In the aftermath of a mass extinction, nature tends to get creative. Those lucky species that survive often explode with Seussian abandon into a diverse array of shapes, sizes, and behaviors, capitalizing upon the ecological opportunities left available by their less fortunate peers. Usually, the oddities produced by these “adaptive radiations” are whittled down by natural selection to only a few surviving forms. But evolutionary biologists are interested in the course these radiations take — the dynamics that result when nature hits the “randomize” button.

Scientists have tried to understand the order underlying this chaos by studying modern animals that have established broad diversity, such as the immense cichlid family of fishes (which encompasses over 1,000 documented species) or Darwin’s finches of the Galapagos islands. But these studies can only work backwards from the species that exist today. To watch an adaptive radiation unfold, a better source is the fossil record, as the University of Chicago’s Lauren Sallan and the University of Oxford’s Matt Friedman discovered in a recent journal article for Proceedings of the Royal Society B.

Sallan and Friedman used fossil databases from two prehistoric mass extinction events: the Hangenberg event, of roughly 359 million years ago, and the end-Cretaceous extinction, which ended the age of dinosaurs. By measuring how surviving fish species changed body shape and size after these ecological disturbances, the researchers could test two common theories of adaptive radiation inspired by studying surviving species. One model proposed a free-for-all “burst” of divergence followed by a long period of relative stability. Another, sometimes known as the “general vertebrate model,” introduced the idea of staged divergences, with habitat-driven changes in body type preceding diversification of head types.

“There hadn’t been any tests of these things using fossils,” said Sallan, a graduate student in the Department of Organismal Biology and Anatomy. “You have all these analyses of diversification, yet not one of them goes back to the fossil record and says what’s happening at this time period, and the next time period, and the one after that.”

When Sallan and Friedman looked carefully at their data, they didn’t find evidence for either of the pre-existing theories. Instead, they saw a staged radiation that started not tail-first, but head-first, with surviving species initially trying out a wide range of head shapes attached to similar bodies. The driver of this diversity may have been a simple factor: food. Faced with far less competition, the surviving fish evolved new types of teeth, jaws, and heads to take advantage of the expanded menu suddenly available. Later, once head shapes stabilized, different body types from broad and flat to thin and eel-like appeared as new species adapted to their surroundings.

“It seems like resources, feeding and diet are the most important factors at the initial stage,” said Sallan, who works in the laboratory of University of Chicago Professor Michael Coates.

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As another year comes to a close we’d like to look back at the fascinating research breakthroughs and inspiring patient stories from 2011. ScienceLife ran 168 posts this year, and while we wish we could highlight all of them, here are a handful of our favorites from each month.

January

Patrick Wilson found out that the H1N1 virus could end up helping us fight all types of flu. Stephen Pruett-Jones studied how some male birds mimic the sounds of predators to pick up the ladies (with an audio clip). We interviewed David Gozal about his study on the link between childhood obesity and lack of sleep, and took a look at NCAA regulations mandating sickle cell testing for athletes.

February

Harold Pollack gave a lecture on why violent crime in urban, minority communities should be considered a public health epidemic. Siri Atma Greeley studied the actual medical benefit of widespread genetic testing. Stacy Lindau wanted to know why so few women get help for sexual problems after surviving cancer. We talked to Bana Jabri about the causes of celiac disease, and Sliman Bensmaïa showed us how the brain processes the basic elements of touch very much like it handles visual information.

March

Sola Olopade educated women in Nigeria about using clean-burning stoves to prevent indoor pollution. Stefano Allesina and Jonathan Levine looked at how rock-paper-scissors helps explain evolution. Joshua Miller went to Yellowstone Park to see what stories the ghostly bones of animals can tell, and Scott Eggener questioned the wisdom of indiscriminate prostate cancer screening.

Photo by Gerald Waddell

Andrea King studied the wide range of responses to drinking alcohol, and why it can be fun for some people and a bummer for others. Cheryl Reed took a ride in a helicopter with our UCAN nurses. Kamal Sharma looked at the genes that control animals’ gait, and Ningqi Hou studied how urban environments can dictate how much exercise people get.

