Archive for heterarchy
June 7, 2008 at 7:19 PM · Filed under bioinformatics, community interaction design, complex systems, cybernetics, heterarchy, making it public, technology
A letter to this week’s Nature describes a study that reveals an interesting model of human movement patterns. The study is the first of its kind for the simple reason that the researchers were able to objectively track people in the natural environment by using mobile phone locations as proxies for their movement.
location tracking phone
Biologists have been performing similar studies on animals for years, using radio tracking devices and similar forms of locations awareness. However, because people tend to be difficult to keep track of, subject to influence from experimental methods, and resistant to monitoring by others, it has been previously difficult to get this kind of accurate data about humans.
Without recapping the study itself (you can read the original abstract and related news stories from the links below), there are many reasons why these data are interesting and useful. The least of which concern us with how people behave and how their behavior translates into public health practice, urban planning, education and communication. For me, the most interesting questions come when we understand what kinds of heterogeneity exist in populations. Understanding what motivates people to behave and respond differently is curious, especially when it relates to their cognitive capacities, their environment, and their learned behaviors. Thus we can begin to ask questions about how systems like architecture or policy, at very different scales, affect systems at other scales–like human reproductive choices for instance.
This study demonstrated that people aren’t really all that interesting in the movements, which is to simply say that we are predictable. We generally stay close to home or work and move in small bursts around these areas most of the time. Occasionally we make wider forays across the landscape.
There are privacy concerns to be negotiated. Many have been critical of the use of this information for the study. To my mind I don’t find the use of the data in the current study problematic for two reasons: 1) there is no identifying information available in the data, and 2) the mobile phones companies have been collecting this data, often out of legal obligation for billing precision, and using it for proprietary purposes with contractual consent from subscribers. I think it is important that some public good be made of the information, even if it means simply bringing to light the fact that these kinds of data are ubiquitously collected under the terms of cell phone contracts. Furthermore, a sample of people in the study explicitly consented to having their movements tracked as part of a value-added service, associated with navigation or weather for example.
Still, the study raises questions and begs for further social questioning and negotiating. I think where it starts to become problematic is when these studies begin to impede personal autonomy. Then again, the negotiations are where all the fun is…
BARABÁSI LAB
For a rundown on how the press is selling the story-via Google
Cellphone Tracking Study Shows We’re Creatures of Habit-NYTimes
Cell phone users secretly tracked in study-CNN
How Will Disease Spread?-ABC News
Mobile phones expose human habits-BBC
May 23, 2008 at 1:28 PM · Filed under biotechnology, cognitive justice, community interaction design, complex systems, cybernetics, design ecology, ecoregionalism, heterarchy, host-parasite, relational aesthetics
I was up this morning thinking about the kinds of spaces, communities and interactions I would like to see. Somewhere between physical computing, synthetic biology, evolutionary ecology, and design is a space where species can speak and be recognized by each other, where urban infrastructure becomes adaptive in the space of days and not decades, where the threshold of difference is lowered to such a degree that new networks between otherwise unrelated groups and individuals can find common ground.
Perhaps for the first time, I am beginning to see how things can be connected for the purpose of builing empathy. Whereas previously, I think the difficult work of etting to know a species was largely out of many peoples’ desires and time banks, perhaps there are now ways of making the opportunities both immediate and resource-efficient.
Rather than always seeking to decouple tightly-linked host-parasite relationships, can we find ways to make new ones…perhaps ones that can grow into mutualisms and symbioses? Is hardwiring a step in the process? What are the costs, benefits, sources and sinks? Can we create or link networks of co-dependence? What models of covariation should we adopt: linear, dominance, epistatic, topological?
May 20, 2008 at 11:18 AM · Filed under bioinformatics, biotechnology, cognitive justice, digital design, genes, genomics, heterarchy, visualization, yeast
Yeast Cell Cycle
Here is a new visualization of the cell cycle using a combination of Virtual Reality Markup Language (VRML), Flash, and database-driven graphics. This new version from Chris Landau and Jamie Cope’s
nformation design demonstrates the yeast cell cycle in 3D cycle stages along with educational information about the process.
Try zooming in and see changes in the nucleus as the cycle progresses.
Yeast Cell Nucleus During Metaphase
This project started as a collaboration at the University of Michigan with Anuj Kumar’s lab in the Life Sciences Institute and first led to the
OrganelleView project.
April 17, 2008 at 7:14 PM · Filed under heterarchy
It took me a long time to warm up to facebook. Eventually it was everyone else’s adoption of the site and its practices that convinced me to once again reaffirm my membership and make connections again. It’s been a good decision in the short-term, if only for the current knowledge of long-lost friends and colleagues.
