Texting has grown from technological fad to a primary route of communication popular around the world. With cell phones in the pockets of people of all incomes and ages, the quick, no-frills conversations enabled by texting have made almost everyone more proficient with their thumbs. Due to such impressive ubiquity, people in health care are starting to ask whether text-messaging can be harnessed as a cheap and user-friendly tool for communicating with patients outside of the clinic - particularly hard-to-reach patients in urban and low income areas.

“People are ignoring that unlike every other technology, mobile phones reverse the digital divide,” said Shantanu Nundy, clinical instructor of medicine at the University of Chicago Medical Center. “More low income patients are using phones for text messaging and internet than other groups. So shouldn’t we then be developing technology for this type of population?”

Nundy and Jonathan Dick, a Pritzker graduate now in residency at Columbia University Medical Center, arrived independently at this same idea after separate trips overseas, where they saw clinics in Uganda and India using text messages as part of their operation. With texts, physicians could follow up with patients with chronic diseases, making sure they were taking medications and doing the types of self-examinations necessary to manage diabetes or HIV - tasks that are just as challenging at home as they are abroad. In some areas of Chicago the diabetes rate is as high as 25 percent, and African-American populations have much higher rates of diabetes complications such as blindness and amputation.

“It seemed to me that we had a lot of the same problems on the South Side of Chicago, so why not try it there?,” Dick said.

To test this premise, Nundy and Dick joined efforts with Medical Center faculty Monica Peek and Marshall Chin, who recently received grants from the Alliance to Reduce Disparities in Diabetes and the National Institutes of Health to look for new ways to improve outcomes in South Side neighborhoods. For a pilot study published last month in the Journal of Diabetes, Science, and Technology, the team recruited 18 African-American diabetes patients to try out a new automated text-messaging communication system that they programmed.

The study participants were not your typical teenage texters, instead reflecting an age range (38-72) more commonly afflicted with diabetes.

“If this is going to work, we needed to look at middle aged people and people in their 60s and 70s. I’m less interested in having this as a hip thing for teenagers with diabetes,” said Peek, assistant professor of medicine. “It needs to be able to work in people I see in clinic. A 55-year-old black woman with diabetes, if it works for her, I’m interested.”

Each participant was asked at the beginning of the study what kinds of text message they would like to receive, with candidates including reminders to take diabetes medications, check blood sugar, or conduct self-examinations to detect potential complications. Participants could also customize when they received the message, and how often they came in over the one-month pilot.

Some were purely notifications (i.e. “Please take your medications now.”) while others required a text response (”How many times did you check your feet this week?”). In one early sign that the messages were reaching their targets, participants often texted back whether a response was required or not, sending an “OK” or a “Thank you” message to what they knew was an automated system. The study reports, “Many participants found that they began anticipating the text messages and readying themselves to answer the questions in an affirmative way, such as preparing the insulin syringe ahead of the expected message.” That enthusiasm was reflected in surveys of the patients after the study period ended, where all but one participant said they were very satisfied with the text reminders.

“In the context of a population that typically has very few interactions with the health care system and may have experiences that are negative or bad or fearful, it was very fulfilling for them to have positive reinforcing messages where they really felt cared for by the system in a way they hadn’t in the past,” Peek said.

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Anyone with a video game console at home can simulate  a variety of occupations: airplane pilot, race car driver, baseball player, Old West zombie hunter. As technology improves, the experience that can be created for these tasks grows ever more accurate and immersive, causing some experts to wonder whether simulation can be used for actual education as well as vicarious thrills. In the aeronautics field, this is old news - pilots have been trained on flight simulators for decades, gaining experience on high-risk, low-frequency tasks such as landing a damaged plane on a river. But in medicine, the use of simulation has only started picking up speed in the last decade, employing a mix of high-tech and low-tech to prepare doctors and nurses for both the usual and unusual.

In their Department of Medicine Grand Rounds presentation last week, Ernest Wang and Morris Kharasch from our partners at NorthShore University HealthSystem described the current state of simulation in medicine on the eve of their state-of-the-art simulation center’s grand opening. But while the idea might sound modern, it’s actually been around for more than 40 years, as Wang illustrated using a clip from the 1972 film Future Shock, narrated by Orson Welles.

Welles’ portentous warnings were a bit premature, it turned out. Never mind the leap from medical simulation dummy to humanoid robot, a generation would pass from when the first dummies were engineered in the late 1960’s before the broader field would accept simulators as a valid training tool for doctors.

“It looked pretty much what our current high-fidelity simulators look like, but didn’t have traction,” said Wang, a clinical associate professor at NorthShore. “There’s a Chinese saying: ‘When the student is ready the teacher will appear,’ and clearly they were too far ahead of their time and the conditions weren’t right.”

However, since 2000 the use of simulation in medicine has gathered momentum. A wide range of technologies are currently used for teaching sessions, from complex simulation environments that fully recreate the experience of being in an operating room to computer programs and table-top gadgets that rehearse medical decision-making and the performance of specific tasks. Medical simulation has grown to the point where a new specialty - the simulationist - may need to be created, Wang said.

“This would be a practitioner of simulation, who takes a recipe of clinically important cases, lessons learned from other industries, computer-driven full body simulators, realistic task trainers, and a dash of theater, to create a memorable learning experience that can be transferred directly to patient care,” Wang said. “In the end, that’s what this is about: education and patient care.”

