semeiotica recombining contemporary art, design strategy and life science
Archive for evolution
July 25, 2008 at 8:04 pm · Filed under cognitive justice, community interaction design, critical theory, evolution, metaphors, semantics
I’m picky when it comes to using metaphors. They reveal so much about the biases and commitments that underscore our thinking and, more importantly, how that thinking gets translated into physical manifestations and action.
Cathy Davidson at HASTAC has written a sharp brief on the use of the word ’selection’ as it pertains to evolution and natural selection. She writes,
Having spent a day pulling book after book after book off my shelf, and looking at the proforma and obligatory evolutionary argument that almost inevitably comes in the final chapter of an otherwise careful description and discussion of brain functionality, I am convinced that the word “selection” has a lot to answer for.
The point she makes in the article is that the use of the word selection is directly linked to ideology. I think she is right here, and it should have been incumbent on the evolutionary biology community to recognize this and have proffered a solution early in its history. My fear is that, to do so, would be seen as a mocking retort to creationists that so recently cloaked their arguments in the guise of intelligent design. Well, maybe that a good thing.
Expanding on the relationship of the selection metaphor and its connection to ideology, Margret Evans, a psychologist at the University of Michigan, studies some of the ways that children, potential users of evolution, acquire evolutionist and creationist beliefs. Evans describes how Western religious and philosophical traditions emphasize essentialism, teleology, and intention, and in the process limit the cognitive appeal of natural explanations for the origins of species. She argues that because these ideas tend to show up repeatedly in public representations, they constrain the inferential reasoning capacities of the developing mind. It’s an observation that suggests science’s own predilection for categorization is at the root of evolutionary biology’s social friction.
Maybe we ought to have namethis.com come up with a new term.
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.
December 5, 2007 at 11:47 pm · Filed under Design, biology, complex systems, ecology, ecoregionalism, evolution, host-parasite
One of the questions that’s been nagging at me is if the CEMA lab that we’ve been building is an applied testing ground for Science, Technology and Society (STS) Theory and Practice. Wikipedia describes Science and technology studies (STS) as:
the study of how social, political, and cultural values affect scientific research and technological innovation, and how these in turn affect society, politics, and culture.
My interpretation is surely unidimensional, and I’m sure there are many examples of experimental media arts and technology spaces where critical questions are being addressed. Are there programs that take a specifically empirical approach to the propositions that come from STS and its metaview of science as it is practiced? Many of CEMA’s projects look at how technology and scientific enterprise are embedded in society and politics. Because we specifically implement creative art & design practices in the process, we seek to generate multidimensional perspectives that can further stimulate the ways in which artifacts are designed, situated, and discussed in culture and society. One of these outcomes may be so-called innovation. My curiosity leads me to wonder if the structures that STS identifies can be tested.
A recent article in Design Issues looked at how products and practices are linked under actor-network theory. The authors, Jack Ingram, Elizabeth Shove, and Matthew Watson, suggest that their concepts have the potential to bridge design and social theory. Studying processes of acquisition, specialization, scripting, appropriation, assembly, normalization and practice can lead one to recognize how artifacts, processes, and principles are tightly linked. These linkages may or may not lead to what Malcolm McCullough calls ‘deskilling’ – where individuals and their environment become increasingly estranged as infrastructural bias accumulates.
I suppose this is why I am excited about one of our students’ projects. Prayas Abhinav has created Not Alone, which is more or less the Indian implementation of TXTmob. TXTmob was successfully used during the Democratic and Republican National Conventions for protesters to actively coordinate their movements and demonstrations. One of the interesting questions to come out of this is how the implementation of this very socio-political technology will fare in India. What concerns and questions need to be addressed? I think Prayas is taking an interesting tactic by formulating the distribution of Not Alone as a form of social intervention designed to aid those in need.
What’s interesting to me is how technologies and scientific structures can be compared across landscapes to reveal how large-scale ecosociopolitical trends shape the differences in how technology and science are practiced and interpreted. Shelia Jasanoff took this approach in her book, Design on Nature, when she compared different conceptions for when life “begins” in the US, UK and Germany. By showing how the differing legal and political approaches led to the formation of different definitions of life, she showed how abortion issues reproductive rights are scripted and normalized (my interpretation).
So I’m thinking about all of this because I have long been interested in male-biased infection patterns which are especially prevalent in affluent countries. I started thinking about these patterns and how they might relate to Malcolm’s description of ‘deskilling.’ Are biological relationships like those between host and parasite affected and influenced by infrastructure and artifacts degrading or biasing over time? Is this a ratcheting effect and, if so, is it at all similar to the ratchet effect experienced by asexual populations as they diminish genotypic variation each generation through selection? Do landscape effects like the differences in infrastructure in the U.S. versus India contribute to this? hmmm…
March 26, 2007 at 4:13 pm · Filed under boundary objects, evolution, host-parasite, interdisciplinary, making it public, relational aesthetics, sculpture, teaching and learning, thesis
The exhibition of Sui generis continues this week in the Windows Room (3rd floor) at Palmer Commons (hours: 7:30 am-11pm Mon-Sat). The exhibition is open to the public now through April 13th, 2007.
A reception will be held on Friday, March 30th from 5-6:30 p.m. at the above location. Gabriel Harp will be on hand to discuss the work.
A presentation entitled, “Network Entrepreneurship in Biology, Art, & Design” will take place on April 2nd, 2007 from 5-6:30 p.m. in the Art & Architecture Auditorium.
