty voids of space. Along one of the few roads on site, there’s a line of towering electrical poles in the shape of the Greek letter pi, a monstrous “capacitor tree,” and a herd of bison. Old farm houses coexist with architectural wonders like the Proton Pagoda – a black box propped up on four 26-foot-tall legs and connected to the ground by two spiral staircases twisted into a DNA-like double helix.

But among all of the oddities in this small world of juxtaposition, the biggest surprise of all is what lies beneath the grassy fields. Hinted at only by low earth berms that occasionally run tangent to the roads, the Tevatron sits quietly in its tomb 25 feet underground. It’s been more than two years since the pride of U.S. particle physics shut down, and while the rest of Fermilab has moved on to new experiments, the Tevatron remains in a kind of limbo – not an exhibit, not on its way to the scrap yard. For now, it lies patiently like a relic from a past civilization waiting to be discovered.

Inside the squat service building set up along the Tevatron ring, Czarapata and I make our way through a forest of electronics and a legion of pipes and dewars built for the Tevatron’s liquid helium cooling system. We eventually come to a flight of concrete stairs that leads down to the 10 foot high, 8 foot wide tunnel undercutting more than four miles of prairie. My excitement grows with each step of our descent until finally we enter the ever-curving corridor, home of the elusive machine I’ve read and heard so much about.

When I ask Roger Dixon what it was like during his early days at the lab, his eyes light up.

“I’d be so excited when I’d come to work back then. Sometimes I’d stay for days without going home, and I would think, ‘We’re really making history here.’ There was that feeling that everybody ought to be able to experience in their life – that what you’re doing is really something unique, incredible and making history.”

Full thesis here: http://dspace.mit.edu/handle/1721.1/92633


Preying on the Predator: The Shark Fin Controversy
Alexandra Morris

The captain cut the motor. The waves had been increasing for an hour. “It’s too rough out here,” he said, anticipating the disappointment that washed over our faces. We had risen before the sun’s rays peaked over the horizon, we’d pulled on our damp wetsuits and climbed with sleepy smiles into the boat. But despite the captain’s best efforts, we were still within sight of Mozambique’s coastline.

Before we could react, he was shouting at us. A whale shark, the largest known fish in the sea, had passed just beneath the boat. My hands shook as adrenaline coursed through my veins. I pulled my flippers over my feet and fastened my snorkel mask. We dove backwards simultaneously off the boat, limiting our disturbance of the animal to one collective splash.

Once in the water, I flanked the group slightly, hoping to secure the ideal viewing position for my first live shark encounter. But when I peered through my snorkel mask, I saw nothing but microscopic fish. How was it possible to overlook an animal the size of a school bus? My anxiety was mounting. Suddenly, a dark shadow emerged just beneath the surface of the water, no more than ten feet in front of me. I held my breath and lowered my face. And there, in the middle of the Indian Ocean, I found myself staring into the open mouth of a feeding whale shark.

When one hears the word “shark,” it’s unlikely a docile whale shark is the species that first comes to mind. It’s more common to imagine members of the toothier variety, such as a great white or a hammerhead. But shark species range considerably. Nocturnal nurse sharks nestle along the sea floor, ambushing crustaceans. Lemon sharks are social butterflies and prefer grazing on fish near the warm surface of the water. Spiny dogfish are the runts of the shark litter, maxing out at just over three feet.

Sharks tend to invoke a sense of fear in humans—the indestructible predators of the sea. Yet they face their own dangerous predator. Sharks kill 12 humans each year, while humans kill 11,417 sharks every hour. A shark’s fin is a gold mine in certain cultures: the pectoral fin of a whale shark is worth more than my Subaru Outback.

Not long ago, a group of shark fishermen came to realize there was little value in carting massive shark bodies to shore when all they needed were the fins. So they sliced off the fins, and threw the still living, rudderless sharks to die in the open ocean. So began the gruesome practice known as “shark finning.” Due to its massive size, luminescent markings, and unique texture, a whale shark fin is the Rolls-Royce of the fin market.

Shark fishing and especially finning has resulted in the addition of dozens of species to the list of threatened and endangered species. Over the past ten years alone, numerous shark conservation groups have emerged around the world. Media campaigns, celebrity advocates, and new government regulations have attempted to curb the demand for shark fins. Yet despite these efforts, the fin market continues unabated.