May

Daniel McGehee looked at the long-term effects of nicotine on the brain. Habibul Ahsan went to Bangladesh to study the health impacts of accidental exposure to arsenic in drinking water. The brain’s overlooked supporting cells got their due at a conference on neuroscience, and we remembered a landmark discovery about a once popular drug taken during pregnancy that we now know can cause cancer.

June

As we headed into summer, Diana Lauderdale used Google to track MRSA. We learned about an extraordinary transplant where a man received a new heart, liver AND kidney. Daniel Geynisman gave us the rundown on whether or not cell phones are killing us (they’re not, as long as you don’t use them in the car), and some UChicago undergrads studied what happens to gorillas on the birth control pill.

July

We spoke to Donald Jensen and Andrew Aronsohn about the new outlook for patients with hepatitis C. Igor Schneider made a time machine to find the genetic switch for limb development. Farr Curlin led a study about the benefits of addressing spiritual needs alongside medical care, and Adam Cifu looked at the phenomenon of scientific study reversals.

August

Stefano Allesina dug into the long, shady history of nepotism in academia in Italy. John Schneider talked about his work addressing sexual health and stigma in India. Michael Becker discovered a new treatment for the Royal Disease, and we had the rare chance to name check a Spiderman villain in a post.

September

Martha McClintock and Suzanne Conzen studied the connection between social isolation, stress and breast cancer. Gallego Romero traveled to India to search for the origins of lactose intolerance. Stephanie Dulawa developed a mouse model for OCD, and Paul Vezina looked at a different kind of obsession, compulsive gambling.

October

Arshiya Baig started a pilot project to help people learn about life with diabetes through pictures. Manyuan Long found that some of the youngest genes are in the brain. Jens Ludwig and Stacy Lindau published a landmark study about the connection between neighborhood poverty and health, and Issam Awad studied a rare brain disease that soon could be treated with a drug instead of surgery.

November

Cathy Pfister and Tim Wootton figured out how to use seashells to track climate change over the years. Lianne Kurina found a link between loneliness and sleep quality. Shantanu Nundy, Monica Peek and Marshall Chin developed a program to send text message reminders to people with diabetes, and Pan Chen looked at the links between childhood abuse and aggressive behavior in adults.

December

Inbal Ben-Ami Bartal, Jean Decety and Peggy Mason discovered that rats can show empathy for their fellow rats in distress. Maciej Lesniak performed a scary but amazing brain surgery on a patient who was awake. Cathryn Nagler searched for the source of food allergies within our bodies, while Stafano Guandalini uncovered the challenges in educating doctors about one of those allergies, celiac disease.

Whew. Hope you were able to click through at least a few of those. We look forward to another great year of research in 2012. We’re taking a break next week, but we’ll be back on January 5. Happy holidays!

Have you ever cheated on a test by glancing over at someone else’s work? Or relied on a fellow student to carry the load on a group project while you coast along with minimal effort? While few will admit to these forms of cheating, they have long been fixtures of the classroom. However, a lazy individual benefiting from the hard work of a colleague is not a trick exclusive to humans. In a recent study of bacterial infections in plants, the laboratory of evolutionary biologist Joy Bergelson demonstrated that these unsavory practices can also be found in pathogens - and that may be a good thing for us.

In the bacterial world, the goal is survival. What we perceive as an infection is merely colonization for the bacterial population, who are establishing a new home where they can happily feed off the host’s nutrients and reproduce. Bacteria build and release virulence factors to achieve this settlement and evade immune system defenses. But because these factors spread out, benefiting an individual bacterium’s neighbors as well as itself, a sneaky bacterium can get by without producing its own virulence factors. In laboratory dish experiments, scientists observed that bacteria engineered without the ability to release factors can still thrive so long as they are paired with normal, pathogenic partners.

Though scientists described this “cooperator-cheater model” in the artificial environment of the dish, nobody had yet observed it in a natural setting. For a study published in September by the journal Ecology Letters, a team led by postdoctoral fellow Luke Barrett discovered the model in action within the cells of the popular genetic model plant Arabidopsis thaliana.

