Medical school isn’t cheap. Today, medical students graduate with an average debt over $155,000, and the need to pay off those mortgage-sized loans drives many a young doctor away from more modestly compensated but sorely needed fields such as primary care and family medicine. To alleviate this financial pressure, many organizations have started scholarships to help with the med school tuition bill, rewarding scholastic achievements and commitments to work in underserved populations. The American Medical Association’s Physicians of Tomorrow program is one such effort, and this week’s announcement of the 2011 recipients [pdf] carried a heavy Pritzker School of Medicine presence.

Two of the 18 (11 percent, but who’s counting) fourth-year medical students receiving the $10,000 scholarship were from the University of Chicago’s medical school. Laura Blinkhorn (left) and Maggie Moore (right) are the two very impressive Pritzker students among the recipients, each with very impressive biographies already built in their young careers. Blinkhorn has done work with South Side neighborhoods as part of the Pritzker Summer Service Partnership, works with the Washington Park Free Children’s Clinic, and is planning to spend 3 months of the next year doing a clinical rotation in the African country of Gabon. Moore volunteered at the Maria Shelter Clinic for Women and Children and the South Side “Girls on the Run” program, and somehow finds time to write poetry about her medical experiences. Because of poems such as “Cadaver Memorial” and a collection called “A Third Year’s Life in Lyrics,” Moore was given the Johnson F. Hammond, MD Scholarships supporting medical journalism by the AMA. Congrats!

New Furniture for Molecular Engineering

When you are building a new house, you’re gonna need some furniture. The same thing goes for building a new research institute - before you can fill it with people, you need somewhere for them to sit. The University of Chicago’s Institute for Molecular Engineering, which was born in December and acquired a leader in March, has this week announced four named professorships made possible by anonymous donations. The funded positions give the institute the power to recruit prominent researchers to help realize the institute’s unique vision blending biology, chemistry, and physics.

“The big job in front of us is to bring together people with expertise in broadly applicable areas of enabling technology, such as synthesis of new materials, biological engineering, new ways of doing computing and quantum information science,” said Matthew Tirrell, the founding Pritzker Director of the Institute for Molecular Engineering and senior scientist at Argonne.

Elsewhere…

The San Diego Union-Tribune Keith Darcé wrote an excellent overview of the Earth Microbiome Project, the global study of the world’s bacterial populations that has previously been featured on the blog. Our own Jack Gilbert is featured (he mentions their current project swabbing bacteria from the animals of the San Diego Zoo), and an interesting hunt for bacteria able to survive in high-salt conditions is also explained.

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By John Easton

Let’s start with a statistic: almost 2,000 citations a year. One paper by Paul Meier, the Ralph and Mary Otis Isham Distinguished Service Professor emeritus of statistics, pharmacological and physiological sciences, medicine, and the college, has been cited more often, by a wide margin, than any other paper in the field. At last count it was the fifth most cited research paper of all time, in any field. With about 34,000 citations to date, Kaplan, E. L., and Meier, P. (1958), “Nonparametric Estimation from Incomplete Observations,” has been cited by another scientific publication about once, on average, for every day of Meier’s long life—he was born in 1924—and still counting.

Sadly, however, that ratio can only increase. Citation counting will continue, but the numbering of days stopped on Sunday, August 7th, when Professor Meier, a world-class statistician who made “extraordinary contributions to statistics and to society,” according to Columbia University - and everyone else - passed away peacefully at his Manhattan home.

The Kaplan-Meier estimator is used ubiquitously in medical studies to estimate and depict the fraction of patients living for a certain amount of time after treatment. This is not as simple as it sounds. Survival curves are complicated by the uncooperative way in which research subjects often behave. Some leave a study part of the way through. Others elect not to die before the study ends. These are known as “censored observations.” The Kaplan-Meier estimate is a simple way to compute the survival curve despite such troublesome behavior.

There was almost a Kaplan estimator and a Meier estimator. Each had submitted a separate manuscript to the Journal of the American Statistical Association, but the editor recommended that their papers be combined into one. It took them four years. “At one place he solved a problem that I couldn’t solve,” Meier later recalled in an interview [pdf]. “Other places I solved problems he couldn’t.” Finally published in 1958, it was only cited 25 times over the next ten years. Then, boosted by statisticians’ increased computing power, it caught on. It has since been applied to data from clinical trials of therapies for every disease from cancer to cardiology to concussion.

Friends and colleagues point out that this was only one of Meier’s fundamental contributions. He published many more studies, was a persistent and outspoken advocate for randomization in clinical studies, helped design some of the 20th Century’s most important clinical trials and trained many of the leaders in the field.

“Paul was a friend and colleague as well as one of the most influential statisticians of an important era,” recalled Stephen Stigler, the current chair of statistics at the University of Chicago. “He left an indelible mark on us, and through his research on the world’s clinic analytical practice. He will be missed and cannot be replaced.”

“I have been so fortunate and privileged to know this truly great, wonderful, helpful, kind man who was always so generous with his skills and wise advice,” said toxoplasmosis expert Rima McLeod, professor of ophthalmology and visual sciences at the University. “He is one of the founding fathers and giants of statistics in the past century. He was at the same time simply a modest, helpful, supportive and warm colleague who only let you know how special he was by the quality and content of what he said and wrote.”

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There’s something quaint and charming about a family business, where multiple generations work shoulder to shoulder to keep an enterprise afloat. But when the business in question is academia and the salaries are paid by tax dollars, suddenly keeping it in the family carries the stink of nepotism. In the public universities of Italy, it’s no secret that nepotismo is the rule, not the exception. Despite repeated legislative efforts to reform university hiring, scandals such as the one at University of Bari’s economics department - where a father, two sons, and five grandchildren all work together - remain a perennial problem in Italy.

