Do simulated conversationalists dream of revolution?

One rough definition of philosophy is that it’s an effort to figure out what’s “good” or “right” for individuals and societies. It's elusive human stuff, with the answers to these questions at the heart of personal and cultural values. Those who study cultural change traditionally identify patterns by analyzing behaviors, institutions, literature, etc., but I was surprised to learn that computer simulation has become a part of the philosopher’s toolbox.

Researchers are now studying the evolution of ideas and values in simulated communities where software-based “agents” discuss hot topics and form opinions. The emerging field borrows from the more traditional uses of simulation, like population genetics and economics.

I came across the idea that the era of digital philosophy has arrived in Matt Windsor’s recent article on the UAB Magazine website. With his permission, I swooped in with follow-up questions for his source, Marshall Abrams, Ph.D., assistant professor in the UAB Department of Philosophy.

Per Matt’s piece, Abrams is building computer simulations of cultural change, the flow of ideas among individuals which, taken together, shape societal mores. In a typical simulation, a few dozen of Abrams' software “agents” might choose from among 50 beliefs after exchanging ideas 30,000 times in 10 minutes.

The agents start out strongly believing what they’re told, but begin to form their own views as they encounter the ideas of others. They more firmly “believe” in something the more they hear it from others and are more likely to share that which they believe in strongly. Nevermind what these simulation rules say about human nature.

Simulations are useful, says Abrams, for examining broad patterns of cultural change across populations. While they will likely never predict future cultural shifts, they may help researchers to determine which shifts underway should be taken seriously.

Strictly speaking, Abrams’ work is not philosophy, digital or otherwise. It’s a brew of philosophy, social sciences, humanistic studies, psychology, evolutionary theory and computer science.  In a larger sense, he is examining whether or not such diverse disciplines can be integrated.

Syntax equals attitude?

Abrams is particularly interested, as Matt writes, “in analogies that describe how we view our relationships and our place in the world.” Those studying culture see analogies used in conversation as “cognitive filters” that reveal something about a person’s worldview. Metaphors and analogies might connect sets of beliefs using simple rules that can serve as models for more complex beliefs. With this in mind, researchers sift through history and anthropology for examples where commonly used analogies can be linked to the values of those using them.

Along these lines, the relationship between a nation and its dictator, for example, may be shaped by the relationships of individuals with their fathers and reflected later in their use of fatherly analogies: “Fearless leader x is the father of our nation.” Abrams is interested in how analogies shift with time and what that says about the world. He suspects that a subtle and complex interplay is underway between each person’s use of analogies and other influences on his or her thinking, and hopes that the simulations can help to describe them.

For more information, Abrams recommends that enthusiasts take a look at the National Endowment for the Humanities’ Office of Digital Humanities, along with the UNC Charlotte Complex Systems Institute. If you are deeply interested in this emerging field, you may want to browse through the following partial list of researchers who have influenced Abrams’ work.

Influences

• Abrams’ simulations are inspired by hypotheses proposed by anthropologist Peggy Sanday to explain how roles in childrearing influence a person's ideas about human origins.
• He is planning simulations based on the research of psychologist Lera Borodisky on how thinking of crime as a disease or as a beast affects what people propose as solutions to crime.
• In terms of research with analogies, psychologist Keith Holyoak and cognitive scientist Paul Thagard offer interesting insights based on which analogy people chose to compare the famous Children’s Crusade, the May 1963 march by Birmingham students against segregation. Did the march destroy a tumor (segregation/racism), fix a light bulb or attack a fortress?  In addition, Abrams' simulations are based on Thagard’s software. 
• Dedre Gentner and Kenneth Forbus have also created excellent computer models of how we process analogies. 
• Patrick Grim and Jason McKenzie Alexander represent other philosophers doing influential work with computer simulations.
• A number of “philosophers of science,” including Paul Humphreys and Eric Winsberg, are interested in philosophical questions about the role of simulations in science.

