Photo by Bruce Powell

Yesterday wasn’t just St. Patrick’s Day for fourth-year medical students around the country - it was also Match Day, the tense and celebratory day when aspiring doctors learn the residency program where they will spend their next 3-7 years. At the Pritzker School of Medicine, green-clad students and supporters absolutely packed the hospital’s Billings Auditorium for the big event Thursday morning, cheering their peers as they were called one by one at random to collect their match envelope. In a local tradition, it literally pays to go last, as students throw into an informal prize pot for whoever has to wait and squirm the longest to pick up their envelope (second-to-last gets a Hershey bar as consolation). In the video below, you can see some of that process - including the outcry when the last envelopes are miscounted - followed by the amazing tension-release of the countdown and unison envelope opening.

The numbers from the day are just as exciting as the video. At Pritzker (recently ranked #12 among medical schools by US News and World Report), 110 students were matched in 24 specialties at 46 institutions, including 23 students who will stay with us here at the Medical Center. The most popular specialties for Pritzker students were internal medicine (25% of the class), general surgery (11%), and pediatrics (11%). Nationally, trends continued to shift for the second consecutive year toward primary care specialties such as internal medicine, family medicine, and pediatrics, according to the National Residency Matching Program, a step in the right direction to meet some of the increased demand for primary care doctors expected in the wake of health care reform. MedPageToday’s Kristina Fiore breaks down the numbers.

Podcast 0.3: Transplants, Rock-Paper-Scissors Ecology, and More

We have settled on a name for our young research podcast: Bench to Bedside. However, we are still keeping the training wheels on as we work out the technical kinks and explore the best ways to deliver audio versions of our latest research and medical stories. Please enjoy the third installment of our podcast, featuring a recent coast-to-coast kidney transplant chain that involved the Medical Center, how Rock-Paper-Scissors can explain biodiversity, the fight against indoor air pollution in Nigeria, and the new numbers on the eating disorders epidemic in the United States. As always, we would love to hear feedback on what we’re doing right and wrong at robert.mitchum@uchospitals.edu or dianna.douglas@uchospitals.edu.

Bench to Bedside Episode #0.3 by robmitchum

Elsewhere…

Some people keep ant farms, some people keep multiple flasks of bacteria growing for 13 years (and counting) to study evolution. Ed Yong writes about experiments from Michigan State University that show “tortoise” bacteria can beat out “hare” bacteria over the long run. (And if you’re a science communicator of any sort, do listen to Ed and Carl Zimmer’s “Death to Obfuscation” session from January’s Science Online meeting)

read more

For three weeks starting tonight, the attention of sports fans around the country will be on the brackets of the NCAA Basketball Tournament as 68 teams are methodically reduced to one champion. The process is somewhat similar to evolution, as a combination of direct competition and environmental luck (determined by a team’s seeding and the results in other games) helps whittle down the field in a survival of the fittest fashion - no wonder the bracket is initially set by the NCAA Selection Committee. Nature, it turns out, conducts its own tournaments to determine which species in a given ecosystem will live on and which will go extinct. Only in this game, it’s a little harder to keep score.

Rock-Paper-Scissors is best known as a childhood playground game, one that gets old once the players realize that no clear winner will ever emerge. But that indecisive quality attracted researchers Stefano Allesina and Jonathan Levine to the simple game as a potential explanation for one of ecology’s greatest mysteries: biodiversity. The ability of similar species to occupy similar niches within an ecosystem has long baffled ecologists, since evolutionary competition between the species should eventually produce a surviving winner and an extinct loser. But in systems like the Amazon, thousands of species appear to have struck a truce, peacefully co-existing.

Yet what looks like peace on the surface may merely be the result if constant rock-paper-scissors-like tournaments behind the scenes, Allesina and Levine report this week online at Proceedings of the National Academy of Sciences. The game is an example of an intransitive relationship, where none of the three options can achieve total dominance: rock beats scissors, scissors beats paper, and paper beats rock. That kind of relationship has been observed in nature, for trios of lizards or bacterial species. But what about intransitive relationships with more than three participants - the rock-paper-scissors-dynamite and beyond of nature?

“No one had pushed it to the limit and said, instead of three species, what happens if you have 4,000? Nobody knew how,” said Allesina, assistant professor of ecology and evolution at the University of Chicago. “What we were able to do is build the mathematical framework in which you can find out what will happen with any number of species.”

