Connectivity is Beautiful
Communicating with plants, environmental sensing, crowd-sourced science, ecosystem monitoring, when species meet…
Archive for March, 2008
Measuring Behavior
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.
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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.
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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.
Hello world!
Well, I’m trying wordpress now instead of blogger, my previous platform. Hang tight; Many changes coming.
Biology, Art, and Witnessing
tiara or crown of thorns?
This afternoon we concluded a week-long workshop in the so-called bioarts (go here for a nuanced discussion of the term) at the National Center for Biological Sciences (NCBS) in Bangalore, India. The workshop, conducted by Symbiotica and organized through a collaboration between NCBS, The Arts Catalyst and the Center for Experimental Media Art at the Srishti School of Art Design and Technology, brought together both Indian and international artists to engage with the tools of biotechnology as a way of investigating opportunities for research at the intersections of biology and art practice.
The capstone to the week was a community discussion among the participants and graduate students and faculty from NCBS. The conversation wa quite lively as it had been all week beginning with a opening keynote from Oron Catts about bioart and its role in cultural and scientific discourse.
Mukund Thattai moderated the discussion and acted as a provocateur by highlighting the potential for artists to become long-term interlocutors within the NCBS community. He particularly asked for skeptics of this art/biology engagement to share their concerns. Some of questions and concerns raised were:
- How does the arts research percolate ‘down’ into culture given that these are two “ivory towers” largely speaking to each other?
- Why is it that artists seem to be so vague in their proposals, seemingly lacking the precision of language to communicate ideas?
- That the sciences practiced in institutions like NCBS are not intended for the average person and that possibly they shouldn’t be involved in it’s production because of the responsibility involved.
- That the artworks produced appear to be superficial.
- That the ideas or concepts presented through the work are already known and aren’t progressive enough to indicate value.
- That biological research is drawing on ancient and traditional ways of knowing that largely obviate the need for any questioning of its categories and ways of understanding life.
- That biologists just need to become better communicators and all of the problems associated with, e.g. acceptance of evolution, will disappear (this was actually raised during our first day’s interaction with the NCBS community).
These questions were sincere and engaging, and I was happy that there was such a good turnout to discuss these issues. People shared many different perspectives that varied widely in their desire for further such engagements, different models of engagement, and skepticism for the value of the kinds of activities that we were engaged in.
I was somewhat restrained from entering the fray directly because one of my main goals is to elicit the widest possible display of concerns from a community like this. Sometimes I feel it is better to just listen and use the issues raised as areas for getting tactically involved.
This brings me to a rationale for art/science engagement that I think deals with many of the concerns raised. Art, when engaged with biology, performs a social function of ‘witnessing.’ Steven Shapin and Simon Schaffer (Leviathan and the Air Pump, 1985) highlights this process in their analysis of Robert Boyle’s experiments with pneumatics and Thomas Hobbes’s critiques of his experimental program. They describe three processes that effectively multiply witnesses to experimentation and the resulting production of scientific knowledge: 1) facilitating replication–so that users can perform experiments themselves, 2) performance of experiments in a social space–i.e. sharing in the embodied experience, and (perhaps most importantly) 3)virtual witnessing–i.e. production in a user’s mind an image of the experimental scene such that it obviate the need for direct witness.
In the context of the workshop, I think this process of witnessing is increasingly relevant for the production of the biological program and its social contract with society. On the one hand, by teaching artists to use the tools of biology, Symbiotica creates an expectation that non-specialists could theoretically repeat experiments for themselves and verify their validity. Indeed, simple hypothesis testing was performed using environmental sampling of microorganisms and transformation of E. coli with a green fluorescent protein marker. Another example where replication of an experimental program is facilitated comes from the Critical Art Ensemble’s Marching Plague in which US military experiments in biowarfare were replicated with a critical eye for how the results did or did not support defense practice and the politicization of biotechnology. Each of these examples demonstrate how the practices of biology can be effectively replicated to allow for a wider social engagement of science and it’s relationship to other social groups and cultural concerns.
The second aspect of witnessing in shared spaces is perhaps the easiest to show. There were twenty residents at NCBS during the week, engaging in shared processes, visiting labs, and discussing the methods and implications of biological research in India. There’s a worldwide trend of artists working in labs with organizations. Kevin Kelly has a nice list of these residencies here.
What follows from these forms of replication and shared space is the dissemination of a virtual reality of the experimental program. I think that what comes out of artists’ engagement is a type of circumstantial evidence for scientifically-produced knowledge. It relies not on fact or even certainty but solely the residue of artistic engagement. Shapin and Schaffer point to these as circumstantial, stylized, accounts that do not exist as pure forms but instead as publicly acknowledged moves towards or away from “the reporting of contingencies.” Contingencies here means events or things that might jeopardize the validity of the experiment. By allowing the full spectrum of the experimental ‘scene’–perhaps through the inclusion of additional perspectives, political persuasions, or ideas–a better picture of experimentation and its context can be understood. The CEMA blog this week documented the workshop in detail. How often do you see that level of detail in the daily working of, say, a genetics lab? Consider also how art exports knowledge into other spaces and disciplines, either though its images or simply through the engagement itself.
Reflecting on all of this (and I’m tired now), I think one of the interesting questions to pursue is to ask what difference artistic engagement makes along each of these three axes. Does it differ from other methods of communication, and if so what are the behaviors and practices that make it so?