Stefano Allesina, an assistant professor of evolution & ecology at the University of Chicago, witnessed the damaging effects of these unfair hiring practices as a student in Italy. While pursuing his PhD, Allesina’s advisor told him not to waste his most productive years trying to get a job in Italy - advice he followed in emigrating abroad to the United States. Many of his Italian peers followed similar paths, while those who stayed behind languished in limbo waiting for scarce tenure track positions to open. Frustrated with the broken Italian system, Allesina decided to apply his talents for creating computational models in ecology to measuring the full scope of nepotism in the university system of his home country.

“In Italy, there is an enormous brain drain,” Allesina said. “Italy is losing so many graduate students to other countries, it’s unbelievable. It’s because the hiring is extremely slow, complicated, and not really based on quality…and I think these kind of hiring practices contribute a lot to this brain drain and the fact that Italian universities are not ranked very high internationally.”

In a study published yesterday in PLoS ONE, Allesina used a public directory containing the last names and fields of study for over 61,000 professors to look for systemic signs of nepotistic hiring. With a simple computer model, Allesina detected unusual clustering of last names within disciplines such as law and medicine, far from the random distribution expected with unbiased hiring.

“It’s not a few bad apples, it’s really bad,” Allesina said. “I found that in many disciplines there are much fewer names than you would expect to find at random, indicating a very, very high probability of nepotistic hires.”

The original model worked like a random lottery, repeated one million times. Over the entire dataset, more than 27,000 different last names were represented. For each discipline, Allesina tested whether certain names appeared more than expected at random. So for medicine, where there are 10,783 faculty members with 7,471 different last names, Allesina programmed his computer to test how likely it was to randomly draw only 7,471 names (or fewer) from the total name pool in 10,783 tries.

“It’s very basic, anybody with a laptop can do this analysis,” Allesina said. “I wanted to keep it as coarse-grained and simple as possible. Because then it’s more powerful - if this works, anything else will work. Even this very simplistic analysis can find that some disciplines are above and beyond what one could expect.”

Under this model, the worst offenders were law, medicine, and industrial engineering, all of which showed only a 1-in-1,000 chance of having so few last names by random. On the other end, psychology, demography, and linguistics  each contained a last name distribution close to random, suggesting that hiring was more fair in these fields. Another analysis, which mapped the likelihood of two faculty members in the same field sharing a name by geographic region, found that indicators of nepotism were stronger in the south - a result that would surprise few Italians, Allesina said.

“For an Italian, this is not that surprising,” Allesina said. “It is a narrative of two separate countries, where in the public sector we have more problems in the south.”

A much trickier task than measuring the breadth of nepotism in Italy is finding an effective solution for ending the unfair hiring practices.

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One of the sectors closely monitoring the debt debate in Washington is the medical world, where hospitals, physicians, and patients anxiously await the final agreement on cuts to Medicare and Medicaid. Of particular concern to academic medical centers [pdf] are proposed cuts to graduate medical education, funding used to pay the salary of residents and fellows who are both training as physicians and specialists and working on the front lines of patient care. In a time when a patient’s wait time to see a specialist grows longer and longer, squeezing the bottleneck of physicians-in-training even tighter could have long-term consequences.

This week, the Medical Center’s executive vice president for medical affairs and dean Kenneth Polonsky took to the newspapers to argue against these damaging cuts. In an op-ed letter published by the Chicago Tribune, he expressed concern that the proposed cuts would “would reduce access to doctors, multiply waiting times and do lasting harm to patients in Illinois and nationwide.”

No one questions the need to rein in spending on health care or the obligation of hospitals to do their part. But we need to maintain a high level of patient care, and to make certain that our country has enough physicians in the future. Policymakers in Washington must maintain their support for graduate medical education and find more equitable ways to distribute the budget-cut burden.

Elsewhere…

Speaking of Washington and health care policy, without the Patient Protection and Affordable Care Act, 63-year-old Glenn Bovard of Valparaiso would not have been able to receive life-saving gift this past Father’s Day: a new heart. The Post-Tribune profiled Bovard’s story and surgery, performed by the Medical Center’s Valluvan Jeevanadam and Jai Raman. “The surgery was a cakewalk compared to the heart attack,” Bovard told the paper.

As many as one-third of patients with epilepsy cannot control their seizures with medication. Local newsmagazine Chicago Tonight profiles efforts by Wim van Drongelen, technical and research director of our pediatric epilepsy center, to develop new ways of helping these patients by modeling how seizures begin and spread in the human brain.

At the end of a long, difficult week, many people like to unwind on a Friday evening with a drink? But does alcohol relieve stress, or prolong it? A new study by Emma Childs of the University of Chicago Behavioral Pharmacology Laboratory and written up by the Gannett News Service suggests a double-edged sword - stress reduces the positive effects of alcohol, while a drink may extend the tense feelings produced by a stressful event.

A cautionary tale about when newspapers twist the words of scientists for sensationalist ends - did paleozoologist Darren Naish really say that the Loch Ness Monster was “more fact than fiction?”

Evolution isn’t only a process that happened in the distant past. Carl Zimmer’s wonderful cover story in the Science Times this week follows New York evolutionary biologists as they hunt for signs of urban evolution in progress for mice, fish, ants, and other city-dwelling critters.