Note: The title of this post is a tribute to the famous sci-fi novel Do Androids Dream of Electric Sheep?, by Philip K. Dick, which served as the basis for the film Blade Runner. Abrams says his “agents” are not smart (designed as simple models for study), but that such work could be combined with artificial intelligence research at some point if someone were interested.

Do sugar-sweetened drinks drive obesity?

Obesity has been linked in media coverage to the drinking of too many sugar-sweetened beverages. Emotions are running high, but is there enough scientific evidence to conclude that consuming fewer sugary drinks will reduce obesity?

The Obesity Society opened its annual meeting, Obesity 2012, this week in San Antonio with a debate on that very subject.

In the debate, David Allison, Ph.D., associate dean for science within the UAB School of Public Health and director of the NIH-funded UAB Nutrition Obesity Research Center, faced off against Frank Hu, M.D., Ph.D., professor of Nutrition and Epidemiology at Harvard School of Public Health.

Allison sat down with The Mix to comment on the debate and on related studies just published in the New England Journal of Medicine.

Show notes on the interview

1:25 Sugar-sweetened beverages have figured centrally in public health discussions about obesity for more than a decade. Some evidence has suggested that such drinks may play a unique role. What’s needed now, says Allison, are rigorous studies to prove (or disprove) that reducing consumption of these beverages actually increases weight loss or slows weight gain.

2:02 Public health as a field changed over the last decade as the obesity epidemic became more evident. Advocacy has wrestled with purely scientific discussion, and emotions are running high.

3:44 Valid, scientific study results are a must when deciding whether or not any one factor contributes to, or reduces, obesity, and the standard for that validity is a randomized clinical trial.

4:38 Up until the meeting, the evidence has not been there to demonstrate that reducing sugar-sweetened beverage intake would reduce obesity, according to Allison. In six of the six randomized clinical trials to date, he argues, the primary analysis of all patients studied showed no statistically significant difference in weight gain, weight loss or BMI between those who kept drinking sugary drinks and those who cut back.

5:26 On top of the six clinical trials mentioned, however, a series of papers were just this minute published in the New England Journal of Medicine. Two of the studies — one in children, one in adolescents — did indeed represent the kind of randomized clinical trials Allison has been calling for. The authors of both studies offer valid evidence, Allison says, that reducing consumption of sugar-sweetened beverages reduced weight gain in specific groups under certain conditions, but more studies are needed to confirm that the patterns apply to everyone.

9:23 While sugar-sweetened beverages remain an important area of inquiry, Allison says he thinks other emerging thrusts in obesity research warrant attention as well. These include the roles of sleep, daily weigh-ins and eating vs. skipping breakfast.

10:32 UAB’s Nutrition Obesity Research Center has joined with six other NORCS and a center in Denmark to organize a randomized clinical trial in 300 patients to generate evidence that having or skipping breakfast in the morning affects body weight.

11:36 UAB meeting highlights beyond the presidential debate included a presentation by Nefertiti Durant, M.D., assistant professor in the UAB School of Medicine's Division of General Pediatrics and Adolescent Medicine, as part of a symposium on adjusting obesity prevention approaches to account for a person’s age. Her talk, titled “Freshman 15 and Beyond,” discussed contributing factors and potential solutions. In addition, James Rimmer, Ph.D., Lakeshore Foundation Endowed Chair in Health Promotion and Rehabilitation Sciences in the UAB School of Health Professions, will be talking about how people with intellectual disabilities have higher rates of obesity than the general public based on several factors, including their living arrangements.

13:10 For good information on obesity, Allison recommends the Weight-control Information Network organized by the National Institute of Diabetes and Digestive and Kidney Diseases. He also points to the U.S. Agriculture Department’s Dietary Health page. For researchers, Allison offers the UAB NORC’s seminar series, which is available to all online, goes back 12 years and discusses a great many aspects of nutrition theory and related scientific evidence.

Also important is a recent editorial in the Journal of the American Medical Association by the director of the National Institutes of Health, Francis Collins, M.D., Ph.D. Of the editorial, which argues that public policy must be founded on valid science, Dr. Allison says he couldn’t agree more.