“We’re showing that cheating actually happens in nature, and that the cheaters persist,” Bergelson said. “You can make cheaters that do well in the lab, and you can show that these systems may be stable in theory, but to show that it is actually happening in nature is novel.”

Recently, researchers discovered that Arabidopsis carried two strains of the bacteria Pseudomonas syringae, a common plant pathogen. While one strain had all the normal pathogenic activity, another was a kind of bacterial pacifist, with a broken system for secreting virulence factors. Surprisingly, these two strains appear with almost equal frequency in Arabidopsis, suggesting that the non-pathogenic strains are far more successful in nature than previously thought.

To test the nature of this relationship, researchers took the two natural strains and experimentally infected plants with only one or the other. When grown alone, the “cheater” strain was not nearly as successful without its more aggressive partner around to unwittingly “donate” virulence factors. Additional modeling suggested that the more aggressive the virulent strain, the more likely it was that cheaters would be found nearby eager to exploit the hard work of their pathogenic peers. The cheater strains are also harder for the host immune system to spot, since the machinery that produces and releases virulence factors is a frequent target of those defenses.

“When you go into the field, it’s kind of a curiosity: why would non-pathogenic cheaters be almost as common as pathogens inside the host?” Bergelson said. “It turns out that the cheaters can do really well as long as they’re with the pathogenic variety, and they don’t pay the price of having to actually make a secretion system or effectors. They also don’t run any risk of being recognized because it is the presence of secreted effectors that causes the recognition events in the first place. So, these non-pathogens have some good things going for them.”

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By Matt Wood

Sometimes scientific discoveries happen by accident. Henri Becquerel discovered radioactivity when a uranium rock he left wrapped up in a drawer with some X-ray equipment imprinted itself on a photographic plate. Alexander Fleming discovered penicillin when he noticed that mold growing in a staphylococcus culture was killing all the bacteria around it. In 2007, Catherine Pfister and her colleague Timothy Wootton made their own accidental discovery. They were studying how species interact in the coastal waters around Tatoosh Island off the northwestern tip of Washington state when they found something alarming about the chemistry of the seawater—a discovery that points to the adverse effects of increasing amounts of fossil fuel carbon in the atmosphere.

As a routine part of their work, Pfister and Wootton were measuring pH levels in the waters around Tatoosh Island. Such readings are usually the boring part of field research, providing context for the rest of the experiments. “If you were studying tree growth you’d always have to be measuring the weather,” said Pfister, an associate professor of ecology and evolution at the University of Chicago, “And this is the weather for us, what the ocean is like.”

Instead of the slight declines predicted by models, however, Pfister and Wootton, a professor of ecology and evolution, found that pH levels in the water were dropping at an order of magnitude faster than expected.

The pH levels in seawater are part of the basic chemistry of the ocean. Plants and animals develop and interact in a certain pH and evolve as it changes naturally over time. What concerned Pfister and Wootton was how the rapid drop in pH they recorded would affect the ecosystem. “We all know that there’s a strong pH dependence of biological reactions, and we don’t know how those reactions will change if pH changes rapidly,” Pfister said.

Rapid decline in seawater pH is a symptom of what’s called “ocean acidification,” or decreasing alkalinity as ocean water absorbs increasing amounts of carbon dioxide from the atmosphere generated by burning fossil fuels. Scientists estimate that the ocean absorbs at least a third of that carbon dioxide.

In 2008, they published their findings about the declining pH levels in PNAS. What they didn’t know at the time was whether those readings were part of a sustained trend or just an unexpected natural variation. “We have a lot of concern about that,” Pfister said. “We haven’t been measuring [pH levels] for that long in the ocean. There’s a very short instrumental record in the ocean, and the instrumental record only goes back to the 1990s.” Most of the pH data on record was also from tropical waters and the open ocean, in areas with less species diversity than the rich coastal waters around Tatoosh Island.

