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.

Click here for a zoomable version

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.

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

I don’t know which category this one falls into, but I do feel it’s worth sharing and making public. Perhaps someone will even comment with improvements. I can only hope.

In any case, this proposal was dependent on a constellation of partnerships (and funding) to make the project move forward–at least from my perspective. Sometime a little cash can help develop needed projects and spur collaboration. This was a submission to the Knight News Challenge which is supposed to announce its winners sometime in mid-June. Since I know I’m already out of the running, there isn’t really a compelling reason not to share—but please tell me if there is!!!

envirocasting logo

Anyhow, here is most of it—-minus some names to protect the innocent—–except one: this logo was created by Zack Denfeld, and we’ve used it on a variety of projects.  For more, you should visit his launchpad.

Describe your project:
Envirocasting adapts global weather information to the cultural and operational needs of local [international disaster preparedness organization] branch offices and communities, supporting their risk assessment and preparedness needs. A wealth of information exists to support disaster preparedness, but a gap exists between the design of information services and their local use-contexts, limiting widespread use and effectiveness. The benefits of these information services are clear to local decision makers, and they are anxious to put the tools and news sources into practice.

However, exposure to digital news platforms is low, and the capacity to use them in decision making contexts is minimal as a result of this disconnect between design and use.

Envirocasting takes a design anthropology approach to inform the design, distribution, and acquisition of digital weather information services to local decision makers. Design anthropology seeks to understand the role of design artifacts and processes in defining what it means to be human. Using this approach, local patterns of information consumption and culture related to futures, information design, and technological metaphors can be identified, allowing for the design of appropriate services. Design principles as well as specific, local use-applications will aid in the distribution and assessment of weather forecast efficacy. Thus, weather news for risk assessment can flow more precipitously to decision makers, allowing them to coordinate the disaster preparedness efforts more quickly and strategically.

Simulation games for local communities will support learning and the application of information services in context. This provides use-case memories of the future and practice in managing uncertainty with minimal risk.

How will your project improve the way news and information are delivered to geographic communities?

Envirocasting aims to localize climate information by making it simple, non-technical, clear, easy to use, and as meaningful as possible. Maps are relevant when their colors, numbers, icons, and scales are relevant and supported by culture and context. Information that connects with specific actions can be used confidently in planning and decision making. Specific use-cases communicated by local communities will drive the development process and will help weave the digital media fabric with aesthetics, narratives, and metaphors. Games support critical thinking and social play to help decision makers and communities explore the dynamics of news and information-based decisions for climate-related disaster preparedness.

How is your idea innovative? (new or different from what already exists)

Envirocasting innovates by translating connections between design and use. When local conditions refract the design and dissemination of information from distant or multiple sources, innovation is an inherent byproduct. Envirocasting is designed with the mind in mind, understanding cultural legacies that influence the recognition of uncertainty and metaphors. It bridges experience, play, and interactions, creating memories of the future. The project identifies appropriate implementations of open-source digital information services and defines a set of prescriptive resources for innovating across disaster risk contexts and cultural processes based on abstractions and lessons from six local communities in three countries.

What unmet need does your proposal answer?

A fact-finding mission conducted surveys, interviews, meetings and workshops over two-month periods in 2008 and 2009.

Explicit unmet needs include:

1. An Increase in the Accessibility and User-Friendliness of Climate Information Products
2. New Products to Fill Information Gaps for Needs–Starting with Improved Flood Forecasting Tools
3. Training in the Use of Climate Tools and How Climate Information Could Trigger Action Such as:
   • Learning to access and interpret climate information tools.
   • Learning how to monitor seasonal forecasts in conjunction with medium and short-term forecasts.
   • Understanding how to take gradated actions.
   • Channels of communication and decision-making to receive and take action based on time-sensitive climate information.

And don’t take my word for it:

What will you have changed by the end of your project?

More-Measurable outcomes:

• Prototypes that adapt weather information services to local use-contexts.
• Documents that communicate design processes for cross-cultural communication.
• Heuristics or ‘rules-of-thumb’ for the design of climate information services for risk assessment.
• Country and local use-context reports that document specific patterns of information acquisition and behavior.
• Relevance of climate information for local decision-makers.
• Ability to align information with decision and action.
• A folktaxonomy of climate information and categories for creating a cultural consensus model (CCM) to realize translations in cognition and practice among cultural contexts.
• An index of context-specific actions and the values associated with them.

