Biodiversity and Entropy

On Tuesday, my Erdos number dropped from infinity to four. That's right: after four years of grad school, I am now officially published!

The article, “A New Phylogenetic Diversity Measure Generlizing the Shannon Index and Its Application to Phyllostomid Bats,” by Ben Allen, Mark Kon, Yaneer Bar-Yam, can be found on the American Naturalist website or, more accessibly, on my professional site.

So what is it about? Glad you asked!

Protecting biodiversity has become a central theme of conservation work over the past few decades. There has been something of a shift in focus from saving particular iconic endangered species, to preserving, as much as possible, the wealth and variety of life on the planet.

However, while biodiversity may seem like an intuitive concept, there is some disgreement about what it means in a formal sense and, in particular, how one might measure it. Given two ecological communities, or the same ecological community at two points in time, is there a way we can say which community is more diverse, or whether diversity has increased or decreased?

Certainly, a good starting point is to focus on species. As the writers of the Biblical flood narrative were in some sense aware, species are the basic unit of ecological reproduction. Thus the number of species (what biologists call the "species richness") is a good measure of the variety of life in a community.

But aren't genes the real unit of heredity, and hence diversity? Is the number of species more important than the variety of genes among those species? Should a forest containing many very closely related tree species be deemed more diverse than another whose species, though fewer, have unique genetic characteristics that make them valuable?

And while we're complicating matters, what about the number of organisms per species? Is a community that is dominated by one species (with numerous others in low proportion) less diverse than one containing an even mixture?


There is no obvious way to combine all this information into a single measure for use in monitoring and comparing ecological communities. Some previously proposed measures have undesirable properties; for example, they may increase, counterintuitively, when a rare species is eliminated.

In this paper we propose a new measure based on one of my favorite ideas in all of science: entropy. You may have heard of entropy from physics, where it measures the "disorderliness" of a physical system. But it is really a far more general concept, used also in mathematics, staticstics, and the theory of automated communication (information theory) in particular. At heart, entropy is a measure of unpredictability. The more entropy in a system, the less able you will be to accurately predict its future behavior.

The connection to diversity is not so much of a stretch: in a highly diverse community, you will be less able to predict what kinds of life you will come across next. Diversity creates unpredictability.

To be fair, we weren't the first to propose a connection between diversity and entropy. This connection is already well-known to conservation biologists. But we showed a new and mathematically elegant way of extending the entropy concept to include both species-level and gene-level diversity. It remains to be seen whether biologists will take up use of our measure, but whatever happens I am happy to have contributed to the conversation.

A Middle/High School That Teaches Complex Systems Through Games??!

A new school is opening in New York for grades 6-12 that completely blows my mind. The Quest to Learn school combines games and complex systems in a way that pretty much would have made my life as a teenager. Hell, I wouldn't mind going back to high school now if I got to go here. I'll let them describe it:

Mission critical at Quest is a translation of the underlying form of games into a powerful pedagogical model for its 6-12th graders. Games work as rule-based learning systems, creating worlds in which players actively participate, use strategic thinking to make choices, solve complex problems, seek content knowledge, receive constant feedback, and consider the point of view of others. As is the case with many of the games played by young people today, Quest is designed to enable students to “take on” the identities and behaviors of explorers, mathematicians, historians, writers, and evolutionary biologists as they work through a dynamic, challenge-based curriculum with content-rich questing to learn at its core. It’s important to note that Quest is not a school whose curriculum is made up of the play of commercial videogames, but rather a school that uses the underlying design principles of games to create highly immersive, game-like learning experiences. Games and other forms of digital media serve another useful purpose at Quest: they serve to model the complexity and promise of “systems.” Understanding and accounting for this complexity is a fundamental literacy of the 21st century.

