Science Metropolis – Boston

Evolution has solved a number of challenges humans face, for instance, flight. (Credit: Museum of Science)

– by Julia Darcey

Harvard undergraduates who take Noel Michele Holbrook’s course on biodiversity often do not end up becoming scientists. The future lawyers and businesspeople listen thoughtfully to her lectures on preserving the variety of Earth’s species, but lacking the passion of a biologist, there is one critical point that they have difficulty understanding. One student finally approached  Professor Holbrook about it. The student explained that she understood that species were going extinct, and that habitats were disappearing, but she still had one fundamental question: “Why does this matter?”

Biologists like Holbrook now have a solid and penetrating argument that preserving biodiversity matters because of its benefits for human health. In a new book, world-renowned scientist Eric Chivian compiles hundreds of studies on how evolution has allowed snails, bears, frogs and trees to solve major medical problems facing humans. He presented the book, titled Sustaining Life: How Human Health Depends on Biodiversity during a public conversation with Holbrook last night at the Boston Museum of Science.

Despite the clear benefits of biodiversity, species are disappearing at an unprecedented rate due to a combination of pollution, development and climate change. Extinction can have a big impact on humanity, Chivian said, because the keys to solving many human health problems already exist in the natural world-we just have to figure out how to use them. 

One example is the medical possibilities in 40,000 distinct toxins made by the 700 species of aquatic cone snails. The shelled slugs bombard their prey with sharp, poison-coated harpoons, the most potent of which hijack the victim’s nervous system. The study of cone snail toxins has already produced the painkiller Prialt, which is 100 times more effective than morphine and does not lead to tolerance.

The trick to preventing disease associated with obesity may also exist in the belly fat of the polar bear.  The polar bear, Chivian said, becomes massively obese before entering its den to sleep for the winter, and yet never develops Type II Diabetes or other obesity diseases.  “If we lose the polar bear,” said Chivian, “we will perhaps lose the secret to a disease that kills 1.5 million people a year.”

A drug for peptic ulcer disease, which affects 25 million Americans, may have once dwelt in the rainforests of Australia, inside the stomachs of gastric-brooding frogs. Females of these species ate their eggs, which would slowly incubate inside the mother’s stomach. The eggs survived by secreting chemicals that stopped the production of digestive enzymes.  However, all research on these frogs came to halt in the 80s, when the only two species of gastric-brooding frog went extinct. 

“Those compounds-which may have evolved over millions of years-are gone forever,” Chivian said.  To him, this is an idea that everyone can understand. Numbers of species lost have not been effective in communicating the urgency of biodiversity loss, partly because it happens far from day to day life, often in rainforests or at the microscopic level.  When educating the public about biodiversity, Chivian said, “the most basic fundamental focus should be on what the impacts on us would be.” 

“We hope that the book will make the connection that humans are not separate from biodiversity,” he said. Written in plain language, it is designed to be used by scientists, the lay public, and even as a textbook. This is the first text that explains in great detail why biodiversity matters, and Professor Holbrook, for one, now includes it on her syllabus. 

Michelle Ridgway prepares for her canyon expedition. (Credit: Michelle Ridgway’s Blog)

– by Jennifer Berglund

West of Alaska is buried one of Earth’s most glorious and unexplored frontiers – the Zhemchug Canyon. The giant cavity, over a mile and a half deep, could consume the Grand Canyon with room to spare. When currents flow into the canyon, they slam against its walls before being thrust upwards towards the ocean’s surface. Within these upwellings, hordes of nutrients amass, feeding some of the largest concentrations of phytoplankton on Earth, which in turn nourishes a thriving cornucopia of life.

Into these dark depths, Michelle Ridgway made her descent.  Ridgway is a marine ecologist from Juneau, Alaska, and one of the last true explorers to plunge into a great unknown. As part of a public lecture series at the New England Aquarium, she shared her experiences in this final frontier earlier this week. Her story begins when she first sat in a tiny, eight-foot long research submarine resembling a backward forklift with pontoons. 