Allesina and Levine built their model to simulate the outcome when different numbers of species compete for various amounts of “limiting factors” with variable success. An example, Allesina said, is a group of tree species competing for multiple resources such as nitrogen, phosphorus, light, and water. Some trees may be better at obtaining nitrogen from the soil, while others may have better access to water or light.

When such a complex model is simulated over time, some weaker species lose and go extinct. But many species remain - some common, some rare, but all balanced in a state of equilibrium. With each additional limiting factor added into the model, more species are able to survive, producing robust biodiversity despite constant competition.

“What we put together shows that when you allow species to compete for multiple resources, and allow different resources to determine which species win, you end up with a complex tournament that allows numerous species to coexist because of the multiple rock-paper-scissors games embedded within,” said Levine, professor of ecology, evolution & marine biology at the University of California, Santa Barbara.

read more

Sen. Dick Durbin tours Argonne National Laboratory with Rick Stevens, Professor of Computer Science (photo courtesy of Argonne)

In Washington, the fight over budget cuts is well underway, as a Republican majority in the House and a Democratic majority in the Senate tussle over the best way to reduce a multi-trillion dollar federal deficit. The first bill of the new House, H.R.1, set federal appropriations for the rest of fiscal year 2011 (ending in September) and snipped $61 billion from the budget, predominantly from discretionary domestic spending. One target of those cuts would be the National Institutes of Health budget, which would lose roughly $1.6 billion of its $32 billion budget for funding scientific research in the United States.

As you might expect, this news was not welcomed by Chicago-area researchers, who turned up in lab coats to support a news conference by Sen. Dick Durbin last Sunday at Northwestern University’s downtown campus. Durbin vowed to fight against the cuts as H.R.1 is discussed in the Senate, saying that interrupting the funding would slow progress toward new treatments for diseases such as AIDS, diabetes, and cancer. (video here)

“When you put these research projects on hold, you can’t ask the laboratory mice to take a nap,” Durbin said. “You can’t ask the cultures to stop growing - we’ll get back to you at the end of the fiscal year. And you can’t expect the professional researchers, the men and women who have dedicated their lives to medical research, to have certainty that next year they’ll have a job.”

Researchers from each of the major Chicago academic hospitals appeared at the conference and talked about how the proposed budget cuts could harm their own projects. Michelle Le Beau, director of the University of Chicago Comprehensive Cancer Center, discussed the biomedical research underway at UChicago thanks to the nearly $300 million in NIH funding received this year and last. Le Beau focused in on her own research examining therapy-related acute myeloid leukemia - a “very cruel and ironic” cancer caused by the chemotherapy and radiation treatment of a prior tumor. Any job losses that follow from NIH cuts could break up the expert team she has formed to study causes and treatment of the disease, she said.

“A lapse in funding will result in dismantling our highly specialized research team, and this leads to a loss of capability, because it takes years to assemble these teams again,” Le Beau said. “These are individuals who have trained for years to apply their extraordinarily unique skills. They have families to support and bills to pay.”

read more

Janet Rowley rides her bike in front of the Gwen & Jules Knapp Center for Biomedical Discovery. (Photo by Jason Smith)

It never gets old hearing the story of how Janet Rowley found the first genetic cause for cancer in the early 1970’s, so it’s a delight to read this week’s New York Times conversation between Rowley and reporter Claudia Dreifus. The interview retraces Rowley’s steps from working with mentally disabled children at Cook County Hospital through her almost accidental training in cytogenetics and her most famous discovery - the chromosomal translocation that causes acute myeloid leukemia. While Rowley has been repeatedly honored for her contribution to the concept of cancer as a genetic disease (and continues to remain a yearly subject of Nobel speculation), she remains understated in looking back at her life’s work.

“People accuse me of being too humble. But looking down a microscope at banded chromosomes is not rocket science. If I hadn’t found it, somebody else would.”

To go with the New York Times interview, the University of Chicago Facebook page put out a call for questions to Rowley, and have received some interesting thoughts. There’s still time to get your question in there for one of the most respected cancer researchers in the United States and a key figure in the history of genetic disease research. [See also Lisa Belkin's post on the New York Times parenting blog about recent research on barriers against women in science, in which she cites Rowley's example.]

Elsewhere…

As a kid growing up in the Chicago suburbs, I remember being trained in emergency procedures for the seemingly infinitesimal chance of a Midwest earthquake originating in the New Madrid fault in Southern Missouri and Illinois. But despite recent rumbles in the Chicago area, it’s been 200 years since the last New Madrid quake to get into the 7’s on the Richter Scale, according to this nice New Madrid By the Numbers post by natural science blog +/- Science. Perhaps those school drills weren’t so crazy after all - the blog points out that in 2003 the U.S. Geological Survey estimated a 7 to 10 percent chance of a major New Madrid earthquake in the next 50 years.

