2004 Thesis Excerpts

Amitabh Avasthi Superfish

Katherine Bourzac Chimeras

Jennifer Frazer Mold Fever

Courtney Humphries New Age of AIDS

Carolyn Johnson Neutrino Capital

Megan Ogilvie Iron in the Ocean

Mara Vatz Flight 191

2003 Thesis Excerpts

Erico Marui Guizzo Shannon's Message

Timothy A. Haynes Basis For Dreaming

Matthew T. Hutson Computing Beethoven's Tenth

Sorcha McDonagh Atlantic Crossings

Maywa Montenegro deWit Genetically Versatile Rice

Anna E. Strachan Chasing Chupacabras

Superfish:
The Coming Blue Revolution
Amitabh Avasthi

Located on the eastern most tip of the North American landmass, St. John's in Canada's Newfoundland province boasts a link with the sea that is older than any other city on the continent. Over a thousand years ago, the Vikings were drawn to the region because of its incredible marine life. When Italian explorer—and fish trader—John Cabot landed there on St. John's Day in 1497 the abundance of fish amazed him and his crew. Cabot returned to England with tales of a "new-found land" where fish could be hauled up in buckets. By 1620, the region was a major supplier of dried cod to countries as far away as Spain and Italy. France and England fought mightily to control this vast fishery business.

Four centuries later, St. John's is now just another exotic travel getaway, a sleepy port town blessed with natural beauty, scenic drives, and historical monuments. But quiet rumblings are taking place there on the molecular level. Genetic tinkering in its laboratories is attracting the interest of the world's fish consumers and industry alike. These fruits of biotechnology promise to match the discovery of fire itself. If the efforts succeed and ecological concerns are allayed, genetically modified fish—bred to grow at a phenomenal speed and resist disease—promise to revolutionize the aquaculture industry and restore St. John's to its formal glory as the center of the global fish trade. But playing with fire has dangers as well. Some wonder if such attempts to remodel nature could have ecological consequences as disastrous and irreversible as a conflagration out of control.

Since the earliest days of animal domestication, humans have tried to improve the quality of their livestock through selective breeding. Though the results have been impressive, the process is generally slow and time-consuming, as it can usually take several generations of such selective breeding to achieve the desired traits in an animal. Breeding efforts are imprecise, and success is mostly a hit or miss affair.

In 1866, Austrian botanist and monk Gregor Mendel demonstrated how physical traits were transferred from parent to offspring through genes. Geneticists later came to realize that if they could somehow collect the genes responsible for specific traits and selectively add them to individual plants and animals, they could make designer plants and animals of their choice. But there was a problem. Science lacked the methods to extract, purify, and manipulate DNA, the molecule that genes are comprised of. Not until 1973 did Stanley Cohen of Stanford University and Herbert Boyer of the University of California, San Francisco, solve the problem by showing how DNA from one organism could be carefully snipped away at just the right point using enzymes as molecular scissors and be replaced with a gene from another organism. This method of gene splicing became the common means of transplanting genes from one species to another and led to the creation of the biotech industry. Scientists once had a dream, now they had the tools to realize it.

Breaking Boundaries:
Chimeras and Species
Katherine Bourzac

Humans and mice are much more distantly related than goats and sheep, but chimeras between the two work surprisingly well. "It surprises me that it's so viable," graduate student Paul Davis said of the chimera model he uses to study disease pathways at Washington University in St. Louis. He and his advisor Samuel Stanley, a professor of medicine and microbiology at the university, repeatedly used words like "surprising" and unexpected" to describe their chimeras.

Goats and sheep are in different genera. Humans and mice are in the same kingdom (animals), phylum (back-boned animals), and class (mammals). We diverge before goats and sheep, at the order level – they scurry off with the other rodents, we with our big brains and opposable thumbs join the primates. But enough has been preserved throughout the course of evolution that tissues and cells from humans and mice can form chimeras.

Stanley's lab implants human fetal tissues into adult mice to model human diseases. Davis explained how they create the chimeras. "We have collaboration with the birth defects center at Washington University and they send us fetal tissue at 90-92 days old. We take those fetal intestines and implant a small, centimeters-long tissue section into the back of the mouse. You slice the mouse open on the dorsal side [the back] and you implant the tissue and just close up the mouse." The tissue grows "and you've got a human intestine" living in an easily accessible spot on the mouse's back.

Stanley and Davis use a strain of mice, called severe combined immune deficient (SCID), bred for deficiencies in their immune system. SCID mice don't have an important class of immune cells – those which, among other functions, cause transplant rejection. "We know we're getting around tissue rejection because we're using mice with no immune system, so they can't really reject the [human] tissue." These mice do not incorporate the human tissues to the extent that goat and sheep became integrated in Anderson's overt chimeras. "You're really using the mouse as a vessel to be the carrier for human tissue," said Stanley.

Davis got involved with this work "because it was absolutely cool. The "first corollary" of microbiology, he said, "can be summed up like this: if you don't have a model, you're screwed. That's the end-all, be-all….If there's not a model in which to study your organism, don't study it." And SCID-human chimeras are "the best model you could ever have…for virtually any pathogen. Not only is it a model, it's probably the best model you can get because it's actual human tissue, not a mouse or ape but actual human tissue."

"You can actually mimic a number of things that would be happening in the human in the mouse," Stanley said. SCID-human chimeras have been used to model a number of processes in the human body. "To look at organogenesis – how an organ develops – it's turned out to be a nice system. The other thing that's been nice is the idea of studying human-specific pathogens," agents of disease like bacteria. Scientists have used the chimeras to test early anti-HIV drugs and model diseases from cystic fibrosis to rheumatoid arthritis to cancer. Stanley and Davis study Entamoeba histolytica, an amoeba that causes dysentery (horrible diarrhea) and liver abscesses among other symptoms.