In evolutionary biology today, it’s the ugly guys who get famous. But that hasn’t always been the case. When paleontologists were assembling a library of prehistoric life in the 19th century, they wanted to find the fossils they could easily categorize. The freaks, the weirdos, and the oddities were less well received, square pegs that wouldn’t fit in the round holes on a tree of life. However, today, it’s those hard to categorize fossils that tell the richest stories to biologists seeking to map evolutionary history, with all of its strange tributaries.

When Ramsay Heatley Traquair first described a 332-million-year-old fossil of a holocephalan (a relative of sharks and rays), he gave it a name that marked it as an outcast: Chondrenchelys problematica. Both parts of the name revealed his frustration with finding the right category for the ancient fish - Chondrenchelys means “cartilage eel” (a kind of oxymoron), and problematica is obvious. But the same features that made it so hard to classify in 1935 - plus a frightful new feature never observed before - made the long extinct species especially interesting to John Finarelli and Michael Coates of the University of Chicago.

Despite their obscurity today, holocephalans are an important group to scientists looking at the origins of jawed vertebrates - a group that would eventually include us. The holocephalans, including still-existing oddballs such as ratfish, the rabbit fish, and the elephant shark, split off from the rest of the fish world 400 million years ago, and have evolved in their own direction ever since. Studying the biology of modern holocephalans can tell us about some of our earliest ancestors, and studying holocephalan fossils gives the field even more direct insight into the early days of vertebrates.

“It represents an awful lot of vertebrate evolutionary history, that’s why it’s important,” said Finarelli, a research associate professor in the Department of Organismal Biology and Anatomy (OBA). “You’re getting down to a fundamental split at a very early point in the vertebrate family tree with what’s around today.”

“You look at these specimens to see what kind of insight you can get into the very general properties or conditions of how to make a jawed vertebrate, because you’re getting this independent pipeline,” said Coates, professor of OBA and senior author of the study.

Yet Chondrenchelys problematica lingered in obscurity until two new specimens were unearthed in the Mumbie Quarry in Scotland, described for the first time last week in the Proceedings of the Royal Society B. More complete than previously described fossils of the species, Finarelli and Coates noticed something unusual and unexpected about the long, skinny fish’s dental structure that sets it apart from other creatures, alive or extinct.

“It’s got teeth where you shouldn’t have teeth. Imagine a full set of teeth in your lips - that’s what this thing has,” Finarelli said. “They’re just fundamentally different from everything else we’ve ever seen in the jaw.”

To confirm that they didn’t just stumble upon mutant representatives of the species, the researchers went back and looked at the older Chondrenchelys fossils. Their re-examination confirmed that the unusual teeth was present in those less well preserved specimens as well, meaning the extra set of choppers was a standard feature for the species - and for no other species seen before or since.

The researchers haven’t yet commissioned an artist to reconstruct the face - “It would be pug ugly,” Coates said - but its homeliness is useful to scientists. Chondrenchelys existed at a time when holocephalans were exploding in diversity and the species newly-discovered weirdness only adds to the possible forms the group can take.

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It’s one of the most significant events in Earth’s history: the moment when a sea creature first stepped - or more likely wriggled - onto land. The momentous occasion 400 million years ago opened up a whole new habitat where life on Earth could evolve and spread out, and made that first bold pioneer and its peers the ancestor to everything from dinosaurs to birds to humans. Obviously, scientists would love to know more about what that brave explorer looked like, and have long hunted for their fossils. But genetics offers another way to journey back in time and look at the biology of the first fish to leave the water, and a study published today by University of Chicago scientists suggests that the genetic tools to make those first historic steps were present long before they actually occurred.

In this case, the genetic hunt was inspired by a famous fossil find, the 2004 discovery of Tiktaalik by a team led by University of Chicago evolutionary biologist Neil Shubin. Tiktaalik was described by its discoverers as a “fishapod” - a transitional species between fish and the four-limbed land-dwelling tetrapods. Though Tiktaalik and its cousins had fin-like appendages, the skeletal structure within those fins was more complex than typically seen for an aquatic species, featuring wrist and hand-like compartments that may have allowed it to do “push-ups” and drag itself slowly across land. Such a sophisticated structure probably didn’t develop overnight, leading Shubin to wonder just how far back the genetic program for developing a limb might have existed in fish.

“This is really a case where knowing something about the fossils and the morphology led us to think about genetic experiments,” said Shubin, the Robert R. Bensley Professor of Organismal Biology and Anatomy and senior author of the study in the Proceedings of the National Academy of Sciences. “Tiktaalik and its cousins showed us that this limb compartment is not an utter novelty in tetrapods, as was thought for a long time. So an antecedent of that program must exist.”

To answer that question, Igor Schneider, a postdoctoral research in Shubin’s laboratory, assembled a genetic “time machine” to look at the origin of a genetic switch for limb development. A genetic switch controls the expression of genes - where and when they are turned on during embryonic development. Schneider took the human sequence of a genetic switch called CsB that controls limb development and looked for similar sequences in a diverse group of animals: mouse, chicken, frogs, zebrafish, and the skate. Though very different today, the animals all share a common ancestor some 400 million years in the past, millions of years before Tiktaalik. Looking at what the CsB switches share in common between those distant relatives today offers a glimpse at the biology of their great-great-great-(repeat 100 million times)-grandfather.

Just looking at the sequences revealed many similarities between the CsB switches of fish species and tetrapods. But the real test was to determine whether the switches performed similar functions despite 400 million years of divergent evolution. To test this required a little bit of mad science: swapping gene sequences across species. First, the CsB switch from a mouse was put into a zebrafish embryo, where it was shown to activate gene expression in the distal fin. The reverse experiment - zebrafish CsB into mouse embryo - was even more exciting, as the primitive fish switch successfully activated gene expression in the developing mouse paw (seen at right).