To find out if their measurements represented a new trend, they turned to a tried and true method of measuring historical ocean environments: sea shells, specifically the shells of the California mussel (cross section pictured above). Mussel shells are made of calcium carbonate and grow annual layers or bands just like trees. Scientists often use hard structures like this to infer things about the environment in which an organism lived, so the chemical composition and growth patterns of these mussel shells can be used to study the chemical composition of the ocean.

The results of this study are published in a new paper in PLoS ONE. Pfister, Wootton, graduate student Sophie McCoy and colleagues from the University of Chicago Department of Geophysical Sciences analyzed carbon and oxygen isotopes in shells that had been growing near their instruments for the past decade, as well as shells collected by researchers 30 to 40 years ago and ones provided by the local Makah tribe from over 1,000 years ago. Carbon isotope levels drop in conjunction with pH. When they compared the shells from the three different time periods, they found that the ones from the last decade showed a precipitous drop in carbon isotope values similar to the pH decline recorded by their instruments in the earlier research. The findings both confirmed the earlier measurements and demonstrated that shells might be used to measure historical pH levels in water when no instrumental record exists.

Unfortunately, Pfister says that they’re left with another mystery. read more

The evidence for recent, accelerating global climate change is very strong, as it is for the role we humans have played in influencing our Earth’s weather. But for the most part, there have been few direct tests of how climate change could affect the organisms that inhabit our planet. Much of the evidence on this point is either anecdotal, correlational, or based upon predictive models, such as reports that 1 billion people will be forced to relocate due to climate changes or predictions of increased extinction risk due to changes in temperature, ocean chemistry, sea level, and other factors. None of these studies get at a crucial question that will determine the true impact of these environmental shifts: in a footrace between climate change and evolution, what will win?

Two studies published today in Science suggest an answer for one particular species, the small flowering plant Arabidopsis thaliana. Just as the fruit fly Drosophila melanogaster has become an important tool for scientists studying animal genetics, Arabidopsis is the model organism of choice for studying plant genes. Researchers around the world - including the laboratory of Joy Bergelson, professor and chair of evolution & ecology at the University of Chicago - have characterized the genome of Arabidopsis and looked at the variation within the species.

“Arabidopsis is pretty much ubiquitous; it’s been collected in most parts of the world. You find it throughout Eurasia, Russia, up through Scandinavia and down through the Iberian peninsula,” Bergelson said. “So, as a community, we now we have thousands and thousands of lines from all over, many of which are housed in this lab.”

Those resources allowed Bergelson’s laboratory and another group from Brown University to study the relationship between climate change and evolution in this plant species via two separate experiments. In the first, a team led by University of Chicago postdoctoral researcher Angela Hancock applied the popular methodology of genome-wide association studies (GWAS) to the plant, with a twist. Instead of looking for gene variants associated with a particular characteristic of the plant itself, the team looked for variants associated with different climate variables, such as temperature, precipitation, and humidity. (If it sounds familiar, ScienceLife wrote about a similar study Hancock performed with human genetics in 2010.)

Their analysis produced a list of climate-associated genes that reflect familiar biological processes, controlling aspects of photosynthesis, growth, energy metabolism, and other activities important to plant health. To test whether these genes were truly related to a plant’s fitness in a given climate, the researchers tested their ability to predict how well a plant would grow when grown in one particular climate, that of Lille France, based on the number of favorable variants that they carried. Happily, the gene variants were truly predictive, suggesting that the variants produced by their GWAS indeed played a role in a plant’s ability to grow and reproduce in a given climate.

“You can actually predict pretty decently changes in the relative fitness of plants just based on the results from our worldwide scan,” Bergelson said. “It didn’t have to work - it was a longshot really - but we were happy to see that it did work.”

But for the future of climate change, the more critical question was how these variants initially appeared in the Arabidopsis genome. For many of the climate-associated variants, the University of Chicago team found evidence of “selective sweeps,” an evolutionary process where a new, favorable mutation appears and spreads rapidly through a species. In the case of Arabidopsis, this finding suggests that the plant adapted to shifts in climate thanks to the random appearance and subsequent spread of these helpful mutations, rather than drawing from pre-existing genetic variation. But in times of rapid climate change, there may not be sufficient time to wait for those genetic changes to occur.