Davis said they hadn't anticipated how well these SCID mouse-human chimeras would work. "It was kind of a grand experiment with no hypothesis – hey, let's see if this would work." They knew the SCID mice would not reject the tissue. "But I think it was to our surprise that it would accept the tissue....we were surprised that it wasn't ignored by the mice," Davis recounted. In other words, the mice go beyond not attacking the human tissue. When you make a new addition to your house that has a sink or a toilet, you add on to the plumbing. The mice do the same thing when the human tissue is added, growing new veins and arteries to provide a blood supply for the human intestine or liver or skin.

Read Katie's entire thesis on MIT's DSpace

Living creatures float in every breath we take. The air is a mist of life that coats every surface exposed to it with microorganisms. This is normal.

Among these organisms are the molds – fungi that specialize in decay. In recent years, these molds have also generated a furor – a storm of fears, litigation, rising insurance premiums, and a small industry specializing in detection and remediation. This is not normal. At least, it's never happened before.

Humans have lived with molds for thousands of years in uneasy peace – especially compared with our tempestuous relationship with other microorganisms. Countless viruses and bacteria infect humans, but the number of major fungal infectious diseases can be counted on two hands. Ebola, plague, smallpox, tuberculosis, and other diseases caused by viruses and bacteria are the subjects of horrific legends and nightmares. Tinea, the fungal cause of athlete's foot, is the subject of mildly amusing low-budget commercials.

But lately molds have been getting new attention. The illnesses some people have claimed are caused by mold are more nebulous, and in some ways, more frightening. Breathing difficulties, headaches, dizziness, flu-like symptoms, unexplained bleeding, hearing or memory loss, cancer…the list goes on and on. And it's not just called mold anymore; it's "toxic mold."

Families come on the evening news to describe how mold has taken over their home – even their car! – making them perpetually sick. Moon-suited remediators are the only ones who enter such contaminated houses, as if they were "hot zones."

Every fall, the news media describe how some public school has developed a mold problem and must be closed for clean-up.

Books and websites warn homeowners about the dangers of "toxic molds", in particular, the black mold named Stachybotrys chartarum ( stack-ee-bot-ris kar-tar-um).

Insidious, silent, and deadly, this new threat has emerged, some claim, to threaten our lives. Others dismiss the concern as mass hysteria, brought out of nowhere by enterprising capitalists, and unsupported by scientific evidence.

"I'm just so fascinated by this phenomenon," said Raymund King, the author of the 2003 book Toxic Mold Litigation. "It's really a phenomenon. I practiced medicine for about 10 years before I became a lawyer, and I see it from two different perspectives." His book, aimed at lawyers, published last July, and priced at $102.85, sold out in eight weeks.

Whatever the true cause, marriages, jobs, and health have all been damaged by close encounters with indoor mold. The insurance industry has also taken a financial beating, as mold claims have skyrocketed nationally. And those looking to exploit or profit on mold fever have caused needless headaches and confusion, sometimes ruining the cases of those with potentially legitimate mold claims.

Why are some people suddenly consumed with fear of "toxic mold?" Have the molds changed? Have our homes? Have we? Does mold truly cause horrific health problems, or is it just hype? The truth, according to a five-month investigation, lies somewhere in between.

Read Jennifer's entire thesis on MIT's DSpace

When a new class of drugs called protease inhibitors emerged from the lab in 1996, everything changed for HIV-infected individuals in the U.S. The following year, studies found that a triple-drug combination reduced the levels of virus in the blood to the point where they were often undetectable. "All of a sudden [patients] just weren't getting sick," Heller said. "And the management of HIV, from the perspective of a doctor taking care of patients, it sort of—I don't want to say became less challenging – but it became more rote."

Heller's patients have simply stopped dying. "I'm trying to think of the last time I saw somebody dying of AIDS," he said, and paused for half-a-minute to think. "I guess it must have been five years ago, at least a patient of mine." And five years ago such a statement would be unthinkable for a physician caring for HIV-infected patients.

Harvey Makadon, a primary care doctor at Beth Israel Deaconess Medical Center specializing in HIV/AIDS, also has not lost a patient to AIDS in four or five years. Not only are his patients living longer, the opportunistic infections that used to plague AIDS patients are now far more rare. "I haven't seen a person with an opportunistic infection in probably three or four years," said Makadon.

For those with access to care, these new medicines have changed the face of AIDS and they have done it far more dramatically than many people in the field would have thought possible. Vastly more people are living with HIV infection than are dying of AIDS. The Centers for Disease Control and Prevention (CDC) estimates that between 800,000 and 900,000 people are living with HIV infection in the U.S., and nearly 400,000 of those are living with AIDS. In 2002, 16,371 people died of AIDS.

Just as insulin treatment changed diabetes from a fatal disease to a chronic one, so HAART has changed the meaning of testing positive for HIV infection in the U.S. In the 1980s and early 1990s, finding out you were infected with HIV often meant dramatic life changes and coming to grips with impending mortality. Some quit jobs and abandoned long-term plans.

But some of these patients, resigned to certain death, received newer treatments and "suddenly it was, 'Here is your life back. You're not going to die,'" said Heller. "And a lot of these people who had put their careers on hold, and their lives on hold, and had not gone into relationships, and had sold their life insurance policies, and didn't both building up their 401Ks" suddenly were given back their lives, but they had already abandoned the things they needed to have a life.

Psychologists dubbed this phenomenon the Lazarus Syndrome, because these patients, if not awakening from death, were returning to their lives after acclimating to the idea that death was at hand. But their new reality was far more complicated than simply waking up to restored health. The suddenly faced the complex financial and medical issues of someone living with a chronic disease. Many had gone on disability insurance during their illness, and now found themselves able and willing to work but afraid to lose their disability by looking for jobs.