Elsewhere they go into a bit more detail about how games are used to teach different subject areas:

At Quest students learn standards‐based content within classes that we call domains. These domains organize disciplinary knowledge in 21st certain ways—around big ideas that require expertise in two or more traditional subjects, like math and science, or ELA and social studies. One of our domains— The Way Things Work—is an integrated math and science class organized around ideas from design and engineering: taking systems apart and putting them back together again. Another domain—Codeworlds—is an integrated ELA, math, and computer programming class organized around the big idea of symbolic systems, language, syntax, and grammar. A third domain—Being, Space and Place—an integrated ELA and social studies class—is organized around the big idea of the individual and their relationship to community and networks of knowledge, across time and space. Wellness is the last of our integrated domains, a class that combines the study of health, socio‐emotional issues, nutrition, movement, organizational strategies, and communication skills.

OMG!OMG!OMG!OMG!

One of my favorite aspects of this school is that they have a separate staff of game designers working together with their teachers. As a former teacher I can tell you that designing good, creative lessons is a relatively different skill-set from actually implementing these lessons in front of a class and following up with your students, and that doing both well requires more time than is physically possible without traveling at relativistic speeds. So having designers who are there at the school and understand the teachers' needs, and who have the time to make great lessons, is a really really good idea.

At IIASA

This is just a brief note to let everyone know I'm spending the summer at IIASA, a scientific policy research institute located just outside of Vienna. IIASA focus on systems analysis of global problems such as climate change, land use, demographic changes, public health, ecology, and energy. They don't seem to use the phrase "complex systems" much, but they're clearly talking about the same thing.

I happen to be one of 53 lucky graduate students to be selected for this year's Young Scholars Summer Program, meaning I get to paid to live in Vienna and do research. Can't really complain about that. Tomorrow I get to hear mini-presentations on everyone's research proposals, which should be very interesting. My own project will be on the long term, gradual evolution of cooperation in spatially structured populations, using a mathematical framework known as adaptive dynamics.

I'm expecting to learn a lot here, and I'll share as much as I can with you readers. Looking forward to it!

The Catholic Perspective on Evolution

As an occasional reader of science blogs, I can't help but notice the extraordinary amount of time and space devoted to the debunking of Creationist and Intelligent Design "science." Certainly there are good reasons for this: the poor reasoning and scant evidence behind such pseudoscience makes it an easy target, and the surprising momentum of the Creationist political agenda represents a genuine threat to American science education.

Still, I can't help but feel that the focus on Creationism's pseudoscientific claims have obscured what is really a debate about beliefs and values, not science. Moreover, the discourse on blogs often reflects a view that religion (of all forms) is inherently opposed to evolution, and that no intelligent person could possibly believe in both.

My partner addressed some of these issues in a final paper for her recently completed Master's of Theological Studies degree from Harvard Divinity School. This paper begins with an anecdote describing the surprising and complex position toward evolution taken by middle school students she taught, and goes on to detail the history of Catholic responses to Darwin's theory. Some of the ideas from her paper are articulated below in the hopes of adding nuance to the evolution blogversation. Neither she nor I intend to present either her students' view or the Catholic view as models for how to reconcile (or not) evolution and faith, but only as voices that complexify the picture of this conversation as a fight between Bible-thumping evangelists on the one hand and atheist scientists on the other.

....

In 2004 I was a new, white teacher at a middle school in Dorchester, Massacusetts. The students in my seventh and eighth grade comparative religions classes were young women of color, and of primarily African and Caribbean descent. During the kind of cheerfully chaotic class that takes place the day before a lengthy school holiday, one of my most inquisitive students surprised me with a question about evolution. She wanted to know who was right: the scientists, or the people we were studying in religion class? Before I could collect my thoughts, a flood of powerful and emotional rejoinders issued from several of her classmates. My limited familiarity with the traditions with which they were affiliated gave me only a vague sense that I might expect a critical stance on the subject. What I had entirely failed to consider were the ways in which the cultural and racial identities of my students intersected with both their religious worldviews and their feelings about evolution. I soon learned that the ways in which many of these young women processed the tense public controversy over evolution and Biblically based accounts of creation were deeply tied to their sense of identity as people of color in a white-dominated culture. Many began quoting their pastors: “You are made in the image of God. You are beautiful, loved, and wanted in this world, and can’t nobody take that away from you.” Others followed with similar, powerful words that affirmed the essential pride and self worth that was instilled in any child of God. Still other students spoke of the historical influence of this notion of essential human worth on abolitionist and civil rights movements. They knew their history. The concept that all humans have been made with great love and purpose by God has historically operated as a powerful political and psychological resource to combat the behaviors of a racist society. Many students made it clear that they saw the promotion of evolutionary theory as a direct attack on the foundations of their personal identity, faith, and value as human beings.