“The key there is that the variant is novel, and so the extent to which a plant or an organism depends on sweeps to adapt to climate means that there is an intrinsic delay,” Bergelson said. “As the climate continues to change, they may not have the standing variation that they would need to adapt. That’s going to slow things down.”

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Writing about science means looking up a lot of numbers. Trying to find a figure for the number of cells in the body or the protein-encoding genes in human DNA or patients diagnosed with ovarian cancer from 1980 through 1995 can eat up a lot of time and internet bandwidth. For some of these oft-cited numbers, there’s a mutually agreed upon estimate that science writers can drop into the articles, such as the 23,000 usually tossed around for the number of human genes. But it’s worth remembering that these figures are subject to change - after all, it was thought as recently as 10 years ago that there were 100,000 genes in human DNA.

A new counting kerfuffle broke out this week for yet another oft-cited scientific figure: the number of species on Earth. Last year, zoologist Robert May proposed in Science that the human race would be “embarrassed” should aliens show up tomorrow and ask how many different types of organisms live on our planet. Depending on the model used, one could argue for a number anywhere between 3 and 100 million eukaryotes, May wrote - and that doesn’t even count viruses and bacteria, which far outnumber the larger species.

But as the authors of the PLoS Biology article “How Many Species Are There on Earth and in the Ocean?” found out this week, picking a number within that range is hazardous territory. Using a mathematical model based on the roughly 1.2 million species we currently know about, the research team calculated a new estimate: approximately 8.7 million species from land and sea. Of those, only 14% of land species and 9% of sea species have so far been cataloged by humans, the authors concluded, and describing those remaining could take over 1,000 years and $364 billion. “Our results also suggest that this slow advance in the description of species will lead to species becoming extinct before we know they even existed,” they wrote.

Dramatic stuff, but what about the math? In Carl Zimmer’s article on the study for the New York Times, the first bubbles of discontent can be felt around the biology world, from fungi experts to entomologists who argue that the 8.7 million number is far too low. Scientists who study microbes were even less pleased with the mathematical model, which they said dramatically under-counted their favorite species. On his blog, Phylogenomics, microbiologist Jonathan Eisen pish-poshed the paper’s estimates of 10,000 prokaryote species: “I think without a doubt the number of bacterial and archaeal species on the planet is in the range of millions upon millions upon millions.  10,000 is clearly not even close.” Two other microbiologists wrote a letter to the Washington Post, pointing out that “a teaspoon of soil contains more than 10,000 species of bacteria.” For the time being, it looks like our alien visitors will have to be satisfied with the answer, “Lots.”

Elsewhere…

Speaking of the importance of bacteria and microbes, consider the discovery of antibiotic-resistance genes in 30,000-year-old bacteria from the Yukon Territory. Though these bacteria lived approximately 29,930 years before the discovery of penicillin, they possessed defenses against the naturally-occurring weapons scientists have seized upon to develop infection-fighting drugs. That long history means outsmarting drug-resistant bacteria may be even harder than scientists thought, and makes the case for even more selective use of antibiotics. “Bacteria share these genes like baseball cards with each other,” Stuart Levy at Tufts University told Nicholas Wade of the New York Times.

Has an important culprit in amyotrophic lateral sclerosis, aka Lou Gehrig’s disease, been discovered? The Medical Center’s Raymond Roos comments on a recent Northwestern University study.

On the blog, we’ve covered the link between sleep loss and testosterone, weight gain, and blood sugar. A new study from UCSD and Harvard now finds a connection between sleep quality and blood pressure. Our sleep research guru Eve Van Cauter commented on the research for TIME.

Just another reminder to check out the Medical Center’s new Facebook page, where this week you can find articles from the blog, information on the DNA Discovery Lab at the Field Museum, and President Sharon O’Keefe’s letter to the editor on hospital charity care. If you like it, please hit that “like” button!