From a medical standpoint, the man we call Bill Dudley is leading a life very similar to that of a patient taking medication for high blood pressure, and he represent the ideal in the medical treatment of HIV/AIDS. In the natural course of AIDS, symptoms of illness appear after a mean of eight to ten years. Dudley was fortunate in that he managed to stay healthy for many years until better medications came along.

In the early days of his infection, he was meticulous about his health, regularly working out and meditating. "Back then you were always prepared for the worst," he said. Now he is less vigilant. "But I think part of that has to do with age. I never thought that I would actually see 50."

Read Courtney's entire thesis on MIT's DSpace

Ray Davis' work at Homestake uncovered what Scholberg called "the famous mystery of the disappearing solar neutrinos." The solution to the mystery was far more complex than physicists anticipated, and Homestake played an important part in revealing the particle's true, rather wobbly identity. Scientists didn't have to revamp their solar models or redesign their directors – they just had to reimagine neutrinos. In order for Scholberg's "neutrino dance" explanation to hold true, the particle must have mass and travel slower than the speed of light. But those ideas didn't hold with particle physics' main theoretical platform, the so-called Standard Model. Perhaps the discrepancy between the old theory and the new result is most apparent in John Updike's verse, which was written before neutrino oscillations were discovered:

Neutrinos, they are very small.
They have no charge; they have no mass;
they do not interact at all.
The earth is just a silly ball
To them, through which they pass
Like dustmaids down a drafty hall.

Neutrinos are indeed, small and chargeless. The poem's popularity among physicists indicates they may be granted the poetic license to "pass like dustmaids down a drafty hall." But things have changed since Updike wrote the poem. Neutrinos do have mass and they do interact.

Physicists are still arguing about what to do with the obsolescent Standard Model. What will fill the gap: string theory, grand unified theory, dustmaid theory? "Physicists," Gilles observed, "aren't anxious to change [theories] unless they're positive." In 2002 Davis shared the Nobel Prize for his discovery, which physicist Kevin Lesko called the "big shift, the paradigm shift in our understanding of the universe." Ken Lande, who lived in Lead with his family for many summers while collaborating with Davis, often directs public attention to the important role that Homestake played in this drama as he canvasses for the scientific drama to continue in a new underground lab. "The…thing that happened here in South Dakota in the Homestake Mine, it started a brand new field: this is the field of neutrino astrophysics. So, it is worth remembering."

Just as Davis was winning his Nobel Prize, the mine that had served as his laboratory was in its death throes. Mining is a destructive business, and companies spend years attempting to erase their footprint on the environment: cleaning the land, the water and the mine itself. Gilles' house looks out over a deep canyon once filled with activity. There's the number five winze airshaft, the area where the cutting-edge tube conveyor (brought all the way from Japan) used to run, the grain elevator-like Ross shaft where cages sped underground. "It was a tough duty when they were starting to tear [the mill buildings] down," he said, describing the loss of a huge complex built into the hillside on the edge of town. "Everything you knew for a lifetime, they were tearing off the mountain. That was kind of discouraging." Later, on our way to dinner we passed the bare hillside in the Murdy's pickup truck. Gilles pointed out the ruined foundations where massive machines once stomped ore to a fine powder. Everyone sighed.

South Dakotans reluctant to abandon Homestake have put their support behind the particle they helped mine from obscurity. "Neutrino: A particle whose time has come" headlines that have peppered the local newspapers since the mine announced it was closing. The Rapid City Journal, which serves the western half of the state, has run 143 articles about neutrinos over the past three years even though it has no science section. In contrast, The New York Times has mentioned neutrinos in only 15 articles over the same time period. Charles Lamb, president of the South Dakota Academy of Science made the minute particles a priority in his inaugural speech among other important issues like cloning, biodiversity, climate change and space. The numerous, but hard to detect Lilliputians of the particle zoo have become the mascot for the proposed underground laboratory and for South Dakota's future.

Read Carolyn's entire thesis on MIT's DSpace

John Martin, an oceanographer from the Moss Landing Marine Laboratory, was one of the first scientists to detect that common species of phytoplankton and zooplankton contained trace metals, such as copper, zinc and iron in their chemical make-up. He realized that trace metals must be integral to phytoplankton growth if the microscopic organisms were using them at the molecular level. Martin developed new techniques for measuring metals in seawater that were clean and contaminant free. Armed with their new equipment techniques, Martin and his researchers went to work cataloging components of ocean water.

The results of the seawater testing shocked the oceanography community. Concentrations of trace metals known to be in ocean waters, such as iron, were detected at orders of magnitude lower than previously thought. And new trace metals, including zinc, cobalt and manganese, that had never before been documented, were found to be common in seawater.

During his trace metal experiments, Martin turned his attention to understanding the role phytoplankton play in regulating the global climate. He was intrigued by the barren ocean waters and set the task to try and figure out why these desolate zones were devoid of life. For lack of a better explanation, up to this point in time most scientists believed that zooplankton feeding on phytoplankton kept the plant-life low in these areas by voracious grazing, much like the way a field of cows eats a grass field bare. But Martin thought that there was something other than overeating zooplankton keeping parts of the ocean barren.

Martin developed a hypothesis that iron was a micronutrient needed for phytoplankton reproduction and growth, and the lack of this trace metal was the sole reason for the barren ocean waters. This became known as the iron hypothesis. Open ocean waters, like those of the Antarctic, equatorial Pacific, and Southern Oceans, Martin reasoned, were too far away from land masses to be naturally fertilized by dust storms blowing off the edge of continents that contained micronutrients, such as iron. According to Kenneth Coale, Martin "was the kind of guy who could put a bunch of seemingly disconnected information together…and whip it up into a theory that was all connected. [His iron hypothesis] was beautiful."