Winning acceptance for medical simulation involves proving its success and determining its most effective uses. At the NorthShore center, educators have focused on designing simulation courses around “high-liability, low-frequency” events, said Kharasch, clinical director of the Center for Simulation Technology & Academic Research. The students in these courses might be residents encountering these situations for the first time, or older doctors who need a refresher on tasks they haven’t performed in many years before serving as an attending on the wards or in the emergency room.

“We’ve learned that as the years go on after you come out of residency, you are less able to do things that you once did as residents,” Kharasch said. “We spend a lot of time training on simple tasks that can be life-saving.”

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Late last year, we relayed the announcement of an exciting new academic program here at the University of Chicago, the Institute of Molecular Engineering. At the time, the IME had a future home (sharing the new William Eckhardt Research Center with the Physical Sciences Division) and a vision, but did not yet have a leader. Yesterday, that crucial headpiece was officially put in place, as biomolecular engineering and nanotechnology expert Matthew Tirrell was named the first Pritzker Director of the IME.

Tirrell will come to UChicago from California, where he has spent time at the University of California campuses in Berkeley and Santa Barbara over the last 12 years. His research specialty is the surface properties of polymers, chains of molecules that can be manipulated for building better materials used for everything from energy to technology to medicine. Those versatile aspirations make Tirrell the perfect leader for the IME, where the mission is to bridge disciplines at UChicago and Argonne National Laboratory and bring the tools of biology, chemistry, engineering, and physics to bear on finding solutions to some of science’s most important challenges.

“This isn’t going to be directed narrowly toward one scientific discipline, but at creating an institute that attacks societal problems from a technological viewpoint,” he said in the official announcement. “Many important societal problems in energy or health care or the environment can be addressed by new molecular-level science. When you are trying to solve problems, you need people from different kinds of disciplines. That’s something the Institute for Molecular Engineering can create right from the beginning.”

In his nearly 300 scientific publications, Tirrell has often studied and discussed how the surface properties of polymers are important for the success of biomaterials. Materials “communicate” with their surroundings through their surfaces, and designing new synthetic devices for technological uses requires a firm grasp on this process. As a result, bioengineers have taken inspiration from how natural materials such as mollusk shells and animal tissue solve surface compatibility problems to understand these interactions on a molecular level.

One application of that accumulated knowledge about biomaterials is novel solutions to clinical problems. In a phone interview Monday with ScienceLife about the biomedical goals of the IME, Tirrell talked about how these new technologies will not be merely passive construction materials, but active biological compounds.

“There are going to be ways of using biology not only to make things but also to do things,” Tirrell said. “Therapeutic organisms can be engineered with the tools of modern biology: living devices, if you will, as well as man-made devices.”

One example from Tirrell’s own research career expands upon designing living machines as a sort of multi-functional Swiss Army knife for diagnosing and treating diseases such as cancer and cardiovascular disease. A 2009 paper, published in Proceedings of the National Academy of Sciences, used a self-assembling lipid sphere called a micelle (pictured at right) to target the fatty plaques that form in blood vessels during atherosclerosis. When those plaques rupture, dangerous clots can form and  block blood vessels. To treat those clots, physicians currently prescribe blood thinning drugs that can produce unwelcome side effects, because the drug is not specifically targeted to the clot and acts throughout the body.

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I’ve said it before, but the AAAS Meeting is my favorite scientific conference, a cross-disciplinary feast of research that’s perfect for omnivores of science. As I wait for the meeting to return to Chicago (2014!), I spent the week attending from afar through the many online recaps. Depending on your preferences, you can get your AAAS download from The Economist (writing about alchemy, of all things), Science News, in podcast form from Scientific American, The Scientist, the inside-baseball view of the Knight Science Journalism Tracker, or AAAS itself. Or you can read more focused recaps of a study that suggests being bilingual can protect against Alzheimer’s disease, the debate over how to effectively communicate climate change to a skeptical public, or monkey video-game self-awareness.

The University of Chicago was represented at the meeting by two talks on very different subjects: the future of health care spending, and the history of human evolution. David Meltzer, associate professor of medicine, argued that cost-effectiveness studies must be performed to control surging health care costs in the United States and other countries. Runaway costs can be partially explained by the flood of new technologies and therapies that are dropped into the healthcare market each year, Meltzer argued. While the FDA makes sure that these new technologies are safe for patients, there is less oversight on whether they actually will offer enough clinical value for their often high price tags. Even old methods, such as pap smears to screen women for cervical cancer, have rarely been assessed from an economic perspective, Meltzer said. Yearly pap smear exams are three times as expensive as exams every three years, but increase life expectancy by only 32 hours compared to less regular screening.

“The value of scientific advance and the resources available for it are greatest when we use scientific advances wisely,” Meltzer said.

On the other end of the spectrum from the future of medicine, Anna Di Rienzo, professor of human genetics, spoke about the history of man. Expanding upon her PNAS study from 2010, Di Rienzo presented genetic data found by her method of using environmental differences to find regional variation. In this case, the search ended in sweat: a gene called keratin 77, expressed in the sweat glands of the body, that has a variant more prevalent in hotter regions of the world. That variant may have become popular in tropical populations due its role in cooling off the body, but in the modern world, such environmental adaptations may be counter-productive.

“We know for sure that a lot of these differences are due to environmental risk factors that differ,” Di Rienzo said, according to Science News. “But there’s also a growing consensus that genetic factors may also contribute to these differences in disease or trait prevalence.”