Blue penguins, and what they have to say about how feather color is produced.

Things are finally getting back to normal in Chicago after last week’s blizzard, but amazing stories of Chicagoans helping each other out during the storm continue to pop up. Here’s one story, from Medill Reports, of a woman who delivered her baby at the Medical Center in the midst of the blizzard Wednesday.

Hillary Rosner, one of the many cool people I met at Science Online 2011, has a new blog at PLoS with the excellent name of Tooth & Claw (from Tennyson’s “Nature, red in tooth and claw,” often associated with natural selection). In her first post, she brings up a fascinating fruit fly name from our own Manyuan Long - “jingwei,” named for a Chinese myth of a woman who drowns and is reincarnated as a bird to have her revenge on the sea. As the 1993 study describes, the gene was once thought to be a “pseudogene” without function, but was later revived and used by Long to study the origin of new genes - an area he still studies today.

Finally, what better way to prepare for Valentine’s Day than reading Brian Switek’s article on dinosaur sex at Smithsonian Magazine. I love the lede.

photo by Cheryl Reed

A quick round-up of science around the web to end a busy, snowy week:

The “facepalm” has become a popular piece of the internet lexicon, alongside peers such as “epic fail” and “OMG.” But, as Ed Yong writes at Not Exactly Rocket Science, humans aren’t the only ones who make the universal expression of disgust and embarrassment. A group of Mandrill monkeys in an English zoo have started to make the expression. However, he writes, they may be signaling something different than facepalming humans: “Why are they doing it? It’s unlikely that they’ve found something stupid on the Internet.”

Jerry Coyne posts another example of purportedly human behavior observed in animals with the green heron - a bird that not only has a crazy expandable neck, but also has been filmed “fishing” by using a piece of bread as bait (yes, there is video). A webpage he links to at Tufts University contains a few other examples of bird tool use.

Earlier this week, in discussing his study on sleep and child obesity, David Gozal theorized that the modern family structure of two working parents has disturbed sleep routines for adults and children alike. Another study, released this week, appears to support that hypothesis, as a team including Ariel Kalil of the Harris School for Public Policy found an association between working mothers and their children’s body-mass index. Lead author Taryn Morrissey of American University stressed to Time magazine that the study is not meant to bash working moms, but rather to remind busy families about the importance of maintaining sleep schedules.”If all moms were to leave the workforce tomorrow, it wouldn’t solve childhood obesity,” she says.

With the Super Bowl coming up this weekend, allow us to point you back to a post written last year at the start of the World Cup about heart attacks in sports fans while watching important games. Some new research has come out in time for this year’s Big Game, including a study of LA fans during the 1980 and 1984 Super Bowls profiled by Ferris Jabr at New Scientist.

When you’re a hospital, you can’t call a snow day. If you’re curious as to how the Medical Center handled this week’s third-snowiest Chicago blizzard ever, here’s your answer: a lot of cots, and free lunch.

University of Chicago chemistry post-doc Niels Holton-Andersen views evolution as a “beautiful, amazingly huge experiment” that has produced elegant solutions to biological problems. His latest discovery is a self-healing, powerful adhesive produced by mussels, published last week in the Proceedings of the National Academy of Sciences. Mussels secrete the substance to stick to rocks in rivers and lakes, and researchers found that tweaking the pH of the adhesive can turn it into a self-healing gel, “kind of like Silly Putty,” Holton-Anderson said. The potential of the discovery was covered by “Green movement” blog Tainted Green.

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.

read more

A male (left) and female (right) splendid fairy-wren in Australia. (photo by Mitchell Walters)

The Friday the 13th and Nightmare on Elm Street movies aren’t typically thought of as mating strategies. But putting on a scary movie is a trick as old as drive-in theaters for encouraging one’s date to jump in fright and snuggle in just a little bit closer. Birds, so far as we know, aren’t into horror movies, but field research published late last year by two University of Chicago researchers suggests that the “scary movie effect” used by humans may also be a mating strategy for some bird species.

Stephen Pruett-Jones, associate professor of ecology and evolution, has been traveling to Australia for more than 20 years to study the splendid fairy-wren, a bird with a very progressive social life. While splendid fairy-wrens are socially monogamous, with males and females forming lifelong pairs, they are sexually promiscuous, mating almost entirely with partners outside of their home relationship. Fairy-wrens also form unusually complex family groups, with young birds sticking around the home territory to help their parents raise offspring rather than flying off to start their own family as soon as possible.