“The genetic switches that drive the expression of genes in the digits of mice are not only present in fish, but the fish sequence can actually activate the expression in mice,” Schneider said. “This tells us how the antecedents of the limb go back in time at every level, from fossils to genes.”

In both experiments, the gene that the switches activated was merely a reporter gene that told researchers where and when the switch was flipped on. The actual genes that cause an appendage to form the skeletal structure for a limb or fin were not present. But could a transplant of the mouse switch and the relevant genes into a fish embryo produce a lab-grown fishapod?

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By John Easton

At 1:30 pm, on Monday, December 12, at its Annual Meeting and Exposition in San Diego, The American Society of Hematology will recognize Janet Rowley of the University of Chicago Medical Center, and Brian Druker of Oregon Health & Science University, with the 2011 Ernest Beutler Lecture and Prize for their significant advances in the diagnosis and treatment of chronic myeloid leukemia (CML), a cancer of the blood characterized by an overproduction of white blood cells.

This is a great honor - and a storage problem.

Rowley has received many prizes over the course of her career: the Lasker Award, the Gruber Genetics Prize and the American Association for Cancer Research Award for Lifetime Achievement. President Jimmy Carter appointed her to the National Cancer Advisory Board. President Bill Clinton awarded her the National Medal of Science. George W. Bush selected her for his President’s Council on Bioethics. She stood with President Barack Obama when he signed the stem cell research bill and she returned to the Obama White to accept the Presidential Medal of Freedom. Then she moved to a new office with a better view, but less shelf space.

Rowley has long been known for brilliant insights, intellectual rigor, and relentless tenacity, but never for extreme neatness. “Her filing system involved piles,” said MaryBeth Neilly, a senior research technician who works with her. When preparing for the move, “we found awards all over the place,” she said. “We knew we needed a place to put them, and that her office was not that place.”

Thus was born the shrine. “Once we moved, but before we unpacked, we ordered a display case,” said Neilly. She and Rowley sorted through the honors and picked the cream of the crop; those that were the most significant, or that looked really cool. Lots of them, some of the trophies, most of the plaques and the vast majority of honorary doctorates, were transported - lovingly, but in bulk - to the University archives.

The display case soon filled to capacity. “There’s a lot of crystal in there, a lot of shiny metal,” Neilly said, such as the National Cancer Institute’s Rosalind E. Franklin Award for Women in Cancer Research, a big carved glass bowl, or the National Medal of Science, a golden medallion.

A few favorites - for reasons aesthetic or sentimental - wound up in Rowley’s office, including the Lasker, the Presidential Medal of Freedom, a large, twisting crystal chromosome from the Jeffrey M. Trent Lectureship in Cancer Research, and a bronze sculpture from the Leukemia and Lymphoma Society. A few more are at Rowley’s house. Two made of a particularly valuable soft, shiny heavy metal, stay at a local bank. The exact positioning of the Beutler Prize has not yet been determined.

Elsewhere…

Vijay S. Dayal, a longtime fixture of the Medical Center’s otolaryngology department, passed away last week at the age of 74. A head-and-neck surgeon and expert on hearing and balance, Dayal was also known as a skilled inventor, obtaining patents for an artificial voice box and a customized “rotating chair” used to test dizziness and balance. “Testing in the chair is not uncomfortable for the patient,” Dayal said in 1991. “It’s like a mild ride on a merry-go-round and it provides us with information we cannot get any other way.” You can read another obituary for Dr. Dayal at the Chicago Tribune.

What’s it like to be a medical student? Pritzker first-year Akash Parekh narrates a day in his life for US News & World Report. Spoiler alert: there’s not much free time, or sleep.

If parents refuse vaccinations for their child, should pediatricians be allowed to refuse to take them as a patient? That interesting ethical question was the subject of an article by the Chicago Tribune’s Deborah Shelton.

The new Scientific American blog network officially launched this week, and provides a new home to many of my favorite science bloggers. For a taste, check out Lucas Brouwers’ post on the evolution of E. coli, and this interview with John Boswell of Symphony of Science (best known for the Carl Sagan autotune track “A Glorious Dawn”).

In zoos, keepers strive to preserve as much of the natural experience as possible for their animals. But not everything can be left up to nature behind zoo walls. While encouraging reproduction can be a zoo mission for captive endangered species, other species can’t be allowed to procreate without limits, lest the zoo run out of room for booming families. In primates, zookeepers turn to a familiar method of birth control - the same hormone-based contraception developed for humans. But does putting a gorilla on “the pill” change more than the animal’s ovulation cycle?

This unusual topic was the basis for University of Chicago graduate Anna Sarfaty’s undergraduate research project. For over a year, Sarfaty and her co-authors closely observed four female gorillas at Lincoln Park Zoo, keeping score of sexual, social, and aggressive behaviors to see if hormonal birth control disrupted their normal activity. Published in the journal Zoo Biology with co-authors Susan Margulis and Sylvia Atsalis, the results offer new information for zookeepers on the effects of contraception.

“Zoos don’t want to separate males from females,” Sarfaty said. “So hormonal birth control is a great option, and we know that it works since it’s been given for many years. But researchers like to understand how animals may be acting differently and understand how the behavior we’re seeing might be different from the natural world.”

Unlike most published studies, Sarfaty’s paper can name names - the stars of the experiment were Rollie, Tabibu, Madini, and Bulera, four of the seven females in the zoo’s gorilla population. Each female gorilla received birth control pills on the same schedule that a female human does - three weeks of estrogen and progestin, followed by one week of placebo pills. Under normal conditions in the wild, gorillas are known to increase certain types of sexual activities known as “estrous behaviors” in the second week of their cycle, near the time of ovulation. So researchers watched their four subjects for 20 minutes a day, four to five times a week, for over a year, to see whether the same behavioral patterns were preserved in the captive, contraceptive-fed females.