Elsewhere…

Last May, we told you about Zoltan Takacs, who spends half his year chasing venomous animals around the world and the other half studying their poisons in the University of Chicago laboratory of Steve Goldstein, professor of biophysics. The good people at PBS’ Nova series got wind of Zoltan’s exciting adventures, and featured him in an episode this week on the potential of deadly venoms to be re-cast as life-saving medications for diseases such as cancer and heart disease. That’s one of his snake photographs up top.

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What the science of science looks like. (From Evans & Foster, Science, 2011)

Perhaps the biggest science story of the week took place, oddly enough, on a game show. The victory of an IBM supercomputer named Watson over human contestants on Jeopardy burned up the Internet, launching a million jokes about impending robot enslavement of humans and comparisons to 2001’s HAL. Now attention is starting to turn to how the best question-answering computer yet invented can next be applied to targets more meaningful than trivia, including helping doctors make medical diagnoses. But the computational methods behind Watson - essentially a giant word-association machine - might also help the world of science take a hard look at its own biases and flaws, according to an editorial in Science last week by two University of Chicago sociologists.

The key word is “metaknowledge,” James Evans and Jacob Foster write, meaning the assembly of knowledge about knowledge. Though the term is a bit on the Orwellian side - “Metaknowledge results from the critical scrutiny of what is known, how, and by whom” - it’s a name for the acquired instincts used by experienced scientists to read between the lines of scientific research articles. A newcomer to the field may only see the methods and results written on the page, but an experienced reader perceives additional information: the reputation of the author, the institution, and the journal, the history of the subject, and the biases and assumptions inherent to any scientific study.

Evans and Foster propose that the shift toward electronic publication and the growing ability of computers to find meaning in massive amounts of data could enable a formal study of this unwritten metaknowledge - and potentially make science more accurate and efficient. A machine trained to detect patterns in scientific literature could help sniff out a multitude of known issues that distort or impede scientific results. Many of the phenomena listed by Evans and Foster have colorful names, such as:

• the “file-drawer problem” - the tendency for experiments with negative results to go unpublished, biasing the literature toward the experiments that showed an effect
• the “Proteus phenomenon” - when scientists flock to a high-profile finding to gain attention by extending or debunking the original research.
• “ghost theories” - when unspoken assumptions of a field (i.e. the use of undergraduates in most psychology studies) influence the results.

Instead of slowly learning these house rules the hard way through the frustrating and slow process of accumulating scientific wisdom, a metaknowledge machine might make the implicit aspects of science explicit. That could help a graduate student avoid wasting time on experiments that have already been done, or help the government route funding to scientific areas that are truly promising, instead of just popular.

“Metaknowledge could inform individual strategies about research investment, pointing out overgrazed fields where herding leads to diminishing returns as well as lush ranges where premature certainty has halted promising investigation,” Evans and Foster write.

Elsewhere…

The crossover of technology into science and medicine doesn’t have to happen at the level of supercomputers - consumer electronics are also making an impact in the hospital wards. Since last fall, medical residents at the University of Chicago Medical Center have been using iPads on their daily rounds to check test results, view X-Rays and MRIs, and order medications for patients at the bedside. Nesita Kwan from NBC News came out a couple weeks ago to report on how these devices are making medical care more efficient, and how Bill Gates himself responded to one resident’s e-mail.

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Eodromaeus, or "Dawn Runner" (Copyright Todd Marshall)

While ScienceLife was away at the Science Online 2011 meeting two weeks ago, our friends in the University of Chicago News Office tried to sneak a dinosaur story past us. Eodromaeus, the “dawn runner,” is the latest edition to the dinosaur discovery menagerie of Paul Sereno, professor of organismal biology and anatomy, discovered in the fossil dig site of Argentina known as the “Valley of the Moon.” While only four feet tall and roughly 10-15 pounds, Eodromaeus was (as Chicago Tribune great Bill Mullen puts it) a “nasty looking little critter,” a carnivorous predecessor to the T. Rex in a time (230 million years ago) when dinosaurs were not yet the dominant lifeform on the scene. [You can watch a cool time-lapse movie of the reconstruction of Eodromaeus here, as well as an interview with Sereno about the discovery and its significance for the rise of dinosaurs.]

As the excellent fossil blogger Brian Switek describes at the Smithsonian’s Dinosaur Tracking site, the discovery of Eodromaeus rearranges scientific theories about the early days of dinosaurs. A previous discovery of Sereno’s team in the same area, Eoraptor or “dawn plunderer,” was once thought to be an ancestor of the larger meat-eating dinosaurs that came later. But comparing the teeth of Eoraptor and its neighbor Eodromaeus suggests that the former was actually an omnivore ancestor of the more benevolent sauropods, with Eodromaeus near at the top of the T. Rex family tree.

“We’re looking at the dawn of the dinosaur era where the fork in the road is still very narrow in the divergence of plant eaters from meat eaters,” Sereno told the Tribune. “That is why Eoraptor and Eodromaeus look so much alike.”

But as in Hollywood, your 15 minutes of fame are very short in the world of dinosaurs. In the mere two weeks since Eodromaeus was unveiled, another thunder lizard has stolen the spotlight: the hilarious-looking Linhenykus, the “one-fingered” dinosaur. Seriously, imagine trying not to laugh as one of these ran towards you (bear in mind that they were also small enough to “s[t]and comfortably in the palm of your hand.”). As Switek points out at Dinosaur Tracking, a current theory goes that Linhenykus, and other dinosaurs with one pronounced digit, may have used their comedically short arms to dig for ants and termites.