Another peculiar benefit was seeing my former labmate’s profile and down there at the bottom, her dog’s profile. I had my first introduction to dogbook.
dogbook
Dogbook it seems is the canine equivalent to facebook. Well, it’s not exactly an equivalent mind you. Rather it allows people to add pictures of their dogs to their profiles, for their dogs to join social networks, and for their friends to send ‘pets’ and other gifts. Here’s their description:
Dogbook allows you to create a profile for your dog, tag your dog in photos, find dogs in your area, and much more!
After doing some searches, it seems that dogbook isn’t the only facebook-hosted social networking site for animals out there. Besides dogbook there’s catbook, horsebook, rodentbook, fishbook and, of course, petbook.
My favorites are the ‘Obese Ann Arbor Squirrel Supporters‘ and the ever vigilant ‘Chihuahuas of NYC – UNITE!‘
More may be on the way as facebook users seem to be requesting ratbook, cowbook, and ferretbook as well.
For me this means that social networking is quick to adopt our companions of other species, or at least to use them as indicators of our own social compatibility. That friends can send gifts such as virtual pets and chew toys ups the ante. The benefit isn’t really for the pets themselves, but it much more for the user own self satisfaction I’m guessing. Of course the ads at the top of dogbook speak volumes. Maybe it’ not for the dogs at all, but rather the people contributing to the billion$+ dog economy…
I asked a friend of mine why she added the application, and here’s what she had to say:
I added dogbook because I love the idea of my dog having friends (and, yes, he does actually visit with and play with the dogs on facebook). I added it since I have so many other friends on facebook with dogs, but so far they are all slackers (or think it is a stupid idea) and so Smudge only has one friend : ( I guess it’s lucky for him he has no clue what it’s all about.
I checked her dogs profile, and it seems he likes, “eating, running, cuddling, gathering all my toys into one pile, barking at chipmunks and pesky cats.” His favorite treats are, “Anything and everything (even carrots and grapes).”
True social physical networking among species is what interests me. How might species engage in ecosystems of care by themselves (with a little intervention from us of course)? What happens when species from different parts of the world are linked by virtual communities of care and neglect? Does it take a village or is a biosphere more appropriate these days? What are the technological links that can make these connections feasible and meaningful for us and our interspecific companions?
April 7, 2008 at 2:39 PM · Filed under biology, design ecology, heterarchy, interaction, relational aesthetics, science
I’m reading a book entitled, When Species Meet, by Donna Haraway. She’s one of my favorite authors, not only because of her subject matter, the relationships between ourselves and other organisms, science, and the stories we use to create meaning for how we act in the world, but because her literary style mixes the meanings of words and maintains her constantly questioning presence in the text.
Potamopyrgus antipodarum under the dissecting scope
In the third chapter of the book, she handles suffering, particularly of organisms in highly-constructed laboratory settings, with great care. By pointing out that we are always linked to killing in one form or another, the questions she raises is not if we do it at all, but rather how we approach, encounter, and leave those organisms that we are inextricably bound to.
My favorite passage from that third chapter is the one in which she asks some of her colleagues in the biological sciences how they demonstrate concern for the organisms in the lab as part of their practice. This is a question very close to home for me because it describes so much about my own motivations for doing science in the lab, how ‘reliable’ data are produced, and what kinds of practices can result.
I’m reminded of that famous quote from Barbara McClintock, also the title of Evelyn Fox Keller’s book, that emphasizes how “Getting a Feeling for the Organism” inserts itself so profoundly into daily scientific practice. This is empathy, yes, but the question Haraway asks is how we learn to recognize and therefore intervene in existing situations to show concern and enact strategies for care.
I think back to my own experiences in the lab, or rather, a temperature-controlled cool room. Others had brought snails back from a mountainous lake region in the southern hemisphere, and I was responsible for their care. These snails happened to be an invasive species in the U.S., requiring an extra level of containment to keep them, their offspring, and the parasites out of the regional ecosystem. My relationship with them meant creating the best possible environment for their growth and reproduction. They were, in effect, prisoners (although escape did have a potentially huge payoff). My role in their care meant feeding, finding and installing balanced spectrum lighting to mimic the ambient wavelengths, bringing in local plants to help filter the water in a huge freshwater ecosystem, making sure the water kept moving, installing irrigation systems to distribute a constant flow across many individual containers, adding sterilized rocks to the containers to allow for micronutrients, bacteria and other microorganisms, and even keeping fish and crayfish in the main tank to help condition and scavenge the water. For me, all of these technologies were about care. For one thing we couldn’t maintain the relationship these snails had with their parasites in the lab because we thought they just weren’t being taken care of well enough. There was this very important relationship, then, between how we cared for these snails and how and what kind of data we could collect about their own tight relationship with the parasites they came with.
For design, I’m thinking of how we script care. How can it be made obligatory as part of the function of a service, object, or process? How is it that we find connections and feel compelled to spend our time and energies attempting to make an environment or artifact more comfortable for another? How are we able to recognize what matters in this equation, especially when there are so many possibilities to misinterpret or just plain get it wrong. I suppose we look for signs of health, reproduction, and activity as indicators that we are on the right track. In doing so we create synergies between ourselves and others. By designing for their comfort, we link our vigor and theirs.
