Ephemerata

My body is a wonderland (and an ecosystem)

2009-07-23T22:07:00.000-07:00

A friend just sent me this posting from Marginal Revolution on a very unique bug I had heard but not read too much on, called Toxoplasma. This parasite is pretty widespread in the vertebrate world, where it was first described to alter the interaction between rats and cats. Basically, the bug lives in the guts of cats, and then gets pooped out into the cat's feces, which are then eaten by rats, and the bug in turn infects the rat hosts. In order to complete the circle of life, though, the bug has to get back into the cat, and it achieves this not apparently very easy task by altering the rat's neurochemistry: it makes the rats less averse to risk, which in turn makes the rats more likely to be eaten by cats, thereby getting Toxoplasma back to its rightful place in the cat's gut. Pretty cool from a community ecology/evolution.

The kicker, though, is that Toxoplasma also lives in humans (lots of humans), and according to recent work, may have the same effect on us it does on rats: Individuals infected with Toxoplasma were six times more likely to get into a car accident than non-infected individuals. Just another reminder that the complex stuff we call a human may be a bit more like an entire ecosystem than just one organism.

Who was charged with possession of drug paraphanelia?

2009-06-03T10:11:00.000-07:00

Great find: picktheperp.com - you get pictures of different, real perpetrators from police mug shots, and you have to pick which perp committed which crime. Fun for all ages! Also, just really interesting to see your own tendencies and thought processes about the physicality of crime. My best streak so far is four in a row.

I found this on Sociological Images, which has a ton of other really interesting stuff which is worth checking out.

truth as approximation

2009-05-14T12:00:00.000-07:00

I just finished watching Obama's speech at the correspondents dinner. First, it's very refreshing to have a president that is circumspect and confident enough to be able to poke fun at himself and his administration. The picture of Obama sitting down for a conference with Captain Hook I thought was particularly tasteful.

But I actually thought the best moment was towards the end of the speech, around 15:25 in the youtube video, when Obama was addressing in a fairly serious manner the state of modern media and their importance in society, etc. When listing a bunch of other values, Obama said "we look to you for truth, even if it's always an approximation," which was followed by a burst of laughter in the audience. Despite the laughter, I had the feeling that it was not actually intended as a joke, and the audience just sort of didn't get it. Either way, though, I think it highlights what a monumental shift we've had from the last man in charge. I mean, recognizing the heuristic difficulties of truth prediction is something of a far cry from "the axis of evil."

The end is nigh...for real

2009-03-27T08:41:00.001-07:00

Oh my fucking god, they finally made a robot with a living brain. Seriously, it's a physical robot attached to a living brain, that grows new neural connections and learns about its environment, built by Kevin Warwick, who is apparently totally insane. Once again, we should have seen it coming.

The Pope is not a scientist

2009-03-20T07:46:00.000-07:00

Overall, I would say the science of public health is probably not the Catholic Church's strong suit:
http://english.aljazeera.net/news/africa/2009/03/20093183550676229.html

Wisdom in the Age of Schizophrenia

2009-03-15T22:24:00.000-07:00

I apologize for the delay in posts for those 3 or 4 of you devoted readers there are. This is a post I've had stewing in my head for a while and am finally getting around to writing down a few preliminary words about.

I've been spending a lot of time thinking about, or more precisely being vexed by, what I perceive to be the shifting and kind of unsteady landscape of knowledge in our modern world. I'm thinking about things kind of across the smorgasbord, from facebook, twitter, and the blogosphere overloading us on connectivity, to cheaper and faster genome sequencing and biotechnology, to the impossibly complex abyss of the financial system. As I immerse myself more and more in this world (for better or for worse), I have a deeply ambiguous feeling about its effects on me, and by extension our modern society. On the one hand, it seems incredibly cool and also incredibly important that knowledge is being democratized. On the flipside, though, I can't help but feel that something, some element of depth of understanding, is being lost in the face of all of this complexity, and this is what I'm trying to wrap my mind around. As a beginning to what I intend on making a series of posts, I just want to bring up a few issues I've been thinking about as of late.

1. Is wisdom a meaningful idea anymore? It seems to me that one of the classical distinctions between wisdom and simple knowledge was that wisdom entailed some sort of intuitive understanding, where knowledge implied simply learning or retaining a piece of information in your brain. Does this have any meaning for us when the things that we are trying to "intuit" are multi-dimensional, microscopic, or beyond the scope of our senses? Is evolutionary computation, which I've talked about a bit before, an example of how we can incorporate the "wisdom" of our decision making into much smarter thinking machines than our own minds?

2. What should be the role of emotion in our decision making? Without going in too deep into details of emotional decision-making theory, it seems pretty clear to me that developing emotions is really important in our ability to cleave through the complexity of the world and ignore some decisions that don't really need to be made. If nothing else, it's a useful filter. In the face of so much information, how is the role of emotions going to change, since in my experience, emotions (at least those involved in decision making) develop slowly, something which seems to be at odds with the current pace of information processing and gathering.

So, just stew on those for a while, and I'll be back with more thoughts soon!

DIY cells

2009-02-17T21:20:00.000-08:00

After watching by this talk by Juan Enriquez, which i highly recommend, I followed up on something he mentioned in his talk that I found kind of amazing. Specifically, Enriquez was talking about the rapid development in the field of engineering cells. In particular, there's been a lot of focus (most conspicuously by bioentrepeneur Craig Venter) on being able to engineer unique living cells that are stripped down to the most basic possible genetic machinery, and this has turned out to be a very promising field. So, the site that I followed up on was this: The Registry of Standard Biological Parts. What a spectacularly mundane name for such an amazing thing. As Enriquez described, it's basically radio shack for cellular engineering. It's a list of "parts," or bits of cellular machinery with very specific functions, with a list of who you can get them from, so that people can put together new cellular machines. Really eerily similar to an electronics catalog...