Though I felt moved and honored to hear the powerful and nuanced ways in which my students articulated the liberative power behind the Biblical account of creation, I was pained to hear how rigidly and antagonistically they conceptualized the “evolution side” of this conversation. I found their monolithic image of “evolutionists” to be a clear example of the troubling state of an important conversation. These young women’s understanding of the relationship between evolution and faith led them to conceive of the scientific claim as only another attack on their sense of self by a hostile, dominant majority ¹. Such an understanding represents a disconcerting deficit of education on both sides of the conversation, effectively eclipsing a range of voices from adding texture to what has become yet another American clash of extremes.

Most contemporary public discussion and media attention on the subject has been shaped by the polarizing rhetoric of certain anti-evolution Protestant American Christians. Those who oppose these efforts by criticizing creationist “science” have largely fallen into the trap of engaging in only reactionary responses. Many on both sides have portrayed this conversation as a conflict of “religion versus science,” ignoring the fact that the Creationist movement has historically been a uniquely American Protestant phenomenon ², which has only in the past couple decades begun to spread to other countries ³.

Ironically, included in the crowd of voices with which my students were unfamiliar were those from the Catholic Church, the tradition upon which their school was founded. Indeed, when I related my classroom conversation to some of my fellow teachers, most of whom were raised within the Church, they expressed great surprise, recalling that the science classes within their own Catholic education had included extensive coverage of the scientific theory of evolution. (In fact, a survey of American Catholic school textbooks published between 1940-1960 found them to be in closer agreement with evolutionary theory than American public school textbooks from the same period ⁴.) Intrigued, I looked further into the historical response of the Catholic Church to Darwin and found a complex story that most certainly disrupts the largely monolithic representation of Christian responses to this scientific theory. It is also a story that is infrequently told, and appears to be largely unfamiliar to much of the American public ⁵.

For almost a full century following publication of “Origin of the Species,” the Church hierarchy avoided any official stance on, or condemnation of, evolution. The first official Vatican pronouncement, Pope Pius XII’s 1950 encyclical, Humani Generis (Human Origins), ackowledged evolution as a possible scientific explanation for the origin of humanity⁶. More recent pronouncements have strongly embraced evolution as a scientific theory, as evidenced in Pope John Paul II’s 1996 address to the Pontificate Academy of Sciences, the current Pope Benedict XVI’s text “Communion and Stewardship: Human Persons created in the image of God,” and the 2009 Vatican conference on “Biological Evolution: Facts and Theories.” These documents express the view that evolution can be regarded as both a random process in the scientific sense, as well as a fulfillment of God’s plan⁷. Thus, while the Church accepts evolution as a scientific theory, it rejects any claims that this theory has no place for God. Significantly, these documents seek to distance the Catholic perspective from that of intelligent design Creationists⁸, and intelligent design speakers were pointedly barred from the recent Vatican conference.

Popular thought about evolution amongst American Catholic laity, scholars, and journalists has been largely supportive of evolutionary theory as well. A literature review of popular Catholic press indicates that responses to the 1925 Scopes and 2005 Dover trials (the former testing a Tennessee prohibition against teaching evolution in public schools, and the latter arguing against the inclusion of intelligent design within public school science curricula) demonstrates a desire to problematize any claims of an inevitable clash between science and religion brought about by the teaching of evolution⁹. For example, one 1925 editorial in a Catholic newsletter argued “[Creationist lawyer] William Jennings Bryan is reported as having said that if evolution is true, then Christianity can’t be true. In this matter as well as many others Mr. Bryan is wrong.” ¹⁰

.....