14:22 End podcast

About the podcaster

Greg Williams @gregscience @themixuab is research editor within Media Relations at the University of Alabama at Birmingham.

Genomic marathon is worth it

Imagine a project so vast that you could work on it for 20 years, spend $4 billion and still have only just moved it off the starting line. Would you ever finish?

Those questions have for years faced the massive effort to understand human genetic material. The Human Genome Project cost roughly $3.8 billion from 1998 to 2003, and a central message afterward was that “we have but scratched the surface in our understanding.” The ENCODE project picked up where the Human Genome Project left off in 2003, seeking to understand which bits of the genome have an active role in human biology despite their not being genes.

While the 20,000 or genes discovered during the Human Genome Project are a central part of the “blueprint for human biology,” ENCODE has helped to confirm that genes represent less than 2 percent of the genome. Genes, it turns out, are surrounded by vast stretches of code, some of which control when, where and how genes turn on and off.

Teams of ENCODE researchers recently published 30 research papers that represent an early round of results, according to an article in the journal Nature. But how far have we come after adding ENCODE’s seven years and $185 million to our monumental investment in the Human Genome Project?

We asked Michelle Amaral, Ph.D., study navigator in the UAB School of Medicine’s Department of Genetics, for her perspective as part of the next generation of genomic researchers. She thinks ENCODE is worth the investment based on its contributions to date and its potential.

In part thanks to ENCODE, doctors today can assess the impact of small variations in a person’s genome on several diseases, and tailor their treatment accordingly. Amaral mentioned Bruce Korf, M.D., Ph.D., chair of the Department of Genetics, as an example of a UAB genomics researcher whose work is already contributing to both personalized medicine and advances against rare diseases.

What’s taking so long? 

More than 400 ENCODE scientists had completed roughly 1,600 experiments on 150 different cell types in time for the recent ENCODE publications. Despite this frenzy of activity, however, efforts to map the function of the entire human genome are about halfway there, with an in-depth description of the genome’s function just 10 percent complete, according to experts quoted in the Nature article.

“Each person’s DNA code consists of about 3 billion chemical units,” says Amaral in way of explaining the “slow” pace. “Sorting them into genes, gene triggers and gene networks is like trying to piece a foreign alphabet into sentences, stories and libraries of stories, and without knowing the grammar rules.”

From another angle, the ENCODE consortium has already done great things. It has assigned a rough function to about 80 percent of the human genome, although critics argue some of this functional DNA is really junk. It has identified the DNA binding sites for about 120 transcription factors, proteins that control when genes switch on and off to express proteins. And it has mapped genome regions “carpeted” with molecules called methyl groups that confer still more precise control over gene expression.

These mechanisms for genetic fine-tuning may explain why humans are so complex, despite having fewer genes than grapes.

Furthermore, ENCODE has identified thousands of points on the genome where a single-letter (single-molecule) difference in the code contributes to a genetic disease, with 90 percent of them falling outside of genes.

Those interested in learning more should visit the ENCODE project website, the National Human Genome Research Institute ENCODE site, or follow ENCODE on Facebook or Twitter.

UAB genomics retreat

UAB faculty, trainees and students will have a chance to learn more about the field, share work and network at the UAB Genomic Medicine Retreat on Tuesday, Sept. 25. The event will be held in UAB’s Alumni Auditorium.

UAB speakers will include Drs. Korf and Amaral, as well as Lynn Holt, program director for the Genetic Counseling Program, Elliot Lefkowitz, Ph.D., associate professor in Department of Microbiology, and Jonas Almeida, professor in the Department of Pathology. Dan Roden, M.D., professor of Medicine and Pharmacology at Vanderbilt University will also speak. Registration is required and may be completed here.

The list of retreat sponsors reveals the power of the genomics collaboration under way at UAB: the Center for Clinical and Translational Science, Heflin Center for Genomic Science and the Comprehensive Cancer Center.

How hard should I worry about West Nile virus?

West Nile virus has taken lives in several states, but how worried should we be? What can we do beyond stocking up on Deep Woods Off and staying away from ponds?