Nabokov’s Hobby

The research of lepidopterist Vladimir Nabokov never quite got the credit it deserved while he was alive and working as curator of butterflies at Harvard’s Museum of Comparative Zoology. Perhaps it was his outlandish ideas, about butterflies migrating from Asia through Siberia and Alaska and down to South America. Or perhaps it was because he was better known as the experimental novelist responsible for Lolita, Pale Fire, and other books. Catching and studying butterflies was a lifelong hobby for the Russian-born Nabokov, but despite publishing at least one manuscript (pdf, found via Carl Zimmer’s twitter) on the evolution of a group of species known as Polyommatus blues, he was largely ignored by the scientific community as an amateur.

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Last weekend, I was one of the fortunate 300 who gathered in Research Triangle Park, North Carolina for the 2011 edition of Science Online. The simplest way to describe Science Online is as a science blogging conference, but the real topic on the table was the broad future of science communication, be it through blogs, podcasts, ebooks, twitter, or plain old paper. Through “unconference” sessions led by panels but driven by audience discussion, workshops, field trips to labs and museums, and good old-fashioned bar conversation, scientists, journalists, and scientist-journalists dissected how science can be best defended and explained in a time where mass media coverage is increasingly scant or poor.

I could spill literally thousands of words on what I learned and discovered at Science Online, but for the sake of my audience, I’ll restrict myself to three subjects most relevant to an academic medical center in the new media environment. For more coverage, see the Columbia Journalism Review’s 30,000-foot view, Ed Yong of Not Exactly Rocket Science on the science-blog echo chamber, and Chris Rowan at geology blog Highly Allochthonous on the elephants of the conference. Or you can wade through the over 10,000 tweets sent from and about the conference.

1) Patients Can Blog Too

The majority of the bloggers who attended Science Online cover science through the lens of peer-reviewed research, government policy, or media criticism. Many of these blogs deal with the long-term picture: how will this laboratory study impact medical treatment in 10 years, or how will climate change policy affect our planet’s future. But a corner of the science-writing world is written by people particularly engaged in what science can do for them immediately: patients fighting serious disease.

As a session on “Patient Blogging as Therapy” proved, social media is a natural fit for patients to share information and support. Dave deBronkart, known on the web as e-Patient Dave, called in via Skype to talk about how his own fight against advanced kidney cancer exposed him to the online world of patient engagement, including the technically-primitive but still-functioning listservs of ACOR. Now, having beat his cancer, he’s the hub of an electronic patient advocacy community that includes other panelists like David Seidman (blogging about his kidney disease and need for a transplant) and Alberto Rocca, who started a website for families of children with the rare lung cancer pleuropulmonary blastoma. deBronkart’s motto of “potent information simply portrayed empowers people” was an inspiring reminder of a different way people use blogs or any other media at their disposal to seek knowledge and truth, and the opportunity for online conversations about health that are two-way streets.

2) A Calm Voice in a Shouting Match

But where will patients, of the blogging or non-blogging sort, receive that potent information? The internet is all about easy access to info on virtually any topic, but the quality of that information often leaves much to be desired. Like the search engine TV commercial, a simple search can be easily drowned out by nonsense and falsities - often, in the case of medical advice, dangerous ones. The magnitude of this problem could be read from the beleaguered company accurate medical information kept in the “Defending Science Online” session: evolution and climate change, two other areas where misinformation very noisily tries to shout down evidence-based knowledge.

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The late December quiet has given way to a post-holiday flurry of exciting research news, most of which I can’t tell you about until next week. But in the meantime, here’s our first weekly roundup for 2011 of the most interesting science and medical news around the web.

Tears for Fears

Scientists have discovered a multitude of ways by which animals communicate through chemical signals, such as those in the urine that dogs use to mark their territory and the path left by ants to guide their compatriots to food sources. But whether such pheromone signals exist in humans has been much more controversial. Martha McClintock, professor of psychology at the University of Chicago, has published many papers showing evidence for communicative signals in human sweat that can influence menstrual cycling, mood, and brain function in other people. But the behavioral effects of human chemical signals have so far been small, producing nowhere near the sensational effects that marketers of “pheromone” perfumes claim on less than reputable websites.

But another mediator of chemical communication in humans may have been traced this week, in a paper published by Science on the ability of women’s tears to affect sexual interest in males. The Israeli study used a hilarious method of collecting their experimental substance, sitting women down in front of sad movies and catching their tears in test tubes (”We obtained negative-emotion tears from 2 donor women who watched sad movies in isolation,” the authors right in scientist-ese). The fluid was then placed under the nose of male subjects, who viewed pictures of women’s faces and rated their attractiveness. As described by Ed Yong at Not Exactly Rocket Science, the males’ sexual interest decreased when exposed to the tears, as compared to being exposed to a control of saline. Differences in brain activity and testosterone levels were also detected while men sniffed the tears of sadness.