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Elsewhere…

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

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The unsung heroes of scientific research are the graduate students*. Graduate students provide the enthusiasm to run experiments 7 days a week and all hours of the day and night to generate data for publications and their own thesis projects. The fresh perspective a graduate student brings to an area of research can also provide new ideas to their mentors and collaborators, spotting connections or opportunities that might have been missed by those with more experience. In even the biggest discoveries, graduate students play a critical role.

That was the take-home message from Neil Shubin’s keynote lecture at last week’s Scientific Diversity: People, Research, Careers Symposium organized by the Biological Sciences Division. Following talks by graduate students, post-docs, and young professors, Shubin delivered a characteristically fascinating and funny tale about his laboratory’s discovery in 2004 of Tiktaalik, an important transitional fossil between sea and land animals. The story of Tiktaalik may have been familiar if you’ve read Shubin’s excellent Your Inner Fish or seen him speak before. But this time around, Shubin put added emphasis on the critical role of his graduate students and collaborators, both in setting the stage for the fossil’s excavation and in the continued quest to learn from Tiktaalik’s remains.

In fact, Shubin said the very spark for Tiktaalik’s discovery came from a friendly argument between him and his former graduate student at the University of Pennsylvania, Ted Daeschler. Shubin and Daeschler had found many Devonian era fossils of fish with primitive limb-like structures in their home state, but wanted to find even earlier examples of the transition from fins to limbs. So they had to pick the right place for an expedition, with exposed rocks of the right age for finding such an elusive fossil.

“Everything changed for us in a conversation in my office in 1998. We were having an argument, as graduate students and their advisors typically do, and we settled the debate with a college geology textbook,” Shubin said. “I was thumbing through the book, and I hit a diagram that changed the course of my career.”

The diagram showed the three areas where the ancient deltas Shubin was seeking were known to be exposed. Two of them had already been the site of expeditions, but the third - a cluster of islands in the Canadian arctic - was largely unexplored. Shubin and Daeschler “ran to the library,” he said, and found a paper that confirmed the region held the exact type of rock they were looking for.

“It was truly exciting; here was a whole part of the world that was unexplored,” Shubin said. “After we saw this, we went to Chinese food for lunch, and my fortune cookie said, ‘Soon you will be at the top of the world.’”

It took six more years for an expedition to find Tiktaalik, embedded in the rocks of Ellesmere Island. It took a further two years for the fossil to be prepared sufficiently (by preparator Robert Masek) for analysis and publication. The rest is history - massive media coverage, a book, and even The Colbert Report. But the story of Tiktaalik isn’t over, and it is graduate students that are writing the newest chapters.

“It’s really a nice system, because so many bones are so well preserved, for us to ask new kinds of questions, and this is where graduate students come in,” Shubin said.

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Field assistant Jared Singer maps a partial elk carcass in Yellowstone National Park. Photo credit: Joshua Miller

Paleontologists often deal with time scales in the hundreds of millions of years, reading the messages of fossils to learn about life on Earth long before humans arrived on the scene. But bones aren’t limited to providing insight on prehistoric ecosystems. The skeletal fragments left behind by animals at their final resting place can be just as valuable as ecological data points when they’re 100 years old as when they are 100 million years old, a new study discovered. The “ghosts” of animals from decades past can give scientists the tools to study more recent ecological changes, due to climate change, invasive species and other threats to global biodiversity.

Yellowstone National Park, established in 1872, was the first of its kind not just in the United States, but in the world. For the past 139 years, the National Parks Service has both protected the western territory and studied it, regularly monitoring the wildlife that lives within its nearly 3,500 square miles of land. So for Joshua Miller, a graduate of the University of Chicago Committee on Evolutionary Biology, the Park offered a perfect testing ground for his study assessing the scientific worth of relatively young bones.

“Yellowstone is phenomenal; it’s one of our nation’s gems,” said Miller, now a postdoctoral researcher at Wright State University. “They have a huge amount of historical data on living populations, so it is a great place to look at the bone record and be able to match up what we see in bones to what we know has happened in the living community.”

