A Model of Mitochondria in the Cell

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.

Transferring the silk thread for the weft from Gabriel Harp on Vimeo.

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.

Preparing the shuttles from Gabriel Harp on Vimeo.

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.

Weaving silk using a mitochondrial sequence from Gabriel Harp on Vimeo.

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

Playpower is a initiative to support affordable, effective, and fun learning games. The project is starting with an existing $10 TV-computer as a platform for learning games in the developing world.

The video below introduces the Playpower Foundation’s mission.

Playpower: An introduction from Playpower Foundation on Vimeo.

Working on a set of social research practices means getting to know or getting NOT to know (depending on how you look at it) the places and practices of the people who can potentially create something valuable from changes to the exiting technology and it uses.

We held a summary and feedback session at the Center for Study of Science, Technology and Policy after their first week of training and observation. They shared their process of ethnographic research gathered feedback to develop it further and begin to implement more observations on a wider scale.

The research team gave a great introduction of their process with some initial results. What followed was a fantastic discussion among approximately 15-20 staff and researchers at CSTEP as well as visitors and the Playpower team.

Many themes began to emerge, and it became clear that the exciting thing about the Playpower project was more than its concept of low cost computing. Instead, I think it raises as many questions as it answers and engages its audience with problems about the role of technology in education and everyday life.

We explored multiple themes in more or less detail, but overall the session was a fantastic success and good model for how to bring about discussions that relate social science, technology, economics, and education in exciting ways.

Questions and themes for further follow-up:

1. What is the role of ethnographic researchers in relationship to the design process and the Playpower project more generally? That is, how do perspectives gained “on-the-ground” compete with held assumptions about the project and its implementation?

2. How do we move from perspectives of technology as a solution questions about peoples’ goals and aspirations? That is, are we working on the Playpower technology as a panacea for educational constraints rather than understanding how family and individual wants and needs articulate their own technology (or otherwise) solutions?

3. Understanding context means that we may need to do some questionnaire redesign – to understand more than just the landscape afforded by people’s lifestyles and incomes towards an understanding of how practice and purpose shape socio-technical interactions.

4. How can the conclusions and assumptions held by programmers and designers be refined? Put another way, do designers or researchers feel free, comfortable, or motivated to redress cultural biases and modes? Also, how is the distinction between game design and development articulated?

5. Does ethnographic research inform through techniques beyond the interview-questionaire-film? What are additional techniques for research?

6. What are the values that Playpower is proposing, advocating, or nominating? For example, are fantasizing, empathy, or transitions in behavior and practice something the project aims to make durable in its presentation and game design? What about the game or software content? How do these values translate into design – e.g. process or pattern knowledge as bird’s eye views and 2nd order perspectives.

7. Can film and cinema provide media and narrative precedents for games and instruction?

8. Did they buy (the original keyboard/game sets) because they are educational? Or for other purposes?

9. Are there game paradigms to move beyond the screen and into interaction and engagement with the real world.

Daal:
1/2 kg moong daal (green gram)
onions, 1/2 kg spinach (shredded), coriander, garlic (crushed),
2 tomatoes, chillies
dhaniya (coriander seeds) powder, turmeric

soak the daal for 5 mins
boil 7 glasses of water with 2 teaspoons of salt
add the daal to it

chop onions and green chillies
heat them in 4 tablespoons of oil
add 1 tbspn dhaniya powder
1 tbspn red chilli powder
a little turmeric
1/2 kg shredded spinach, 2 tomatoes
when the daal has boiled enough, add chopped coriander leaves and mix

daal seasoning: heat 2 tbspn oil, add jeera (cumin seeds) when oil is hot enough and add the chopped garlic. add it all to the daal when ready.

Baati:
1 and 1/2 kg atta (wheat flour)
add some salt and water and knead the dough (thick consistency)
make balls of the dough.
cook them on a bonfire (or bake).
optional: then lightly fry the baati in ghee (clarified butter) or regular butter

you can also make a nice sweet dish to eat with the dal by then tearing bits of the baati and mixing well with jaggery (unprocessed sugar).

wattersupplybangalore8801

This graph represents the difference between demand and supply in Bangalore from the years 1988-2001. Blue circles are per capita supply of water in Liters per day.