Purity (or why Woody Guthrie refused to eat at the kitchen table)

2009-02-10T10:13:00.000-08:00

I've been reading along a couple of divergent lines recently. I'm taking a class on conservation biology, so I'm reading a lot about species diversity and disruption and how landscapes change in response to human activities. On the flipside, I also just finished reading "It Still Moves" (by Amanda Petrusich), a book about finding the roots of Roots music, or Americana, told mostly through a road trip to a splattering of important American music cities and filled with vignettes about local business shacks, Cracker Barrel meals, and hours on the highway. Despite the differences in content, however, there is a theme blaring out from the pages of these two readings, and that theme is purity.

I'm not sure I really have anything particularly profound to say about this subject, but it just struck as odd that what lies at the heart of so many different arenas of life is ultimately the search for purity of some kind (usually paired with a not-so-glancing blow at the evils of modern life which are continuously spoiling the pure and lovely past).

In music, and especially in American "folk" music, there is a wide following for finding, documenting, and preserving the purest, most unadulterated American music. This is more or less explicitly why lots of the old folkorists and archivers would go to jails to make field recordings, because these were presumably little time capsules where artists that learned to play before they were put into jail remained untouched by modern music. Although this is certainly not true of all folklorists, and certainly not all folk musicians, there is undeniably a strong tendency within folk and roots music to have a bias towards the past as pure and the modern as almost viral.

Conservation Biology is just bathed in the same kind of contradiction. There is some inherent value in untouched wilderness and areas that have not been altered for long periods of time, whereas anything that has been tainted by modern man loses something automatically. In some ways, I find this kind of backwards. There's no inherent reason why a "pristine" wilderness is any different than one that has been affected by human activity, and it seems rather that change and adaptation are quite the norm in the natural world, seeing as 99% of species that lived in the "pure" past just didn't make the grade and went extinct. Ultimately, I just wonder why there seems to such a universal psychological drive to maintain the past as pure and valuable.

Possibly my favorite story about this subject is about that legend of cowboy and american music, woody guthrie. Guthrie is often turned to as a potent symbol of the rambling singer/songwriter, outlaw, drunkard, romantic, dabbler, and just about every other sign you can tack onto him. He provided source material and inspiration for a whole generation, including the likes of Dylan, Seeger, later Wilco, etc. Guthrie was also seen by many as the living proof of an otherwise theoretical construct in the minds of lots of folklorists of the wandering dust-bowl refugee, the working man's hero. My favorite deflationary story about this myth is when he was at the house of the famous folklorist Alan Lomax. Guthrie was often welcomed into the Lomax home, and they offered him lots of basic comforts, which he would often refuse. He refused to sleep on the bed offered to him, and instead slept on the floor covered in a jacket, just like a hobo. Instead of eating at the dining room table, Guthrie would only eat at the sink. Bess Lomax found his antics "annoying," and complained that he was only pretending to be a hobo. For this, Guthrie is one of the great enigmatic symbols of American history, I think. Maybe he was only comfortable in the wayfaring life he had indeed lead, and didn't know how to exist in the comforts of modern society. Maybe he was just trying to inflate his own personal mythology. Maybe he did it because it annoyed the Lomaxes. Maybe all of these, who knows. Either way though, it was very american.

Competition, Farms, and the Democratization of Innovation

2009-01-25T17:44:00.000-08:00

Undeniably, we are now living in a world that is exceptionally complex. Although the world may not be any more complex and dynamic than it was a few centuries or millenia ago from a physical perspective, it seems clear that from a social perspective the world has skyrocketed in its complexity, especially since the industrial evolution and the process of "globalization." It also seems clear that this trend will almost certainly continue exponentially in every sector of life. From the personal and social connections we make to financial markets and international governance, the world is getting bigger and more interconnected.

In general, I find this to be a pretty hopeful and beautiful thing: knowledge is being democratized (by the internet, as well as big-minded projects like PLOS and One Laptop Per Child) and I think for the first time we are really able to actually imagine the solutions to problems that are fundamentally international in nature (e.g. the drug trade, hunger, poverty, and especially global environmental issues).

This new kind of world, though, is also going to bring about a whole new set of problems. This was highlighted for me recently during the beginning of the economic shitstorm when I was listening to an NPR interview, which was actually about artificial intelligence. What stuck with me about the interview was the discussion of the computer programs that determine what happens in the financial markets. Obviously, the financial markets are too complex for anyone to predict in their specifics. And so, lots and lots of shareholders (which i think include private, small-time investors, although I could be wrong about this, I know embarrasingly little about the world of money) put sort of preset "sell" mechanisms on their holding. So, if the values of certain stocks fall below these setpoints, it can start a sort of wave of selling, which then can sort of reveberate out through the market. What was amazing, and sort of shocking to me, was to hear that not only is this very complicated (and apparently important) system being run at least in part by a bunch of computers, but that the effects were so complicated that nobody could figure out what happened, so that they had to write other computer programs to figure out what the other computer programs were doing!

So, this is scary because (a) the machines are taking over (huge vindication for all the sci-fi nerds), but also because (b) it represents how we've created mechanisms in the world that can themselves gain complexity and then sort of go beyond our ability to easily understand and control.