To test his iron hypothesis Martin sent a team of researchers to the Antarctic Ocean to collect samples of phytoplankton-barren seawater. Iron was added to some seawater samples, while other samples, the controls, were left untreated. After several days under the same conditions, phytoplankton was thriving in the samples containing iron. The control samples were still barren. Further bottle experiments strengthened the hypothesis's standing, and rocked both the oceanographic and the remainder of the scientific community. The iron hypothesis was, as Barber mentioned, a paradigm shift for oceanographers.

Martin then took his hypothesis even farther and suggested that the iron-ocean interactions may be partly responsible for past ice ages. During the ice ages, the climate was much drier than it is today. The atmosphere was a grimy swirl of dust swept up from vast stretches of deserts covering the land. If large amounts of this iron-rich dust were blown into areas of the ocean that lacked iron, the fertilized ocean would increase photosynthesis in plants, thereby sucking more carbon from the atmosphere into the ocean and cooling the planet.

Seeing the possibility of how close iron limitation may be linked to the global climate, Martin followed this conjecture with another, even more provocative speculation: dump enough iron into the ocean and you could reverse global warming. At a lecture at the Woods Hole Oceanographic Institute in 1988, Martin uttered what is undoubtedly his most famous quote: "Give me a tanker of iron, and I'll give you an ice age."

After publishing the results of his iron hypothesis bottle experiments and his ice age claims in the prominent British journal, Nature, Martin was courted by the press. His findings were published in many of the major science magazines, and the iron hypothesis – and the man behind it – soon surfaced in popular magazines and newspapers. Martin found himself on the talk-show circuit, discussing his iron hypothesis on Good Morning America, CNN, and the United Kingdom's BBC.

Even though Martin's bottle experiments strengthened his hypothesis, he faced doubts from other oceanographers, as it was yet to be shown that iron was the limiting nutrient to phytoplankton growth in the real world: the open ocean. Martin was challenged at every turn. According to colleagues, this contentious atmosphere was the kind he liked best.

To help resolve the controversy, Martin proposed to conduct ecosystem enrichments of the open ocean. But many scientists believed that experiments on whole ecosystems were risky, and it took several years to convince the National Science Foundation to endorse and fund an iron fertilization experiment.

Though Martin died of cancer shortly before the first iron fertilization experiment, dubbed Ironex I, his colleagues insisted that his research be continued. The first iron addition to the equatorial Pacific Ocean took place in the fall of 1993. Scientists involved with Ironex I fertilized a 64 square kilometer patch of ocean with iron. The results were astounding. The phytoplankton levels increased threefold. By all accounts, the ocean turned green.

Read Megan's entire thesis on MIT's DSpace

American Airlines Flight 191 began its long-haul trip to Los Angeles without trouble, although delays at O'Hare had put it a few minutes behind schedule. It was a mild spring day, 63 degrees with clear skies. At 3:02:38 Chicago time, the control tower cleared American Airlines flight 191 for takeoff on runway 32R heading northwest. A few seconds later, Captain Lux confirmed, "Ah—American one ninety-one underway." That was the last communication Flight 191 had with the control tower.

As the plane accelerated down the runway, the cockpit voice recorder (CVR) picked up the voice of first officer James Dillard calling out the plane's speed as it passed through eighty knots. Everything sounded normal until just two seconds before lift-off, when the CVR recorded a thump, followed by the word "damn" one second later—the last recorded sound in the cockpit. A controller in the tower watched as the plane lifted off. What he saw was almost beyond words. He shouted to the other controllers in the tower, "Look at this—look at this—blew up an engine. Equipment—we need equipment. He blew an engine. Holy ____."

But the plane continued to gain altitude in what looked like a normal climb. The controller radioed to the captain, "American 191, you wanna come back and to what runway?" But there was no response. "He's not talking to me," the controller said. The plane began a shallow left turn. The turn got steeper and steeper—too steep. "He's gonna lose a wing," the controller said. "There he goes—there he goes." The plane, only 580 feet and 20 seconds into the air, began to dive and plunged to the ground.

The plane crashed into an old out-of-service airport field that had long since been overshadowed by O'Hare. The space was being used as K-9 training grounds and extended right up to the edge of a trailer park, where mobile homes lined a few loops of pre-planned streets. Just on the other side of the park stood several oil storage tanks—an array of massive white cylinders with staircases winding around the outside that make the scale of the tanks look impossibly large. "If he'd a kept going, he'd a hit the oil tanks," says Ken Miller, a man now in his fifties who has lived in the trailer park for over twenty-five years and today works in the park's front office. "For miles around would'a been devastated if he'd a hit the oil tanks."

Pieces of the shattered plane carved through some of the trailer homes and the fire on impact took the lives of two people on the ground. But the residents of the area still count themselves lucky. "He knew what he was doing," says Miller. "Going down, he put it in the best place he could. We still credit that pilot."

Miller was working in nearby Skokie at the time, and got a call from his boss who told him he'd better head home because there had been a plane crash. He says he could see the smoke from miles away. He rushed home to find that the streets were all blocked off. "There were nothing but fire trucks and hoses, everywhere," he remembers. "The fuselage was out in the street over here," he said, pointing through the window to the shady street that borders the old airfield.

The damage to the aircraft was extensive. "The air frame was, of course, severely broken up," said investigator Henry C. Martinelli, a manager of aircraft systems engineering for American Airlines. Because the plane crashed with a full load of fuel, most of it was destroyed by the immense fire. The largest portions remaining were the engines, the landing gear and part of the tail. For weeks afterward, people sifted through the ashes, looking for parts and pieces of the airplane and for human remains. The whole area was under tight security, but even so, there were a few thefts. "There were some sick people," Miller recalls. "One person parked on the toll way and walked over. He wanted to take something from one of the bodies, he wanted to take some lady's ring. They caught some people trying to take pieces of the plane, but you know, they need every piece to put it all back together."

