Dancing Computer Science Professors

TOPIC: bright spot on a gray day

A few days ago I came upon one of my academic colleagues, ipod in hand, dancing along a country lane. I was touched. "A bright spark in an otherwise gray day," I wrote to her later.

Those of you looking for a great college, come to

Sewanee: The University of the South,

nestled on a wooded mountain top in southern Tennessee, teeming with deer and rabbits and squirrels and wild blackberries, where even the computer science professors can be caught (occasionally) dancing along the country lanes.

Computer Simulation of the Evolution of Religious Belief

TOPIC: evolution of religion

Adding to the general melee that is the debate about the evolution of religious belief, here's some stimulating news about a computer simulation created by evolutionary anthropologist James Dow (Oakland University in Rochester, Mi):

Religion is a product of evolution, software suggests
[NewScientist.com, 5/27/2008]

and the original research paper can be found here: Is Religion an Evolutionary Adaptation?

I'll take some time soon to blog more carefully on the original paper, but immediately tantalizing was the general concept: a computer simulation of interactions between "believers" and "non-believers," with the believers eventually flourishing! How cool … but of course this all depends on the assumptions built into the simulation. How were "believers" and "non-believers" defined? What type of interactions were being modeled? And how was adaptive fitness defined?

Dow used a co-evolutionary agent-based model allowing for influences of both genetically determined behavior and learned behavior. Dow explains that

The model does not include a large external storehouse of cultural memory, such as books or databases, from which agents learn. Therefore, it is more applicable to an early, pre-literate culture than to a modern civilization. The brain underwent most of its evolution when people lived such cultures. [§2.4]

The simulated agents have both inherited and learned capacities to communicate "real information" vs. "unreal information." The assumptions here are that:

Real communication carries information about the environment that the receiver can use to increase its fitness. Unreal communication carries no information about the environment and may decrease the fitness of the receiver by diverting its attention. Religious communication is of the unreal type. Although religious communication has benefits, these have nothing to do with the information in the communication. It is precisely the lack of material real-world information that defines religious belief. The simulation examines how unreal communication can evolve by means of social selection. [§2.5]

So "believers" are essentially defined as communicators of unreal information, and eventually fitness is manifest in terms of the number of offspring an agent leaves when it dies. Agent fitness is affected in the simulation, though, through the complex interactions (communications) among the multiple agents. Basically: agents that receive real information increase in fitness; agents who receive unreal information decrease in fitness. But an agent's tendency to communicate either type of information is affected by the type of information being received from other agents, a form of cultural learning.

In most of the simulations, the general population increases and the non-believers dominate the believers — under these basic conditions, populations increase, but the gene frequencies for real communication rise and those for unreal communication fall.

The interesting variant occurs, prompting the article title and the pop media coverage, when Dow plays with the greenbeard parameter that determines with whom an agent communicates. [see the Green-beard effect on wikipedia]. The simulations mentioned so far used greenbeard = 0, designating that the agents with whom an agent communicates is chosen randomly from a uniform distribution of the agents (i.e. no agents are preferred for communication). When Dow incorporates the greenbeard effect, then "If one agent sees that another agent is more likely to communicate unreal information, it can select that agent as a recipient of its communication with a greater probability." Basically, Dow simulates a situation in which agents are more likely to communicate with agents that themselves are more likely to disseminate unreal information.

Under such conditions, we see the population of believer agents eventually thrive.

Now, why would one implement such a greenbeard effect in the simulation? That's not clear, and makes a nice topic for another post.

Related References

Dawkins, R. (1976) The Selfish Gene. New York: Oxford University Press.

Dow, James (2006). The Evolution of Religion: Three Anthropological Approaches. Method and Theory in the Study of Religion, 18(1), 67-91.

Dow, James (2007). A Scientific Definition of Religion. Anpere: Anthropological Perspectives on Religion <http://www.anpere.net/ccount/click.php?id=13>.

Dow, James (2008). Is religion an evolutionary adaptation? Journal of Artificial Societies and Social Simulation, 11(22) <http://jasss.soc.surrey.ac.uk/11/2/2.html>.

Science is a Way Of Life — Brian Greene, 6/1/2008

TOPIC: Science (general)

Here's a nice New York Times op-ed piece by Brian Greene (6/1/2008), author of The Fabric of the Cosmos, and The Elegant Universe.