One year ago, Ridgway was on a mission to explore the deepest depths of the Zhemchug canyon and to document all traces of life that she could find. Out of a 200-person crew on the Greenpeace ship Esperanza, she was one of only five pilots allowed to operate the tiny sub. This status gave her the privilege to personally explore the canyon’s depths. 

As Ridgway descended, she took her first glimpse of the canyon wall.  Spots of bright oranges, blues and purples filled her view. Although the water was just a few degrees above freezing, it was indeed coral, a staple of tropical reefs. With her sub’s robotic arm, she reached out and grabbed the end of a 9-foot-tall piece. Much of the coral Ridgway found in the canyon had yet to be described.

Nearby, the mouthparts of tubeworms lined the rock walls, resembling the mountainsides of tropical rainforests speckled with ferns.  Between the coral and tubeworms hid an orange speck – a tiny prickly crab.  It was the younger version of a giant King Crab, one of the most sought after crab species in the world. Only a few millimeters long as a youth, it can grow to be nearly five feet in diameter as an adult. 

Ridgway’s sub was soon a fifth of the way down Zhemchug canyon and suddenly incapable of handling the enormous water pressure. She began her retreat, stopping for a moment at the top of the canyon.  The seafloor below resembled a desert, sandy debris gathered in waves and what appeared to be the coral reef’s rejects moved sporadically on the floor around her.  A large greenish-brown flatfish stared with two eyes that seem to have bumped into each other on one side of its head.

As Ridgway ended her dive, she quickly gathered a few more samples. She found a giant brown ball resembling a rock, which, when later examined, turned out to be compacted dirt. It was determined to contain traces of various species of ice algae, many of which scientists thought to have been extinct for 15,000 years. 

Ridgway returned to her research vessel full of stories, specimens, and enthusiasm for her next big dive. It was only 1of 25 in this particular mission – the first of many fruitful expeditions to come.  

– Upcoming Aquarium events include: “Whales: Candles, Cheeses and Pigs in Disguise” on Oct. 5, “Tuna: A Love Story” on Oct. 14, and “Journey with a National Geographic Photographer” on Nov. 10. 

The history of the street pigeon is revealed in  Courtney Humphries new book Superdove. (Credit: Vizero.com)

– Story by Roxanne Palmer

Look!  Up in the sky!  It’s a bird!  It’s a plane!  No- actually, it is a bird. 

Street pigeons- also known as Columbia livia, rock doves, or, to quote Woody Allen, “flying rats”- are a common sight on the streets of Boston.   Most city-dwellers ignore them, many revile them, and a few feed them.  In the portrait of the urban landscape, they are mere background objects, neither endangered nor exotic enough to inspire our interest, let alone lavish PBS documentaries.  Pigeons, it seems, just don’t seem natural.

Courtney Humphries, a graduate of the science writing program at MIT, brings these birds into the foreground in her book, Superdove: How the Pigeon Took Manhattan… and the World.  The author recently gave a talk at the Harvard Natural History Museum, where she gave a brief overview of the historical relationship between people and pigeons.  Though they’ve gotten a bad rap as disease-carriers (untrue) and annoying pests (somewhat true), the pigeon is an amazing evolutionary success story.

Humphries pointed out that the first chapter of The Origin of Species focuses on the variation observed in domestic pigeons.  Darwin himself owned specimens from several breeds of fancy pigeon, from the peacock-like Fantail to the Jacobin, which sports a large, feathery frill around its head.  By breeding his pets and extensively questioning pigeon enthusiasts (of which there were many in Victorian England), he was able to fully flesh out his ideas on descent from a common ancestor.  While even the most casual of science hobbyists has heard of Darwin’s finches, it is really Darwin’s pigeons that we should thank for the theory of evolution.

From its beginnings, the history of the pigeon was heavily influenced by mankind.  After being domesticated in ancient Egypt, some of the birds naturally escaped their owners.  However, unlike other feral animals, they never actually left.  Buildings erected by men provided a habitat as equally suited to them as the rocky cliffs where their wild cousins nested.  Food was plentiful and there were few natural predators.  Thanks to the efforts of people, feral pigeons flourished in the cities.