The full text of the paper, which delves more deeply into how science becomes appropriated as a "cultural resource" and gives recommendations for teaching, can be made available on request. Again, our purpose is not to espouse or promote the Catholic view, but merely to present it as evidence that Creationists do not represent all, or even most, religious (or even Christian) views on evolution, and to highlight some of the hidden cultural factors underlying this debate.

Footnotes:
¹ While I affirm that it is crucial for my students to develop a more nuanced understanding of the scientific community, it is important to note that, as young women of color their anger and anxiety is certainly not unfounded. The history of science as practiced by dominant culture is guilty of repeatedly producing scientific data and discourse in ways that either exploit or promote racist ideology. The American eugenics movement and the Tuskegee Syphilis Study are but two examples of this phenomenon.

² Eugenie C. Scott, Evolution vs. Creationism (Westport, CT: Greenwood Press, 2004), 85-134.

³ Simon Coleman and Leslie Carlin, Cultures of Creationism (Burlington, VT: Ashgate, 2004), ix.

⁴ Gerald Skoog, “The Coverage of Human Evolution in High School Biology Textbooks in the 20th Century and Current State Science Standards,” Science and Education 14(2005):412-413.

⁵ Ronald L. Numbers and John Stenhouse, eds., Disseminating Darwinism (Cambridge: Cambridge University Press, 1999), 2. This text is one of many that notes the lack of both scholarly research and public knowledge on the Catholic position toward evolution.

⁶ Humani Generis, Chapter 36.

⁷ “Communion and Stewardship,” Chapter 69.

⁸ Ibid.

⁹ Christopher M. Hammer, Reconciling Faith, Reason, and Freedom: Catholicism and Evolution from Scopes to Dover (MA Thesis, University of Virginia, 2008), 3.

¹⁰ F. Gordon O’Neil, “The Week,” Monitor and Intermountain Catholic, June 6, 1925, 1.

Nature Minus Humans?

From the "nothing is quite so simple" department, a Boston Globe article this week points out a hidden legacy of the conservation movement: The expulsion of native peoples from their land.

Starting with Yosemite in the late 19th and early 20th centuries, the pattern of forcing indigineous civilizations from their ancestral land in order to create wildlife reserves and national parks has been repeated across the country and the world.

The conflict is... compelling the conservation movement to grapple with the effects of its own century-long blunder, and with its origins as an American movement driven largely by nature romantics and aristocratic men determined to protect their hunting grounds. Not only has it dispossessed millions of people who might very well have been excellent stewards of the land, but it has engendered a worldwide hostility toward the whole idea of wildland conservation - damaging the cause in many countries whose crucial wildland is most in need of protection.

The article describes how indigineous peoples threatened with displacement across the globe have begun to band together to force a change in the conservationist mindset that humanity and nature are antithetical.

Reporting like this is why the Boston Globe needs to stay in business.

The Human Dimension of Climate Change

A New York Times Magazine article raises an issue I've been thinking a lot about lately.

If you are, as I am, a scientist concerned about global climate change, you may find yourself asking, "What kind of research could I be doing to best contribute to a solution?"

According to some, it may not be to study the climate itself. We may not know enough to predict exactly what will happen when, but we do know that drastic changes are coming whose magnitude will be determined by the actions we take now. It may not even be to study technologies such as alternative energy or policies such as cap-and-trade that can help combat global warming. Because while these policies and technologies are surely necessary, global warming is a problem created by human behavior, and our behavior will need to change if we are to make the individual and group decisions necessary to mitigate it, including the implementation of these policies and technologies. It may therefore be that the most important scientific questions in the fight against global warming are questions about humans, human behavior, and what we can do to change it.

The climate change puzzle presents a number of interesting questions about human behavior. The global environment is the ultimate "commons" game: We have a shared resource, and we can individually decide how much effort to put into preserving it. Only, we don't see the fruit of our individual efforts directly; only the sum total of everyone's efforts determines how well the resource is preserved. In the case of climate change, there are further complications: the effects of our actions now may not be seen for another fifty years, and some argue that the entire problem was fabricated by misguided scientists. Combining these factors, it is not hard to understand why many people feel little incentive to take action against global warming.