After acknowledging the standard reasons cited for "why science matters," such as the fact that science is "woven into the fabric of our day-to-day activities … affects the quality of our lives" and is critical for problem-solving and making informed decisions, Greene continues:

But here’s the thing. The reason science really matters runs deeper still. Science is a way of life. Science is a perspective. Science is the process that takes us from confusion to understanding in a manner that’s precise, predictive and reliable — a transformation, for those lucky enough to experience it, that is empowering and emotional. To be able to think through and grasp explanations — for everything from why the sky is blue to how life formed on earth — not because they are declared dogma but rather because they reveal patterns confirmed by experiment and observation, is one of the most precious of human experiences.

Later in a paragraph I would like to send to all my students who complain that science sucks out all the mystery and wonder of the world, Greene points out that:

It’s one thing to go outside on a crisp, clear night and marvel at a sky full of stars. It’s another to marvel not only at the spectacle but to recognize that those stars are the result of exceedingly ordered conditions 13.7 billion years ago at the moment of the Big Bang. It’s another still to understand how those stars act as nuclear furnaces that supply the universe with carbon, oxygen and nitrogen, the raw material of life as we know it.

Read the whole editorial yourself. It's a short and worthwhile read. I hope more and more people eventually agree with Greene that "Science is the greatest of all adventure stories …"

Related References

Easter, R., Greene, B. R., Jackson, M. G., & Kabat, D. (2005). String windings in the early universe. Journal of Cosmology and Astroparticle Physics, 2005(2). [doi: 10.1088/1475-7516/2005/02/009]

Greene, Brian 1999, original hardcover). The elegant universe: superstrings, hidden dimensions, and the quest for the ultimate theory. W. W. Norton & Company.

Greene, Brian (2004, original hardcover). The fabric of the cosmos: space, time, and the texture of reality. Knopf Publishing Group.

Greene, B., Schalm, K., Shiu, G., & van der Schaar, J. P. (2005). Decoupling in an expanding universe: backreaction barely constrains short distance effects in the cosmic microwave background. Journal of Cosmology and Astroparticle Physics, 2005(2). [doi: 10.1088/1475-7516/2005/02/001]

Dropping Babies for Good Luck & Good Health

TOPIC: bizarre, sad, religious rituals

You are not alone if you think superstitions and religious beliefs are innocuous personal choices and harmless forms of self-expression. But check this out — a brief video of religious devotees tossing babies off a building in some kind of "good luck" ritual:

http://www.youtube.com/watch?v=MV9EsQU5YgE
A brief description can be found all over the web now as various news agencies and blogs have picked this up. For example at:

http://news.sky.com/skynews/article/0,,30200-1314661,00.html
But we all might benefit from the moderating influence at a site devoted to renewed anthropological perspectives in this article focusing on anthropology and the popular media:

http://openanthropology.wordpress.com/2008/05/02/
Also very interesting right now: despite the almost month-long time since the original story, there's a surprising dearth of real information about this particular ritual and its practitioners &hellip I've been looking but have found only hundreds of copies (some more true to the original than others) of some original news blurb and lots of hysteria. I'll post again when I find further, perhaps less sensationalized, information.

UPDATE: the original news piece seems to be the following from CNN

http://edition.cnn.com/2008/WORLD/asiapcf/05/01/babies.tower/index.html#cnnSTCText

Summer Camp, Hold The Religion

TOPICS: religion, summer camp, popular press

As a child, I was truly puzzled by the religious beliefs of family, of friends, and of adults in general. The beliefs and belief systems seemed so . . . blatantly irrational, and the vigor with which people espoused their fantastic beliefs seemed inversely correlated with the humanity with which they lived their lives and treated those around them. But as a youngster, this was difficult to articulate.

Difficult in part because I was too young, too inexperienced, to understand what I was seeing and feeling, often leading me to simply dismiss the beliefs and associated behaviors as unimportant — because (my innocent self thought) how could such irrationality have any great force in the world? Wouldn't that be bizarre? So (my naive self concluded), such irrational beliefs and related behaviors must not, could not, be terribly important or influential in the day-to-day “real world” of people and things and schools and governments, etc. It must be merely some odd quirkiness of human society, so I thought. Older now, but not much wiser, I still feel that pull of amazed disbelief. How could someone be so … blatantly irrational? Surely such irrational beliefs and related behaviors couldn't (and couldn't be allowed to) influence society in any but the most superficial ways? But the amazed disbelief is increasingly tempered with outrage, disgust, and discouragement: how can people be so … blatantly irrational? And how can such irrationality be so pervasive, insidious, and so forceful?