Behaviors were scored according to an “ethogram” - a dictionary of behaviors that is “more difficult to write than you would think,” Sarfaty said. The catalog, reproduced in the article, is extensive: listing everything from social play and grooming to biting and chasing to more risque actions such as mounting and masturbation. The researchers also monitored how much time the females spent in the vicinity of the group’s dominant male silverback gorilla, which is a provocative move in gorilla culture.

“Because the gorilla social system is so strict, just sitting close to the silverback male and doing nothing is still a big deal,” Sarfaty said.

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Around the pediatric cancer wards at Comer Children’s Hospital, he was known by the rhyming nickname of “Doc Nach” and for delighting patients with his Mickey Mouse watch. On a ward where a smiling face goes a long way, Dr. James Nachman was always happy to provide a cheerful presence. Behind the scenes, he was also a dogged researcher, developing new protocols for children who didn’t respond to the standard treatment for acute lymphoblastic leukemia (ALL) and working to save the limbs of children diagnosed with sarcoma, a cancer of the bones.

Sadly, Nachman passed away last week at the age of 62, while on a rafting trip in the Grand Canyon. This week, Medical Center colleagues remembered “Doc Nach” for his skill with patients and scientific expertise.

“Jim was an outstanding clinician, teacher, and clinical researcher,” said John Cunningham, professor of pediatrics and chief of pediatric oncology. “He made seminal observations in leukemia and lymphoma that have impacted the lives of many children and adults with these diseases. He was an outstanding doctor, beloved by his patients, their families, and his colleagues. He was an irreplaceable member of our cancer team. We will miss him deeply.”

Patients’ families also were quick to pay tribute to Nachman. At the ChicagoNow blog “Ay Mama,” Laura Lutarewych wrote a moving post about her encounters with Nachman during the treatment of her 2-year-old daughter, Atia.

He’d walk into a room with a smile asking, “How’s my favorite girl?” It didn’t matter who the patient was - they were all his favorite, so it was fitting and each child wore their title proudly.

Without exception, he’d hold out his wrist and ask, “Who’s on my watch?” Atia especially loved that part, because she knew the script; she didn’t even have to look at the watch. With a huge smile, she’d point at it and exclaim, “Mickey Mouse!”

Earlier this year, we shot a video with Nachman for a series of informational segments on pediatric cancer topics that you can view below. Even in answering technical questions about how ALL is diagnosed and treated, you can see the good cheer and optimism in Nachman’s demeanor that was so comforting to his patients. For all of the people he touched during his life, that positive attitude will be missed.

“He was an optimistic, sunny person,” his brother Robert Nachman said in the Chicago Tribune obituary, “and his eyes lit up whenever he was talking about children.”

Elsewhere…

Linkage was off last week, so we didn’t have a chance to post this excellent front-page Chicago Tribune article about the neuroprosthetics research program here at the University of Chicago. Reporter Cynthia Dizikes also penned an online supplement that explains the link between assistant professor Sliman Bensmaia’s favorite Star Wars scene and his research on the neural mechanisms of touch.

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Teaching with Treadmills

Inside the Biological Sciences Learning Center on the Medical Center campus is a laboratory that looks more like a gymnasium. Six state-of-the-art treadmills and six futuristic exercise bikes sit around the room, each connected to a computer alongside modified oxygen masks and suction cup sensors. Instead of dissecting frogs or mixing chemicals, students show up to lab sections in shorts and running shoes, prepared to sweat for science. In Mark Osadjan’s “Metabolism and Exercise” course, part of a two-quarter Exercise and Nutrition sequence, there’s no sitting on the sidelines.

Since joining the University of Chicago as a senior lecturer in 2003, Osadjan has designed courses that teach undergraduates about biology by connecting with what most college students care about: keeping fit, and sex. As part of the UChicago core curriculum, every undergraduate must fulfill a biology requirement, even if their interests lie in political science, music theory, or philosophy. With his “Metabolism and Exercise” and “The Biology of Gender” courses, Osadjan has met these science-shy students halfway, filtering instruction on evolution, physiology, and genetics through their own personal hobbies and interests. The efforts have been such a success that Osadjan’s courses fill up soon after registration is opened.

Today, Osadjan was announced as one of this year’s recipients of the Quantrell Award for Excellence in Undergraduate Teaching, an esteemed UChicago honor that goes back to 1938. Last week I met with Mark to talk about his award and his career path, from a graduate student studying Antarctic fish to an instructor of graduate-level science to his current position, teaching predominantly undergraduate non-biology majors.

“It’s always a trick to figure out how to teach with enough enthusiasm, such that it spills over to the students,” Osadjan said. “It’s our challenge not only to teach these students a certain number of facts, but to show them why those facts are important, relevant, and worth thinking about throughout life.”

You can read more about Osadjan and the other Quantrell winners in the award package at The University of Chicago news site.

Elsewhere…

Most college students spend their summers traveling the country or working an internship, but 20-year-old Rachel Garneau had other plans: donating a kidney. On Tuesday morning, Garneau came to the Medical Center and made the rare gift of an altruistic kidney donation, triggering a kidney swap chain that helped patients in need of the organ in New York and Madison. Neil Steinberg at the Chicago Sun-Times followed the story before and during the surgery, and got some great play-by-play commentary from Yolanda Becker, professor of surgery and director of the kidney and pancreas program.  For instance: “‘The pancreas is the bitch of the abdomen,” she confided.’”