So, long introduction, but this got me thinking about how things like innovation, regulation, and control are going to have to change in this new way-too-complex future. In particular, I think we're going to have to come up with "smart" systems for understanding and controlling these very complex global systems.

One model for this that I find very intriguing is called "evolutionary computation," from computer science. From what I understand, evolutonary computation is a name for lots of different styles of computation that involve creating iterative programs that will progress slowly towards a "fitter" solution through many generations of calculation.

One example is from architecture. Imagine there is some leeway in how you can arrange some structural elements (maybe "struts") spatially in a building, but you want to find the best arrangement. And you know that you want to maximize some aspect of the building, let's say "toughness." People are creating programs that will randomly generate a whole variety of different arrangements of struts (the parallel of mutations in a natural population), and then they test all these different arrangements for "toughness." The specific arrangements of struts that perform best get to have "offspring," or new arrangments that are roughly like them but with some more mutations, and then the whole process is repeated. The result is basically that the program roughly imitates the smart processes of evolution and designs something all on its own.

Although this is a rough example, I think it still points to a useful direction in how we can sort of "decentralize" the analytical thought process. I think the same kind of thing can apply to societies. If we can figure out ways to bring innovation and analysis away from central "brains," such as centralized policies or governments, and out into the rest of the world, this opens up tons of new possibilities. And, it may even be the only way to move forward as the mechanisms of the world (such as financial markets and the internet) become too gigantic for a centralized brain to handle easily.

So, as a final endpoint, I want to bring this around to what I've been getting really interested in recently: local farms. I've recently started volunteering at a local organic farm, and I've been incredibly impressed with the innovative and dedicated work that is being done with basically no resources and very little overhead support from either a government or an academic institution. They're working on projects to build a solar-powered kitchen, expanding the visibility of good food by bringing it to impoverished communities for very cheap, having a roving biodiesel delivery system for their crops, and tons of other stuff. My point is that this is what we need more of: small-scale, decentralized innovation and problem-solving. In the spirit of Thomas Friedman, I think the best way for us to stay competitive in the modern world is to decentralize the system of innovation and encourage people to make change on the grassroots level (something that would seem especially appropriate in the age of Obama). There's lots of smart people out there with ideas that could make swift and effective change. Let them do their thing.

Rhythm and synchronicity

2009-01-18T18:10:00.000-08:00

This excellent TED lecture by Cornell mathematician Steven Strogatz has really gotten me thinking about the role of rhythm in life, biological, human, and otherwise, and I highly recommend it. The lecture covers some really interesting examples of how rhythms, or what he calls examples of "sync" arise spontaneously in everyday situations.

One familiar example from the biological world is schooling (in fish and birds, etc), where are all of the movements of tons of individuals are coordinated to give the impression of choreographed action. As it turns out, schooling works on some pretty straightforward principles. He shows a mathematical model of schooling each individual's behavior is determined by some exceptionally simple rules: each individual is only aware of those nearest to it, all individuals tend to line up in the same direction, and that all of the individuals are attracted to each other, but keep a set distance between them.

Strogatz also goes over some less animate examples of spontaneous sync. He shows that two metronomes will sync up if you give them a way of "communicating" with each other mechanically, which in this case was a mobile platform that he put both on. Also pretty cool was the example of how people's footsteps tended to get into rhythm at the opening of the Millenium Bridge in London in 2000, which caused the entire massive bridge to start wobbling and had to be temporarily shut down.

Pretty cool examples of how rhythms can arise between individuals spontanteouly, and they all seem to really interesting example of the larger idea of emergence. Since watching the lecture I've been thinking about the pervasive rhythms are in life that I don't really notice most of the time (traffic patterns, cadence of conversation, moods, everything seems to have its own rhythm on some scale).

More than anything though, it reminded me of all of the old church, gospel, country, and other "americana" music I've bene listening. Especially in the old gospel stuff (especially Goodbye, Babylon and Classic Southern Gospel), there's some really energetic in so many of the songs that's hard to put my finger on, and I can't help connecting it in my mind to this sort of spontaneous development of alignment and rhythm between people. Many of the recordings are field recordings, so the recording quality is often poor, but the blistering energy and rhythms come through clear, and it's kind of amazing that people would so frequently and so universally get together to make music. I mean, it sounds like a silly question, but why does it make so much sense for people who are thinking something (about God, or poverty, or teen angst, or love, or whatever) to get together and make sounds in rhythm together, from the church choir to the transcendent drum circle to the dance club? It would make a lot of sense to me that people are expressing something really fundamental and instinctive that comes out in music, something that stretches way beyond human life into the rest of the living and even non-living world. Well, in addition to it just being fun...

With a wave of his (very long) finger...

2009-01-13T12:01:00.000-08:00

...the trader made lots of money.

Apparently, according to a new study in PNAS, the size of men's fingers might be to blame for the financial crisis (sort of). The study found that there was a direct correlation between the relative size of a male trader's ring finger and how much money he made in the market. Specifically, the research measured the ratio between index finger length and ring finger length, so that a low ratio means you have a relatively long ring finger.

Even cooler is that there is a potential mechanism for explaining this relationship. Previously, it's been shown that having a low index:ring ratio (and therefore a long ring finger) means that a man will be more sensitive to changes in testosterone levels. This means quicker reactions and more willingness to take aggressive risks, which are also apparently useful in trading. I wonder if a hand print will now become part of the application for i-banking.