The investigators didn't have much to put back together; the damage to the plane was so complete. But they did have one major piece of the puzzle, a piece that hardly needed any putting together at all. Back on the runway, the left engine and pylon assembly (the structure that attaches the engine to the wing) was almost completely intact. And to many—though not to the NTSB—that was answer enough. Why did the plane crash? Because the engine fell off.

Of course, nothing is so simple. Like a child incessantly demanding to know "why?", investigators are constantly searching for causes. In any investigation, answers along the way tend to open the door to more questions. The engine fell off, but why? Maybe it had pre-existing structural damage. If so, when, how, and why did the damage occur? It could have fallen off because of an explosion on board—terrorism or sabotage may have been involved. Again, who, when, why, and how?

Even these answers wouldn't be enough. Understanding why the engine fell off was one thing, but figuring out why that caused the plane to crash was another. After all, DC-10s are designed to be flyable under catastrophic circumstances, even in the event of a complete engine loss. Why, then, couldn't the pilots bring the plane back for an emergency landing? Maybe weather was a factor; or maybe the pilots were at fault. How experienced were they; were they well rested; what had they had to eat or drink the night before? All these questions and more needed to be addressed.

The investigation of Flight 191 very early on splintered into two clear but separate tracks. First, why did the engine fall off, and second, why did the loss of an engine cause the plane to crash? Behind every possible solution is at least one person—someone who caused, or more likely, failed to prevent a dangerous set of circumstances from arising. . . .[I]t can be almost impossible to distinguish between human and technological actions. Investigators could go back and forth forever and trace the line of causation back through time ad nauseum. As it turned out, perhaps the most difficult part of conducting the investigation was knowing when to stop.

Read Mara's entire thesis on MIT's DSpace

If information theory doesn't have an origin myth, it has a very clear beginning. The field was founded in 1948 when Shannon published the paper considered his masterwork, "A Mathematical Theory of Communication." The fundamental problem of communication, he wrote in the second paragraph, is that of reproducing at one point a message selected at another point. A message could be a letter, a word, a number, speech, music, images, video—anything we want to transmit to another place. To do that, we need a transmission system; we need to send the message over a communication channel. But how fast can we send these messages? Can we transmit, say, a high-resolution picture over a telephone line? How long will that take? Is there a best way to do it?

Before Shannon, engineers had no clear answers to these questions. At that time, a wild zoo of technologies was in operation, each with a life of its own—telephone, telegraph, radio, television, radar, and a number of other systems developed during the war. Shannon came up with a unifying, general theory of communication. It didn't matter whether you transmitted signals using a copper wire, an optical fiber, or a parabolic dish. It didn't matter if you were transmitting text, voice, or images. Shannon envisioned communication in abstract, mathematical terms; he defined what the once fuzzy concept of "information" meant for communication engineers and proposed a precise way to quantify it. According to him, the information content of any kind of message could be measured in binary digits, or just bits—a name suggested by a colleague at Bell Labs. Shannon took the bit as the fundamental unit in information theory. It was the first time that the term appeared in print.

In his paper, Shannon showed that every channel has a maximum rate for transmitting electronic data reliably, which he called the channel capacity. Try to send information at a rate greater than this threshold and you will always lose part of you message. This ultimate limit, measured in bits per second, became an essential benchmark for communication engineers. Before, they developed systems without knowing the physical limitations. Now they were not working in the dark anymore; with the channel capacity they knew where they could go—and where they couldn't.

But the paper contained still one more astounding revelation. Shannon demonstrated, contrary to what was commonly believed, that engineers could beat their worst enemy ever: transmission errors—or in their technical jargon, "noise." Noise is anything that disturbs communication. It can be an electric signal in a telephone wire that causes crosstalk in an adjacent wire, a thunderstorm static that perturbs TV signals distorting the image on the screen, or a failure in network equipment that corrupts Internet data. At that time, the usual way to overcome noise was to increase the energy of the transmission signals or send the same message repeatedly—much as when, in a crowded pub, you have to shout for a beer several times. Shannon showed a better way to avoid errors without wasting so much energy and time: coding.

Coding is at the heart of information theory. All communication processes need some sort of coding. The telephone system transforms the spoken voice into electrical signals. In Morse code, letters are transmitted with combinations of dots and dashes. The DNA molecule specified a protein's structure with four types of genetic bases. Digital communication systems use bits to represent—or encode—information. Each letter of the alphabet, for example, can be represented with a group of bits, a sequence of zeroes and ones. You can assign any number of bits to each letter and arrange the bits in any way you want. In other words, you can create as many codes as desired. But is there a best code we should use? Shannon showed that with specially designed codes engineers could do two things: first, they could squish the messages—thus saving transmission time; also, they could protect data from noise and achieve virtually error-free communication using the whole capacity of a channel—perfect communication at full speed, something no communication specialist had ever dreamed possible.

Read Erico's entire thesis on MIT's DSpace

It was 1953 at the University of Chicago. Eugene Aserinsky—college dropout, dental school dropout, social work dropout—had washed up on the doorstep of Nathaniel Kleitman—physiology professor and sleep expert—and been taken in as an assistant dream researcher. At this point in time, dream research was dominantly Freudian, but Aserinsky wasn't interested in why we dream or in what dreams mean, he wanted to know why our eyes twitch when we sleep. No one expected eye-twitching to revolutionize neuroscience; other people in history had noticed and recorded eye-twitching, but no one had bothered to study it.

Rummaging through the university basement, Aserinsky dug up a junked electroencephalograph and wired it to the sleeping eye of his eight-year old son and waited for twitching. Once the eyelids were moving, the EEG would erratically spike and dive into jagged peaks and troughs. Aserinsky assumed the machine was broken—wouldn't be the first time—so he hooked up a second EEG to his son's other eye. Same results. The two machines recorded the same wild fluctuations. Funny, the EEG readouts look a lot like the brainwave readings taken from fully awake patients.

