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.
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Change of address1 year ago in Variety of Life
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post doc job opportunity on ribosome biochemistry!11 years ago in Protein Evolution and Other Musings
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Lab Rat Moving House14 years ago in Life of a Lab Rat
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in The Biology Files
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.
Freeman Dyson on Climate Change
The New York Times has an article on eminent physicist Freeman Dyson's skepticism of climate change arguments. Several passages struck me in particular:
In a long-term sense, he is completely right. Life on earth has survived much greater shocks in the past and will likely continue to adapt and evolve as long as the sun is shining. We humans are a particularly adaptable bunch; we don't need to wait for genetic evolution to change our behaviors. We have devised ingenious solutions to our problems in the past, and we could probably think of something to carry us through whatever changes may come.
But the problem with this argument is the short-term. Humanity and life in general may be infinitely adaptable, but the fact is that, for the moment, we have adapted to life on the planet the way it is. We depend on certain plants and animals for food. These plants and animals in turn depend on other plants and animals, as well as certain chemicals and climate conditions. Every step in this chain is, for the moment, perfectly adapted to the climate of the present. Nature has even devised its own mechanisms to keep the current climate in place: for example, ocean bacteria help regulate the earth's temperature and atmosphere. We are, at present, in a state of equilibrium.
Massive increases in carbon dioxide, leading to rapid temerature growth, would push us out of equilibrium. Nature's homeostatic (equilibrium-maintaining) mechanisms would be insufficient to maintain our current climate, and large changes would occur. Food chains would have to be restructured as intermediate links go extinct. Some species would win and some would lose in the scramble to adjust to the new status quo.
Ecologists know that an ecosystem pushed out of equilibrium will eventually reach some new equilibrium state. But the details of this new state are impossible to predict ahead of time. Which species will dominate? What new food chains will form? This is the big question of climate change; no one can really say.
As far as we humans are concerned, the odds that this new state will be better for us are pretty low. Consider, for example, that the typical American diet is built from a relatively small variety of fruits, vegetables, grains, and animals. And the genetic variety within these crops is decreasing as breeds become standardized within the agriculture industry. It's unlikely that the specific plants and animals we depend on will be winners in the new equilibrium, since they, like us, are adapted to what we have now. We will have to scramble to change how we eat, as well as where we live, thanks to sea level changes. Millions of lives will be disrupted in this change. We have to ask ourselves, as a society, if we this disruption is an acceptable tradeoff to maintain our current energy habits a little longer.
As mathematician and ecologist Simon Levin said, “Nature is not fragile... what is fragile are the ecosystems services on which humans depend."
Dyson agrees with the prevailing view that there are rapidly rising carbon-dioxide levels in the atmosphere caused by human activity. To the planet, he suggests, the rising carbon may well be a MacGuffin, a striking yet ultimately benign occurrence in what Dyson says is still “a relatively cool period in the earth’s history.” The warming, he says, is not global but local, “making cold places warmer rather than making hot places hotter.” Far from expecting any drastic harmful consequences from these increased temperatures, he says the carbon may well be salubrious — a sign that “the climate is actually improving rather than getting worse,” because carbon acts as an ideal fertilizer promoting forest growth and crop yields. “Most of the evolution of life occurred on a planet substantially warmer than it is now,” he contends, “and substantially richer in carbon dioxide.” Dyson calls ocean acidification, which many scientists say is destroying the saltwater food chain, a genuine but probably exaggerated problem. Sea levels, he says, are rising steadily, but why this is and what dangers it might portend “cannot be predicted until we know much more about its causes.”and
Beyond the specific points of factual dispute, Dyson has said that it all boils down to “a deeper disagreement about values” between those who think “nature knows best” and that “any gross human disruption of the natural environment is evil,” and “humanists,” like himself, who contend that protecting the existing biosphere is not as important as fighting more repugnant evils like war, poverty and unemployment.His basic argument seems to be that, yes, human activity is causing global temperatures to rise, but this may not be a bad thing. Life, and humanity, will adjust to life in the new climate through adaptation and evolution, and may even emerge richer and stronger.
In a long-term sense, he is completely right. Life on earth has survived much greater shocks in the past and will likely continue to adapt and evolve as long as the sun is shining. We humans are a particularly adaptable bunch; we don't need to wait for genetic evolution to change our behaviors. We have devised ingenious solutions to our problems in the past, and we could probably think of something to carry us through whatever changes may come.