Over the course of studying these unique behaviors, Pruett-Jones and others observed another odd quirk of the splendid fairy-wren. When disturbed by the call or sight of a predator or threat - such as the butcherbird, or a clumsy human researcher - the small, blue males of the species don’t fly away and hide as you might expect, but sing their own distinct call, called Type II song. While a graduate student working with Pruett-Jones, Emma Greig studied the timing of those calls and found that the male fairy-wren responds almost instantaneously to the song of his predator.

“The male begins his Type II call immediately after the butcherbird begins to call, so they’re basically right on top of each other,” Pruett-Jones said. “It sounds like a duet.”

But the purpose of that communication remained mysterious. Was it an alarm call to other fairy-wrens in the area? A display of their bravery and physical fitness to attract mates? Or an effective means of capturing the attention of any females in the area?

The latter theory was tested by another round of field experiments, conducted at Brookfield Conservation Park in South Australia. Using an iPod filled with bird-call audio files, Greig played different songs for female fairy-wrens, using Type I song (a territory-marking call), butcherbird songs, and Type II songs in various combinations. The females responded most strongly when the butcherbird-Type II song combination was played (listen below), as measured by looking in the direction of the call and responding with their own song.

Butcherbird and Male by robmitchum

“We have shown that females do, in fact, become especially attentive after hearing butcherbird calls,” said Greig, currently a postdoctoral researcher at Cornell University. “So, it seems that male fairy-wrens may be singing when they know they will have an attentive audience, and, based on the response of females, this strategy may actually work!”

read more

Even before the very rules of life were changed by the discovery of an arsenic-based microbe in a California lake (or were they? More next week.), this week seemed to be full of strange and interesting science involving animals. While ScienceLife works on a bunch of research that is under embargo until later this month (disclaimer: none of them involve extraterrestrial life), here are a few bullet-pointed studies that inspired awe and wonder this week.

• Optogenetics is the technique of creating mutant mice with cells that can be modulated with flashes of light, which is awesome. For example, a scientist can introduce a gene into a mouse strain that makes motor neurons sensitive to light, and when light is shined at those neurons, the mouse starts running. Now, researchers from Stanford and UT Southwestern have used optogenetics in the frontal cortex of a mouse strain, and found a way to produce anti-depressant-like effects (pdf). As covered by David Dobbs at Wired, the technique may offer a new non-invasive way of treating depression way down the line; for now, optogenetics requires a brain implant, which is less than ideal clinically.

• Telomeres, the long repeated sequences at the end of chromosomes, were a fashionable scientific buzzword before optogenetics was even a glimmer in science’s eye. With their companion enzyme telomerase, telomeres were hyped to be the genetic key to the  “fountain of youth,” the biological source of the cell damage that accompanies aging. But despite being the subject of last year’s Nobel Prize in Physiology or Medicine, the excitement about telomeres seemed to have faded out. But an exciting new study published in Nature this week may reignite that flame, as scientists at Harvard reversed the premature aging of a special mutant mouse with telomerase treatment. Wired, Ars Technica, and the Wall Street Journal discussed this “Ponce de Leon” effect, but Discover blog 80beats urges patience for those waiting on anti-aging pills.

• Scientists have long used animal models to study the neurobiology of fear in laboratory settings. But how do you realistically recreate situations that would cause a rat to be scared in the wild in the predator-free world of the animal facility? For one group of scientists, the answer was Robogator, a simulated predator designed to leap out at rats as they moved foraged for food in their lab environment (you can download video clips here). Researchers looked at how close the rat would approach Robogator before and after a lesion of the amgydala, a brain region thought to be involved in fear response. Before the lesion, the rats would only get food 10 inches or less from the entrance to their chamber, but after the lesion, they would go as far as 50 inches, sometimes even approaching and investigating the robot (video) without fear.

• Here’s a novel effect of environmental pollution upon wildlife: when ibis birds of South Florida are exposed to the most potent form of mercury, they opt for homosexual pairings over heterosexual matches.

Fangs You Very Much, Evolution

Where did the snake get its fangs? It sounds like the lead-in to a Rudyard Kipling Just So stories, but it’s a legitimate evolutionary biology question about one of nature’s deadliest weapons, one that goes back 20 million years ago to the oldest snakes in the fossil record. But even those ancient snakes had fangs similar to the poisonous snakes of today, with a hollow tube running through the tooth to inject venom into some poor prey like a hypodermic needle. How snakes (and other venomous reptiles) evolved such an elegantly dangerous mechanism was a mystery, until a new study published this week by University of Chicago’s Jonathan Mitchell and colleagues.