Consulted by the New York Times, McClintock said the study “really broadens the possibilities of where signals are coming from,” but expressed skepticism that the tears’ effect would be restricted to sexual behavior. “I have no doubt that it affected sexuality as they report, but I would be very surprised if it doesn’t turn out to affect other emotions in other contexts. Maybe it’s affecting some deeper, more fundamental psychological process that drives the effect that they’re reporting,” she told the newspaper. Other critics have asked whether the chemical signal lies in the tears themselves, or are collected by the tear from the skin as they roll down a subject’s cheeks. The nature of the chemical still remains to be found, but the evidence suggests another entry in the previously hidden chemical vocabulary of humans.

Fraudulent Science, Human Cost

Last year, the infamous 1998 Lancet paper purporting to show a link between the measles, mumps, rubella vaccine and childhood autism was finally retracted after years of criticism for biased selection of subjects and unethical behavior. But the research, led by Andrew Wakefield, went beyond scientific mistakes to fraudulent falsification of data, a new report from the British Medical Journal released this week discovered. Investigative reporter Brian Deer found that Wakefield, who was being receiving payments from a lawyer seeking to file a lawsuit against vaccine manufacturers before he started the study, changed the timeline of autistic symptoms appearing in patients to make it look more like vaccines were the cause. The article is a rigorous and thorough deconstruction of a scientific fraud that has had concrete consequences for children around the world - in the  12 years since the article was published, measles cases have spiked in England and America as vaccination rates have dropped, and other vaccination-sensitive diseases such as whooping cough have also made a resurgence.

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ScienceLife ran 219 posts in 2010, and choosing the best of them is as hard as picking a favorite gene.  So here’s a month-by-month scan of a busy year at the University of Chicago Medical Center, full of exciting discoveries in the laboratory and the clinic. The impact of some of this research is already being felt by patients receiving improved, evidence-based medical care. For other studies, the clinical benefit may be years in the future, and may take unpredictable forms. As a closing message for 2010, we’ll re-quote the recently departed Eugene Goldwasser, whose laboratory research isolating and purifying the hormone erythropoietin has helped millions of people worldwide.

“It is a particularly impressive example of how basic research can pay a dividend that could not be anticipated at the start,” Goldwasser wrote about his life’s work, “and it is a pity that the lesson still has not been learned by those who control public funding of science.”

January: Tong Chuan-He looked at how cancer may result from cells who don’t want to grow up. Scientists studied how sleep affects the language learning skills of starlings (with painstakingly acquired video of the experiment!). Richard Jones combined two laboratory staples - Western blots and DNA micro-arrays - to develop a new method for studying protein networks. While physicians such as Tammy Utset treat patients with lupus, UChicago scientists are looking for the genetic origins of the autoimmune disorder.

February: Many Medical Center employees returned from volunteering with relief efforts in Haiti, and we filmed video interviews with Rex Haydon, Tiffany Cupp, Richard Cook, and Dima Awad on their experiences. Most of the human genome is “junk” between protein-encoding regions, but Marcelo Nobrega developed a way to find important regulatory elements in that genetic sea. Like birds, human learning can be affected by sleep, and Leila Kheirandish-Gozal reported on the impact of obstructive sleep apnea upon learning in children. Can a single protein in the brain create behaviors associated with drug addiction in rats?

March: Everyone knows air travel is stressful, but did you know that eastbound flights cause stronger cortisol changes than westbound trips? The laboratory of Milan Mrksich found a way to direct stem cells to form fat or bone by shaping them into stars or flowers, a brilliant example of bioengineering. Computational neuroscientists discovered how touch is like vision in the brain, knowledge that could be used to someday re-engineer Luke Skywalker’s robot hand. Dartmouth president and Partners in Health co-founder Jim Yong Kim visited to talk about a new, needed area of research: health care delivery.

April: Researchers at the Field Museum and the University of Chicago teamed up for the Emerging Pathogens Project, an effort to find new viruses in animals before they jump to humans. Cardiologist Martin Burke tested out a new type of internal defibrillator device that can go under the skin, instead of into the heart (the clinical trial, reported in May, was a success). In a lecture to the MacLean Center of Clinical Medical Ethics, transplant surgeon J. Michael Millis described his efforts to bring American organ transplant practices to China.

May: A trial testing the erectile dysfunction drug Viagra for a rare, untreatable lung disease failed, but pulmonologist Imre Noth found a silver lining. Lauren Sallan and Michael Coates uncovered evidence of a previously unappreciated mass extinction event 360 million years ago that changed the path of life on Earth. Researchers from the University of Chicago and around the world presented science at the frontier of biotechnology at the annual BIO conference.

June: In a study that is literally the size of an entire country, epidemiologist Habibul Ahsan measured the toll of a tragic, accidental exposure of millions to arsenic in Bangladesh. Putting a gene from fireflies into the pancreas of mice isn’t mad science, it’s an imaging tool that will help study cures for diabetes. Epigenetics, the modifications that turn genes on and off, took off in 2010, and cardiologists Stephen Archer and Jalees Rehman linked one epigenetic factor to pulmonary artery hypertension.

July: Scientists don’t often get to see the fruits of their research in the flesh, but the Celebrating the Miracles gathering of diabetic children weaned off injected insulin thanks to genetic research was a moving exception (video of the event can also be viewed). Another hot topic in science and medicine this year was the use of computational analysis to sift through rapidly accumulating data, topics explored by Gary An and Andrey Rzhetsky. Or you can build a computer model of a brain network to study the dynamics of epilepsy, like neurologist Wim van Drongelen.