But the problem with this argument is the short-term. Humanity and life in general may be infinitely adaptable, but the fact is that, for the moment, we have adapted to life on the planet the way it is. We depend on certain plants and animals for food. These plants and animals in turn depend on other plants and animals, as well as certain chemicals and climate conditions. Every step in this chain is, for the moment, perfectly adapted to the climate of the present. Nature has even devised its own mechanisms to keep the current climate in place: for example, ocean bacteria help regulate the earth's temperature and atmosphere. We are, at present, in a state of equilibrium.
Massive increases in carbon dioxide, leading to rapid temerature growth, would push us out of equilibrium. Nature's homeostatic (equilibrium-maintaining) mechanisms would be insufficient to maintain our current climate, and large changes would occur. Food chains would have to be restructured as intermediate links go extinct. Some species would win and some would lose in the scramble to adjust to the new status quo.
Ecologists know that an ecosystem pushed out of equilibrium will eventually reach some new equilibrium state. But the details of this new state are impossible to predict ahead of time. Which species will dominate? What new food chains will form? This is the big question of climate change; no one can really say.
As far as we humans are concerned, the odds that this new state will be better for us are pretty low. Consider, for example, that the typical American diet is built from a relatively small variety of fruits, vegetables, grains, and animals. And the genetic variety within these crops is decreasing as breeds become standardized within the agriculture industry. It's unlikely that the specific plants and animals we depend on will be winners in the new equilibrium, since they, like us, are adapted to what we have now. We will have to scramble to change how we eat, as well as where we live, thanks to sea level changes. Millions of lives will be disrupted in this change. We have to ask ourselves, as a society, if we this disruption is an acceptable tradeoff to maintain our current energy habits a little longer.
As mathematician and ecologist Simon Levin said, “Nature is not fragile... what is fragile are the ecosystems services on which humans depend."
Reader Show-and-Tell
One of the joys of writing a blog like this is receiving comments from people I've never met in real life, but who have stumbled upon my blog from somewhere in webland, and found something on it worth responding to. It's really great to know my ideas are bubbling out and reaching people.
So this time I'd like to put aside my usual format and get to know some of my readers a little better. If you don't mind, I'd be very grateful if you can drop a comment answering these:
1. Who are you? (student, researcher, generally interested person, ...)
2. How did you find this blog?
3. What topics interest you most within those I've discussed?
4. What else interests you, either within or outside of the complex systems field?
Those who I do know in real life are also quite welcome to respond!
So this time I'd like to put aside my usual format and get to know some of my readers a little better. If you don't mind, I'd be very grateful if you can drop a comment answering these:
1. Who are you? (student, researcher, generally interested person, ...)
2. How did you find this blog?
3. What topics interest you most within those I've discussed?
4. What else interests you, either within or outside of the complex systems field?
Those who I do know in real life are also quite welcome to respond!
Two great links about the economy
1. Eduardo Porter has an excellent Op-Ed in the New York Times comparing the evolution of huge bonuses for bankers to the evolution of excess blubber on bull elephant seals--good for the individual seal (bank) but bad for the species (financial sector.) I couldn't agree more.
2. The collaboration between This American Life and NPR news that brought us the excellent show about the mortgage meltdown are back again with the clearest explanation I've heard to date on how our banking system is screwed.
2. The collaboration between This American Life and NPR news that brought us the excellent show about the mortgage meltdown are back again with the clearest explanation I've heard to date on how our banking system is screwed.
On the Definition of Life
Last post we discussed a theory for the origin of life on earth, and we found that a proper definition of life is necessary to even begin addressing the question. This post, I'd like to dig deeper into the definition issue.
I strongly feel that life is a process, and should be defined in terms of what it does, not what it's made of. But adopting a process-based definition of life means we must consider whether our definition applies to entities that we think of as non-biological. For example (as my dad pointed out upon reading my previous post) crystals replicate their structure. Should they be considered alive? Computer viruses reproduce en masse; are they alive? Are "25 things about me" Facebook posts alive?
The example of crystals, more than anything else, convinces me that although reproduction is the central feature of life, it is not sufficient for defintional purposes. Crystals have not changed their nature since they first appeared on the earth. Their abitily to "adapt" is limited to conforming to the shape of their environment; they have produced no novelty in their billions-year history.
A glance at the wikipedia page on this subject gives us several other criteria we may wish to include, such as homeostasis (the ability to regulate one's internal evironment), and metabolism (the ability to convert raw materials to energy.) But these also seem peripheral to what I would consider the principal feature of life: its abilty to create new innovations in the world. These innovations are the product of evolution, so (as faithful reader samineru suggested), we should focus on entities that don't just reproduce, but evolve.