Aserinsky realized that something was awake that theory said shouldn't be. Theory said the brain rested when the body rested; that sleep was a chance for mind and body to recoup from the rigors of waking life. Even today, this is a popular misconception and a logical belief, based on all outward observation. What shocked Aserinsky: the EEGs said that the brain is often fully awake when the eyelids are twitching, even though the outward body appears practically paralyzed.

Aserinsky shared his results with Kleitman, and together they began rigorous experimentation to determine what those twitching eyes and spiking brainwaves meant. They woke people up when their eyes were twitching and their brains were active according to the EEG and discovered that around 90 percent of people awakened at this stage were in the middle of vivid dreams. Less than 10 percent of people woken up in other stages of sleep were found to be dreaming. They ran five years of experiments on hundreds of test subjects to conclusively establish that—contrary to popular belief—the mind is incredibly active while sleeping, particularly during REM (Rapid Eye Movement) sleep. These experiments also demonstrated that dreaming was somehow linked to the active brain patterns observed during REM sleep.

Aserinsky and Kleitman's work was the modern revolution that brought the dreaming brain into focus for researchers and freed scientists and philosophers from the belief that sleep existed to rest the mind. It has since been shown that dreaming—or at least the patterns of brain activation that coincide with dreaming—occur in all mammals (and only in mammals). The obvious questions arise: if sleep does not simply rest the mind, what does sleep do, and why is dreaming an inescapable part of evolved mammalian physiology? Since nature is economical and avoids unnecessary energy waste, then what necessary evolutionary function is realized in dreams? It is our task as rational, curious thinkers to explore what this function is.

Einstein wrote: "Philosophy is like a mother who gave birth to and endowed all the other sciences. Therefore, one should not scorn her in her nakedness and poverty, but should hope, rather, that part of her Don Quixote ideal will live on in her children so that they do not sink into philistinism."

Science has done well in divesting us of many archaic misconceptions and in turn providing us with a new understanding of the world, but when it comes to uncovering the nature of the mind, even the best minds of neuroscience are still philosophers in practice, even if not by their own admission. And in no part of neuroscience is the role of philosophy more important than in probing this terra incognita of why we dream.

Michel Jouvet, one of Europe's leading neurophysiologists and dream researchers, wrote in 1999 that: "People know very well that sleep is a complicated problem and that dreaming is perhaps the last frontier of neurobiology: we shall certainly understand perception before we understand dreaming."

His point is well taken: that dreaming is the most misunderstood and mystical function of mammalian physiology. We all dream and none of us can definitely say exactly why. The more progress that is made in understanding the brain, the stronger our foundation from which to speculate on dreaming—and enormous progress has been made in the last fifty years—but dreaming is still one of the ultimate Quixotic windmills, right next to what preceded the Big Bang? or how many dimensions are there, really?

Why are dreams? is the type of question that can really keep you up at night.

Artificial Intelligence and Musical Creativity:
Computing Beethoven's Tenth
Matthew T. Hutson

The first time I heard of David Cope's Experiments in Intelligent Music (EMI, or, more affectionately, Emmy) was in 1999. The cognitive scientist Douglas Hofstadter, author of Gödel, Escher, Bach, came to my university to give a lecture on the EMI phenomenon. When Hofstadter first learned of EMI, he visited Cope and soon went on a lecture tour presenting EMI and his interpretations of it. EMI does not just compose music; it can compose music in the style of any given artist. Feed it the scores of Beethoven's first nine symphonies, and it spits out his tenth.) One might argue that composing in an existing style is not creative, but that would mean that Beethoven's symphonies 2-9 weren't creative.) Hofstadter is an amateur composer and a passionate fan of Chopin, and the fact that EMI could produce Chopin-like pieces disturbed him. During the lecture he offered three sources of pessimism, which he later reprinted in Virtual Music, a 2001 book by Cope:

"1. Chopin (for example) is a lot shallower than I had ever thought.
 2. Music is a lot shallower than I had ever thought.
 3. The human soul/mind is a lot shallower than I had ever thought."

Faced with these options, one can perhaps empathize with the German musicologist's anger at David Cope.

But generating music with an algorithm is really nothing new. An algorithm is just a series of rules, usually followed in sequential steps; the algorithm for getting dressed might be: put on pants, put on shirt, put on socks, etc. Algorithmic music is much older than computers. In the 17th century, Giovanni Andrea Bontempi designed a wheel with numbers on it assigned to notes, and an accompanying set of rules for using the wheel to compose. The methods appeared in his 1660 work, New Method of Composing Four Voices, by means of which one thoroughly ignorant of the art of music can begin to compose. In 1787, Mozart devised a game called Musikalisches Würfelspiel that involved arranging precomposed sections of music into a minuet by rolling dice. Mozart and other great composers adhered to a set of rules restricting tonal music given in 1725 by Johann Joseph Fux in his The Study of Counterpoint. Example rule: "From one perfect consonance to another perfect consonance one must proceed in contrary oblique motion." (A consonance is a combination of notes that sound nice together; its opposite is dissonance. Motion refers to the relative motion between overlapping melodies or voices; oblique means that one voice goes up or down while the other remains steady, and contrary means they move in opposite directions.)

Any kind of constraint or formalism placed upon composition defines an algorithmic process. The haiku is an algorithm; you're required to write the poem in three lines of five, seven, and five syllables, respectively, and the theme must refer at least indirectly to a season. Many constraints remain invisible, such as the very idea of 12-note tonal music. Constraints also result from the methods of notation, and from how certain instruments can be played. (A chord for a solo piano piece can't contain three widely spaced notes, as humans usually have only two hands.) Cope argues that all composers are algorithmic and that it would be insulting to argue otherwise, because they've spent years learning the techniques and processes of their school and those musicians who came before them.

