2015 Thesis Excerpts

Rachel Becker, You Smell: The Mysterious Science of Scent
Christina Couch, Life After Hate: Recovering from Racism
Cara Giaimo, The Mascot and the Refugee: Survival Strategies for the New Urban Jungle
Michael Greshko, There and Back Again? Reproducibility and the Hunt for a Human Compass Sense
Anna Nowogrodzki, Sex, Drugs, and Women’s Desire
Sarah Schwartz, Owning the Code of Life: Human Gene Patents in America
Joshua Sokol, The Reef at the End of the World

You Smell: The Mysterious Science of Scent
Rachel Becker


Life After Hate: Recovering from Racism
Christina Couch

Christian Picciolini was fourteen when he encountered his first white power skinhead. It was 1987 and Christian was smoking pot with a friend in a back alley near his home in Blue Island, Illinois, when he was interrupted by a dark muscle car that pulled into the alley, spitting gravel and skidding to a stop just a few feet away.

“He came out of the passenger’s seat, beelined it straight to me with a dead look in his eyes,”Christian says. “He just looked at me and said, ‘Don’t you know that that’s what the communists want you to do?’And like in a kung-fu move, just pulls the joint out of my mouth and smacks me in the head…From that moment on, I knew I wanted to be like this guy.”

That’s when Clark Martell, a former member of the American Nazi Party who is largely credited with building the early racist skinhead movement in the United States, told Christian about how white men stay enslaved—through advances made by so-called “less intelligent”races, through drugs that calm the mind and draw focus away from the real fight, through greater opportunities for immigrant business owners, ironically just like Christian’s Italian parents.

“From that moment on, I knew I wanted to be like this guy.”

Christian was mesmerized, not only by the Doc Martens-clad skinhead standing before him but also by the idea of being part of a social movement much larger than himself. Christian spent the next seven years involved in the white power movement. He eventually became regional leader of a group that was once one of the most prominent white power skinhead gangs in the country.

More than a decade later, Christian co-founded Life After Hate, a nonprofit organization dedicated to helping former right wing extremists transition out of the lifestyle. In addition to offering support for recovering racists and those they’ve hurt, Life After Hate also works with government sectors and community organizations to help people outside the supremacist community understand how these groups work.

Now they’re broadening their impact. With grant funding from the Department of Justice, Life After Hate is partnering with the research nonprofit, RTI International, to conduct a three-year study that examines behavior patterns of former right wing extremists. By gaining a better understanding of the motivations behind joining and leaving extremism, Christian and RTI hope to create a psychological assessment that can help organizations like Life After Hate understand who’s ready to leave the extremist lifestyle and what they’ll need to make a successful transition.

Full thesis here: http://dspace.mit.edu/handle/1721.1/101359


The Mascot and the Refugee: Survival Strategies for the New Urban Jungle
Cara Giaimo

The earth has only so much room, and humans are taking up more and more of it. Our population grows by a little over one percent per year, and the cities that house the majority of us swell in turn. To connect them, we web the spaces in between with roads and railways, with sky-high wires and underground pipes. To repair, power, and feed them, we clear-cut rainforests, dynamite mountains, and parcel valleys into cow pastures and fruit orchards. Other creatures that find their stomping grounds chopped, paved, or highway-sliced are left with a decision: stay on their shrinking ranges (and deal with the crowded consequences) or strike out into the un-wild.

Those who choose the second option are called synanthropes, from the Greek words for “with” and “humans.” Defined by ecologists as “wild species that settle in human habitations of their own accord,” synanthropes find niches and make homes all over what we call civilization. We’ve got skunks in our garbage dumps and coyotes on our golf courses, hawks in our high-rises and rats in our sewers. No block is too developed; no phylum too untamed. Sand flies swarm around Brazilian hydroelectric power plants, drawn to the water in the retaining dams. House sparrows open automatic doors. The Thames Estuary—the rivermouth that, as Joseph Conrad had it, launched “the dreams of men, the seed of commonwealths, the germs of empires”—houses, now, a thriving population of harbor seals.

Austin, Texas, is a case study in synanthropy. Interspecies encounters are as much a part of city life as outdoor music and taco trucks (indeed, the grackles have been known to imitate electric guitars and to steal tortilla chips from hapless Tex-Mexers). I have met, on different twilit jaunts through the city, raccoons camped out in roadside culverts, coyotes howling at the Moon Towers, and a pair of falcons perched on adjacent telephone poles, scoping out prey. The reasons are practical: Austin has been growing steadily since its founding nearly two centuries ago, and its mild climate and embrace of green space are as appealing to animals as they are to people. But the results are palpable, experiential; it feels as though, with no more frontier left to explore, all that wild Texas energy turned inward and started attracting furrier, scalier pioneers. Even the species represented seem freakier than average, as though the animals, too, have read the bumper stickers, and have committed themselves to the business of Keeping Austin Weird. Any old city has pigeons. Austin has feral parakeets.