Bizarro Me

2009-01-08T13:05:00.001-08:00

Just found this guy's website. "Jimmy-Jimmy" aka James Crall. I think I see the future

Selecting for Cuddliness (aka Cultural Evolution and the Future Parameters for Species Survival)

2008-12-30T11:33:00.001-08:00

I feel like I've been inundated recently by all kinds of info on saving endangered species and how important it is to preserve habitat and dedicate funds to their protection. Just yesterday, I visited the Harvard Museum of Natural History, which had a special little section on the birds of North America (Ivory-Billed Woodpecker, Passenger Pigeon, etc) that have disappeared due to habitat destruction, hunting, and all kinds of other, uniquely human, sins. I was also particularly alarmed while watching the BBC Planet Earth episode on the poles and saw a cuddly little (and by "cuddly" and "little," i mean "really dangerous" and "fucking huge") polar bear swimming farther and farther between bits of melting ice. Loads and loads of guilt have ensued.

I began to notice something a bit striking about the skew of the publicity that different species get for being endangered. In the most recent issue of Scientific American 3.0, all about sustainability and environmental concerns, there is a graphic about endangered species. The graphic depicts lots of individual pictures of different species, with a certain number sort of faded out, representing the number of species that are in danger in the near future. After a brief inspection, I noticed that every one of these species had a backbone, and most had fur.

This may not seem like a big deal. lots of things have backbones, and lots have fur. Especially the ones that we consider very cute. As someone who spends lots of his time thinking about bugs though (which do NOT have backbones), I'm a bit miffed by this. For a little bit of taxonomic background, things with backbones are called Vertebrates, and things with fur (and mammary glands) are Mammals. Mammals are just one of many classes of Vertebrates. Vertebrates, in turn, belong to one Phylum (chordata). This phylum is one of 38 phyla in the kingdom Animals alone. Animalia is in turn one of four kingdoms (plants, fungi, and protists are the others) that make up one of three Domains of life. My only point with all this jargon is that, taxonomically speaking, what was represented in this visual on endangered species is hugely skewed toward a very narrow group of species.

And so, finally, as I was wallowing in my own bitterness of studying an underappreciated section of life, what I realized is that, if public recognition of the endangered-ness of a species is predictive of how much Endangered Species funding they get, and this funding actually results in their preservation and continued existence on the planet, then this represents a potential fundamental shift in what kinds of things are being selected for in animals.

Let me try to explain that a bit more coherently. I think that now, and probably increasingly, we are selecting for certain characteristics in animals. It seems to me that the attention and funding that goes to certain groups over others (I'm thinking in particular of mammals and other vertebrates) is greatly skewed, and this is based not on anything as practical as ecosystem functioning or potential usefulness for biomimicry, etc., etc. Rather, it seems to me that we are selecting species for how cuddly they are, or rather how much they appeal to our public sentiments and sensibilities, more than anything else. Their symbolic value may be more important than their ability to function in the natural world. I imagine a future for the biological world in which the defining traits of a species are not how well they survive and reproduce in the wild, but how well the concept of them survives and reproduce in our minds. In brief, perhaps in the future, the future genetic evolution of species will depends largely on the evolution of these organisms as memes in our own human minds.

Ode to Home Heating

2008-12-19T20:25:00.001-08:00

In the back of my mind, I spend lots of time denigrating modern civilization, with our obvious pitfalls, egoism, environmental destruction, and otherwise unending parade of travesties. But every now and then, I am starkly reminded of just how nice it is to live in the world we live in. For the last few hours, Boston has been getting pounded by a snow storm, freeing winds, etc. I just came back from walking down the street to drop off some mail. No more than a few hundred yards, but my cheeks were rosy, my shoes were filled with snow and I was chilled to the bone. And then, and then I stepped back into my 65 degree apartment, where my computer and guitar and cat and books and oven and food for months were all waiting for me, and it was lovely. Indoor heating, I love you...

We are still evolving (and how!)

2008-12-17T10:48:00.000-08:00

Recent common sense in general science and among biologists has been that humans are no longer evolving. Natural selection is a process which depends on differential rates of death, and we've gotten so good at avoiding death (at least before reproductive age) that lots of people with theoretically disabling genes still get to pass those genes on (I, for example, have horribly flat feet and a genetic disposal to tear my ACLs. While not great for my athletic career, this probably will not, fingers crossed, affect my ability to reproduce).

Some recent work in the field of genetics, however, is possibly turning this assumption on its head. Mostly through projects like the HGP (Human Genome Project), and advanced techniques for processing very large amounts of data, we can now compare and trace lots of different genes in the genomes of lots of different people. When examined on this level, there is some preliminary evidence that our genome is actually going under extremely fast selection, in geo-historical terms. It could be that 10% of our genes are actually under some kind of active selection, which is very much on the high end for evolution. Most of this work is pure statistics, and based on the assumption that if mutations are inherently random, and we see a whole bunch of alleles (specific versions of genes) changing in the same direction over some appreciable amount of time, then this is indicative of active selection for these specific alleles. With a few notable exceptions (like some work on selection for the gene that allows adult humans to digest lactose), these genetic changes cannot be linked to specific functions, and so we don't know exactly what kind of gene is being selected for. But, from a certain perspective, it makes lots of sense that we are actually under greatly accelerated natural selection, since the rate of changes in our lifestyles, as well as the increased rates of disease evolution that are likely from increasing population densities, are in the big scheme of things, very recent phenomena. Either way, very interesting to think that for all of our medicine and modern mumbo-jumbo, our genes are still being aggressively selected.