On the one hand, West Nile fever and severe West Nile disease are scary, having caused 87 deaths nationwide. The 1,993 infections so far this year represent the highest number ever reported through the first week in September. The virus is carried by 64 different species of mosquito and has now spread through 48 states, including all of Alabama. Furthermore, the CDC says the number of West Nile virus infections is “grossly underreported.”

On the other hand, most people infected with WNV have no symptoms at all, let alone become ill, and you can protect yourself with insect repellant. To put the WNV numbers in perspective, even the low end of the CDC’s estimate for annual flu-related deaths is 3,000, with the average closer to 10 times that.

Maybe what makes WNV so distracting is that it’s unpredictable from year to year and from person to person based on their age and other factors. I have kids aged five and eight, and my WNV worry meter amped down when I saw that cases in children are rare. But with a mother approaching 70 and a grandma in her 90s, my concern grew again when I learned than more than half of West Nile deaths are in people aged 70 or older, who have weaker immune systems.

The severity of WNV infection in any given year depends on things like the number of mosquitoes out there, which depends on how cold the previous winter was, says Qianjun Li, Ph.D., assistant professor in the UAB School of Medicine’s Division of Infectious Diseases. Last winter was warm, so the mosquito population has swelled.

Also important is the outcome of the annual evolutionary battle between the virus and the immune defenses of birds and humans, says Li. Viruses change their makeup with every generation, forcing immune defenses to scramble to recognize the new versions. One side may gain the upper hand in any given year. Complicating matters, some people’s bodies and brains react to viral invasion so strongly that that the reaction itself threatens to become life-threatening. The fever and inflammation that come with viral infections are the body’s doing.

Despite the media coverage, WNV disease is rare. That means that government funding for related research is limited, and the willingness of pharmaceutical companies to invest in therapies or vaccines is even more constrained, says Li. Thus, the work moves slowly, with the arrival of both vaccines and antiviral medications, in Li's estimation, more than five years away.

A visit to Clinical Trials.gov reveals six vaccine trials and two antiviral drug trials underway in WNV, but none of them will deliver immediately. As pointed out in a recent piece by my colleague Nicole Wyatt, self-protection will be the key during the many WNV seasons that will pass before vaccines and treatments arrive.

Li’s research focuses on mosquito-transmitted viruses, such as yellow fever, dengue fever and WNV. He is exploring the theory that human immune response against WNV infection may become deadly as chemicals released by immune cells to fight the infection — chemokines and cytokines — build up to the point that they kill surrounding human tissue.

He is also working to develop tests that can accurately measure whether WNV drugs currently under development are nontoxic and effective, lessons that may apply to WNV relatives like the dengue virus. The ultimate goal of Li’s work is to understand the interactions between viruses, mosquitoes and the immune systems of birds and humans, and to develop new anti-viral therapeutics that prevent and control infections.

Li recommends that those interested in learning more visit the CDC West Nile page or the West Nile Virus Information Exchange.

Stem cell studies a long way from autism answers

A recent post in the Nature blog Spoonful of Medicine talked about how the Sutter Neuroscience Institute in Sacramento has started recruiting kids for a clinical trial on an experimental stem cell therapy for autism. The author, Kathleen Raven (@sci2mrow), reported that the research team there hopes their study answers questions about a disease with "few, largely ineffective treatments."

The California team will recruit 30 autistic children between ages 2 and 7 who have cord blood banked at a Cord Blood Registry near the institute. That’s because the Sacramento study will use each child’s own stem cells as treatment, and because cord blood is a stem cell source that avoids the debate surrounding embryonic stem cells. Other autism stem cell trials underway include a Chinese study using cells donated from other children’s cord blood, and a Mexican study where stem cells will be harvested from each child’s fatty tissue.

We asked Alan Percy, M.D., professor in the UAB School of Medicine’s Division of Pediatric Neurology, and Fred Biasini, Ph.D., associate professor in the Department of Psychology, for their take on the studies. Their short answer was that the three studies are unlikely to soon answer the question of whether or not stem cells can treat autism. The Chinese study is complete but has not published any papers and the Mexican study is still recruiting.