August: Air pollution is a problem indoors as well as outdoors in developing countries where dung and firewood are used to cook food - a problem being tackled in a project led by Sola Olopade. A study of the hormonal changes induced by a stressful test revealed a surprising protective effect of marriage and long relationships. Microbiologist Olaf Schneewind’s laboratory developed two new strategies against MRSA, the most-wanted cause of hospital-acquired infections.

September: To study multiple sclerosis, neurologist Brian Popko’ s laboratory developed a new mouse model that can replicate the disease, then spontaneously recover. Meanwhile, a new drug to treat MS, originally isolated from fungus found in wasps, was approved by the FDA and is being studied for broader uses at the Medical Center. The micro-organisms that live in humans were analyzed as part of a “microbiome” study looking at the protective effects of breast-feeding against a intestinal disease.

October: Common wisdom on quitting smoking says to stay away from cigarette-associated cues, but research from psychiatrist Harriet de Wit’s laboratory revealed that abstinence could make craving even worse. A study of how getting a good night’s rest affects dieting results suggested that “sleeping off the pounds” isn’t merely a fantasy. Graduate student Daniel Matute solved a 100-year-old riddle about how quickly new species become reproductively incompatible with each other.

November: In perhaps our favorite study of the year, geneticist George Perry found a way to acquire the genomic information of endangered species from…poop. The evolutionary biologist Leigh Van Valen passed away, but his Lewis Caroll-inspired Red Queen Hypothesis lives on. Sometimes statistics don’t tell the whole truth, as in the curious case of the aspirin paradox - why the cardio-protective drug may actually predict worse outcomes after heart attack.

December: Evolution textbooks may need a rewrite after geneticist Manyuan Long’s laboratory discovered that new genes can be just as essential as old genes. A study by neurobiologist Nicholas Hatsopoulos proved that the only thing better than a thought-controlled device is a thought-controlled device equipped with a robot arm. Ripped from the headlines: microbiologist Jack Miller weighed in on the hype over arsenic-based bacteria, and ethicist/physician/friar Daniel Sulmasy discussed the Presidential Bioethics Commission’s report on synthetic biology.

All told, it was a great year of science and medicine. Let’s do it again in 2011! Regular posting will resume Jan. 3rd. Happy Holidays.

Artist's rendering of the new Eckhardt Center (Courtesy of HOK/JCDA/AJSNY)

Today, the University of Chicago announced plans to construct the William Eckhardt Research Center, an innovative new building along Ellis Avenue that will be home to many researchers in the physical sciences.

But just as newsworthy as the new building is one of its prominent tenants: the Institute for Molecular Engineering, the largest new department launched at the University since the Harris School of Public Policy in 1988. The Institute, called the IME for short, will serve as a bridge between the Physical Sciences Division and the Biological Sciences Division for shared goals in research and education.

But what exactly is molecular engineering? The specific mission of the IME will be set next year when a director is named, but the general direction of this exciting new discipline was summarized last year by a faculty committee appointed to evaluate the IME’s creation. ScienceLife talked to a few of those committee members to learn about what molecular engineering is, what kinds of problems it might solve, and what kind of students it will create.

Biology and medicine is increasingly focused on how small scale interactions are important for both normal function and disease. Simultaneously, engineers grounded in physics and chemistry are looking toward biological systems for ideas and solutions. Increasingly, physical and biological sciences are speaking the same language, said Raphael Lee, Paul and Ailene Russell Professor of Surgery, Medicine, and Organismal Biology & Anatomy.

“On the molecular scale, behavior is described by laws of physics and chemistry,” Lee said “The rules of biology and physics are identical at the molecule scale. That’s where the fields boundaries blur and overlap.”

At this common ground, molecular engineering provides a skill set for the next generation of scientists to address the world’s biggest problems. The knowledge gathered through basic science in biology, chemistry, and physics laboratories can be combined and applied to major issues, such as providing clean water to undeveloped countries, or developing more efficient energy sources.

“This is making the science much more applied: we know how it works, so let’s try to make it better. How do we apply that knowledge to these problems that we see,” said Erin Adams, Assistant Professor of Biochemistry and Molecular Biophysics.

Molecular engineering innovation may also lead to the development of new technologies for medical care. Scaffolds for stem cell treatment might be designed through engineering, chemistry, and biology collaboration. Animals that have evolved natural self-healing abilities could inform the design of materials that repair themselves, which could in turn be used for the design of industrial products and medical devices.

“I think it’s entirely possible that new kinds of tools could be generated in molecular engineering that would have therapeutic implications,” said Julian Solway, Professor of Medicine and Pediatrics. “The problems that we’re addressing are the same problems, and the solutions that we want to find are well-suited to be approached by both camps.”

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Ultrasound imaging is best known for pictures of developing fetuses; 3D is typically associated with monster movies. But when you put the two together and aim the technology at the heart, they create a valuable tool that is changing the way heart disease is treated. Three-dimensional echocardiography is a cutting edge imaging technique used to obtain a detailed look at a patient’s heart in motion, figure out what may be wrong, and determine the best way to fix it.

The high-definition images collected by “3D Echo” can detect holes in the heart, problems with the valves that let blood pass between chambers, and irregularities in muscle contraction and blood flow. Information gathered during an echocardiogram can help surgeons create detailed plans for procedures to correct heart problems and can give them immediate feedback in the operating room after the surgery to make sure it was successful. For the increasing number of procedures that can be performed with cardiac catheterization instead of open heart surgery, a 3D echocardiogram provides live information to help guide cardiologists in their repairs.