Are clinical trials handicapped by their own success? A new analysis from Anup Malani and Tomas Philipson of the University of Chicago Law School finds that trial enrollment for a given disease plummets when a treatment is found to be effective, using AIDS clinical trials after the approval of anti-retroviral therapy to illustrate the point. Richard Schilsky, professor and section chief of hematology/oncology at the Medical Center, agreed with the findings at Nature News: “There are so many options that patients are not flocking to get into clinical trials like they used to.”

Read how turtles move to warm areas to bask - even in their own eggs as embryos. Adorable photos and interesting commentary (are they determining their own sex?) at Not Exactly Rocket Science.

That news about the World Health Organization adding cell phones to their list of possible carcinogens? Here’s an article from Cancer Research UK to reassure your fears. Another reassuring fact: it was placed by the WHO into the same risk category [pdf] as coffee, dry cleaning, and pickled vegetables.

Can jazz musicians tell the difference between another musician improvising or following composed music? A new study finds the answer, and a ScienceNOW article gives you the chance to test yourself.

Did you know UChicago evolutionary biologist Neil Shubin does a regular science news roundup on local newsmagazine show Chicago Tonight called Scientific Chicago? Well he does, and the latest edition discussed a story familiar to readers of the blog: the mass extinction 360 million years ago that ended “The Age of Fishes.” Watch the video here.

A Magic 8-Ball for Cardiac Arrest

Cardiac arrest is one of the most common ways that people die, and hospitals need to be constantly vigilant about the threat of heart stoppage in their patients. So physicians have long sought to develop a way of predicting who is most at risk for cardiac arrest when checked into the hospital, such that extra care and surveillance can be taken. At the 2011 international meeting of the American Thoracic Society, held this past week in Denver, two Medical Center fellows presented research refining these early warning systems to make them a more effective hospital tool.

In the first study, pulmonary and critical care fellow Gordon E. Carr connected cardiac arrest with another frequent sight on the hospital ward: pneumonia. Carr’s study found that patients admitted with pneumonia are at elevated risk of cardiac arrest over the next three days after admission, and that almost 40 percent of these cardiac arrests occurred while the patient was outside of the intensive care unit. “We found a compelling signal that some patients with pneumonia may develop cardiac arrest outside of the ICU, without apparent shock or respiratory failure,” Carr said in a press release. “If this is true, then we need to improve how we assess risk in pneumonia.”

Adding extra caution about cardiac arrest to the care of patients with pneumonia is a specific way to improve surveillance. But to apply to more patients, a broader scale is needed, one that can be easily assembled from the vital signs that are already routinely measured in the wards. One such scale, called the Modified Early Warning Score or MEWS was tested by pulmonary and critical care fellow Matthew Churpek as a predictor of cardiac arrest, who found it to be better at predicting a cardiac arrest in the next 48 hours than any individual vital sign. But MEWS was designed for general risk of death, not specifically for cardiac arrest, and Churpek suggested a more specialized risk score could be calculated for use by hospitals. The benefits of such a measure, he said in a press release, would be immense.

“Rapid response teams are a complex and resource-intensive intervention, so providing evidence-based criteria for their activation is crucial,” Churpek said. “Our patients will do better if we can detect who is at high risk early enough to intervene and prevent a cardiac arrest.”

Doctors Against Ronald McDonald

Childhood obesity is a growing problem in the United States, and doctors point the finger of blame directly at increased consumption of junk food and fast food. Chains such as McDonalds have made noise about making their food healthier, especially for children, by posting calorie counts on menus and offering snacks such as apples and carrots instead of fries. But according to an open letter signed by over 500 health care professionals and placed in newspapers around the country this week, they have not done enough.

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An enzyme from three different species is compared, with structural "flaws" shown in green. (From Fernández & Lynch, Nature, 2011)

One common misconception about evolution is that it produces “better” organisms with time - a seductive opinion to humans who would like to think of themselves as the pinnacle of natural selection. In a way, it’s an easy error to make, for who would look at a single-celled bacterium next to a human and think that the four billion years of evolution between the two species hadn’t produced some improvements? But when Ariel Fernández and Michael Lynch compared the proteins that bacteria and humans share, they found that the unicellular organisms held a surprising advantage. Though the overall shape of the proteins were the same, the human proteins were leakier, more vulnerable to the destabilizing effects of water than those of the bacteria.

But according to the paper published yesterday by Fernández and Lynch in Nature, those protein flaws may have been the key spark that led to the evolution of complex organisms.

“We hate to hear that our structures are actually lousier,” said Fernández, a visiting scholar at the University of Chicago and senior researcher at the Mathematics Institute of Argentina (IAM) in Buenos Aires . “But that has a good side to it. Because they are lousier, they are more likely to participate in complexes, and we have a much better chance of achieving more sophisticated function through teamwork. Instead of being a loner, the protein is a team player.”

The engineering advantage of bacteria over humans boils down to one simple fact: they will always far outnumber us. Billions of bacterial organisms can fit into a single Petri dish, and in a single human body there are over 100 times more bacterial cells than there are humans on Earth . When a genetic mutation with a negative effect pops into existence in these huge populations, natural selection quickly disposes of it, preserving the integrity of the protein that gene encodes. But when a mildly negative mutation appears in a relatively small population, such as that of humans or elephants or pine trees, selection is less efficient and the mutation may spread - a phenomenon called genetic drift.