My concerns as a youngster were difficult to articulate also because I never, ever encountered anyone else questioning such things. Friends, family, children and adults around me … the only criticism I witnessed of religious belief was leveled by others with a different religious belief. Our irrational belief system, they seemed to say, is better than that irrational belief system over there. As a kid, who was I going to talk to about my lack of belief? And why did I feel embarrassed when confronted with weird religious beliefs and rituals of my friends? I wasn't embarrassed for them — I was truly embarrassed myself.

I think I would have really appreciated an escape to something like Camp Quest, described on the Camp Quest website as “The Secular Summer Camp” founded explicitly to

… provide children of freethinking parents a residential summer camp dedicated to improving the human condition through rational inquiry, critical and creative thinking, scientific method, self-respect, ethics, competency, democracy, free speech, and the separation of religion and government guaranteed by the Constitution of the United States.

USAToday picked up a piece on Camp Quest by Valerie Bauman of the Associated Press.

Camper Caitlin Fox, 16, said the camp has helped her build confidence.

“Before I attended I used to feel really embarrassed,” she said. “I was afraid my friends would reject me if I didn't believe in some higher power.”

Bauman points out, of course, that

Critics say the camps appear to espouse a particular point of view.

Erika Chopich, a psychotherapist, chaplain and founder of the nonprofit Hope America Ministries Foundation, said the invisible creatures in the exercise are obvious metaphors for God. "It's clearly meant to teach that God cannot possibly exist," Chopich said. "... There's obviously some teaching going on, there's some philosophy there. It's not completely neutral."

Chopich has a good point, of course, although it's not the point she intended. Rational thought is never neutral when used to confront nonsense.

And I wish I had such support when I was a kid.

Quick note: try a Google search on this topic — it's amazing (and encouraging? I don't know) how many sites have picked up this news item.

Mindfulness-Based Therapies in The New York Times

TOPIC: mindfulness, popular press

Here's a great article by Benedict Carey in the New York Times on the increasing clinical interest in mindfulness-based practices and therapies:

Lotus Therapy, a New Old Path (NYT 5/27/2008)

Lotus therapy? Yes … well, in addition to the ridiculous title, someone decided to throw in two really silly pictures, one of a pseudo-Freudian-looking man, presumably a psychologist, floating in a lotus position with pen and notepad in hand, and the other an equally silly picture of Zindel Segal titled “a psychologist, demonstrating meditative therapy.” [see below, originally captioned as “ANXIETY AID Zindel Segal, a psychologist, demonstrating meditative therapy. Jim Ross for The New York Times.”].

I don't mean that Zindel Segal himself is silly, of course. I can just imagine some poor staff photographer sent over to get pics for this article and discovering that . . . there's nothing to photograph.

Photographer: well, maybe you could demonstrate the technique, you know, for a picture to go along with the article.

Segal: the technique?

Photographer: yeah, you know, like doing something mindfully?

Segal: you want to take a picture of me doing something mindfully?

Photographer: yeah, like just for a few seconds do something mindful and I'll take a few snaps and get out of here.

Segal: Hmmm. OK. [sitting down and crossing legs] How's this?

Photographer: Uh huh. Well, could you do something more active? I mean, something more obviously mindful?

Segal: So people will see it in the picture?

Photographer: yeah man, exactly.

Segal: no.

Photographer: well that sucks.

DESPITE that silliness, the article itself is a treat, mentioning all in one place a good handful of pioneering researchers in the field of mindfulness studies and applications (in order of appearance): Zindel Segal, Jon Kabat-Zinn, Marsha Linehan, J. Mark G. Williams, John D. Teasdale, & S. Helen Ma, and striking a reasonable balance between the pros and cons, the positive and negative results flowing from research into mindfulness-based applications to physical and mental health.