The article focuses on Columbia's Center for Research on Environmental Decisions, which performs experiments on people's decision-making processes. One finding jumped out at me as interesting and perhaps counter-intuitive: we tend to make better decisions as groups rather than as individuals. For example, one researcher studied decisions made by farmers in Southern Uganda as they listened to rainy-season radio broadcasts. If they listened to it in groups, they would typically discuss it afterwards and come to consensus on the best planting strategy in response to the weather. They ended up more satisfied with their yields than other farmers who listened to the broadcasts individually.

Our response to climate change will obviously involve a great variety of individual and group decisions, but it may be that if we can force more of the critical decisions to be made in group settings, where participants have not made up their minds beforehand (research shows this is crucial) we may find ourselves more able to put aside the parts of our human nature that would impede progress, and make the decisions that are in all of our best interests.

Gangs and Homeostasis

"To live outside the law you must be honest"
-Bob Dylan

I just finished "Gang Leader for a Day", a memior in which sociologist Sudhir Venkatesh recounts his days as a University of Chicago graduate student, most of which were spent hanging out in the Robert Taylor Homes with one of Chicago's most successful crack selling gangs.

My personal interest in gang culture began with my teaching days on the west side of Chicago. Over the course of my first year I gradually realized the extent to which gang affiliations were affecting the culture of my classroom and the school at large. Four sesasons of The Wire widened my interest by showing how the drug trade intersects with every other aspect of city life.

Venkatesh's story starts with an ill-advised trip to a local housing project as a first-year sociology student, in which he tries to get anyone to answer the asanine survey questions he has prepared (question one: "How does it feel to be black and poor?") He is detained overnight and nearly killed by the local gang members on suspicion of being a scout for a rival gang. But their leader, J.T., recognizes Venkatesh for the naive outsider he is, and advises him to dispense with the surveys. "With people like us, you should hang out, get to know what they do, how they do it."

The rest of the book, and indeed Venkatesh's entire graduate research, is predicated on the unlikely interest J.T. takes in Venkatesh and his project. He believes Venkatesh will write his biography (Venkatesh does little to contradict this misconception) and gives him guided tours on nearly every aspect of the gang's operations, often trying to cast himself as a philanthropic community organizer. In time, Venkatesh's research branches out to other forces in project life: prosititutes, odd-job hustlers, community workers, religious leaders, CHA (Chicago Housing Authority) representatives, and police, each playing complex and often morally ambiguous roles.

There is much of interest here from a complex systems perspective, but the place to start is probably the multiple roles the gang plays in project life.

First and foremost, the gang is a business. It exists to make money, most of which goes to the upper management. In the case of the Black Kings gang that ran the towers in this story, the business was primarily crack cocaine, though they also extorted "protection" money from other formal and informal businesses in and around the towers.

However, because of the nature of the business, it wouldn't do to have cops, social workers, and other civil servants roaming around the projects. The gang was largely effective in keeping these unwanteds out, but this meant there was a vacuum in terms of keeping order, resolving disputes, and looking after children. The gang stepped in to fill part of this vacuum. They helped negotiate conflicts between tenants, and mete justice when it seemed necessary. Sometimes they even helped clean the tower hallways. And J.T. instituted a rule that no one could join the gang unless they had graduated high school.

Despite J.T.'s talk of helping the community, the primary reasons for this behavior were financial, not altruistic. Any violence in the building would attract the attention of the cops, which in turn would disrupt operations and scare away customers. It was therefore in their interest to resolve disputes peacefully, or to administer punishment so that a wronged party would not take matters into their own hands. Keeping teenagers in school would also cut down on unwanted violence, and produce workers better able to handle money.

The relevant complex systems principle here is homeostasis: the regulation of one's internal environment. In order to compete effectively against other forces (gangs, police, etc.), the Black Kings had to reduce competition and discord within their own gang and the community in which they operated.

There's so much more to Venkatesh's story than I could possibly relate here, so I'll end by giving the book a full-throated recommendation. Although his naivite is often cringeworthy, his experiences provide a window into a complex world that operates so differently from the societies most of us inhabit.