About the work:
Sui generis is a large-scale tectonic, systems-based installation designed to take into account related conceptual attributes of a chapel, scientific laboratory, carnival, and children’s nursery. Sui generis offers a cognitive retreat, a place for reflection, and a chance to come into close physical proximity with other organisms and ourselves. A rules-based activity based on the concept of asexual reproduction continues through the duration of the exhibition. A selection from Lewis Carrol’s Through the Looking Glass often used to explain and ideate contemporary theories about the evolution of sex and recombination accompanies the artwork.
In order to experience the installation, visitors will be invited to raise their heads through one of the two holes in the floor underneath. When inhabiting the interior, the two viewers will be confronted not only with the shadowscape, but also with each other. As the architecture is elusive in its source, it invites diverse interpretations–a carnival sideshow, a Zen garden, a Victorian greenhouse, a virus, or perhaps even a flower awaiting pollination.
The title Sui generis indicates an idea, an entity or a reality that cannot be included in a wider concept. In intellectual property law, exclusive rights are granted for the creation and development of plant breeds, databases and traditional knowledge (among others) to reflect that the subject matter is a product of the intellect.
For more background, explore a database of terms and concepts associated with the design of Sui generis as well as documentation of the construction process.
About the Artist:
In his work, Gabriel Harp recombines visual art and life science (epistemology) through the processes of critical design and network entrepreneurship. Often working at the interfaces of evolutionary biology, bioinformatics, education, and visual culture, his work investigates the roles of metaphors in education, science and policy and the primacy of visual signals in the discourse surrounding genomics and biotechnology. Collaborating with Zack Denfeld and others, Gabriel is currently developing a visual map of patent claims on the human genome.
March 10, 2007 at 9:26 pm · Filed under Design, bioinformatics, boundary objects, digital design, evolution, genes, genomics, making it public, maps, molecular biology, network entrepreneurship, visualization, yeast
The collaborative work of graduate student Gabriel Harp and Chris Landau (MFA ‘06) on the Organelle View project was published in the January issue of Nucleic Acids Research.
“The project makes a gigantic leap in the distribution of biological data–moving it beyond the conventional representations of names and numbers to embrace the visual and organismal aspects of cellular and molecular forms”, says Harp.
“Organelle View is a scientific visualization application allowing users to dynamically generate a visual interpretation of data from Organelle DB. Organelle View presents a searchable interface with a three-dimensional representation of an archetypical cell. Rather than representing organelles and subcellular structures by text, Organelle View offers an artist’s rendering of a cell and its major organelles. At present, we have chosen a budding yeast cell (S.cerevisiae) as the model for Organelle View, largely because protein localization has been studied quite extensively in yeast; future versions of Organelle View will incorporate additional cell types from other organisms.”
(Wiwatwattana, N., Landau, C.M., Cope, G.J., Harp, G.A., & Kumar, A. (2007). Organelle DB: an updated resource of eukaryotic protein localization and function. Nucleic Acids Research, 35, D810-D814.)
full text via PubMed
January 13, 2007 at 12:43 pm · Filed under boundary objects, evolution
Now more than ever, the concepts, practices, and influences of evolutionary biology communicate experiences of evolution in contemporary life and culture. How do we understand these experiences? The mechanisms of natural selection, sexual selection, migration, mutation, and genetic drift are common in biological systems, yet they are frequently misunderstood. How do we understand and interpret these mechanisms in society? How can we communicate these concepts in ways that also engage our senses?
We broadcast a call for creative work that explores the diversity of forms communicating,commenting on, and engaging mechanisms of evolutionary change and the science of evolutionary biology.
The responses varied. We received submissions largely from artists in six countries and across many different types of media and traditions. In this exhibition, we brought together those works that, through their forms and content, demonstrate the comical, impassioned, and sometimes sublime experiences of everyday evolutionary mechanisms.
January 13, 2007 at 12:16 pm · Filed under evolution, sculpture, sexual selection
mixed media
2006
Interview on Michigan Public Radio real media
January 13, 2007 at 11:48 am · Filed under evolution, sculpture
Piece of Mind in Uncertain Times!
Mixed-media
4′x4′x3′
2005
visit the documentation site
January 13, 2007 at 11:19 am · Filed under biology, ecology, evolution, host-parasite, photography
Pictured is a comparison of an infected (top) and uninfected (bottom) freshwater snail, Potamopyrgus antipodarum. The parasite is called Microphallus, and can colonize the snail hen the snail passively ingests Microphallus eggs while feeding. The snail serves as an intermediate host for the parasite–meaning that the parasite needs the snail’s resources to develop and reach its next host. Often these final hosts are waterfowl, though in the lab mice are used for experimental purposes.
This images was made in the lab of Curt Lively at the Department of Biology at Indiana University, Bloomington.
Digital Print
1′x1′
2003
January 13, 2007 at 11:09 am · Filed under biology, ecology, evolution, photography
The cover photograph demonstrates sexual dimporphism in a flowering plant, Silene latifolia. I made the image while working as a research assistant in Lynda Delph’s lab in the Department of Biology at Indiana University in Bloomington. The
Pictured are the female (left) and male (right) reproductive organs. Notice the extreme differences in size. There is enough genetic variation in many populations of Silene latifolia such one can reduce or expand the degree of dimorphism by artifically selecting on a physical trait such as calyx width or flower number.
Gender and Sexual Dimorphism in Flowering Plants. 1999. M.A. Geber, T.E. Dawson, and L.F. Delph, Eds. Springer, Berlin.