Evolution requires that:
These requirements rule out crystals: It would be hard to say that crystals are competing in any meaningful sense, and variations in the structure of a crystal are not (as far as I know) passed down onto other crystals seeded by it. "25 things about me" posts also don't compete, and small innovations in one post are not typically passed down into the other posts inspired by it. So neither crystals nor facebook memes are alive by this definition.
Computer viruses are more tricky. I don’t know of any viruses that mutate and pass mutations on when they spread. But one can imagine this happening in the near future: viruses producing their own innovations and finding ever more devious ways to infect other computers. If they did, would we call them alive? By this definition, we would.
Such questions are central to the field of artificial life. Artificial life (or “alife”) researchers write computer programs in which entities compete and evolve according to abstract sets of rules. There is debate in this community over whether they are actually creating life with these programs, or merely simulating it.
Many other intelligent people have written on the definition of life; I recommed these articles for further reading.
I strongly feel that life is a process, and should be defined in terms of what it does, not what it's made of. But adopting a process-based definition of life means we must consider whether our definition applies to entities that we think of as non-biological. For example (as my dad pointed out upon reading my previous post) crystals replicate their structure. Should they be considered alive? Computer viruses reproduce en masse; are they alive? Are "25 things about me" Facebook posts alive?
The example of crystals, more than anything else, convinces me that although reproduction is the central feature of life, it is not sufficient for defintional purposes. Crystals have not changed their nature since they first appeared on the earth. Their abitily to "adapt" is limited to conforming to the shape of their environment; they have produced no novelty in their billions-year history.
A glance at the wikipedia page on this subject gives us several other criteria we may wish to include, such as homeostasis (the ability to regulate one's internal evironment), and metabolism (the ability to convert raw materials to energy.) But these also seem peripheral to what I would consider the principal feature of life: its abilty to create new innovations in the world. These innovations are the product of evolution, so (as faithful reader samineru suggested), we should focus on entities that don't just reproduce, but evolve.
Evolution requires that:
- Entities compete for the chance to reproduce, based on their characteristics.
- Whenever an entity reproduces, its characteristics are passed on to its offspring, with slight variation.
These requirements rule out crystals: It would be hard to say that crystals are competing in any meaningful sense, and variations in the structure of a crystal are not (as far as I know) passed down onto other crystals seeded by it. "25 things about me" posts also don't compete, and small innovations in one post are not typically passed down into the other posts inspired by it. So neither crystals nor facebook memes are alive by this definition.
Computer viruses are more tricky. I don’t know of any viruses that mutate and pass mutations on when they spread. But one can imagine this happening in the near future: viruses producing their own innovations and finding ever more devious ways to infect other computers. If they did, would we call them alive? By this definition, we would.
Such questions are central to the field of artificial life. Artificial life (or “alife”) researchers write computer programs in which entities compete and evolve according to abstract sets of rules. There is debate in this community over whether they are actually creating life with these programs, or merely simulating it.
Many other intelligent people have written on the definition of life; I recommed these articles for further reading.
On the origin of life
First of all, you may have notied something a little different here. I am now a member of Field of Science, a new network of science blogs. You can investigate the other blogs in this network through the links at the top and bottom of this page. All the content from the original blog has been imported here (including your lovely comments), and the original address redirects here, so no need to update your links. At the moment, we're looking a little plain in the visual department, but some massive redecoration plans are in the works.
On to today's topic: life. How exactly did a collection of random chemicals give rise (eventually) to sentient beings? Where did it start?
This question supposes that at some point, a collection of chemicals that were "not alive" found a way to organize themselves into an entity that was "alive." But we immediately run into another, more fundamental issue: what, exactly, is life? How can we distinguish life from whatever came just before it?
Some researchers (see this Wikipedia article, for instance) consider chemicals such as DNA or RNA to be the distinguishing feature of life, and reduce the question of life's origin to looking at how these chemicals were synthesized.
But this perspective, in my opinion, misses the point. Life is a process, not a chemical. The distinguishing feature of life is not what it's made of but what it can do: namely, it can reproduce itself. More precisely, we can define the process of life by this picture:

