This talk gave a broad overview of international issues and policies in agriculture and food security, and showcased three research projects that explore Agricultural BioDiversity, Genetically Engineered Crops and the difference between European and United States food laws.
The Distribution of Intellectual Property Claims on the Human Genome. Source Data: Jensen and Murray (2005) Intellectual Property Landscape of the Human Genome. Science 310:239.
Click on the image for a Processing animation of patent locations.
Approximately one quarter of human genes are protected by intellectual property regulations. Little information about the number and distribution of gene patents is available in a manner empowering to members of the public. Existing gene patent resources rely almost exclusively on verbal search strategies for access in contrast to visual interfaces that promote exploration and discovery. This can be traced to the relative immateriality of genes which cannot be seen and whose effects are experienced through a web of medical, environmental, and social constructors.
One solution to this problem is to create a visual map of patent claims in the human genome. By representing the location, number, functional, and patent characteristics of genes, such a map could provide immediate visual access and cues for further investigation. Maps are created through the contributions of multiple constituencies and exist as objects for discussion, reflection, and mediation. Using patent data from the human genome developed by Jensen and Murray (Science 310: (2005) p239-240), we have started this project as a series of creative sketches. CAMBIA continues to update these data in accordance with current information.
Genes involved in human health, disease, and drug discovery tend to be heavily patented. A map would provide reasonably accessible information to non-specialists and help to scaffold conversations surrounding these issues. It is helps to document regions of positive selection, where specific genes are being disproportionately valued, by social and technological actors operating on human and non-human life processes.
The word mitochondrion comes from the Greek μίτος or mitos, meaning thread and χονδρίον or chondrion, meaning granule (thanks! wikipedia). But this isn’t about the mitochondrion itself. Rather, this is a story about how the genetic information that helps mitochondria reproduce and silk threads are rewoven together.
What is a mitochondrion? It’s an organelle (kind of like an organ in your body) for a cell. They generate much of the chemical energy used by a cell to carry out its different processes.
I have been working on a project for the last few months that extends work on what I call Silking Systems. By calling it Silking Systems, I’m trying to emphasize the patterning of silk and textile production as a set of relationships, things and interactions to accomplish varieties of silk/non-silk relationships, rather than as modes of behavior or production which are static – or should I say pre-threaded?
In 2008, some of my students researched How Silk is Made (after How Stuff is Made) for my class on Design for Sustainability. Their work documents the collection and processing of the silk fiber from cocoons to the thread you find in finished textiles.
Steps to a square cocoon.
About a year later, I worked with students at CEMA to develop square cocoon. Yes, a square cocoon. However, we also succeeded in learning a lot about sericulture – the raising of silk moths and worms – for silk cocoons which are then turned into thread. You can see some of process for making a square cocoon – as well as a lot of other aspects of silk production – in this flickr set documenting some of our work on Silking Systems.
In attempting to learn about sericulture from scratch, I visited some local producers in Karnataka, India and pulled in some textual research and advice – including Joseph Needham’s classic series on Science and Technology in China (1998 ed).
The most recent concept that I want to document here is pretty simple. Human mitochondrial genome sequences are woven in sequence using silk to produce a pattern that matches the mitochondrial nucleotide patterns.
Ashwathnarayann
Before I go further, I should acknowledge the assistance of Ashwathnarayan who aided me tremendously is becoming knowledgeable about silk production and weaving. He also did all of the weaving by hand with some help from me in reading the sequence. Nonetheless it was a true collaboration throughout. David Matthew was also instrumental in helping to build some of the loom pieces as well as providing emergency translation from Kannada to English when my conversations with Ashwathnarayan became difficult or too complex. At the beginning too was Millie who accompanied us to a silk production house in Vijayapura, Karnataka – just north of Bangalore. Millie did some great translation acrobatics using her English and knowledge of Tamil to translate for me and to speak with Ashwathnarayan – who in turn was speaking with the silk producers in Kannada.
Checking the loom's warp.
I have a few implicit goals and a few explicit ones as well. An implicit one is that I am attempting to push the relationship between craft, production, economic agency, and hybridity. I am drawing to some extent from the idea that economic value is generated through recombination – that goods and/or services emerge and create value when they are mixtures of other (especially unrelated) things.
Eric Beinhocker details this concept of value through hybrids along with an evolutionary algorithmic perspective on economics in his book The Origin of Wealth (2006). The book was recommended to me by Cesar Hildago, a Research Fellow at Harvard University’s Center for International Development. Cesar’s work on complex networks has also influenced this project, starting with his article on the Product Space of Nations (2007) and continuing with images like figures 1 and 2 which came out of his research. The network graphs make it easy to see how different economies differ in the products they export.
