Thursday, September 27, 2012

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.

  • 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.

Friday, September 21, 2012

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.

Friday, September 14, 2012

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.

Friday, September 7, 2012

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 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.