Selecting for Cuddliness (aka Cultural Evolution and the Future Parameters for Species Survival)

2008-12-17T10:37:00.000-08:00

Selfish chromosomes, evolution, and arpiar saunders

2008-12-08T19:51:00.000-08:00

I wanted to give a shout out to Arpiar Saunders, not only because he's a friend of mine but because he is the co-author of a really good article out in Science this week about chromosomal evolution with the intimidating title "Centromere-Associated Female Meiotic Drive Entails Male Fitness Costs in Monkeyflowers". Although the old no-one-really-says-this-but-it-fits-my-point saying about Science is that "if it makes it in Science, it's got to be interesting" is not alway true, and although female meiotic drive may not be particularly self-explanatory as to why it's so interesting, I'll try to convince you that it's actually a really cool addition to how we think about evolution and selfishness in the biological world (I apologize, Arpy, or anyone who actually understands this science better than me, for the butcherin' that's a-comin').

First, we need a quick reminder about high school biology and cell division. So, most cells in your body have two copies of each chromosome (these are the little Xs that your genes hang out on, and we have twenty three different chromosomes), one that came from your dad, one from your mom. combined when your parents bung. When you, as a biological, adult, are going to combine your genes with another person's (what was once called "sex"), you are only going to pass on one of those two copies to your sperm or egg, which each only have one copy of each chromosome (then they get together so that the fertilized egg, later "zygote," has two copies of each chromosome).

So Mendel (papa bear of genetics) assumed that each trait in genetics had an equal probability of being passed on. In modern genetics, this would mean that each of the two chromosomes, each containing a bunch of genetic info, has an equal opportunity of being passed into the sex cells. Then natural selection determines which of these genes (which are sitting on chromosomes) is best "fit" to the environment, and those combinations of genes that are most successful in the environment reproduce more and make more copies of those genes, and presto, evolution.

The traditional focus of evolutionary theory, then, has been put mostly into the arena of adult fitness, or animal performance. What really matters though, is what genes get passed on. So, what Arpiar Saunders and Lila Fishman (at the University of Montana) studied was how genes can exploit and be successful at a very different moment in evolution. Using some genomics voodoo, they tracked a gene that preferentially gets passed on during female meiosis (i.e. makes it more likely that its chromosome gets passed on versus its homologous chromosome in the same cell). Most interestingly, however, individuals who were homozygous for this gene (they had two copies of the same gene, one on each chromosome) showed decreased pollen viability. So, boiled down to a tiny nugget of information, this is an example of how genes can compete on the molecular level, and how certain genes can become relatively prevalent in a genetic population, despite decreasing overall performance of the organism they're hitching a ride in. Selfish douchebags.

For all you weird scientists...

2008-12-07T13:04:00.000-08:00

The now-annual Dance Your PhD contest, where scientists turn their PhD research topic into a choreographed dance. Personal favorite: Flaming hula hoops at night-time as an interpretation of "Hydrodynamic Trail Detection in marine Organisms."

Family Matters (for amoeba)

2008-12-04T07:40:00.000-08:00

Very cool article on social behavior in amoebae. Amoeba? Social? For real?

Even a sack of molecules as simple as an amoeba can have social behaviors. Apparently, ameobae will group together into larger blobs when food gets scarce to move faster and find more food. Unfortunately for some, creating this larger blob requires some individuals to sacrifice themselves (a pattern pretty common in insects, but pretty impressive for a single-celled organism). A new study in PLOS has shown that these the amoeba will only cooperate, however, only with closely genetically related amoebae. Nepotism has deep roots...

Swapping bodies

2008-12-03T08:10:00.000-08:00

This experiment (succintly described by Ed Yong) is possibly the craziest psychology experiment i have ever heard of, and very very cool. In brief, a couple of psychologists, using pretty simple camera setups and mannequins, convinced people that a mannequin's body (and then another human's body) was their own. Eventually, the subjects were so convinced that these other bodies were their own that when the mannequin bodies were threatened with a knife, their own bodies showed typical physiological fear and stress responses (sweat on the neck, etc.). Brings up so many interesting issues and implications about how we sense the world and ourselves in it, video games and reality, I don't even know where to begin. Maybe I should rename this blog "we are living in the future."

Recession = bad news for cuddly critters

2008-12-02T08:32:00.000-08:00

So, we've been in a recession for nearly a year now, which jives pretty well with what most of us feel I think. Beyond our pocketbooks, though, I think the recession is gonna be bad news for lots of agendas in environmental policy (For example, the international policy toward sustainable use of bluefin tuna, which seems to have gotten waylaid because of economic concerns). It seems inevitable that in the wake of the current economic crisis, investment in long-term environmental concerns, such as sustainable use of resources, will take a backseat to more immediate and pressing economic concerns, and that we will see a retraction away from what seemed like an increasing momentum in the direction of everything sustainable, organic, local, efficient and generally green. Although i don't really see any plausible way of avoiding this retraction, I fear the fallout that we will see from this in the coming decades. Or maybe this crisis will provide an opporunity for economic restructuring based on renewable energy? A man can hope...

Restless Leg Syndrome or "my culture is making me ill..."

2008-11-30T17:57:00.000-08:00

If you currently, or have ever, or have even thought that maybe you do, suffer from RLS, or Restless Leg Syndrome, I am sorry. I do not believe you.

This topic has been simmering in the back of my mind for many years now, and a weekend of listening to The Corrections (by Jonathan Franzen) while driving to and from a snowy camping trip in Vermont, away from the insanity of modern society, spurred me to voice my thoughts, at least in a preliminary way.

Particularly, my thinking has been focused on the distinction between diseases (or "syndromes," "infections," or whichever other piece of medical nomenclature) and simple states of existence. On the surface, this seems to be an intuitively simple question, but I actually find it to be very problematic.