Ulat bansi from CEMA on Vimeo.

The teams also took part in a competition in which the winning team is invited to present their work at the Microsoft Research Design Expo, part of the Faculty Summit held in Redmond, WA in late July. We’re all looking forward to attending because we are very proud of the students’ accomplishments.

The ‘Moon Vehicle’ project consisted of a system to create interactive storytelling experiences around themes of the moon, space exploration and colonization, and India’s forthcoming launch of the Chandrayaan-I moon satellite.

Screen captures from the \'Moon Vehicle\' project design.

The Moon Vehicle team’s design developed in part from the Bangalore Space and Culture Initiative, an interdisciplinary endeavor of artists, scientists, designers, and technologists that began in late September, 2007 and coordinated by Srishti, NIAS, and ISRO.

The Play Revolution project changed many times, but it was always focused on the idea of building a socio-econo-technical system for improving the knowledge-networking opportunities of children living in slums in and around Bangalore.

The lab itself and the social interactions were influenced in part by the GROCS lab at the University of Michigan. Thanks go to Linda Kendall-Knox for her willingness to share aspects of their process.

The course started as a relatively straightforward user interface design series of topics, but this plan was quickly abandoned for a more socially-embedded model that would adapt to the different concerns and questions we were going to encounter. The primary article guiding this process was entitled “Products and Practices: Selected Concepts from Science and Technology Studies and from Social Theories of Consumption and Practice” (Ingram et al. 2007). The article stressed six stages of technological adoption: acquisition, scripting, appropriation, assembly, normalization, and practice.
We used these stages to guide our design process.

The students were given a design brief that consisted of two challenges: one consisting of Srishti’s existing commitments to cultural, educational, artistic,and design-based engagements with society, and another consisting of a more general challenge to design a user interface and/or interactive experience around the theme of learning and education. They were asked to develop a project that synthesized these challenges into one unique approach that incorporated the concerns, commitments, and constraints that were implicitly and explicitly embedded in the issues raised.

The theme of this year’s competition was “Learning and Education”, and students were challenged to design a user interface and/or interactive experience around the theme of learning and education that improves the daily life of a wide variety of users through learning and education, promotes creativity and curiosity in new topics, demonstrates novel ways of providing instruction, and rethinks education systems and tools.

For more on the project, visit their site.

This is a short video about the Center for Experimental Media Arts, the lab where I work.

This semester a group of my students undertook the task of documenting the silk production process as it occurs in Karnataka. They visited several sites ranging from a rural handloom enterprise to industrial mills and retail outlets. They prepared themselves by looking at precedents from similar art and design students looking at how things are made. They also focused their investigations by first reading the Design for Sustainability Guide. In this way, they managed their engagement for the purposes of producing actionable knowledge to foster sustainable design practices.

One of the outputs of their research is this account of silk production. I found it detailed, well-researched (though I would have preferred more footnotes and cited references), and informative. I think it also illuminates the degree to which these students understand their processes and are willing and able to identify parts of the systems for further exploration.

Screenshot of one of the mapunity community interfaces.

Last week I visited the Mapunity folks who are building projects at NSRCEL in the Indian Institute of Management, Bangalore. They are a really great, super-keen group dedicated to building IT solutions for the purposes of development…often using geographic systems as a segue to action. I think they are most well-known for their work on the Bangalore Traffic Information System, which, if you’ve visited Bangalore recently, you know how bad the traffic is here.

The Mapunity folks are creating tools for users to make their own maps for whatever purpose they choose. The ones I like the most are these, dealing with innovation in rural parts of India. Here is where local, user based solutions to problems like disease control in cumin crops or remedies for animal wounds can be mapped to particular areas and described.

http://honeybee.mapunity.org/main
and a regional innovation listing here: http://ruralinnovations.mapunity.org/main

More projects are in the works, and they were working on a new interface even as we talked. Go check them out…maybe even create your own community!