“This is progressing very quickly and in many diseases, it really, really changes the way that people think about cardiology,” said Roberto Lang, professor of medicine and the director of the Noninvasive Cardiac Imaging Lab at the University of Chicago Medical Center. “We can look at the heart and tell the surgeon what he or she is going to encounter at the time of surgery.”

At this month’s American Heart Association meeting in Chicago, Lang presented research and participated in panels on the latest uses of 3D echocardiography. Since its submarine-sonar-inspired origin in 1953, the sonogram has been applied to cardiac function in many ways, through 2D images (similar to today’s fetal ultrasounds), through 3D reconstructions built from 2D data, to today’s instantaneous 3D view. Though real-time 3D imaging was only made possible 8 years ago, it is rapidly sweeping into the hospitals around the world, and new uses are still being discovered as the technology improves further.

During the AHA meeting, Lang presented what he calls “fusion imaging,” a combination of 3D Echo and computed tomography (CT) scanning to help determine the best place to implant a pacemaker for restoring normal heart contraction. Another presentation focuses on how 3D Echo can collect information about problems with the mitral valve - the portal between the left atrium and left ventricle of the heart. The precise location of leaks and other abnormalities can be mapped from the same angle the surgeon will see during surgery, Lang said, minimizing surprises on the operating table.

The best way to grasp the value of 3D echocardiograms is to see one, and last year, a production company came to the Medical Center and filmed Lang at work and talking about his field. Watch the results below.

“When we do these studies, we use all the different modalities and integrate them into a simple study,” Lang says in the video. “You want to be a detective and find out exactly what is happening to the patient, so you use all the technologies available and integrate them in order to come up with a good question or a good answer.”

[Thanks to Philips and Tomorrow Media for the video footage.]

Photo by John Amend/Cornell

I’ve always been fascinated with the rock solid bags of coffee bought at the store, which have all the density of a brick until opened, when they crumble into scoopable grounds. Turns out that’s a physical concept at work, known as “jamming transition,” when separate, particulate materials are pushed so close together they act like a solid structure. It turns out jamming transitions are useful for more than just compact packaging, but can also help solve a persistent, basic problem in robotics: how can you make a robot “hand” as good as the human hand at picking up objects?

An answer was published this week in the Proceedings of the National Academy of Sciences by researchers from the University of Chicago, Cornell University, and private company iRobot. The scientists created a finger-free “universal robot gripper” by filling a balloon-like elastic bag with particulate material - such as, yes, coffee grounds - pressing the bag down on to the object, then removing the air from the bag, triggering the jamming transition and creating a perfectly shaped, tight hold. There’s video below, demonstrating some of the objects and functions the device can be used for. But when will they be installed in prize claw machines?

[Coverage from Engadget, Gizmodo, and Wired]

Resurrection of the Beagle

The HMS Beagle was the Royal Navy ship that transported a very special passenger, a naturalist named Charles Darwin, around the world in 1831. What’s left of the ship may currently lie at the bottom of a marsh, but the name has lived on as a favorite for ambitious science projects. First, the Beagle name was attached to the Mars space probe Beagle 2, and now it has been affixed to the University of Chicago Computation Institute’s newest toy: a 150-teraflop supercomputer, one of the 50 fastest supercomputers in the world. Housed at Argonne National Laboratory, this Beagle will sail the seas of data produced by researchers in physics, biology, and medicine.

As discussed previously on ScienceLife, the next wave of science will be less about collecting data and more about actually doing constructive things with it. The Beagle’s maiden voyages will be to help projects such as the Membrane Protein Structural Dynamics Consortium, the UChicago-led effort to study the shape and function of cellular machines. Other immediate uses may be for genomics projects, where scientists have struggled to keep up with analysis of the data created by cheaper and cheaper gene sequencing technology. In the Beagle’s announcement, Conrad Gilliam, UChicago’s dean of research for the biological sciences division, looks forward to a time when electronic medical records provide valuable data for the development of more effective treatments.

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Yesterday we talked about how Kathleen Cagney’s research appeared to reveal an effect of the 9/11 terrorist attacks on the body mass index of people more than a thousand miles away in Dallas. By coincidence, Discover magazine published a book excerpt (from “Origins: How the Nine Months Before Birth Shape the Rest of Our Lives” by Annie Murphy Paul) yesterday that touches on how the fall of the World Trade Center might have caused post-traumatic stress disorder not just in people near the towers that morning, but also the fetuses being carried by pregnant women near the towers. Can PTSD be transmitted from mother to unborn child? And did 9/11 leave a wide swath of medical impact across the country? Fascinating research.

Oh cruel search for alien habitable worlds: new data released at an astronomy symposium this week appears to refute the existence of Gliese 581g, the “Goldilocks” planet that had everyone daydreaming of intergalactic travel two weeks ago. Though the debate over the planet’s existence is far from settled, it’s a quick, nasty reminder that leaping from a handful of data points to bold claims of Earth-like planets and alien life is a dangerous gamble. (Also, Google News hits for original Gliese 581g story = 1407 articles. For the “Gliese 581g may not exist” story = 91.)