There is an obvious biological answer: a "disease" (et. al) is a state which puts your physical existence into some kind of detriment or danger. AIDS is clearly a disease, because there is a not-at-all unclear connection between having AIDS and risk of death. This seems fairly unproblematic.

A definition such as this just doesn't work for "mental illness" however. There is no clear way in which not being able to pay attention in class, or having a leg that itches too much (maybe getting out and doing a bit of physical activity might be a good "prescription" for this "disease") poses any danger to our physical well-being.

Well, then what's the problem? The problem is a psychological and social one, and not biological. These conditions do not endanger or damage the physical lives of people, but their social/mental lives. These conditions disrupt the act of being or becoming a healthy and productive member of society. "Healthy" and "productive," however, are clearly not universal or easily definable terms, however. Rather, they are very specific to certain cultures and certain times.

I think the fact that ideas of health will depend highly, if not completely, on culture, is an inevitable, and not necessarily bad, fact. What seems insane to me, however, is the fact that in our culture, we have a very small subset of our population (our medical institutions) defining what it means to be "healthy" for the rest of us, and then selling us drugs to conform to these "normal" mental habits. When a child is prescribed Ritalin because he can't sit still in the classroom, no longer does this mean that he doesn't like math, but rather that he has a disease (ADD) that prevents him from the reaching the normal state of being able to strap yourself down in a chair and silently filter information into your mind. This disease has to be treated, and so culture actually steps in to not just affect an individual's personality through typical, external, cultural influence, but now through the biological and medical process of directly affecting mental states. Remind anyone of lobotomy? (also, note the shift of responsbility, and therefore autonomy, away from the individual). Now it certainly seems like certain mental states are more conducive to individuals leading productive lives within the given contemporary social constraints given to them, but it seems to me that these alternative (perhaps to be generalized as "creative") mentals states are actually very important and very influential in society as a whole, and may be necessary as we enter a period in human history where change is accelerating (TED seems to be a good example). I'm reminded of the portfolio (or diversification) effect in ecology (drawn from the finance realm) where diverse ecosystems tend to be the most stable over long periods because they are able to weather a wider variety of inevitable environmental changes.

I know I sound like a conspiracy theorist, and I apologize, but the undeniable truth of this thang just keeps on popping up in my face. See John Stewart for a much more insightful, and much lighter, treatment.

cancer as an infectious disease

2008-11-20T07:30:00.000-08:00

The New York Times just posted a very interesting piece (by Erica Rex) on cancer in the population of Tasmanian Devils (yes they are real) in Australia. The Devils have recently been added to Australia's endangered species list because of a widespread cancer that is devastating the population.

Although seeing a new species added to the endangered species list is, unfortunately, sort of a routine and utterly not-fantastic event today, this particular species is decline is especially fascinating (and frightening) from a biological perspective. This is because the cancer devastating the Devils is working as an infectious disease, spreading throughout the population.

In humans, cancer is a product of a person's own cells dividing out of control. Typically, cells in your body are stopped from dividing ad infinitum by a series of cell cycle regulating molecules, and typically cancer is a result of malfunctions in any of a variety of these regulatory molecules. From this perspective, then, cancer has really very little to do with a person's immune system, and cancers in humans are not known to be at all infectious, but are rather largely genetic.

The cancer taking out Tasmanian Devils is different, however. As a brief review of the immune system, your body uses a set of molecules called the MHC (for major histocompatibility complex). These are little markers on the outside of all cells which work like a language to figure out which cells are supposed to be in our body and which aren't, and then other cells in your immunse system digest the stuff that's not supposed to be there.

It's a great system, until something learns to work around it. It is the misfortune of the Devils to be a sort of experiment in evolution, where certain cancerous cells have evolved to not have any of the cellular markers that tell the body that it is foreign, or from another organism. This means that this cancer can begin to act as an infectious disease, spreading between individuals.

Typically, if cancerous cells from another human were to invade your body, your immune system would quickly recognize these cells as foreign, mark and digest them, and the cancer would not be able to proliferate within your body. In the Devils however, this is no longer true, and a single cancer has begun to spread throughout the population. Amazingly, this entire cancer is probably the product of a mutation in one cell in one tasmanian devil, and this cell has now begun to divide out of control and spread throughout an entire population. Frightening, but very cool.

Evolution, Death, and the Free Market

2008-11-19T18:08:00.001-08:00

Since the beginning of the current economic crisis, I've been thinking about the general parallels between biological systems and economic systems, and particularly about concepts of how each of these systems works toward becoming "better," whatever that means for each respective field. (Disclaimer: my understanding of the biological world has quite a bit more nuance than the economic, so I apologize ahead of time for all of the butcherings, false claims, oversimplications, and general prostitutings of economic ideas that follow).

Despite tons of differences, there are some overarching and important similarities between the economy and evolution. Both Adam Smith and Darwin were (explicitly or not) influenced by the thinking of Malthus, emphasizing the limited nature of many (if not all) resources. From this style of thinking, both Smith and Darwin realized that competition was an essential aspect of progress. Perhaps more fundamentally, each viewed their respective system as being spontaneously self-organized by limited resources and competition. (I see both of these systems as examples of the larger theme of emergence, a subject on which i will post in the near future).

Smith saw that in a system of economic exchange, competition was the most important driving force behind change. If you start with the premise that resources (money, time, goats, whatever) are limited, and that each individual is going to act in their own self-interest, society is bound to get better. Self-interest (importantly, combined with the ability to individuals within society to freely choose between a given set of options) leads to lowering prices and spurring innovation within markets and so on, the "invisible hand" of fundamental self-interestedness becomes the driving force behind socio-economic change, and the modern free-market economy is born.