The direct effect of these mild mutations would be to introduce minor flaws into the structure of proteins. If the change in protein function was too severe, it would cease to function and likely kill the organism. But if the change was just a small nick in the armor of the protein, making it chemically more vulnerable to water, the mutation might stick around long enough to be passed on to offspring. That theory informed Fernández and Lynch’s hypothesis: proteins from species with small population sizes would contain more of these flaws than those from species with large populations.

Their idea was proven true: compare the same protein between, say, humans, flatworms, and bacteria, and you’ll find a descending frequency of protein flaws. Even within a single species, the difference can be measured. Some bacteria have both endosymbiotic populations that live inside other organisms and larger, free-living populations, and the proteins from the endosymbiotes were found to contain more structural errors than their free-living peers.

But the exciting part is what happens after those errors accumulate. read more

More Honors for Shubin

In 1863, in the midst of the Civil War, Abraham Lincoln signed an order creating the National Academy of Sciences, an organization bringing together the country’s most esteemed scientists to “investigate, examine, experiment, and report upon any subject of science or art.” From the original 50 members, the group has blossomed to 2,100 today, with roughly 200 of those Nobel Laureates. Any club with a 10 percent Nobel ratio is pretty exclusive, so being elected to the Academy’s lifetime membership is a thrilling honor for a scientist.

This week, evolutionary biologist Neil Shubin was the latest UChicago scientist given the honor of NAS membership, part of this year’s class of 72 new members and 18 “foreign associates.” Shubin becomes the 40th current member of the NAS located at the University of Chicago, and joins Medical Center faculty such as Janet Rowley, Martin Weigert, Donald Steiner, Bernard Roizman, Robert Haselkorn, and David Jablonski, who was elected last year (Fermilab director and professor of physics Pier Oddone was also elected in this year’s class). Election is no simple matter - each new member must pass a 10-step process [pdf] and be voted in to the academy by their potential peers.

Shubin is most famous for the discovery of the pivotal fossil named Tiktaalik roseae, a transitional species between ancient fish and the first limbed creatures to walk the land. But Shubin’s research is more than just fossil-hunting, as he studies the genetic programs that control development of limbs in the embryos of species such as sharks and salamanders. On the blog, we recently featured a paper by Shubin and former graduate student Andrew Gillis, where the embryos of strange creatures called holocephalons revealed some of the earliest steps in limb evolution.

In all likelihood, Shubin’s election was helped by his scientific communication skills as well. From his book about the discovery of Tiktaalik and the story of human evolution, Your Inner Fish: A Journey Through the 3.5-Billion-Year History of the Human Body, to his appearances as a correspondent on WTTW, to his anatomy teaching duties at Pritzker Medical School, Shubin has proven himself eager to educate the public at large about science. Appropriately enough, a second honor announced for Shubin this week was the Distinguished Service Award for Enhancing Education through Biological Research from the National Association of Biology Teachers. Once again, he finds himself in good company, as previous recipients include James Watson, Stephen Jay Gould, and Richard Dawkins.

“I am deeply honored to receive the NABT Distinguished Service Award. In an age where the ideas and tools of biology are increasingly playing a role in our lives, it is a deep honor to be recognized by those who are at the front lines of educating the next generation,” Shubin said.

The Science of Killing Bin Laden

A news story as big as the killing of Osama Bin Laden spares no beats, and there were plenty of science stories written this week in the aftermath of Sunday night’s surprise news. The most direct scientific angle was in the identification of the terrorist leader’s body, a step U.S. officials wanted to prove beyond a doubt before going public with the news. Like many of the events surrounding the raid, many of the details remain classified. But that hasn’t stopped science writers from writing explainers on how biometrics and DNA matching likely would have been used to make sure the Navy SEALS really had killed Bin Laden. President Obama himself confirmed that DNA testing was used to confirm they had the right body, but one fascinating mystery is where the DNA used to make the comparison was gathered. Nature blog The Great Beyond describes the candidates - from Bin Laden’s half-brothers and half-sister to one of his purported 26 children - and talks a bit about the recent history of using DNA identification techniques in criminal matters, including one crook busted by DNA he left on a slice of pizza.

Elsewhere…

The creation of new drugs, and the death of old drugs - Medical Center researchers commented on both sides of the pharmaceutical life cycle in newspaper stories this week. In the New York Times blog Fixes, reporter David Bornstein looks at the “valley of death” in developing new drugs for less-than-common diseases, and focused on the Myelin Repair Foundation and researchers such as Brian Popko (who we have featured twice). Then yesterday, the Chicago Tribune’s Bruce Japsen wrote about the upcoming patent expirations on the popular drugs Plavix, Lipitor, and Actos, and talks to our Caleb Alexander about the implications for health care.

How do you make a new species in the lab? It’s easier if you find a lizard species that is entirely female and can reproduce by cloning. Ed Yong at Not Exactly Rocket Science describes genome mash-ups, asexual reproduction, and the trickiness of species-naming in this great post.

A retired nurse and research coordinator at the Medical Center talks with Dawn Turner Trice about her experiences working with a small rural clinic in Ghana.

Ancient fish feed on crinoids before the extinction. (Art by Robert Nicholls)

At the core of ecology is the perpetual battle between predators and their prey. The relationship typically works like a see-saw: when more predators come into an environment, the prey population drops, until the predators start going hungry and dying off, allowing the numbers of prey to rebound, and so on. Ecologists have observed these dynamics in the wild as new predators are added to ecosystems or eliminated through extinction or relocation. But for the first time, this kind of predator-prey relationship has been observed in the fossil record, thanks to a newspaper article and a 360-million-year-old mass extinction.