“These birds are very successful because of us, and what we’ve done… we created them,” Humphries said.

While pigeons are not the subject of many scientific studies, people still find them to be useful creatures.  Pigeon are still a food source across the world, especially in Asia.  Homing pigeons have carried messages as recently as World War I.  Superdove even relates the account of how the behaviorist B.F. Skinner developed a prototype for a pigeon-guided missile.

During the question and answer session, an audience member asked if Humphries had ever thought of eating the subject of her research.  She laughed, and confirmed that she had ordered pigeon at a French restaurant, where it is euphemistically listed on the menu as “squab”.   She called it “a richly flavored bird- not fatty like duck, and not bland like chicken.”

Yes, she recommends the pigeon- in more ways than one.

(For the more adventurous readers of Science Metropolis, Clio Restaurant in Back Bay offers pigeon accompanied by black truffles, spaghetti squash, pistachio croquant and baby leeks, for a cool $38.)

It doesn’t take a philosopher to answer the question of “What is life?” According to science writer Carl Zimmer, the popular blogger behind the Loom, the answer can be found by studying Escherichia coli, a common bacterium living in your gut. “E. coli is an oracle,” he says, that tells about life and how life works.

Zimmer is a recent expert in the beauty and history of this bacterium, the topic of his new book “Microcosm: E. coli and the new science of life.” Wearing a tie covered in pictures of microbes, he told fans at the Harvard Book Store yesterday evening that he wanted to write about this “unjustly neglected” player in biology, because its scientific contributions are often unknown to the general public.

German pediatrician Theodor Escherich first discovered the bacterium in 1885 while investigating a string of childhood illnesses. As he looked at samples of sick children’s diapers under a microscope, he observed thousands of fast-growing rod-shaped bacteria. Since then, the bacterium has become a model organism for many scientific experiments. A French researcher once said, “What is true for E. coli is true for the elephant.”

The bacterium is popular because it is easy to grow, a crucial characteristic for bioengineering. The gene for insulin, a hormone produced by the pancreas and used in the treatment of diabetes, is routinely placed in E.coli. As the bacterium multiplies, scientists harvest the insulin and sell it in giant vats – much better than the previous method of stealing pancreases from butchers.

Zimmer, with the help of a fist-sized stuffed model, gave an enjoyable description of E.coli. He demonstrated the way it coils its hair-like flagellum to move forward, and then uncoils them to tumble around a Petri dish as well as the “nose” it uses to detect which tasty molecules to move towards. He even showed E. coli sex, which consists of a bacterium protruding a long tube to another bacterium, and exchanging genes.

Just as E. coli redefines the meaning of sex from the “exchanging of gametes” to the “exchanging of genes,” it also redefines other aspects of living organisms. Different strains of E. coli are found in nature, and even more are produced daily in labs. Despite their genetic differences, they are still considered the same “species,” making biologists question the definition of species. E. coli has been manipulated so much that some strains have fragments of DNA matching no other organism.

So, next time you hear mention of E. Coli, don’t think food poisoning – think knowledge.

Story and photograph of Carl Zimmer by guest blogger Mai Nitta.

Despite her status as a best-selling author of books about cadavers and the afterlife, a signing event with science writer Mary Roach is great fun. Over a hundred people abandoned this evening’s cool spring air to listen to Roach speak about her newest work, “Bonk: The Curious Coupling of Science and Sex,” at the Brookline Booksmith, an independent bookstore near the Coolidge Corner T stop. Luckily, sex research is anything but sober, and the audience laughed out loud as Roach candidly discussed some of the more surprising findings.

One of her favorites was the list of items emergency room employees regularly remove from patients’ rectums. From light bulbs to spectacles and a magazine, the list goes on and on. Another surprise, learned from her interviews with scientists. is the number of recipes for synthetic semen used for experiments. Each recipe, said Roach, yields one ejaculate, to which she joked about doing a “Bonk” cookbook. Another notable interview, Roach mentioned, was with a woman who could think herself to orgasm within a minute. Roach asked the woman if she did this constantly. ”I’m usually too tired by the time I get home,” the woman responded.