Among any number of nice bits of information, Carey quotes Segal as thinking “… a big part of [the rising interest in mindfulness] is that more and more therapists are practicing some form of contemplation themselves and want to bring that into therapy.” In fact (something Carey probably didn't have the space to point out), there are at least two other significant aspects to that particular influence — not just the therapists bringing contemplative practices from home into the office, but also taking mindfulness practices home to help with the stress of the job and using mindfulness practice to make themselves better therapists/practitioners. Just a few examples of recent research include:

Carson, S. H. & Langer, E. J. (2004). Mindful Practice for Clinicians and Patients. In Haas, L. J. (Ed) Handbook of primary care psychology, 173-183. New York:Oxford University Press.

Christopher, J. C., Christopher, S. E., Dunnagan, T., & Schure, M. (2006). Teaching Self-Care Through Mindfulness Practices: The Application of Yoga, Meditation, and Qigong to Counselor Training. Journal of Humanistic Psychology, 46(4), 494-509.

Grepmair, L., Mitterlehner, F., Nickel, M. (2006). Promotion of mindfulness in psychotherapists in training and treatment results of their patients. Journal of Psychosomatic Research, 60(6), 649-650.

Grepmair, L., Mitterlehner, F., Loew, T., Bachler, E., & Rother, W. (2007). Promoting mindfulness in psychotherapists in training influences the treatment results of their patients: A randomized, double-blind, controlled study. Psychotherapy and Psychosomatics, 76(6), 332-338.

Shapiro, S. L., Brown, K. W., ; Biegel, G. M.(2007). Teaching self-care to caregivers: Effects of mindfulness-based stress reduction on the mental health of therapists in training. Training and Education in Professional Psychology, 1(2), 105-115.

Stratton, P. (2006) Therapist mindfulness as a predictor of client outcomes. Dissertation Abstracts International: Section B: The Sciences and Engineering, 66(11-B), 6296.

Wexler, J. (2006) The relationship between therapist mindfulness and the therapeutic alliance.Dissertation Abstracts International: Section B: The Sciences and Engineering, 67(5-B), 2848.

Carson & Langer (2004), e.g., note that “Increasing mindfulness rather than mindlessness can help patients recast their experiences in a different light as well as help clinicians approach patients' problems from a different perspective,” and argue that “a mindful perspective can have a useful impact on the decisions of a mental health professional regarding diagnostic issues and coordination with the primary care physician and staff.”

Carey points out that “Many researchers now worry that the enthusiasm for Buddhist practice will run so far ahead of the science that this promising psychological tool could turn into another fad.” The enthusiasm, of course, is building in both the professional health-care system and in the general public.

But this just reminds us that we need to carefully evaluate the science, continue to do the critical research, and remind ourselves that no single treatment will be effective or appropriate for complex human behaviors with multiple underlying causes.

Some Related References

Hahn, T. N. (1987). The miracle of mindfulness: an introduction to the practice of meditation. Boston: Beacon Press.

Kabat-Zinn, J. (1994/2005). Wherever you go, there you are: mindfulness meditation in everyday life (10th anniversary edition). New York: Hyperion.

Kabat-Zinn, J. (2005). Coming to our senses: Healing ourselves and the world through mindfulness. New York: Hyperion.

Segal, Z. V., Williams, J. M. G., & Teasdale, J. D (2002). Mindfulness-based cognitive therapy for depression. New Tork: The Guilford Press.

Prebish, C. S. & Baumann, M. (Eds) (2002). Westward Dharma: Buddhism beyond Asia. Berkeley: University of California Press.

Scientists vs. Non-Scientists

TOPIC: Science Humor

Ever wondered about the fundamental differences between scientists and non-scientists? Logic? Creativity? Rationality? Skepticism? Hmmmm … try this:

http://xkcd.com/242/

Confirmed: The Phoenix has Landed!

Here's one of the first images from Phoenix — a look at the northern polar region of Mars. (photo courtesy of the NASA website at http://www.nasa.gov/mission_pages/phoenix/main/)

Photos from an alien world. What an amazing way to end the weekend.

The Phoenix has Landed!

TOPIC: science news, current events

Looks like a successful landing for Phoenix! Check this out at NASA’s own web site:

http://www.nasa.gov/mission_pages/phoenix/main/
and a report at the New York Times web site:

NYT: NASA Spacecraft Appears to Have Landed on Mars

And this is really cool — watch the NASA control room live:

NASA Control Room TV

Alzheimer’s Disease As Infection

TOPIC: science & health news

COULD Alzheimer’s disease (AD) be caused in part by infection?