Or in words:
An entity is alive if it can produce copies of itself using the free energy and materials that are available in its environment.
There are other caveats we may want to add, such as that living entities can tolerate a certain amount of mutation or environmental change without losing their reproductive ability. But self-replication is a good starting point.
Now the question becomes, how could such a process have arisen? Scientists have managed to synthesize a few self-replicating molecules, but the sponaneous formation of such molecules from inorganic matter seems highly unlikely.
On the other hand, nature is full of chemicals that do this:

In this diagram, A plays the role of a catalyst, helping to synthesize B from other chemicals in the environment. The ubiquity of catalysts led Stuart Kauffman to hypothesize that life may not have started with a single self-replicating molecule, but with a collection of catalysts, each catalyzing another in a cycle:

or in a more complex network:

Kauffman called such collections autocatalytic sets. If such a set of chemicals were able to surround themselves with a membrane, and eventually produce enough of themselves so that the membrane would split in two, we could have our very first example of a living cell.
This idea has a number of interesting implications, which I intend to explore in the very near future. In the meantime, enjoy the new site!
On to today's topic: life. How exactly did a collection of random chemicals give rise (eventually) to sentient beings? Where did it start?
This question supposes that at some point, a collection of chemicals that were "not alive" found a way to organize themselves into an entity that was "alive." But we immediately run into another, more fundamental issue: what, exactly, is life? How can we distinguish life from whatever came just before it?
Some researchers (see this Wikipedia article, for instance) consider chemicals such as DNA or RNA to be the distinguishing feature of life, and reduce the question of life's origin to looking at how these chemicals were synthesized.
But this perspective, in my opinion, misses the point. Life is a process, not a chemical. The distinguishing feature of life is not what it's made of but what it can do: namely, it can reproduce itself. More precisely, we can define the process of life by this picture:

Or in words:
An entity is alive if it can produce copies of itself using the free energy and materials that are available in its environment.
There are other caveats we may want to add, such as that living entities can tolerate a certain amount of mutation or environmental change without losing their reproductive ability. But self-replication is a good starting point.
Now the question becomes, how could such a process have arisen? Scientists have managed to synthesize a few self-replicating molecules, but the sponaneous formation of such molecules from inorganic matter seems highly unlikely.
On the other hand, nature is full of chemicals that do this:

In this diagram, A plays the role of a catalyst, helping to synthesize B from other chemicals in the environment. The ubiquity of catalysts led Stuart Kauffman to hypothesize that life may not have started with a single self-replicating molecule, but with a collection of catalysts, each catalyzing another in a cycle:

or in a more complex network:

Kauffman called such collections autocatalytic sets. If such a set of chemicals were able to surround themselves with a membrane, and eventually produce enough of themselves so that the membrane would split in two, we could have our very first example of a living cell.
This idea has a number of interesting implications, which I intend to explore in the very near future. In the meantime, enjoy the new site!
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