Miller’s plan was elegant and simple: take a census of the bones he could find lying on the ground (no digging required) at different locations in Yellowstone, and see how well the story of the bones matches up with historical data on the local living species. Specifically, Miller would look at the bones of large mammals such as elk, bison, and mountain goats, estimating the abundance of each species over the last century by counting their skeletal remains. While a straightforward idea, and building off of work by researchers with similar interests, Miller said he initially received skepticism from Park officials who didn’t believe that a researcher could find enough bones to make estimates about historical animal populations. That assumption was proved untrue almost immediately, he said.

“It turns out everywhere you go, you run into bones,” Miller said. “We went up to the Arctic National Wildlife Refuge [on a later project], landed the plane and right next to the wheel was an antler. Bone accumulations are just rampant.”

In Yellowstone, Miller and his field assistants spent three consecutive summers laboriously analyzing forty different plots of land. The assistants walked slowly over a one kilometer area, planting flags wherever they came across animal remains. Miller, who had spent months at Chicago’s Field Museum looking at specimens and memorizing their bones, would then investigate their discoveries to identify the species. He also estimated how long the bones had been lying there, either based on how weathered the remains were, or by taking a small sample for radiocarbon dating.

Partial elk carcass in Yellowstone National Park. Photo credit: Joshua Miller

Slowly, a unique database of population changes over the history of Yellowstone was built by Miller. He then was able to compare his bone data to population surveys collected the old-fashioned way - by flying over the Park and counting the animals. Excitingly, there were few surprises, as the bone database matched known fluctuations in animal populations within the Park over many decades. For instance, the reintroduction of wolves in 1995 produced a decrease in elk populations, a shift reflected in Miller’s database by the high number of older elk bones contrasting with the lower number of more recent elk bones. The predictability was a good thing - it meant that the bone record was accurately depicting known ecological history in Yellowstone, and could therefore be used as a proxy for studying population changes in regions without historical survey data.

Other discoveries were totally unexpected and made little sense - at least initially.

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Imagine if your comfortable existence was suddenly and traumatically disrupted by a disaster. Your home is destroyed, food becomes scarce, and social structures suddenly break down. Even the most civilized people would respond to this situation with desperation, doing whatever it takes to survive in the short-term without the usual considerations for the long term.

Now imagine you are a bacterium, living inside the human gut (this might take a bit more imagination). For as long as you can remember, everything has been cool there - a steady stream of nutrients pass by to feed on, the police force of the body’s immune system does not perceive you as a threat, and a happy society has been established with the thousands of other bacterial species in the area. But suddenly, the world as you know it is shaken. The human in which you have made your home contracts a serious illness, and undergoes surgery and intense antibiotic treatment. Millions of your fellow citizens are killed, the food supply dries up, the immune system declares martial law. Facing this desperate situation, bacteria tend to act just like humans would - they riot.

This pattern of ecological collapse leading to chaos may underlie one of the most difficult problems facing health care today: hospital infections. Since surgeon Joseph Lister discovered in the 1860’s that carbolic acid can be used to sterilize surgical instruments and wounds to reduce infection rates, hospitals have grown obsessed with cleanliness to protect patients from bacterial invasion. Yet even perfect diligence cannot prevent serious infections from occurring in a small population of patients, causing scientists such as John Alverdy, professor of surgery at the Medical Center, to ask: Could the threat of bacterial infection be coming from within?

“It’s a new way of thinking about infection, because we’re already doing already we can - washing our hands, sterilizing the site, giving our patients antibiotics - and yet some of the infections seem to be getting worse,” Alverdy said. “There has to be a strategy change, and I think we’re at the forefront of understanding that.”

Alverdy’s group has spent the last decade studying a member of the gut microbiome (the world of bacteria living inside our digestive system), called Pseudomonas aeruginosa. Most of the time, Pseudomonas is a passive colonizer of the human body, an “accidental pathogen” that we pick up through our diets or other environmental exposure that causes no harm. But when the body is severely stressed by a surgical procedure, illness, chemotherapy, or radiation, Pseudomonas occasionally panics and becomes an extremely dangerous inhabitant. Alerted to the body’s emergency by immune system factors and starved for food, it begins tunneling through the lining of the gut to invade the unfortunate patient’s blood. Once the bacteria goes on the attack, it’s very difficult to treat, giving it the highest mortality rate of any hospital infection.