To study the evolution of snake fangs, Mitchell and his team were forced to go to a non-snake reptile - the mysterious Uatchitodon, a roughly 200 million year old reptile known only by its teeth. But in this case, the teeth were what the scientists cared about, and they compared the dental fossils from Uatchitodons found in Virginia, North Carolina, and Arizona. Interestingly, the teeth of older specimens appeared to show a kind of proto-fang, with a “canal” running down the outside of the tooth for the delivery of venom. This style of venom delivery is more similar to the modern-day Gila monster, the authors wrote, which “chews” its venom into its victims (shudder).

Later Uatchitodon teeth display a new form more similar to modern snakes, with the once-external groove now hidden inside the tooth. “This fossil really suggests that you can’t get hollow fangs any other way,” says co-author Wolfgang Wüstertold Nature News. Indeed, modern snakes even demonstrate a fast-forward highlight reel of this evolution, with grooved “replacement fangs” that give way to the mature, tubular model. It’s also a demonstration of the kind of transitional, evolutionary process that intelligent design supporters absolutely hate, demonstrating that the highly successful fang mechanism didn’t just appear out of nowhere, but through a series of intermediate steps that were also functional in their own right.

Another Bridge to China

The effort to help Wuhan University revise their medical school curriculum, described here yesterday, is not the only current collaboration between the University of Chicago Medical Center and Chinese hospitals. Last month, a delegation from Comer Children’s Hospital and the Department of Pediatrics visited Shanghai, where they signed an agreement establishing an educational, clinical, and research collaboration with Shanghai Children’s Medical Center (SCMC).

The relationship between the two pediatric hospitals sprouted from a training program started by Donald Liu, professor of surgery at Comer, who has taught minimally invasive techniques to surgical fellows from the Shanghai hospital for the last 10 years. For a disease called gastroschisis, where an infant is born with their bowels on the outside of their body, Liu’s instruction helped SCMC improve survival rates from 30 percent to 95 percent in 10 years. The success of that informal program and a successful visit from SCMC leadership to Chicago last year inspired the expanded collaboration, which will begin next year.

read more

Many people consider human evolution to be a done deal, something that happened in our distant, wild past. But as Nicholas Wade wrote last week in the New York Times, there is increasing scientific evidence that natural selection has continued to act upon humans, producing observable evolutionary changes as recently as 3,000 years ago. Studies have found that everything from high altitude tolerance in Tibet to dry earwax may have evolved in relatively recent human history, producing subtle but significant population differences in the frequency of certain rare gene variants.

One of the genetic approaches cited by Wade in his article is the work of Anna Di Rienzo, professor of human genetics at the University of Chicago. In a paper published earlier this year in the Proceedings of the National Academy of Sciences, a group from Di Rienzo’s laboratory led by graduate student Angela Hancock went looking for recently evolved human genes in an unusual way. Their results uncovered new ways humans evolved in the recent past, with consequences still felt in our modern age of obesity.

Many genetic studies take an intentionally “naive” approach to such a genetic hunt, comparing gene variants between regional populations with no preconceptions so as not to bias the data. But sometimes a little bias doesn’t hurt; in fact, it may help find differences that fall through the cracks of a broad, unbiased sweep. Hancock and colleagues hit upon the idea of filtering their comparisons by predictable selective pressures expected to drive evolution, such as ecology and diet.

“A lot of the studies done before have been done in a way that was sort of agnostic to the selective pressure,” Di Rienzo said. “We are using aspects of human environments to learn about natural selection and the way humans adapted specifically at genetic level. We use genetic as well as ecological data, and we think that this combination allows us to tap into a set of genetic adaptations that are not accessible by other studies.”

To do this, the team took a particular variable expected to drive evolution, such as polar ecoregion. Because modern humans first arose in the tropical temperatures of Africa, those populations who migrated to a colder environment would be expected to need dramatic genetic changes to survive. So the researchers (using data from the Human Genome Diversity Project, the International HapMap Project, and their own original sequencing) compared the genomes of polar populations against non-polar populations, to see if it revealed specific gene variant differences.