Atlantic Crossings
Sorcha McDonagh

It is a still night, and to the north of the Greenland ice cap, the emerald veils of the aurora borealis are fluttering like ghosts. The Brent family is flying southeast, breaking the silence with the steady beating of their wings, with their panting, and with an occasional honk at one another. The sound races out into the night and echoes off the ice-canyon walls. This is the second leg of their journey to Ireland, a 500-mile flight across the ice sheet that will take the geese about ten hours to complete. They are bound for the fjords and bays near Ammassalik, an island on Greenland's east coast. Natives refer to the east coast as "Tunu," the back side of the country, because it is so sparsely populated compared with the western seaboard.

The adult geese recognize the terrain below and know their way through the icy valley. They know the look of Baffin Bay, too, with its bluish ice floes; the jagged outline of Qeqertarsuaq; and the patchwork fields of Northern Ireland with the Mountains of Mourne to the south. The geese may even pick out the city lights of Reykjavik and Derry. This method of navigating by landmarks, known as piloting, is one of the first things that pilots of light aircraft learn. On cross-country flights, they look for landmarks that are easy to pick out from the air: intersecting highways, reservoirs, mountains.

Ornithologists think that birds form mental maps, much as people remember the prominent features of an oft-made journey. Even the stars feature in these maps—they are cosmic landmarks, familiar, sparkling arrangements on the velvet hemisphere above. Lindbergh and Columbus referred to the constellations on their Atlantic crossings, and there are yachtsmen who still navigate by the stars; some say it is more authentic, the mark of a true sailor. In his book, Sea Change, Peter Nichols writes with pride about using a sextant on his solo Atlantic crossing in a small yacht.

As well as using the stars and landmarks, birds use them to establish direction. The distinction between navigation and orientation is an important one: navigation means using landmarks and bearings to find something—like staging grounds or a food source—whereas orientation means knowing north from south. In the 1960's, behavioral ecologist Stephen Emlen released Indigo buntings in a planetarium, the northern sky displayed on its dome, and found that the birds turned to face the direction of their migration. When he rotated the dome image by 180 degrees, the buntings changed direction too. But when Emlen excluded the North Star and the region around it from the planetarium's display, the birds became confused. To test the birds' reliance on the North Star, Emlen blotted out the star itself and some other constellations from the rest of the sky. The birds all turned to face the right way, suggesting that the constellations around the North Star, which include Draco and Ursa Minor (which the North Star is a part), mattered most to the buntings. This region of the night sky is their reference point, the anchor around which the sky seems to revolve.

The "star compass," as it is known, is one of three compasses that birds employ on their travels. The first one to be discovered was the Sun compass, over fifty years ago, when German ornithologist Gustav Kramer observed the behavior of caged starlings around the time they would normally migrate. The birds were restless, agitated by the migratory drive, the Zugunruhe. When they could see the Sun, they all tended to face in the direction of their migratory route. When the Sun was hidden by clouds, they did not all face the same way. But when Kramer used mirrors to change the direction of the Sun's rays, the birds all turned to face what they thought was their direction of migration, relative to the reflected light.

Kramer concluded that the starlings used sunlight as a directional reference. The theory made more sense when some of Kramer's colleagues found that birds' circadian rhythms enabled them to compensate for the Sun's changing position over the course of a day: they know where the Sun should be, and when. Starlings and carrier pigeons can use the Sun compass at the poles—even when the Sun does not set—and penguins use it as they slowly make their way across Antarctica's ice fields. Even the orange monarch butterfly orients itself by the Sun's position on its annual migration from the United States to Mexico and back.

The third compass birds have is magnetic, one that gives them a sense of north and south that is as natural as our sense of up and down. Biologists had long thought that birds could perceive Earth's magnetic field, but it was not proven until 1968, by ornithologist Wolfgang Wiltschko and some European robins. By placing electrical coils in a bird cage, Wiltschko shifted the direction of the magnetic north inside the cage, fooling the birds.

Over thirty years later, we still don't know how birds perceive Earth's magnetic field. One theory is that a bird's photoreceptors, the light-sensitive cells in its eyes, may double as magnetoreceptors—cells that are sensitive to magnetic fields. It is likely that crystals of an iron ore called magnetite, found in the back of a bird's mouth, have some connection to birds' magnetic sense. Because Earth's magnetic field varies with location, getting stronger at the poles and weaker at the Equator, birds may be able to construct mental maps based on the planet's magnetic topography.

Together, the innate orientation skills and the acquired knowledge of the landscape—geographic, stellar, and magnetic—enable thousands of migrating species to cross Earth's diverse terrains every year.

Rice: How the Most Genetically
Versatile Grain Conquered the World
Maywa Montenegro deWit

On an overcast day in late January the rice fields in Crowley, Louisiana are chocolate-brown and barren. Except for a few remnants of rice stubble and tractor trails, there is little to suggest that anything more than earthworms grow here. In a matter of weeks, however, this landscape will begin to transform. The first brilliant green leaves of rice will poke their heads through the soil, specking the dark earth with the promise of the harvest. Throughout the early months of summer, the plants will grow taller and fuller, and will sprout multiple branch-like tillers. The tips of each of these will blossom into a head of small white flowers, giving the fields, from a distance, the look of a sugar coating. As the flowers mature, seeds will form and begin to fill with starch. The rice plants—now top-heavy with the weight of the grain—will bend forward in a graceful bow. Soon the rice grains will harden and the stalks will dry out, turning the fields a rich golden brown. Some ninety days after the first hardy spikelets emerged, the rice will be ripe and ready for harvest.