Percy says the most important, eventual achievement of the California trial may be to prove with rigorous science that such treatments do not work. The problem, he says, is that some parents are so hungry for answers that they will pursue therapies even If the science is not there. In many cases they leave the U.S. to gain access to treatments in places with much less rigorous patient protection laws in place. Percy sees many pursue this course but no evidence of treatment success.

While the techniques used in the Sutter study have a very small chance of working, Percy says, they may provide insights into better ways to use a patient’s own stem cells in future attempts to create treatments.
The idea that stem cells might improve an autistic child’s ability to speak is based on the theory that the disease has some autoimmune roots. Immune cells in the brain mistakenly attack brain cells to cause inflammation. The hope is that injected stem cells would recognize the ‘autoimmune’ cells as foreigand clean them out. The problem, says Percy, is that such cells would have to enter the central nervous system, an obstacle that has stymied many promising treatments.

UAB is one of the 14 study sites within the Autism and Developmental Disabilities Monitoring (ADDM) Network, says Biasini. Funded by the Centers for Disease Control, the network had been working in recent years to determine how common autism is and how that changes over time and by region. So far, they have determined that about 1 in 88 children have a confirmed autism spectrum disorder.

Biasini also mentioned the following as samples of key UAB autism research:

• An effort led by Biasini and Maria Hopkins, Ph.D., an assistant professor of psychology in the UAB College of Arts and Sciences, seeks to understand how the ability to interpret facial expressions, or not, affects social skills in children with autism with the goal of improving social interactions.
• Work by Sarah O’Kelley, Ph.D., assistant professor in UAB Department of Psychiatry and Behavioral Neurobiology, who is studying social interventions such as the organizing of social skills groups, to see which are most effective in improving social skills in children and adolescents with ASD.
• Kristi Menear, Ph.D., associate professor in the Department of Human Studies within the UAB College of Arts and Sciences, is looking at the impact of exercise on cognitive and social development in adolescents with an ASD.  Exercise has been shown to reduce the impact of various mental and physical health conditions, and her study will look at whether the effect is there in autism as well.
• Irena Bukelis, a psychiatry resident at UAB, is examining the types of medications prescribed to children suspected of having an ASD, which typically include antipsychotic, ADHD and antidepressant drugs. The work will help researchers understand the medication-related issues faced by families as they seek to address a child’s cognitive, social and language challenges, often before they receive an official diagnosis of ASD.

For more information on the state of autism research, Biasini recommends a new and thorough review of current work just published by the Interagency Autism Coordinating Committee (IACC), organized under the auspices of the U.S. Department of Health & Human Services.  Another strong source of information, research resources and registries is Autism Speaks.

Tornado/hurricane shelter and the 9/11 anniversary

When I heard my first tornado siren this spring, it reminded me of the experience of living through Sept. 11, 2001, in New York City, a tragedy now two weeks from its eleventh anniversary.

My wife and I lived in a small apartment on the Upper East Side of Manhattan. That morning we saw a seemingly endless caravan of fire engines rushing downtown as the news flashed the first images of planes hitting the World Trade Center. We spent the day huddled without power, and breathed in dust from the fallen towers as it blew in through our windows.

The same career that had taken me to Manhattan carried me south late last year to UAB. I arrived about six months after the April 27, 2011, tornadoes that took so many lives in Alabama, and we often felt echoes of the storms' aftermath. Our son played his first Alabama baseball in Cahaba Heights near neighborhoods that had been stripped of trees, and where many homes had been recently repaired.



On March 2 this year, we sat up at 3:30 a.m. listening to the storm sirens echo across Vestavia Hills, me getting pings on my phone from UAB’s B-ALERT system. I remember feeling that same nervous dread I felt on 9/11.

My family’s current plan is to huddle in an internal closet should a tornado hit, with our options improving if we have more notice. We would have the kids put on their baseball helmets, but of course getting them into a storm shelter would be the best thing.