As part of the “It Gets Better” campaign reacting to the recent run of tragic suicides by homosexual teenagers, Scientific American’s psychology blogger Jesse Bering begins a long, detailed look at the evolutionary history of suicide. Why would an organism evolve the capacity to kill itself? Bering dials down to insects that are cannibalized after copulation and explains a mathematical equation for suicidal motivation in the first part of his series.

If University of Chicago evolutionary biologist Jerry Coyne is too prolific for you on his blog, Why Evolution is True, you can get a primer on his views regarding the incompatibility of science and religion from his USA Today editorial this week. There were, of course, letters,  and a blog response from Albert Mohler of the Southern Baptist Theological Seminary.

An in-depth Reuters article about the increasing use of cardiac assist devices and the end-of-life ethics questions they raise talks to our chief of cardiac and thoracic surgery Valluvan Jeevanandam, among other experts. For more on the topic, see our post on ethicist Daniel Sulmasy, who has written about when it is ethical for physicians to turn off a person’s cardiac device, knowing that it may hasten death.

Personalized Medicine: The Brake vs. The Accelerator

A recurring theme on the blog - and presumably on every other medicine and science blog - has been the push toward personalized medicine, the utopian future where every patient receives individualized care for a disease or even the genetic risk of disease. But the road to that future world of health care has been slower than some experts anticipated, with disappointing clinical trials, scientific setbacks and regulatory hurdles all acting as speed bumps. Those obstacles are partially why National Institutes of Health director Francis Collins was dinged this week in a New York Times article for promising “a complete transformation in therapeutic medicine” within a decade or two of the Human Genome Project’s completion…ten years ago.

So it was interesting to see Collins’ revised opinion on the timeline for personalized medicine this week in the New England Journal of Medicine, in an editorial co-written with FDA Commissioner Margaret Hamburg. It’s a strange partnership in some ways: the country’s top scientist and the country’s top regulator. The editorial reads accordingly, with a first half marked by the go-go optimism of Collins followed by the “woah, let’s slow down” realism of Hamburg.

Still, there are some interesting initiatives within. Collins gives the glass-half-full version of the New York Times’ Human Genome Project assessment, stating that hundreds of disease-related gene variants have been characterized and are now promising drug targets. The issue, Collins claims is the lack of financial incentives for companies to pursue those targets, something he hopes to fix by allowing the NIH to step in and do the preclinical “Valley of Death” work that scares off pharmaceutical companies. Collins also promises an expanded effort to establish tissue banks and genetic databases from clinical trials and epidemiological studies such as the Framingham Heart Study, to enable better research into biomarkers that predict disease or response to treatment.

On the flipside, Hamburg argues that extreme caution should be employed in approving tests for those very biomarkers. Her argument - that most current tests are inaccurate or misleading - is backed up by the FDA’s recent move to more aggressively regulate test marketed for at-home use. While the editorial offers a table of three tests approved to predict a patient’s response to a cancer drug such as Gleevec or cetuximab, Hamburg writes that some 2,000 genetic tests are currently used by clinical laboratories - some FDA-approved, some not. The editorial promises a genetic testing registry that will offer consumers and physicians information about the tests, but promises that the agency will keep a close eye on tests that “are broadly marketed to laboratories or the public.”

If that sounds all a bit good cop/bad cop, it’s true. The key will be in the balance between the forces pushing personalized medicine forward and those entrusted with testing its validity. As Collins and Hamburg put it, “When the federal government created the national highway system, it did not tell people where to drive - it built the roads and set the standards for safety…We are now building a national highway system for personalized medicine.”

More World Cup Science

When I wrote my World Cup science piece last week, I didn’t realize that several scientists were holding back their timely soccer-science articles until the tournament was in full swing. But sure enough, a flood of new research has crossed the wires in the past week, about everything from the controversial vuvuzela horns to the age-old debate of “soccer” vs. “football.”

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Last month, we told you about a new cardiac defibrillator device that was implanted for the first time in the United States here at the University of Chicago Medical Center. That procedure - performed by Martin Burke, professor of cardiology, on 38-year-old mother of four Brooke Bergeron - was also the first of a global clinical trial that hopes to test the subcutaneous implantable cardioverter-defibrillator (S-ICD) in more than 300 people. But a new medical device doesn’t just jump straight to the world-testing stage; the current trial was built on the foundation of several smaller trials that worked out the kinks of the device and proved its effectiveness in smaller pools of patients.

The data from those trials were published this week in the New England Journal of Medicine, and portray an instructive case study in how a new device is developed and tested without endangering the patient. In trials conducted in New Zealand and Europe over the last 10 years, different configurations of the device were compared, software was refined, and a slow, careful roll-out of the S-ICD in more and more patients was achieved. With a majority of successes along the way, the researchers set the stage for the wider testing of the device currently in progress while exciting many in the field of cardiology.

“This could be a game changer, if indeed this is the direction this technology goes,” Richard Page, president of the Heart Rhythm Society, told Bloomberg News.

Interestingly, the first step was an engineering challenge - figuring out the best configuration for the device’s leads, which both sense the heart’s rhythms and deliver the shock if necessary. The classic implantable defibrillators have an advantage in this respect, since the leads are actually placed inside the heart. But with subcutaneous leads placed under the skin near the sternum, the same task can be accomplished from farther away with a stronger, but still safe, shock. All the same, the device’s designers wanted to minimize the amount of electricity required to reset the heart’s rhythm, and thus tested four different configurations (pictured above) to find the one that performs its function with the least firepower.

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