Fig 1. This image maps the products produced by the United States in 2000. The squares are things they are good at – in the US's case vehicles, chemicals, forest products, for example.
Fig 2. This image maps the products produced by India in 2000. The squares are things they are good at – in India's case textiles, chemicals, and diamonds, for example.
My thinking is that by challenging some aspects of the status quo in silk and textile production, new value propositions might be found. This comes, perhaps, by demonstrating that square cocoons are possible or by remixing molecular genetics and weaving to create a series of silk stoles based on a mitochondrial haplotype found frequently in southern India.
Another goal is to simply visualize the mitochondrial genome – and to make it as accessible for teaching and learning as possible. Making it tactile and making it in silk allows people to touch, feel, and to see individual sequence variation. Silk thread is a good scale for this sort of thing – not too small and not too big either. So in viewing these stoles (which measure about 5 meters each in length) one is challenged to look for patterns and they are rewarded with the same.
The mitochondrial sequence used to produce the pattern next to shuttles that carry the silk thread through the warp.
The process is pretty simple. I started with the stored Genbank sequence of the M2 haplotype which is traceable to early settlers of India. I took the nucleotide sequence information (atctcgctagatagacat, etc) and printed it out in BIG type so that we could follow the pattern easily. By assigning a color to each base type, patterns will reveal themselves. For our first prototype, I chose yellow, blue, green, and red. These are used commonly in genomic sequencing and prediction software (at the University of Michigan, for example) and I wanted to start with something that would resonate with biologists and would also suggest a playfulness associated with childhood and formative development.
Checking and threading the warp. You can see the silk fibers and how thin a single one is. It takes years to master silk weaving because it is a very delicate and dexterity-rich process.
Weaving the pattern is excruciatingly slow. In fact, this kind of work goes against a lot of how silk waving is organized from a production standpoint. There are no repeated patterns and each thread is individually sequenced – that’s the point! We accepted that we might introduce our own errors into the fabric, but then that fits well with the concept; as we try to speed up we might lose fidelity with the original sequence. There are a handful of good correspondences between the weaving process and DNA replication, and they are themselves teachable moments for students that encounter the project. It also gets them thinking critically about what correspondences do or do not exist, as a way of developing their own comprehension.
Finished pattern stretched on the loom.
I’ll expand this article as the project develops further, but I’ll end now with one nagging curiosity. The pattern that is being produced is engaging and pleasing. It makes me wonder if it in some ways exploits a bias we humans may have towards certain arrangements. Specifically I’m thinking about pink noise patterns…but I need to search more.
References
Needham, J., & Kuhn, D. (1988). Science and civilisation in China: spinning and reeling. Vol. 5. Chemistry and chemical technology. Pt. 9. Textile technology. Cambridge University Press.
Beinhocker, E. D. (2006). The origin of wealth: evolution, complexity, and the radical remaking of economics. Harvard Business Press.
Hidalgo, C. A., Klinger, B., Barabasi, A., & Hausmann, R. (2007). The Product Space Conditions the Development of Nations. Science, 317(5837), 482-487. doi:10.1126/science.1144581
The CEMA homepage is showing an image of scanner that has opportunistically been colonized by ants (anyone know which species?). I was present at the offending attack, and I have this to say. I didn’t see it so much as an attack as it was (more perversely) an underanticipated observation that ants had quietly moved into an (apparently) unused and undisturbed piece of late 20th century technology- that of the document scanner.
While this may have been felt by some as an attack on our morals of human-hood and right-living (ants and scanners shouldn’t mix, right…er…right?), to me this was much more the most delicate and profound expression not of nature but of the social world in which we live. The most amazing thing to me is that a colony of ants could have arrived and decided that a scanner would make a good home. Perhaps there were some legacy muffins adding allure to the crystal glass and step-motor, but maybe the ants were looking for something held up in the ambient waves of electrical heat left over from un-nourished scans of students’ faces, buttocks, book chapters, and collages.
No..I think this is exactly where we want to be…where mixes and happenstances converge out of nothing more than the desire to find place, continence in the “other”, and the cheap thrill of being where you aren’t supposed to.
On checking up on their status, they are gone from the scanner…pupae and all. I’m not sure if they left on their own accord or if they were kicked out. Where did they go? The water cooler perhaps? As for next time, I’m keeping my fingers crossed that discovery doesn’t correlate with disentanglement. I’d like to keep my scanner ants…who knows…they may have figured out something that we haven’t.
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?
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.