“I have seen some people postulate that Pseudomonas isn’t a very virulent pathogen, and I say ‘what are you talking about?’,” Alverdy said. “If you provoke it the right way, it will kill everything in its wake. It’s very virulent.”

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Since the time of Linnaeus, scientists have loved classifying the world around them. But while centuries of biologists have worked to collect and categorize the plants and animals of Earth, all that work likely only covers about a minute fraction of our planet’s life. As much as 99 percent of the biodiversity on Earth is smaller than 2 microns - bacteria, viruses, and tiny eukaryotes - and most of these remain to be discovered by humans. There are more microbial cells on earth (1 nonillion, or 1×10^30) than there are stars in the sky, and all of this new life exists in soil, in seawater, and inside animals, plants, and even us.

“You are mostly microbes,” Jack Gilbert told the Institute for Genomics and Systems Biology in a lecture last month. “The world is mostly microbes, and yet we have less of an understanding of how microbes run the universe than we do of the universe itself.”

Gilbert, an assistant professor of evolution and ecology at the University of Chicago, is part of an international project to remedy that shortage of knowledge about the microbial world. The Earth Microbiome Project, a group bringing together scientists from several different institutions, is dedicated to filling in these gaps in the tree of life and, more importantly, figuring out how they may be secretly pulling the strings of Earth’s ecosystems. In his talk, Gilbert rapidly narrated the group’s aims and his own research projects until he ran out of breath, leading an hour-long tour around globe in search of nature’s smallest and most abundant participants.

Classically, microbiology has taken place in cell culture dishes and incubators, as scientists grew bacteria in the laboratory in order to study its identity and function. But the field has benefited greatly in recent years from genetic advances opening up new paths of discovery. As the price of accurately sequencing DNA and its products has exponentially dropped - driven largely by the demand for human genomics - ecologists interested in microbes have borrowed the technology for their own uses. Now, instead of growing bacterial populations in the laboratory, microbiologists can take a genetic sample of whatever environment they wish and use the genes in that sample to reconstruct its microbial denizens. This process is called “metagenomics,” and it is expanding our knowledge of the bacterial world in leaps and bounds, Gilbert said.

“We can take a sample, sequence it, look at the microbial taxa in there, and identify things we couldn’t culture,” Gilbert said. “There are four trillion base pairs of genetic information in a millileter of seawater, in one teaspoon. In a gram of soil, there are about 4 quadrillion base pairs.”

With so much information out there waiting to be discovered, one of the most important questions is where to start. The Earth Microbiome Project is overseeing dozens of projects, each with their own hypotheses and environmental targets. Gilbert outlined just a few: analyzing samples from near the site of the Gulf of Mexico oil spill; comparing soil samples - some as old as 135 years old - from China, France, Australia, and South America; characterizing the microbial communities from the vaginal canals of fertile and infertile pandas in the San Diego Zoo (seriously). Importantly, the procedures used to analyze such widely different samples are being standardized by the project to ensure that comparisons between different research groups and samples are possible.

“The goal of this project is to systematically approach the problem of characterizing microbial life on Earth,” Gilbert said. “We’re reaching a zenith point in our ability to do things individually, and if we want to start generating synthesis of our understandings, we need to start working as a team, as a group, like the physicists do. We want to do the same thing: Come together as a group and say ‘we have a really good idea, a life-changing idea that will change the way we live on this planet, we just need to do it in a systematic and well organized fashion.’”

As a discrete example, Gilbert offered one of his own research projects, conducted before he relocated to Argonne National Laboratory last summer. As senior scientist at Plymouth Marine Laboratory in England, Gilbert and his team studied a section of the English Channel that has been sampled by scientists every week since 1864 - interrupted only by the two World Wars. Since 2000, the team has taken samples suitable for metagenomic analysis, and has methodically characterized what microbes live in this patch of water and how that population changes.

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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)

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