All these animals have settled into the city’s ecological rhythms, finding ways to eat and sleep and mate despite the streetlights and the concrete. But when humans take over a space, they do more than change the landscape. A city like Austin has systems and dimensions beyond the physical. It’s a political, social, and economic entity, not just a bunch of side-by-side dwellings. Cities have laws, goals, and values that overreach their individual residents. They run on super-resources—money, power, attention—that draw competitive focus and determine access to more traditional assets like food and shelter. Just by being around, synanthropes get cast in these human dramas. How well they perform can mean the difference between life and death.

Full thesis here: http://dspace.mit.edu/handle/1721.1/101361

There and Back Again? Reproducibility and the Hunt for a Human Compass Sense
Michael Greshko

Full thesis here: http://dspace.mit.edu/handle/1721.1/101362

Sex, Drugs, and Women’s Desire
Anna Nowodgrodzki

It happened gradually when Barbara Gattuso was in her mid- to late-thirties. She was married and had three kids, the youngest of whom was a toddler. Her husband Greg was wonderful, and their marriage was going great. But she slowly lost her desire to have sex with him.

It wasn’t that she didn’t enjoy sex once it was happening. “When you’re in the act, you have desire. You like it when it’s being done,” she says. But beforehand, she felt no desire to have sex. This caused her “terrible stress.” She’d get up earlier in the morning than her husband, go to bed later, or pretend to be asleep just to avoid the possibility. “It was awful,” she says. “A horrible, horrible deception in a marriage.”

She talked to gynecologists, and none of them knew what to do. “If you find something, please let us know,” she says they told her. She called a “couple PhDs” who “claimed to be in sexual medicine.” When she explained her problem, she says they hung up on her. So she didn’t try sex therapy. She tried some over-the-counter remedies—nothing helped.

Barbara’s situation lasted for over 20 years. She never told Greg about it. One day in 2011, she saw a notice somewhere—on TV or in something she read, she doesn’t remember—of a clinical trial for a drug called flibanserin. “I was really excited,” she says.

Flibanserin was not yet approved, and it worked by altering levels of the neurotransmitters dopamine, norepinephrine, and serotonin. It was originally proposed as an antidepressant, first described in a 1997 paper, but it wasn’t found to be effective at treating depression in any of its nine Phase II trials. Many antidepressants carry a side effect of lower libido, and the later Phase II trials for flibanserin measured sexual dysfunction with an assessment that included the question, “How strong is your sex drive?” Women on flibanserin had higher sex drives than women on a comparable antidepressant, and, to the researchers’ surprise, higher sex drives than those on the placebo. So the Germany-based pharmaceutical company that owned flibanserin, Boehringer Ingelheim, began developing it as a drug to treat low desire.

Barbara hoped flibanserin would work to increase her desire or maybe as an antidepressant—either way, she could use it. “My dad was really ill at that time, and we lost our home in a fire. All this happened in six months.” She thought, “I have nothing to lose.”

Soon, Barbara was talking about her sex life in front of a couple hundred strangers. In a gray blazer with her blonde hair swept up, she looked determined and controlled sitting at the front of the FDA conference room in White Oak, Maryland. Other patients and their representatives clustered at circular tables in front. They were all there for the FDA’s patient-focused drug development public meeting on female sexual dysfunction.

Low desire has historically been considered a psychiatric condition, which means its diagnosis is defined in the Diagnostic and Statistical Manual, or DSM. When a group of experts met in 2000 to discuss updating the definition of female sexual dysfunction, “95 percent of them had financial relationships with the drug companies hoping to develop drugs for the very same condition,” wrote Ray Moynihan in his book Sex, Lies and Pharmaceuticals.

Full thesis here: http://dspace.mit.edu/handle/1721.1/101363

Owning the Code of Life: Human Gene Patents in America
Sarah Schwartz

On the banks of New York’s East River, several sleek white buildings form the Weill Cornell Medical Center. On the thirteenth floor of one of those buildings, Christopher Mason’s office provides a view of rooftops and a hazy uptown sky. Mason is a geneticist, a fact expressed in his office decorations. There’s a stuffed chromosome pillow leaning against the window; the wall displays complex genome maps and an illustration of a Holstein cow and a chicken staring at a cow-patterned egg between them. “I was fascinated by the fact we started as one cell and all the instructions later, become the entire panoply of cells in your body,” Mason says. “And so all you need is time and the right cues, and it’s amazing that it works as well as it does.”

Mason’s laboratory works to understand how to read the genetic code that controls this process. He observes extreme mutations, and also looks at the evolution of the genome, studying DNA, proteins, RNA and its regulation, and more. “If you add it all up, it sounds like we do everything,” Mason says. “But we kind of do a little bit of everything…because I’m, like, ADHD and barely function as a scientist.” He is presumably joking, but he does seem to be managing several things at once, sometimes pausing our conversation to check up on a grant application or a rescheduled meeting later in the afternoon. His wide range of focuses also helps explain his interest and involvement in law.