Darwin most likely drew directly on the work of Adam Smith in his own revolutonary theories on the biological world. When applied to the biological world, the same basic principles of limitiations, competition, and self-interest emerge. Ultimately, there are not enough resources in the world for all species to reproduce infinitely. Given this fact, and the fact that there are differences between individuals in terms of their ability to reproduce, those individuals who reproduce more (through faster generation times, higher survival, sperm competition, or any of a gajillion other evolutionary mechanisms) will pass their traits onto the next generation in greater numbers than others, and the world will look a little more like them. Through the self interest of genes (for lots lots more, see Richard Dawkins, The Selfish Gene) the world is in a continual process of change and progress (depending on your perspective).

So this, very briefly, covers, evolution and the free market. In both society and the biologocial world, there are lots of discrete actors (in society, us, in biology, genes) fighting for limited resources in a slf-interested way, and this leads to a change in the landscape of society/biology. In general, I think this overarching analogy between are fairly well explored and acknowledged, despite lots of infighting over piddling details among academics. But now, I want to talk a little more about why i actually posted this up here, and this is death, and how it relates to this analogy.

Death is a sad, nasty thing in almost every way. It is the opposite of all meaning, inherently. Oddly, however, it is fundamental to any coherent understanding of evolution. The nice way to word evolution is that there is "differential survival" between individuals, which is another way of saying that some survive and some die (or are never born). Without death, there cannot be any overall change in the genetic structure of a population. These overall genetic changes in the long run improve the robustness of a species, because this species becomes more adept at survival in the face of a set of particular environmental changes.

Evolutionary thinking is frequently applied to the economy, both academically and colloquially (i.e. the "survival of the fittest"). Certain parts of this analogy, such as competition, limited resources, and progress through self-interest, transfer fairly directly and I think cleanly from evolution to the economy. I would argue that in addition to these, however, the role of death also tranfers to the economy. If we allow a "free market" system that runs in parallel to evolution, then there are obvious examples of market "death," the most obvious examples being bankruptcies and recession.

It seems to me that is an inevitable part of the analogy between evolution and the economy, and one deserving of attention. Clearly, death is a necessary part of the evolutionary system, both in the form of individuals deaths (analogous to bankruptcies) and also in the form of more devastating events such as the KT Event or the Permian extinction (analogous to major recessions and/or depressions) which usher in major systemic change in how a system functions.

The question that we face, I believe, is whether or not we are willing to accept the costs (i don't really think they're risks, because they are in some global sense inevitable) of having a free market system that is largely analogous to an evolutonary system. Are we willing to accept the effects of "market death," (i.e. widespread joblessness and inumerable social tolls)? If the answer is no, then this probably implies a move toward higher levels of market regulation (as well as increased social safety), which seems to be the direction in which we're heading. It seems obvious to me that some level of regulation is necessary, and that individual members should indeed be shielded from at least some effects of the free market (health care is for me, the most obvious and pressing example of this), but do these regulations weaken our economy as a whole, and its robustness in response to the larger economic environment?

To add a bit of personal complication, i find it kind of odd as I think through these issues that when I think strictly about politics and the economy, free of biology, I am a strong supporter of regulation and a more socialist system. But when i apply an evolutonary perspective, it is hard for me not to think about the pitfalls that seem to be associated with interfering with "death." I guess the ideal system would be one where we can allow the dynamics of the evolutionary/market environment (the competition, success, survival and death inherent in the market) to play out on a level that is removed from the lives of members of our society. And thoughts on how that could actually happen will be fodder for another post.

The Best Day of My Life

2008-11-06T08:19:00.000-08:00

Possibly an exaggeration. But maybe not. As a young person, my entire adult life has been spent under a government that I have absoutely no trust in. It is not simply that I am opposed to the policies of the Bush administration: I have lost all confidence that they are making decisions that are in my best interest, and making those decisions intelligently and responsibly.

Inevitably, there are questions of how policies and certain agendas should be executed and the real world warps all ideals as they come into formation as actual policies. Ultimately, all ideals become compromised and that is a reality I am happy to accept. But not trusting in the intentions and entire ideological drive of the government of which you are a citizen is a deeper, much more alienating problem.

Tuesday night, for the first time in my life, I felt uncontrollable adoration for the person who would be the leader of our country. For the first time, I saw American ideals like equality and liberty (which I just finished critiquing) not as abstract and fictitious, but instead as real, possible, and important ideas that can and should actually having a shaping force in our world. And I saw them embodied in a person who I admire, and who is actually in the most powerful position in the world. For the first time, I was actually proud to be an American. What an odd feeling...

It's also good to know I'm not the only one who is excited. I've never experienced such mass, communal joy before, and i have to say it feels good.

Freedom from liberty

2008-11-02T11:32:00.000-08:00

This is an idea I've been thinking about for a few days after listening to an NPR interview with MT Anderson, author of The Astonishing Life of Octavian Nothing. I have not read the book (and don't really plan on it), but there was an interesting, short bit of the interview where they were discussing the idea of "liberty." The basic idea, as I remember it (or as I have shifted it in my selective memory) was that there were at least two, competing conceptions of liberty in early American history, and especially during the period of the civil war. One conception of liberty was that argued for by abolitionists who believed in the fundamental liberty of man and used this to argue for slaves' right to freedom. On the other hand, secessionists also invoked liberty to justify their own political stance. Jefferson Davis, for example, argued for liberty against "the tyranny of an unbridled majority" (From wikipedia.)