“Doing a book on sex, there’s a lot of room for embarrassment,” Roach said. This couldn’t have been more true when she and her husband “performed coitus“ as Dr. Jing Deng, a senior lecturer in medical physics at University College London Medical School, took a 4-D ultrasound. She compared the experience to getting a colonoscopy because of its medicalization. Plus, said Roach, ”I was taking notes the entire time.”

Roach also shed light on the rate at which sex researchers historically experimented on themselves and their staff. ”Everyone in the Kinsey Institute was performing on film,” said Roach, referring to Alfred Kinsey, the biologist famous for his research into human sexuality throughout the mid-1900s. The current practice today, says Roach, is to entice undergraduate students with course credit.

For more on these stories and answers to questions like – Can a woman find happiness with a machine? –  and - Is the clitoris a tiny penis? – be sure to pick up a copy of “Bonk” today.

Where do you shelve a book written by a surgeon? This morning, I wouldn’t have thought this to be a trick question. When Dr. Atul Gawande, a surgeon at the Brigham and Women’s Hospital in Boston and best-selling author writes a book, copies fly off the science and medicine stacks. Then I listened to Dr. Allan J. Hamilton, a professor of surgery at the University of Arizona Health Science Center, and learned the real answer — it depends on the surgeon.

Dr. Hamilton came to the Harvard Coop in Cambridge this evening to sign copies of his first book, “The Scalpel and the Soul: Encounters with Surgery, the Supernatural, and the Healing Power of Hope.” As the title reveals, the book fuses medicine and faith. Here is a surgeon who writes about “the soul,” “the creator,” and “miracles,” alongside his experiences removing brain tumors and immunizing children in developing nations. So, where in the bookstore can we find Dr. Hamilton?

According to Amazon.com, “The Scalpel,” is in the top 25 bestsellers in the Spiritual Healing category. At The Coop, it can be found within the New Age section. Even the location of the book signing, held on the third floor between rows Bibles and Marxist texts, seemed to remove Dr. Hamilton’s medical authority. Leading medical writer, Dr. Gawande, also writes about ethical and philosophical issues – especially the imperfections and humanity of medicine – but doesn’t come to conclusions based on faith. What separates Dr. Gawande from Dr. Hamilton, then, doesn’t seem to be medical experience, but interpretation.

Dr. Hamilton told a story from his days as an intern at Massachusetts General Hospital about a boy who suffered severe burns and fell into a coma. As he continued to reject several skin-graft surgeries, the boy’s father, perhaps from the stress of the whole thing, had a heart attack and died. The boy’s mother asked if the father’s skin could be grafted, in the chance there might be a genetic match. The doctors tried and after the surgery, Dr. Hamilton was called into the boy’s room. “What happened to my father?” the boy asked. Dr. Hamilton, not wanting to upset him after his sudden recovery, told the boy his father was fine. “If that’s so, why is he standing at the edge of my bed?” the boy responded. “What a miraculous thing to happen,” concluded Dr. Hamilton. Would Dr. Gawande have called this a miracle or peppered his words with a bit of skepticism?

At the end of his talk, Dr. Hamilton discussed some ways spirituality can help in recovery, although, what he called spirituality could be interpreted as a self-generated placebo. One of his rules is to not let statistics, which doctors rely on to gauge the course of a disease, predict the outcome. Although controversial, his advice is a tool for potential patients, and that’s who Dr. Hamilton’s audience is. He did not write a collection of essays recounting the peculiar world of the OR, he wrote a book of stories to help patients and medical professionals incorporate their spiritual selves into the often-cold environment of the hospital.

While this book may just be a work of pseudoscience written by a surgeon, it does no harm. Since many patients identify as religious or spiritual, the positive thinking one can take away from “The Scalpel” may be just as good a medicine as anything Dr. Gawande orders.