Not that the rice in these fields will ever make it to the supermarket shelves. Here at the Louisiana State University Rice Research Station just outside Crowley, the rice fields are giant petri dishes and Oryza sativa L—better known as rice—is the experimental organism. On small one- to two-acre plots, scientists plant seeds from a stockroom containing thousands of different rice varieties—from strains that tolerate being sprayed with herbicides to types that smell like popcorn. And the researchers probe many aspects of rice production, from fertilization, soil, and water management to breeding of new varieties and, nowadays, genetic engineering. Founded in 1909, to improve rice production through "varietal improvement and the development of agronomic practices that increase production and maintain profitability", the LSU Rice Research Station claims the oldest, and yet still one of the most prolific rice breeding programs in the country. Over forty percent of rice acreage in all southern states, and seventy percent in Louisiana, is planted with Cypress, a long-grain variety born and bred at the LSU Rice Station. The leading medium grain rice in the United States, a variety known as Bengal, also comes out of the Crowley cradle. The Rice Research Station brings together a colorful array of rice experts—from lab scientists and plant breeders to farmers and policy-makers. And each group brings to the station its own unique brand of rice knowledge. Plant pathologists examine the diseases and viruses that afflict rice, while entomologists tackle the pestilential bugs. Rice breeders make careful crosses between different rice varieties, while geneticists decipher what it is at the molecular level that determines a "variety" in the first place. Farmers contribute by "field-testing" experimental rice and innovative farming methods; more importantly, they contribute something less tangible—a familiarity with rice that comes from decades of working the land.

Looking much like farmers themselves, the rice researchers are no goggle-masked scientists in latex gloves and lab coats. Bluejeans and cowboy boots are standard lab attire in Crowley, along with button-down plaid shirts and Kelly-green John Deere caps. And while the research conducted at the LSU station is some of the most sophisticated in agricultural science, the scientists are only secondarily concerned with publication for academia. Or as Dr. Qi Ren Chu, a plant geneticist and rice-breeder at the Research Station puts it, "here we try to reach the rice community rather than go to international symposia to present fancy papers." Instead, the focus in Crowley is on production: from determining optimal planting time to testing methods for weed management—the goal is always how to coax more grain from the soil per unit of time, energy, and money. This, indeed, is the holy grail of any rice farmer, and it is a preoccupation whose success determines the welfare of more than half of humanity.

Chasing Chupacabras:
Why People Would Rather Believe in a Bloodsucking Red-eyed Monster from Outer-Space than in a Pack of Hungry Dogs
Anna E. Strachan

In his last book, The Demon-Haunted World, the late Carl Sagan wrote that people embrace pseudoscience in proportion to their misunderstanding of real science. In January of 2003, I approached fifty Puerto Ricans on the street—half of them men, half of them women—and asked, "Do you believe the Chupacabras exists?" Twenty-four answered "Yes." Nine of those twenty-four people said they believed because of the "evidence" or the "dead animals they found." Five of the twenty-four said they believed because "people have seen it," and another five said they believed because the "news" or "science" said the Chupacabras exists.

But the "evidence" they cite—the dead animals, the eyewitnesses, the science and the news—never led any authorities to suspect a bloodsucking monster. So why do these people believe? Sagan would have blamed a superficial understanding of science; people are fed the findings of science in soundbites and textbooks, but the process of science rarely gets on the menu. When Puerto Rican scientists were quoted in the island's media, reports tended to emphasize the scientists' speculations of what the attacker could be (it's a dog! It's a monkey! It's dogs and monkeys!), while few emphasized what the autopsy reports proved the attacker could not be—a bloodsucker. This allowed some people, like Roberto Nogal, to assume that the studies were never carried to conclusion, that "the cases were shut tight," when in reality, science—in Sagan's words—"gropes and staggers" toward truth. Still, the different speculations offered over several weeks of media coverage may have allowed people to roll the "Chupacabras" into the same mental drawer with every trashed model of the universe and "cure" for cancer, concluding that scientists haven't got a clue. But even that doesn't explain why believers would still choose to believe in the highly improbable—a super-intelligent bloodthirsty biped—over the probable hungry stray dogs.

One possible explanation for people's belief in the Chupacabras is a phenomenon psychologists call the "confirmation bias," which holds that people tend to selectively notice or ignore things according to their already-held beliefs. For example, hypochondriacs are at the mercy of the confirmation bias, interpreting every ache as indicative of a serious illness. But psychologists have found that the confirmation bias is a fundamental tendency in human thinking. An example can be seen in Mayor Chemo Soto's analysis of the Goatsucker attack "patterns":

"Now, listen there's something about this: there's something about bodies of water. It appears near water, little creeks, waterfalls. Every time it appears there is a big noise, a deafening sound, a sound of a turbine. It never appears close to the houses, but in the hills. We have run after it when we heard that noise, and when we get there, there is a terribly strong smell of sulfur. That's everywhere that the Chupacabras has been—sulfur. A violent stink in the place where the noise has been. It's very strange. The other day, a meteorite fell by the mountain and when it fell, there was a terrible smell of sulfur too. So I started thinking, analyzing... so it has to be from outer space. Because of the smell and the noise."

How about the times when people reported a "wet dog" smell instead of sulfur, or didn't notice any smell at all? Or the reports of silent attacks beside people's homes? What did he think of the Goatsucker attacks reported in arid, waterless environments such as those in central Puerto Rico, Mexico, or Texas? No, he replies, he hadn't considered those. But he insists they weren't important. He does, however, have a keen memory for the details and events that confirm his hypotheses: "When it was attacking around here, you could always small that terrible stink. You would go to the hills, and you would know it had been around there, because of that terrible stink of sulfur."

In one psychology experiment conducted by researchers at Iowa State University, ESP believers and skeptics read a scientific paper either supporting or debunking ESP. Then they were tested on their memory of the paper's content. The ESP believers who read the paper undermining ESP not only remembered very little of it, in some cases they "remembered" that the paper upheld ESP rather than challenged it! And "normal" beliefs are subject to the same bias. In a similar experiment at Stanford University, people were asked to read studies arguing for or against capital punishment, and they consistently judged the one confirming their own view as "better conducted" and "more convincing." Everyone was more critical of the study attacking their previously held belief, regardless of which belief they held.