Reflecting on how these contradictory political agendas could both be justified in the name of liberty, i began to appreciate the complications that arise from using this word. When we are speaking of universal liberty, are we talking about each individual's liberty? Or a territory or a state's liberty? The reality is, there is no set agenda on this. When people talk of liberty, they can be speaking on almost any level of analysis.

To add complication to this, "liberty" is used largely interchangeably with "freedom," which opens up another pandora's box of problems (i.e. the difference between positive and negative freedom, or the difference in definition between "freedom" in politics and in philosophy). It seems fundamental that liberty is constrained in a whole bunch of ways. A really interesting, and relevant, form of constraint on freedom in economic: We are all certainly constrained from certain actions for certain economic reasons, and the contours of these restraints depend on your income. I am restrained from buying a new car and lots of luxury items. Other people are restrained by their economic status from completing even more basic tasks, like buying food for their family. Wealthy individuals are constrained too just in a different way. Maybe they really want to buy a trip to space, but they just bought their 11th house, and so they can't quite afford it right now. This obviously sounds absurd when placed next to the other examples, but it is indeed on some level a constraint on action, however frivolous that action may be.

My goal here, though, is not to engage in the ongoing philosophical discussion on conceptions of freedom and liberty, on which subject many others have thought much longer and harder and have written much more eloquently.

Instead, when I was hearing about this historical complexity in the idea of liberty, I began to think about modern politics, and I realized that this complication has not disappeared at all. "Liberty" and "freedom" are invoked in almost any discussion or speech of American foreign (e.g. practically every Bush speech in the last eight years). There is part of me that thinks that the ideal of liberty has at least some good in itself, and we all have some instincts about it, even if we haven't engaged in deep philosophical thought about. We all have the general idea that liberty is good thing in the world. But the civil war example really begins home the fact that there may not be any inherent good in the idea of liberty at all. My thought then, is that if this is true, then "liberty" and "freedom" may have become very dangerous concepts in modern politics, because they subsume a huge variety of motives and policies under a word that has such strong historical weight behind it. Perhaps it would be better for us to stop using these words altogether...

It's not just the friendly conversation...

2008-10-27T11:28:00.000-07:00

...that makes coffeehouses such lovely places. Apparently, just holding a hot beverage will actually make you nicer to other people. Yet another reason to maintain my coffee addiction...

Why do people do things NOT for money?

2008-10-25T22:03:00.000-07:00

First, I just want to address a few quick things, it beings my first blog post and all. The picture I have posted is something I came across today and found absolutely incredible. The smaller, brighter insect is a jewel wasp, and it is on top of a common cockroach. Apparently, some scientists recently discovered that these jewel wasps inject their larval young into the cockroach to grow. Simple parasitism, not that interesting. More interesting is what the jewel wasps do afterward: the wasps inject a small amount of venom directly into the brain of the cockroach (micro brain surgery), and this bit of venom works to inhibit the role of octopamine, a hormone that essentially gives the cockroach motivation to walk. So, the cockroach just sort of decides to sit down and relax, alive but zombified, while the larvae slowly eat away its insides. Gross, but very cool. Just the idea that organisms have evolved to actively manipulate the neural pathways and brain chemistry of others is absolutely incredible to me. There are a whole bunch of other cool examples here.

Second, the name: Ephemerata. Part of the inspiration for the name comes from the ephemeroptera (or mayflies). I study insect flight and they were probably among the earliest fliers. I've always liked their named, however, because it puts on an emphasis on the short, passing life span of individuals. At the same time, however, there is a coherent order and whole (the species and its continuation) to which each brief and ephemeral individual contributes. Order and continuity out of passing, discontinuous events.

Finally, my first bit of thinking to download: I watched a TED talk by Mihaly Csikszentmihalyi today (By the way, TED.com, if you don't already know it, is a must). One of the basic questions from which his research began is why people do things that are not motivated by what we understand as common motives such as prestige, sexual endeavor, and of course money. It's kind of interesting and shocking questions in itself, I think. I find that our culture is very used to explaining most all actions in terms of one or another kind of self-interested motive. Perhaps the most outspoken proponents of this idea are certain cultural evolutionists and evolutionary biologists, who have inherited a darwinian focus on self-interest and "survival of the fittest." More on them later, however.

Mihaly's partial response to this question came from his studies of deeply creative and engaged people, especially artists. What he focused on was the state of mind during the creation of art, at the peak of engagement in some action. One common thread in the artists he studied was the feeling of a loss of self. An artist, a composer, said of this creative moment that "you are in an ecstatic state, to such a point that you feel as though you almost don't exist." Mihaly deemed this state as "flow."

The explanation given for the loss of self during this state of flow was, oddly, sort of a simple processing problem. The brain can only process so much information at once. Flow appears only to happen during tasks that present not only the highest challenge to the mind, but also when the mind has the most skills and preparation for these tasks, or essentially when the mind will be the most engaged. Since the brain can only process so much information, it simply can't devote RAM to thinking about stuff like "I wonder if I addressed appropriately for this party" or "Maybe if I make a good impression this guy can get me a job." Self-awareness is traded in for full engagement in some activity. Flow also seems to apply to all kinds of different mental activities, not just art. People can be in "flow" at work, while hunting or fishing, or apparently pretty much any other activity.

To tie this all in together, then, maybe people are drawn to these activities not because they serve any overtly self-serving purpose in themselves, but simply because the acts themselves are pleasing. A scientific explanation of why certain mental states can indeed be ends unto themselves.