Doctors declaring themselves “trans-friendly” may be guilty of false advertising, said panelists discussing “Trans Issues in Healthcare” today. No, not a fondness for trans fats, a subject close to the hearts of many science news connoisseurs, but sensitivity to people, who are transitioning, or have transitioned from one gender to another.

Of the healthcare issues unique to transpeople, as laid out by panelist Gunner Scott, director of the Massachusetts Transgender Political Coalition, knowing what to expect from a “trans-friendly” doctor is the easiest to fix. Other problems – like counselors who hold clients in therapy, charging them for months before writing the letter legally required for sex reassignment surgery, as well as insurance companies not covering these kinds of operations – would require fierce policy battles. (The ongoing fight for equal rights was a sub-theme of this weekend’s conference on “TransLaw,” sponsored by Harvard Law School, where the healthcare panel took place.)

Some of the mistakes doctors make when treating transgender patients involve basic communication. Diego M. Sanchez, AIDS Action Committee PR Director and recently elected superdelegate, explained that if in the initial phone call to a new clinic, the receptionist uses gender-specific phrases like sir or madam to address a transgender caller, this is automatically disengaging. Other trans-insensitive policies include identifying patients by name rather than a number in the waiting room and using anatomical terms during a medical examination when, “I’m going to use this speculum below your waist,” works just fine. Another experience, which arises especially with mental-health providers, is for the patient to be told their situation is just homosexuality, a phase or a fetish, said Thomas, a conference attendee who asked that his last name not be used.

Some of this insensitivity may stem from doctors’ inexperience with transgender patients, but this soon may change. While the numbers of transpeople in the United States has never been counted, it wouldn’t be farfetched to assume that with the increase in civil rights laws, the population is growing. Monica Roberts, the blogger behind TransGriot, estimates the ratio of males who undergo sex reassignment surgery to become female is 1 in 2500.

Those who already advertise as “trans-friendly” are usually doctors who identify as gay, lesbian, or bisexual. Being gay, however, doesn’t mean you are automatically sympathetic and knowledgeable of issues specific to transpeople. “There are providers in our community who claim they are ‘trans-friendly,’ when the stories that result are horrendous,” said Sanchez. While there may be some overlap among the experiences, one of the only ways to educate all providers, gay or straight, is through training.

At the moment, no funded training or certificate programs exist to familiarize doctors and therapists with trans issues. According to Sanchez, an organization called TransHealth used to exist through the Justice Resource Institute, but was defunded.

What should a patient expect from a “trans-friendly” provider? According to Thomas: A provider who listens, has a clinical space welcoming to difference, is able to ask the right questions to experts, not hold things off and believes what you say is true. “Transpeople should expect what any client should expect, no more or no less,” he said. “Trans-friendly doesn’t have to mean trans-perfect. It means that if there is a breach of sensitivity, I can speak up.”

For those looking for care in the Boston area, Fenway Community Health is a good place to visit, although according to Sanchez, there is “opportunity for improvement.” For people under 29, there is the Sydney Borum Jr. Health Center. Other more mainstream providers include Boston Medical Center, Massachusetts General Hospital and, depending on the relationship, your general-care provider.

Resources for doctors and patients on this topic:

- The World Professional Association for Transgender Health

– Gay and Lesbian Medical Association

Every Wednesday, Boston University’s School of Public Health hosts the Public Health Forum, an opportunity for students, staff and members of the community to hear the latest research straight from scientists. Today’s forum brought Dr. Francois Venter, a South African clinician and leader in HIV/AIDS treatment. His talk titled, “South Africa & HIV: Crisis – What Crisis?” focused on the failures of prevention and politics to contain the epidemic in his country. Venter, (No relation to artificial-genome synthesizer Craig), described the current state of HIV treatment as depressing. Scientists are feeling defeated as rates of new infections increase worldwide and trials for vaccines, microbicides and diaphragms fail.