Indeed it did. Several genes were found to appear at different frequencies in the polar populations, and most were found to have the kind of function one would expect to be selected for in a cold environment. Genes that helped people regulate body temperature, for instance, were more likely to have changed in a polar population. Energy metabolism also appeared to have been selected for, with the genes for enzymes that degrade sugars showing differences. The results lined up nicely with a 2008 paper by Hancock and colleagues that used a different analysis method to detect a relationship between climate and genes associated with metabolic disorders.

read more

Photo from Island Adventures (biobay.com)

Bioluminescence has become an important tool in the laboratory, with the glowing components of jellyfish and fireflies applied to help scientists visualize and manipulate cells that don’t normally produce light. I’ve toyed with neurons expressing green fluorescent protein (taken from the jellyfish Aequorea victoria under the microscope, and have caught a few lightning bugs in my day. But until last week, I’d never swam in bioluminescence, or seen it sparkling down my arm like I had dipped my hands in stars. It was, um, pretty cool.

My opportunity to swim with the bioluminescents occurred on the island of Vieques, 8 miles off the coast of Puerto Rico. Formerly the site of a U.S. Navy base and controversial bomb testing, the isolated island remains largely undeveloped and undisturbed, with long, empty beaches and diverse wildlife. That has made Vieques a popular site for eco-tourism, and the “Bio Bay” is considered one of the island’s top attractions. Though there are other bioluminescent bodies of water around the world, many of them have found their glow dampened by both light pollution and regular pollution - in some cases, the ironic result of gas-powered boats used for tours of the waters.

But the single-celled dinoflagellates, called Pyrodinium bahamense, of Vieques’ Mosquito Bay have continued to flourish, thanks to the bay’s remote location and careful handling by the local tour operators. My wife and I opted for the pollution-free electric pontoon boat ride from a company called Island Adventures, founded by a former science teacher and the first company to offer Bio Bay tours on Vieques. Unlike the kayak rides also offered for tours of the bay, the boat ride included the opportunity for swimming in the bioluminescence, an opportunity we could not pass up.

One of the intriguing qualities of Vieques is the odd mix of environments nestled against each other on the island: one bay would be humid and still, while walking 10 minutes to the next bay would find a dry and breezy environment. Mosquito Bay is still another micro-climate, surrounded by mangroves and connected to the ocean by only a small opening. That combination creates the perfect swimming pool for Pyrodinium bahamense, which feast on vitamin B12 from leaves dropped by the surrounding plants and grow to concentrations of 700,000 per gallon. When disturbed, the plankton spark a glow through a reaction of the chemical luciferin and the enzyme luciferase - the same elements used by University of Chicago scientists to monitor pancreatic beta cell regeneration in diabetic mice. 

Surprisingly, the scientific literature on Pyrodinium bahamense is pretty sparse - scientists have isolated and genetically transferred luciferin to a wide range of organisms, but the natural purpose of the plankton’s glow remains a mystery. A 1969 paper studied Pyrodinium and two other species of bioluminescent microorganisms in the laboratory and in nature, finding that P. bahamense can produce a glow up to 4,000 times it’s size. But the authors conclude, “there does not appear to be any selective advantage to the bioluminescence of dinoflagellates.” A different variety of P. bahamense has also been implicated in cases of puffer fish poisoning in Florida and elsewhere, through the production of a chemical called saxitoxin which blocks sodium ion channels. The variety found in Mosquito Bay are thought to be nontoxic - or at least I hope.

Just getting to the bay, which involved a loud, crazy ride through thick vegetation on a rickety old school bus that had to carefully navigate the unpaved, pothole-ridden “road,” was quite the experience. And swimming in a pitch-black bay (during a short window when the full moon was behind thick clouds) was a bit on the frightening side. But producing hazy-blue clouds of light with every movement of one’s limbs quickly changed fear to wonder, as did the strangely discrete points of light that the dinoflagellates produced while dripping off my hands. The tour guide called it “one of the best ways to directly experience nature,” and I had to agree - even when my wife was stung by a jellyfish, an even more direct experience. Immersing one’s self in biology for a tangible, wondrous few minutes is an unforgettable, almost indescribable reminder of the natural, microscopic world ever present around us…even if it occasionally bites back.

Lauren Sallan and Michael Coates in the lab (photo by Jason Smith)

In the Devonian Period of roughly 400 million years ago, fish were the masters of Earth, filling the seas and rivers with enormous diversity from the 30-foot-long Dunkleosteus to lobe-finned fishes like the modern lungfish. Then, 359 million years ago, something happened. The fossil record tells a clear before-and-after story: Dunkleosteus and its family members, the placoderms, disappear, and the ray-finned fishes that we currently think of when we think about fish went from underdog to dominant. Shortly thereafter, a few survivors figured out how to crawl onto land, and the rest was vertebrate history.