March 21, 2008 at 11:17 AM · Filed under art, biotechnology, ecoregionalism, heterarchy, interaction, relational aesthetics
Communicating with plants, environmental sensing, crowd-sourced science, ecosystem monitoring, when species meet…
BotanicallsTwitter
March 17, 2008 at 10:49 PM · Filed under biology, ecology, evolution, heterarchy, host-parasite, interaction
This is actually a really old post from when I was doing my master’s work in host-parasite biology. Nonetheless, it turns out that I’m revisiting it in preparation for an upcoming project.
Behavioral differences between the sexes may explain sexually dimorphic patterns of infection. The risk of infection may be one such factor that an analysis of movement paths can predict. For example, if males spent more time than females foraging for food and, as a result, passively ingest more parasites while doing so, then their risk for infection would generally be greater than females. The tortuosity (or crookedness) of movement paths between the sexes were compared to see if any differences in movement (e.g. foraging) could suggest an explanation for male-biased infection. These differences may suggest that males and females experience their environment at different scales.
Image Analysis
The first thing that needs to be done is to plot the movement of the snails. This can be done by hand, but time-lapse digital photography can help to automate the process. The easiest way to do this was to set up a tripod with the camera pointed down. A white container was used to hold the snails and create the highest contrast background for the photography. Pay attention to the reflection of your light source on the surface between the subject and camera (in this case, water and plastic container). A picture was taken approximately every minute, and to make things simple for the analysis program, I used only two snails per trial- one female and one male. Once I had a stack of pictures (over the course of an hour or two), I loaded them into the image analysis program.
ImageJ is the java implementation of an image analysis program developed by the National Institutes of Health. ImageJ allows you to track the movements of individuals on the screen and outputs a list of XY coordinates for each subject. The first thing that had to be done though was to import the images as a greyscale stack. Once that was done, I cropped out the uninteresting parts of the frame to show only the subject of interest. Further processing was needed to create a binary (black/white) image source for the analysis. Using Process>Subtract Background, I created more contrast with the subject and background. Finally, using the Process>Binary>Threshold, I was able to make the stack be completely composed of black and white images with no greytones inbetween. This is crucial if the analysis algorithm is going to separate the subject from the background. Some parameters may need adjusting for optimal results, but it usually works without too much toying. The final step in ImageJ is to apply the Plugin “Tracker”. This plugin tracks the subject(s) on the screen and outputs a datafile with the coordinates of the movement path. These can then be saved into a text file for later use. I used only two individuals per trial because Tracker is limited to only two subjects. A plugin called MultiTracker is available, but I found it difficult to keep it focused on both individuals. When individuals overlap in space MultiTracker assigns both sets of coordinates to a single individual.
Movie 1. Male and female movement played back after image processing and before tracking analysis.
Measuring the Fractal Dimension of the Paths
I found a great program for measuring the fractal dimension (D) of the snail movement paths. This measurement is thought to measure the scale at which an organism percieves its landscape. Differences in D for different populations would suggest that the populations utilize their landscape differently- perhaps as a result of their perception. The program for measuring D is called Fractal (Nams 2003), and it allows you to import the XY coordinates (after you pare them down to the basic data in excel or something like it). It also allows you to do this as a batch process, making large datasets more manageable. Fractal will give you D for your sample along with confidence intervals. I used a paired-sample t-test in my final analysis. It turned out to be important that I paired similar individuals in the trials; the results did indicate a positive relationship between D and body length. Luckily, I put males and females of the same size in each trial. You’ll have to look into the guidelines for using Fractal yourself if you are going to take a stab at it, but the descriptions are pretty easy to follow. With a bit of doing, it shouldn’t pose a problem to measure these types of behaviors yourself.
A comparison of movement paths for a male and female in maps generated by Fractal.
Selected Bibliography
Bascompte, J., C. Vila. 1997. Fractals and search paths in mammals. Landscape Ecology 12:213-221.
Dicke, M., P. A. Burrough. 1988. Using fractal dimensions for characterizing tortuosity of animal trails. Physiological Entomology 13:393-398.
Escos, J. M., C. L. Alados, J. M. Emlen. 1995. Fractal structures and fractal functions as disease indicators. Oikos 74:310-314.
Nams, V. O. 1996. The VFractal: a new estimator for fractal dimension of animal movement paths. Landscape Ecology 11:289-297.
Nams, V. O. 2001. Using animal movement paths to measure response to spatial scale. submitted.
Turchin, P. 1996. Fractal analyses of animal movement: A critique. Ecology 77:2086-2090.
With, K. A. 1994. Using fractal analysis to assess how species percieve landscape structure. Landscape Ecology 9:25-36.
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