One year ago, Lauren Sallan and Michael Coates of the University of Chicago published a paper on the Hangenberg Event, a mass extinction event that brought the prehistoric period known as “the Age of Fishes” to a catastrophic end. To pinpoint when the extinction occurred, Sallan built a new database of vertebrate fossils during and after the Devonian period, which ran from 416 to 359 million years ago. For 15 years after the Hangenberg extinction, they discovered that the formerly thriving ancient fish of sea and freshwater largely disappeared during a period known to paleontologists as Romer’s Gap.

Sallan and Coates’ study was covered by websites, radio shows, and newspapers, including a Los Angeles Times story that ran concurrently in the Chicago Tribune, and was spotted and clipped by the father of Thomas Kammer, a geologist at West Virginia University. Kammer studies the fossils of crinoids, species similar to modern sea lilies and related to starfish, and had been stumped by a mystery in his own database - a sudden burst of abundance and diversity known as the Age of Crinoids. When Kammer was sent the newspaper article, a missing piece of the story clicked into place.

“I read the article and it was like one of these light-bulbs going on over your head,” Kammer said. “We’ve been puzzled for many years as to why there were so many species and specimens of crinoids. There had to be some underlying evolutionary and ecological reason for that.”

Perhaps, he thought, the crinoids’ time of dominance may have been a consequence of the mass extinction of fishes. Some fish feed on crinoids to this day, but proving that crinoids were a part of the diet of ancient fishes that lived hundreds of millions of years ago is much harder. As Kammer put it, “You don’t actually find the evidence of a fossil fish with a crinoid in its mouth very often.”

Kammer reached out to Sallan for a collaboration, an effort that was joined by Lewis Cook of WVU and William Ausich of Ohio State University. In a study published by Proceedings of the National Academy of Sciences, the team analyzed the two fossil datasets side by side, and found that the timing of the fishes’ abrupt decline and the crinoid’s rise were indeed related. What’s more, as fish populations slowly returned to their former prominence, the crinoid numbers dropped back down to their earlier levels.

“It really tells us about recovery from mass extinctions, especially mass extinctions that involved loss of predators,” Sallan said. “Even if you have a group like the crinoids which makes it through the extinction unscathed, the death of their predators affects them for a further 10 to 15 million years.”

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The University of Chicago is the birthplace of nuclear energy. So like proud but concerned parents, UChicago has kept a close eye on the benefits and challenges of nuclear power over the years since the first self-sustained nuclear reaction under Stagg Field. Thus, the battle to manage the consequences of the damaged reactors at the Fukushima I Nuclear Power Plant in Japan has drawn the University’s interest, and the short-term and long-term effects of that ongoing situation were the subject of a unique panel held on campus yesterday, “Lessons from Fukushima.”

Though nuclear power was created by scientists, discussing its use requires input from political and economic spheres as well. So the panel, assembled by the University of Chicago Alumni Association, brought together nuclear technologists (Hussein Khalil, director of the nuclear energy division at Argonne National Laboratory, and Mark Peters, deputy director of Argonne), nuclear policy watchdogs (Kennette Benedict, executive director of the UChicago-based Bulletin of Atomic Scientists), and energy economics experts (Robert Topel, director of the University of Chicago Energy Initiative). With such different perspectives, it didn’t take long for the panelists to find points of debate, reflecting the tug-of-war over nuclear power that has gone on for several decades.

Nobody disputed the magnitude of the Fukushima incident, with workers at the plant still struggling to limit core meltdown in at least three of the reactors as well as re-cooling spent fuel rods at the site. As well, the panelists agreed that the incident was very relevant to nuclear power in the United States, where roughly one-fifth of electricity is provided by nuclear plants, many of which use the same model as the Fukushima reactors. But opinions differed on what those consequences would be.

Khalil pointed out that this was the first natural disaster to cause “grave damage” to a nuclear power plant in nearly 60 years of their use, and that a similar occurrence was very unlikely in the United States. But Benedict argued that “very unlikely” wasn’t good enough for “the most dangerous technology on Earth,” and that not every safety precaution possible had been taken at Fukushima. Topel agreed with the latter point - “why build generators on the ocean side in a country that coined the term ‘tsunami’?” he asked - and noted that the renewed attention to the long-term dangers of nuclear power would only make it more difficult to build new reactors.

In fact, no new nuclear reactor has come online in the United States in 32 years, Khalil said. So while Argonne continues to research new designs for nuclear plants and new strategies for containing nuclear waste, the economic (and possibly now public opinion) barriers are too large. The most likely rescue for nuclear power may come from an unlikely source: climate change.

“If other technologies turn out to be a bust, and if we really are serious about reducing our carbon footprint and carbon pricing becomes important, then there is a technology we have that can produce a lot of energy at relatively low cost compared to the alternatives,” Topel said. “Then, nuclear energy will prosper.”

By the end of the 90-minute discussion, the panelists came back to common ground on a hopeful note. If a thin silver lining could be found on a disaster that hasn’t yet been completely averted, it’s that the events at Fukushima have re-opened the international dialogue on nuclear power - its immense benefits and equally immense costs.

“One of the positive externalities of the Fukushima accident is that many more people are interested in nuclear energy, and I think that’s terrific,” Benedict said. “It’s unfortunate that it takes an accident to do it.”

Elsewhere…

The conversation about cancer is changing, from a single disease classified by the organ where it appears to multiple diseases grouped by genetic and biological similarities. As ScienceLife has written before, the Chicago Cancer Genome Project is our local contribution to this strategic shift against “the emperor of all maladies.” This week the Los Angeles Times examined that research effort and others like it, speaking with project leader Kevin White and many of the Medical Center’s cancer experts collaborating on this new vision of how to classify and battle cancer.

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