For paleontologists, extinction events are the chapter markers in the story of life, marking profound shifts in the course of evolution. Scientists have long focused on one such marker occurring near the end of the Devonian Period: the Kellwasser Event, considered one of the “Big Five” extinctions in Earth’s history. But evidence for the Kellwasser Event 374 million years ago was based on invertebrate fossils such as clams and mussels, which are abundant and easy to find. The vertebrate fossil record of the time, consisting largely of fishes, is less complete, making it difficult to do the detective work necessary to pinpoint a critical extinction event.

That is, until now, when Lauren Cole Sallan and Michael Coates applied analytic techniques from the field of ecology to a richer dataset of vertebrates fed by recent fossil discoveries. The research, published today by the Proceedings of the National Academy of Sciences, looked at the pattern of vertebrates in the late stages of the Devonian Period, and found a different chapter break - not at the Kellwasser Event, but at the “Hangenberg Event,” 15 million years later.

What’s more, the global species shakeup that resulted from the Hangenberg Event would set the stage for the evolution of all modern vertebrates, including humans. By significantly reducing the species pool, the extinction created a bottleneck effect that allowed a small set of survivors to re-diversify and re-populate.

“There’s some sort of pinch at the end of the Devonian,” said Coates, professor of organismal biology and anatomy at the University of Chicago. “It’s as if the roles persist, but the players change: the cast is transformed dramatically. Something happened that almost wiped the slate clean, and, of the few stragglers that made it through, a handful then re-radiate spectacularly.”

“Everything was hit, the extinction was global,” said Sallan, a graduate student and lead author of the paper. “It reset vertebrate diversity in every single environment, both freshwater and marine, and created a completely different world.”

read more

flickr photo by fourstuarts

Last week was Earth Day, and panels, celebrations and events were held all across the University of Chicago campus. On the Medical Center side of campus, I attended a talk that wasn’t technically a part of the Earth Day blitz, but which nevertheless offered an elegant environmental solution applying the latest genetic tools to a farming trick almost as old as agriculture itself.

For thousands of years, farmers have employed crop rotation to keep their soil from being depleted of essential nutrients, particularly nitrogen. One group of plants long known to be particularly useful for this function are the legumes, such as peanuts, alfalfa, blue bonnets (pictured at right), or soybeans. As Sharon Long, professor of biological sciences at Stanford University explained in a lecture last week, the nitrogen-fixing talent of legumes lies in a strange partnership between the plants and bacteria - a symbiotic relationship that essentially creates tumors on the plant’s roots.

This fascinating symbiosis is the focus of Long’s research, which she presented in the 5th annual Margot and Robert Haselkorn Visiting Lectureship. Robert Haselkorn, a professor of biochemistry and genetics at the University of Chicago, studies bacteria with the ability to fix nitrogen - the process of converting nitrogen into bioavailable ammonia. So Long was a logical invite, as she has dedicated her work to decoding the genes and signals that allow legumes to be nature’s soil saviors.

The environmental aspect comes in with how most modern farms replenish the nitrogen in their soil: fertilizer. To create artificial fertilizer requires extreme heat, which is typically generated with fossil fuels. Besides gobbling up a dwindling natural resource (3-5 percent of natural gas goes to fertilizer manufacture), the process also makes fertilizer prices sensitive to fluctuations in fossil fuel prices. That can lead to food shortages, Long said, as the price of fertilizer becomes too much for farmers in poorer countries to purchase and use, leading to nutrient-depleted soil.

However, legumes offer a potential natural answer to that problem, Long said. When particular species of bacteria infect the plants, they form “root nodules” - tumorous growths that enable the bacteria to harness the plant’s photosynthetic energy for the fixation of nitrogen.

“Nitrogen fixation cannot be carried out by any eukaryote; only bacteria can,” Long said. “It’s not an accident that so many legumes have big, fat, whopping, protein-rich seeds. It’s because for legumes, nitrogen is not a problem, and that’s due to this symbiosis.”

read more

An African Pygmy Kingfisher (Ispidina picta) from the Malawi expedition. (photo by Jason Weckstein)

The scenario played out last spring when “swine flu” suddenly became a household name. As public health agencies sprung emergency policies into place, scientists set about tracing the new H1N1 virus back to its source, following it from person to person and eventually to the animals where it originated. Understanding how the virus’ genes mutated in pigs could help scientists determine how it jumped to humans, and give clues as to the most effective ways to fight the disease. But in the time it took to reconstruct the origins of swine flu, thousands and thousands of people were were newly infected with the virus.