As a graduate student at Yale, Mason had stumbled across a 2005 research paper that detailed the breadth of genetic patents and their effect on research. The paper suggested that nearly 20% of human genes were patented. Mason had just begun to study human genes associated with autism, combing through them to search for disease-causing mutations. The paper stunned Mason, who remembers thinking, “That means that almost every day, I’m infringing on someone’s patent.” It seemed too weird to be true, he says, but he soon discovered that it was.

The average human gene needs between 10,000 and 15,000 nucleotides (around 3,000-5,000 amino acids) to encode its specific instructions. But when Mason went looking through patents, he found that patent protection was applied to much shorter stretches of DNA. In fact, the magic number seemed to be…15. Not 1500, not 15,000, but 15 individual nucleotides.

Patenting 15 nucleotides of the human genome presents a problem when repetition of these nucleotides occurs in multiple other genes. It’s akin to having legal protection on the letter “s,” when the average word is ten letters long. That means that “sandwiches,” “schoolwork,” “settlement” and “shantytown,” though clearly different in meaning, all contain the same patent-protected letter. And “sandwiches” is the biggest violator, because it contains that patented portion twice. (Nothing says that the words have to start with s, either, so “racecourse,” “filibuster,” and “generators” all infringe the imaginary “s” patent as well.)

Using the coding language Perl, Mason went through the National Center for Biotechnology Information’s open database of gene sequences, looking for matches of specific nucleotides. “It only took maybe an hour to write that script,” he says. “Within

the language of Perl, it’s an extraordinarily easy thing to do.” In fact, the challenging part of his study was navigating the semantics of the patents, he says, not analyzing the genes themselves.

His results were dumbfounding. When he compared 15-nucleotide sequences covered by gene patents to the genetic code of all human genes in the open database, Mason found at least one patented sequence in 100% of known genes.

Full thesis here: http://dspace.mit.edu/handle/1721.1/101364

The Reef at the End of the World
Josh Sokol

We’ve arrived at a location tagged on Google Earth, an innocuous spot in the deep blue lagoon between Palau’s islands and the barrier reef that rings the archipelago. Palau’s most populous island, Koror, is a few miles behind us to the southeast. Nestled in the back channels of Koror is Nikko Bay, where I swam with Barkley. Diagonally south and to the west of Koror are the other Rock Islands, gumdrops and sinuous crests of green, a maze with karst walls and paths through turquoise shallows.

Ahead of our boat, on the barrier reef crest, there’s a sliding glint as a line of about-to-break waves crumbles from right to left, the foam after the crash extinguishing each reflection of the Sun before it alights on spot a little farther down the row. “I love that it’s so quiet you can hear the waves breaking,” Shamberger says, listening for the soft roar.

Then she drops a cylindrical flask into the water, snaps it shut, and pulls it back up to the boat. Methodically, using a plastic tube, she rinses a glass bottle out three times with seawater from the flask, then fills the bottle to the brim. Her grad student Andrea Kealoha injects a tiny amount of mercuric chloride into the bottle, which will kill any stowaway bacteria that might further alter the water’s chemistry.

That’s a water sample: the bread and butter of ocean chemistry in general, and of ocean acidification field work in Palau in particular. It’s the staple crop, the jump shot; the basic building block of an entire scientific case. Shamberger twists the cap on and holds up the full bottle to catch the sunlight. It looks like a bottle of clear seawater.

The samples need to get taken at intervals to match the range of tides, which leaves plenty of down time. And since each sampling run takes seven or eight hours out on the boat, a red cooler is fully stocked with snacks. I sit with Shamberger, munching, and we fill the time with talk of ocean acidification.

The sample she’s just taken is infinitesimal progress, a lone pixel in the slowly enhance-enhance-enhancing image scientists are building of ocean acidification. It will be shipped back to Woods Hole along with hundreds of other indistinguishable bottles of seawater. Then twenty minutes of somebody’s life, probably Barkley’s, will go into testing its carbon chemistry. That’s because ocean acidification is not a problem of acid per se, but of carbon.

It’s certainly caused by carbon. There were 350 molecules of carbon dioxide per million molecules in the Earth’s atmosphere in the late ‘80s. That climbed to 370 parts per million at the dawn of the new millennium, then 400 parts per million in 2015. It’s still ramping up. Putting global warming aside for a minute, wind and waves are churning that extra atmospheric carbon into the ocean.

And despite what the name implies, ocean acidification is not an issue of reefs dissolving in vats of acid. The ocean is merely moving from a pH of 8.1, about the same as an egg, toward the acid side, to a value in the high 7s. By definition, anything from pH 14 down to neutral pH 7 is basic, making the ocean of the future still less acidic than pH-neutral shampoo.

But that’s not to say ocean acidification isn’t a problem. The pH scale is logarithmic, like the Richter scale for earthquakes. Even the pH decrease of 0.1 that the oceans have experienced so far is more dramatic than it sounds: the world’s oceans are even now about 30 percent more acidic than they were in pre-industrial times and counting. Marine organisms will rue this change.

Full thesis here: http://dspace.mit.edu/handle/1721.1/101365