semeiotica recombining contemporary art, design strategy and life science
Archive for biology
July 25, 2008 at 12:04 pm · Filed under bioinformatics, biology, interaction, visualization
A comparison of interaction records in two group of hens. This figure illustrates the comparison feature of the music notation program showing the interaction records in two groups of hens interleaved in two-hour blocks.
Ivan Chase demonstrates a compelling use of musical notation for visualizing social interactions and (conceivably) networks using musical notation. Chase suggests that:
music notation graphs can be of particular help in a variety of fields interested in social interaction in humans, animals, and machines such as behavioural ecology, behavioural economics, social organization in animals, development of social networks in humans, human conversational analysis, and the coordination of actions in social robots.
Read the entire article: Frontiers in Zoology 2006, 3:18
May 20, 2008 at 5:57 pm · Filed under art, biology, biotechnology, boundary objects, visual culture
Regine Debatty discusses biology, art, and technology
April 26, 2008 at 8:23 pm · Filed under Uncategorized, bioinformatics, biology, boundary objects, genes, genomics, making it public, maps, visualization
Here is a sketch I made showing the locations and extent of intellectual property claims on 22 chromosomes and the X and Y. These data are from 2005. The extent is larger today.
Click on the image to visit the full-size sketch.
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 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.
March 14, 2008 at 9:56 am · Filed under art, biology, biotechnology, interdisciplinary, making it public
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?
January 29, 2008 at 9:34 pm · Filed under art, biology, biotechnology, molecular biology, teaching and learning
National Centre for Biological Sciences, Bangalore
March 10-14 2008
Call for Participants
Srishti School of Art, Design and Technology and the National Centre for Biological Sciences, in collaboration with the Arts Catalyst and SymbioticA, is organising an intensive 5 day workshop for artists and others interested people. It will be led by SymbioticA’s Director Oron Catts and his scientific collaborator Greg Cozens from the University of Western Australia.
This is a hands-on workshop where the tools of modern biology are demonstrated through artistic engagement, which in turn gives voice to the broader philosophical and ethical exploration into the extent of human intervention with other living things. It involves exploration of biological technologies and issues stemming from their use, and serves as a theoretical and practical introduction to the creation of biological art and is aimed at educating artists from India in issues of biotechnology and the life sciences.
The workshop will cover hands-on engagement with these technologies in order to be able to carry out and critique manipulation of living systems from an informed practical perspective. The practical components include DNA extraction and fingerprinting, genetic engineering, plant and animal tissue culture and basic tissue engineering techniques.
The workshop will present work of contemporary artists dealing with biotechnology. Scientists will be involved discussing ethical issues raised by artists’ work in this area and leading visit to NCBS laboratories. At the end of the week, the ideas explored in the workshop will be opened out with a public discussion event at a venue to be announced in Bangalore.
Attendance and Conditions:
Attendance at the workshop will be by selection through open submission or by invitation. The selection will be made by Srishti, SymbioticA, the artist in residence at NCBS, and the Arts Catalyst’s curator, currently in residence at Srishti. Artists are expected to be available and present for the entire week-long workshop, as this is an intensive process of learning and social interaction. Artists should be based in India, or nearby countries in South Asia.
There is no cost to selected participants to attend the workshop, but travel and other expenses will not be covered. Limited accommodation is available at NCBS for artists travelling from outside Bangalore. Subsidised meals will be available for participants at NCBS.
The organisers believes that the effects of the workshop will be felt in the long-term, as the artists, having learned the technology, will start working on their own biotech projects, or at least feel their work is informed by the experience.
About SymbioticA:
SymbioticA is part of The School of Anatomy and Human Biology, Faculty of
Life and Physical Sciences, University of Western Australia. SymbioticA is an artistic laboratory dedicated to the research, learning and critique of life sciences. SymbioticA is the first research laboratory of its kind, in that it enables artists to engage in wet biology practices in a biological science department.
SymbioticA sets out to provide a situation where interdisciplinary research and other knowledge and concept generating activities can take place. It provides an opportunity for researchers to pursue curiosity-based explorations free of the demands and constraints associated with the current culture of scientific research while still complying with regulations. SymbioticA also offers a new means of artistic inquiry, one in which artists actively use the tools and technologies of science, not just to comment about them, but also to explore their possibilities.
Links to the organisers:
www.symbiotica.uwa.ed.au
www.srishti.ac.in
www.ncbs.res.in
www.artscatalyst.org
www.cema.srishti.ac.in
Please send an expression of interest in attending as an email, including a CV and brief bio, by February 8 2008 at the latest to Meena Vari, Srishti: meena@srishti.ac.in
This workshop has made possible thorough the generous support of part of The School of Anatomy and Human Biology, and Faculty of Life and Physical Sciences, University of Western Australia, NCBS and the Sir Rattan Tata Trust.
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…
July 24, 2007 at 10:56 pm · Filed under art, biology, complex systems, critical theory, genomics, interdisciplinary, metaphors
Gabriel A. Harp
Leonardo. August 2007, Vol. 40, No. 4, Pages 376-381
Evidence from language, history and form suggest an analogy between the cinema and the genome. The author describes some of the relationships between cinema and the genome and points to opportunities for discovering unmarked categories within the genome and new methods of representation. This is accomplished by evaluating existing metaphors presented for the understanding of genetics and revealing how current scientific understanding and social concerns suggest a cinematic alternative. The formal principles of function, difference and development mediate discussion and serve as heuristics for investigating creative opportunities.
July 3, 2007 at 9:21 am · Filed under art, biology
Make sure you check out the bio catagory at we-make-money-not-art.com
They do a nice set of interviews, reviews and other what-nots in the world of contemporary art and biology, particularly in Western Europe.
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