Fortunately, last year’s novel H1N1 virus ended up fizzling out into a run-of-the-mill flu - still deadly in a small percentage of people, but not the runaway killer it threatened to be in its earliest days. But we might not be so lucky with the next disease to jump from animals to humans, so monitoring potential threats before they crossover is a scientific priority. While the genetic sequences of more and more organisms are cataloged every day, the viruses, bacteria and parasites those organisms living inside those animals have barely been characterized.

That knowledge gap is the target of the Emerging Pathogens Project, a collaboration between scientists at the University of Chicago and the Field Museum announced Tuesday morning at the museum’s very cool DNA Discovery Center. Blending the centuries-old practice of gathering animal specimens on field expeditions and the bleeding-edge technology of large-scale genomics, the project hopes to give scientists advance warning and knowledge about tomorrow’s epidemics.

“We plan to treat each one of these animals as an ecosystem in and of itself,” said Shannon Hackett, head of the bird division at the Field Museum and co-leader of the project. “We’re really interested in what lives in and on these organisms.”

Those animal ecosystems were collected during an expedition last fall in the African country of Malawi, a trip that brought back roughly 1,100 bird and mammal specimens. A sampling of those (pictured above) were on display at the announcement of the project; just one shelf from the tens of thousands that store critters of all types in the museum’s vast collection facilities. In categorizing those specimens, the museum has moved increasingly to genetic analysis, but the Emerging Pathogens Project brings those efforts to a much larger scale.

That’s possible thanks to the genomics infrastructure established by Kevin White, director of the University’s Institute of Genomics and Systems Biology and Hackett’s leadership partner in the Emerging Pathogens Project. Having previously launched massive projects to study genetic regulation and the genetic makeup of tumors, White said there was still time to take on another scientific challenge. Gesturing at the DNA laboratory that was the backdrop for Tuesday’s event, White aid that the high-throughput sequencing technology now available could do an amount of work equivalent to several million of such labs.

read more

A Familiar Idea of the Year

One of my favorite year-end wrap-ups is the New York Times Magazine “Year in Ideas” issue, a far-flung digest of creative innovations across multiple fields. This year’s issue comes out on Sunday, but is already viewable online, and a sneak-peek led me to a familiar idea - Stefano Allesina’s model of ecological food webs based on Google’s search engine algorithm. We wrote about Allesina, an assistant professor of evolution and ecology, and his research back in September, as did a lot of media outlets who couldn’t resist the Google angle, but it’s great to see his work receiving even more prominent attention. Excitingly, the blurb talks about how some researchers are looking to apply Allesina’s Page Rank-based model to other topics, such as financial markets and cell signaling. And there’s a really snazzy graphic too!

There’s other great science stuff in the Ideas issue, such as how named cows produce more milk, a glow-in-the-dark dog, and how to write music for animals (and why tamarin monkeys prefer Tool and Metallica)

A Plague of Earworms

Speaking of music science (my favorite topic of all), there has been a flood of interesting articles on the science of music lately, including an entire issue of the journal The Psychologist devoted to the topic. From that issue, I learned that:

• “fans of rock and rap were more likely than others to consider suicide and to self-harm,” but “thoughts of suicide and self-harm precede an interest in rock.”
• Various studies have found an effect of music upon variables such as foot pain, pulse, blood pressure, chronic pain, stress hormones and even allergic responses
• Dogs like Beethoven more than Black Sabbath: “The classical music was arguably the most soothing, and it is interesting that it led to the dogs spending more time resting, more time quiet, and less time standing. In contrast, arguably the least soothing music, heavy metal, led to more time barking.”

Another fascinating scientific study of music has to do with a phenomenon common to most people: earworms, otherwise known as having a song stuck in your head. These crafty creatures, also known variably as stuck song syndrome, brainworms, or involuntary musical imagery, have been featured in popular books on the brain and music such as Daniel Levitin’s This is Your Brain on Music and Oliver Sacks’ Musicophilia, but have been reported as far back as Mark Twain in an 1876 Atlantic Monthly article. However, despite all this attention, there is very little scientific data about earworms, other than some vague notions that they may be related to obsessive-compulsive disorder, may be more common in musicians than non-musicians, and may be more commonly associate with jingles and TV show themes than other types of music.

read more