Evidence has gradually accumulated to suggest that this theory about the etiology of Alzheimer’s disease (AD) should be taken up more seriously. And the serious tone is evidenced now in a series of articles in a special May 2008 issue of the Journal of Alzheimer’s Disease as reported on ScienceDaily and EurekAlert! (Both ScienceDaily and EurekAlert have good summaries of the news, so I'm not attempting a summary here — just passing along the news.)

But hasn't public scientific discussion of AD centered primarily on the genetic bases for the disease, for which we have good accumulating evidence? (See e.g. Ertekin-Taner, 2007, below.) And doesn't the apparent genetic basis/susceptibility for AD rather contradict an infection-based theory about the causes of the disease?

Yes … and most definitely No. The approaches are quite compatible. After all, genetics can determine in no small part, for example, one’s susceptibility to certain types of infection. So a disease may have significant genetic and environmental components — essentially a diathesis-stress model of disease.

Moreover, roughly 95% of cases of AD are non-familial late-onset Alzheimer’s disease (LOAD), also called “sporadic” AD, which has a number of known genetic risk factors — but risk factors aren't the same as determinants of the disease. Somehow such risk factors interact with environmental factors (in the broad sense of that phrase) to ultimately determine the course (if any) of the disease.

The work on AD is exciting and our growing understanding of its causes inspires hope that we'll eventually be able to treat and prevent this awful affliction.

Related links.

Fisher Center for Alzheimer’s Research Foundation [http://www.alzinfo.org/]

Journal of Alzheimer’s Disease [http://www.j-alz.com/index.html]

Wikipedia: Alzheimer’s Disease [http://en.wikipedia.org/wiki/Alzheimer_disease]

Related references.

Ertekin-Taner, Nilüfer (2007). Genetics of Alzheimer’s disease: a centennial review. Neurologic Clinics, 25(3), 611–667.

Balin, B., Little, C. S., Hammind, C. J., Appelt, D. M., Whittum-Hudson, J. A., Gerard, H. C., & Hudson, A. P. (2008) Chlamydophila pneumoniae and the etiology of late-onset Alzheimer’s disease. Journal of Alzheimer’s Disease, 13(4), 371–380.

Hammer, N. D., Wang, X., McGuffie, B. A., & Chapman, M. R. (2008) Amyloids: Friend or Foe? Journal of Alzheimer’s Disease, 13(4), 407–419.

Itzhaki, R. F. & Wozniak, M. A. (2008) Herpes Simplex Virus Type 1 in Alzheimer’s disease: The Enemy Within. Journal of Alzheimer’s Disease, 13(4), 393–405.

KRamer, A. R., Dasanayeke, A., Craig, R. G., Glodzik-Sobanska, L., Bry, M., & de Leon, M. J. (2008) Alzheimer’s disease and peripheral infections: The possible contribution from periodontal infections, model and hypothesis. Journal of Alzheimer’s Disease, 13(4), 437–449.

Miklossy, J. & Martins, R. (2008) Preface: Chronic inflammation and amyloidogenesis in Alzheimer’s disease: The emerging role of infection. Journal of Alzheimer’s Disease, 13(4), 357.

Miklossy, J. (2008) Chronic inflammation and amyloidogenesis in Alzheimer's disease – role of spirochetes. Journal of Alzheimer’s Disease, 13(4), 381–391.

Schwab, C. & McGeer, P. L. (2008) Inflammatory Aspects of Alzheimer Disease and Other Neurodegenerative Disorders. Journal of Alzheimer’s Disease, 13(4), 359–369.

Scott, L. C., Hammind, C. J., MacIntyre, A., Balin, B. J., & Appelt, D. M. (2004) Chlamydia pneumoniae induces Alzheimer-like amyloid plaques in brains of BALB/c mice. Neurobiology of Aging, 25(4), 419–429.

Urosevic, N. & Martins, R. N. (2008) Infection and Alzheimer’s disease: The ApoE e4 connection and lipid metabolism. Journal of Alzheimer’s Disease, 13(4), 421–435.

Weinberg, E. D. & Miklossy, J. (2008) Iron withholding: a defense against disease. Journal of Alzheimer’s Disease, 13(4), 451–463.