Full thesis here: http://dspace.mit.edu/handle/1721.1/92635


Taking Nature’s Pulse
Abi Nighthill

Text to come


Succulent and Spiny: The Bahamas’ Quest for a Sustainable Lobster Fishery
Jennifer Rood

Full thesis here: http://dspace.mit.edu/handle/1721.1/92634


I Carry You in My Heart: Facing an Incurable Prenatal Diagnosis
Emma Sconyers

When it comes to an abortion, it’s not always as straightforward as deciding yes or no. State laws are shifting every day. Women find themselves straddling the line of whether or not their abortion will be legal—even if their child has an incurable disorder. The anatomy scan, given at 20 weeks to determine the gender of the baby, is often the time when abnormalities come to light. It also happens to be the cutoff for legal abortions in much of the South and Midwest, and falls dangerously close to 24-week limitations in the rest of the United States.

The day before Dawn went to her 20-week appointment, she was frantically cleaning the house. She found herself increasingly agitated and every other word out of her mouth was a snap at her husband. She didn’t know why, but she felt like something wasn’t right. The next day, still on edge, Dawn dropped her three-year-old daughter off at daycare before driving to the ultrasound appointment with her husband. She turned to him and said, “I think something is really wrong.” Her husband assured her everything would be fine. But just a few weeks prior, the morning news had announced that Georgia had introduced a 20-week abortion ban. She kept turning that number over and over in her mind. What they would do if the baby was really sick?

Dawn’s doctor gave her a grim prognosis, without any guarantee the baby would be born alive. Even if by some small chance the baby was not stillborn, she would face constant medical care: diabetes, an inability to maintain her temperature, endocrine issues, and kidney issues. The list seemed endless.

Although Dawn supports pro-choice for other women, she had always been pro-life when it came to her own pregnancies. Her entire opinion shifted after the diagnosis. She didn’t know if she and her husband could handle that kind of care. A future with a child that sick seemed insurmountable.

Dawn’s doctor didn’t perform abortions, so she sent Dawn to a specialized clinic. The abortion clinic only saw women that far along in their pregnancies, past the first trimester, on Fridays and Saturdays. It was five days before she went in to have an abortion. “I guess some people treasure those times, whatever time you have with your child,” Dawn says in an interview about a year after her termination. “But it felt cruel and like torture to me because I knew what the end was.” She starts to cry, “I knew what we were going to do and I didn’t want to prolong her suffering any more than I had to.” She had trouble sleeping the week before her appointment and started developing panic attacks. She changed her mind one way or the other every night before bed, worrying herself sick. Her husband kept her grounded. “He was 100 percent sure we were making the right choice and if you ask him today he would say he’s 105 percent. He just knew,” she says.

Full thesis here: http://dspace.mit.edu/handle/1721.1/92632


Seizing a Species: The Story of the Great Salt Lake Brine Shrimp Harvest
Sam Wotipka

When you talk to the scientists and state workers that were around during the nascent years of the harvesting industry, the phrase “wild west” tends to get thrown in a lot. There are tales of boats bieng used as battering rams, physical confrontations and drawn guns.

Jensen and his comrades smirk and roll their eyes at teh suggestions. “More like primitive equipment and hillbillies,” says Stenerson.

As a twenty-two-year-old, Stenerson relocated to Utah from Elkhart, a small town in northern Indiana known for being the RV manufacturing capital of the world. He got his start in the brine shrimp industry in 1989 at BAI, where Jensen had recently been hired as captain. Stenerson spent his first season in the company’s warehouse rinsing batches of cysts in potassium permanganate, a disinfectant, then drying and packaging them. The next season, he joined the harvest crews out on the lake. After a few years, he jumped ship for Jensen’s newly formed company where he eventually became a captain himself, operating a 34-foot Kvichak skiff that was used as a haul boat.

The crews out on the boats are a hardy bunch. A lot of them work the commercial salmon and king crab fisheries in Alaska during the summer, migrating south in the winter to make a little extra cash harvesting brine shrimp. Jensen staffed his boats with fellow river guides. “When shit hits the fan, they’re not afraid,” he said.

Even for seasoned fishermen and river runners, being out on the Great Salt Lake in January and February can be trying. Utah winters are cold and the lake waters are often subfreezing. Snow and wind are commonplace, as are stomach-turning waves, which roll across the surface of the lake and can reach several feet in height. Owing to the water’s elevated density (a product of its saltiness), the waves can pack a substantial punch.

Full thesis here: http://dspace.mit.edu/handle/1721.1/92636