In South Africa, which holds 5 million people living with HIV in its borders, the most of any country, the numbers are rising despite increased condom use and widespread education campaigns.New data reveals up to 91% of new infections in Uganda and South Africa are not the prostitutes or drug users normally associated with HIV, but married women and widows. Dr. Venter doesn’t know why this is the case, but it is clear we don’t understand the transmission dynamics or sexual behaviors. He describes South African culture as very conservative compared to bare-it-all America. The majority of the country’s population is Catholic so no one claims to be homosexual and married couples say they are faithful. This image does not support the data, however, and research to find out more on how HIV is being transmitted in South Africa may be prevented by social acceptability.

Once people are infected, doctors in South Africa are facing what Dr. Venter calls “The Treatment Gap,” thanks in part to their health minister. She needed to be in the hospital and unable to work before they could pass a 5 year plan that would improve the number of drugs reaching pregnant women, nurses and adult patients.

What’s even more shocking is the bureaucracy is being difficult when it is projected 1 in 2 South Africans will be HIV+ within a decade, the projected number of AIDS orphans will reach 2 million and 1 million of its citizens have AIDS with only 20% receiving treatment. Despite South Africa’s status as a middle income country, life expectancy there will soon drop to 50.

“We will never treat our way out of this epidemic – but we need to treat,” said Dr. Venter. What he suggests for now is providing access to drugs and testing to people in South Africa, which unfortunately, requires a restructuring of the health system. Although the media tries to hype the good news about HIV/AIDS, the reality is, things could be better.

Some people collect stamps, others collect bugs; I collect autographed science and medical books. My newest addition is a book by Dr. Neil Shubin, a fish paleontologist and author of “Your Inner Fish: A journey into the 11-million-history of the human body” who spoke at Harvard Book Store this evening. 

When attending a lecture titled: “Does spatial position in the nucleus influence transcription,” one doesn’t expect a crowd. But when such a topic is discussed at Massachusetts General Hospital’s Simches Research Building, the people will come.As med students and hospital employees finished poured in, Dr. Wendy Bickmore, a senior scientist at the Medical Research Council’s Human Genetics Unit in the UK opened her PowerPoint file and revealed the following:

All genes are not created equal, at least not according to the nucleus. There is a bit of favoritism going on in all our cells, and it concerns gene expression. Research in the past five years has found chromosomes containing the instructions for the most important or abundant proteins (11, 17, 18) are more likely to be found in the center of the nucleus. Chromosomes with less important, or genes with environmental-specific roles (4, 13, 16) are tethered to the nuclear periphery where enzymes keep them silent.

How chromosomes become positioned in the nucleus is not well understood. Although those closer to the center are thought to be pushed there by cell transport molecules, it does not seem to be the case for the silenced periphery chromosomes. Since all chromosomes go to the periphery during mitosis, it may be as daughter cells are forming, some just remain on the sidelines.

Those that make it to the center of the nucleus meet clusters of RNA polymerase, the enzyme responsible for making RNA from DNA. Contrary to what was originally thought, the proteins in charge of gene expression aren’t everywhere in the nucleus, they are localized in the center, explaining why the area is so gene rich.

Experiments by Dr. Bickmore have confirmed many of these relationships, but she is quick to point out this does not dictate expression of all genes for all chromosomes. These findings are most applicable for genes requiring high amounts of regulation such as the well-conserved HOX on chromosome 4, which plays a major role in development. Chromosome 4 also contains housekeeping genes, which despite their location on the periphery, are still active.

Although most of the data fits with Dr. Bickmore’s model, there are exceptions. Cell biologists recently found gene expression actually increases at the periphery around nuclear pores, holes in the nucleus allowing transport of key molecules. Why this happens is not yet understood. Also, even if a chromosome is in the center, surrounded by RNA-making machinery, it is trancription factors that determine gene production before anything else.

Can this research be useful in medicine? Dr. Brickmore says she has no idea how, but it is a thought. She is more interested in finding out if mislocated chromosomes can cause human disease.

She predicts this research may also add to our understanding of X-inactivation, the random silencing of either the maternal or paternal X chromosome in females, especially if it shares similar mechanisms with peripheral silencing.

With many unanswered questions and experiments to conduct, this work promises to at least provide the nucleus with a bit of personality.