For that reason, I was fascinated to learn about the work of Uday Vaidya, Ph.D., professor within the UAB Department of Materials Science & Engineering, who is designing a new high-tech tornado shelter.  The panels making up the shelter just passed the tornado threat test from the National Storm Shelter Association (NSSA).

In a feat of materials science, Vaidya and his team used thermoplastic and fiberglass resins, foams and fibers to make panels that are stronger in some ways than the steel in many current shelters. Some of the same materials are used in the latest armored vehicles, and in the UAB team's case they're recycled from discarded oil rig pipe insulation that would otherwise be piling up in landfills.

In the NSSA test, 15-pound two-by-fours fired from a pressure cannon were unable to penetrate the panels in a dozen attempts. The wooden missiles hit the panels at 100 mph, the speed at which projectiles typically exit a tornado funnel spinning at more than 200 mph. Such a storm would rate EF5 on the Enhanced Fujita scale and be capable of leveling well-built homes. Take a look at our recent article and the included video for details.

The successful NSSA test represents a first step toward commercial availability, which the team hopes to achieve by the 2013 tornado season. They started the effort after Hurricane Katrina, and have been working even more urgently since last year's tornadoes. The NSSA test was on Aug.1, and the team just filed its patent applications on Aug. 24.

For more information on tornadoes, please see the National Oceanic and Atmospheric Administration site or its storm prediction center. To follow the design project, look up the UAB spin-off company led by Vaidya: Innovative Composite Solutions.

Guest post: stronger laws may mean less childhood obesity

A New York Times piece earlier this month reported on a study that found Body Mass Index (BMI) increases were smaller for students from the 5th to the 8th grade in states where strong laws govern what foods can be sold at schools outside of the federal meal program. These “competitive foods” include products sold in vending machines, at cafeteria ala carte lines and in school stores.  

The study, published on Aug. 13 in the journal Pediatrics, was titled “Weight Status among Adolescent in States that Govern Food Nutrition Content.”  Its findings establish an interesting correlation for public health advocates like me who have been looking for evidence to support a more global approach to our fight against the childhood obesity epidemic. The Times piece links to the Centers for Disease Control, which reports that about one fifth of American children are obese.

Among the strengths of the study is that it objectively rates 40 states on how strong and specific their laws are concerning the types of foods sold in schools. The research team also used data gathered on the actual, competing foods obtained rather than relying on self- reports from parents or children. The study also appropriately stopped short of stating that stricter states laws were the cause of the lower BMI increase because this type of study could not answer that question. But the correlation seen in their data does raise the possibility that stronger state laws could help.

BMI overall increased from 5th to 8th grade for the 6,000 students in this study, but for the kids in the states that had stronger laws, the BMI gain was not as great. This is hard to interpret for individual children because I have taken care of some adolescents who have medical conditions, or are underweight and need to gain. From a population perspective in a country with an epidemic underway, however, any change that can slow weight gain is a plus. For many children, especially in Alabama, laws that promote the slowing of BMI increases should be welcomed.

Speaking of Alabama, I am left to wonder how we did in this study. The authors did not disclose how each state ranked in terms of their scale of strong to weak. There were data license restrictions and they could not report this. They did mention that, at the start of the study in 2003, 70 percent of the students in states with strong laws lived in the South.

Alabama was given a “B+” grade in 2006 by the Center for Science in the Public Interest in regards to policies for competitive foods in school.  In 2009 the “F as in Fat Reports” funded by the Robert Wood Johnson Foundation reported that Alabama has a nutrition standard for school meals and snacks that exceeds government standards, nutritional standards for competitive foods and limited access to such competitive foods. That said, Alabama, along with several Southern states, continues to rank among the highest in terms of childhood obesity levels. The research presented in Pediatrics does suggest that stronger laws could help slow the obesity epidemic facing our children.

Guest Blogger: Stephanie Wallace, M.D., is an assistant professor in the UAB Department of Pediatrics who is active in UAB's Pediatric Weight Management Program.