Less-measurable outcomes:

• Perception of the design process and innovation pathways for news and information about climate-driven risks.
• The relationship between information providers, researchers, designers, policy makers, and implementing offices providing the opportunity for continued support, training and dialogue necessary to realize the potential benefits of using climate information.
• Channels of communication between information providers and decision makers and between decision makers and community constituents (incl. digital information services).
• The scope of the implementing organizations to conduct cross-cultural research and information adaptation projects.

How will you measure progress and ultimately success?
The uses of weather and hazard preparedness information can be measured using surveys, interviews, meetings and workshops and compared to current estimates of use and use cases, but those data are useful differently for different people including the decision-makers, their constituents, their supporting agencies, and funders of this project. Thus, we intend to cast progress in varied terms for the different stakeholders and partners.

Some of these guiding questions include:

• What are the iterations, changes, and improvements to existing systems?
• What does the trajectory of individual decision-maker’s tasks or questioning look like?
• How do other elements of the media ecology change and what stakeholders are invoked or leveraged in the process?

Success, on the other hand, is more elusive. Disasters are sporadic and may not always afford a direct link between information effectiveness and risk reduction. However, existing case studies show that these types of information, when combined with specific actions, can lead to significant reductions in both the vulnerability and negative effects of a disaster such as flooding. The key to assessment it to engage in a continual processes where we value choices and transitions in practice. The design of this project take into account the high-stakes involved in the decision-making and information uses by providing opportunities for both high stakes (post-hazard) and low stakes (simulation-games) assessment.

Do you see any risk in the development of your project?

The biggest risk at present is that the organizations listed do not have a history of working together (this is indicated by the generic names rather than their proper ones), but this is also where the opportunity exists. The leadership (particularly of the larger orgs) is wary of their participation in the project without first-hand knowledge of all partners and/or certain funding. This conversation is ongoing at the time of this application and continues to develop. If the proposal moves through to the next round, we should at that point be able to name each of the partners in more specific terms.

Supply-side risks (design-mediated)

• Inability to generate meaning either through lack of empathy or translation of needs to designers
• Research products are not absorbed and implemented during the design processes because they are non-normative, unclear for direct application, left uncommunicated, or other
• Partner coalition denatures from lack of shared goals or mental models
• Emphasis on technological development or information diversification over use-context and user needs
• Existing insights, stakeholders, and methods are unknown or unengaged
• Irrelevance, inability, or non-linkage of digital mediums and meaningful information services
• Cultural heterogenetiy too great for scaling of appropriate information services
• Ability and capacity of project managers to recognize and adapt to other sources of risk
• Expertise of project partners is missing or unleveraged
• Translation of local use-contexts into primary research is distorted or biased

Demand-side risks (user-mediated)

• Low frequency acquisition of technology platforms, information services, and/or symbolic systems
• Scripting of use and application to local decision making is unclear
• Appropriation for local use-cases is nonexistent
• Assembly does not fit into the local context of everyday life
• Cannot be integrated into normal practices, culture, and concerns
• Practice with information and platform is sparse

What is your marketing plan? How will people learn about what you are doing?

The conduits for marketing are, in many respects, already in place. The organizational structure and extent of [intl. disaster preparedness agency] branch offices will facilitate branding and distribution using existing networks of community organization, tactical planning, and response offices. Though the value of the services should be self-evident in the design and cognitive acquisition of the services, the goal is to help users to practice using and applying these information services. We also recognize that aesthetic values can elevate the recognition of value and the maintenance of that value through everyday use. Thus, arriving at these values will be a principle objective for all participants.

In order to increase domain knowledge, the outcomes can be shared among the participants, their centers, and via professional and interest networks including the design research community which actively engages with similar project goals. Because some of the project partners include university centers, schools and research organizations, the outcomes will be shared with emerging professionals including graduate students and visiting fellows.

Tactically, the marketing plan for simulation game-based training is slightly more difficult because it requires additional preparation, training, and presentation. Nonetheless, with a bit of effort, these games will reinforce the marketing strategy for the primary goal of adapting weather information using the same local community branch office network structure. We also expect to develop videos that demonstrate our process as well as the use and value of the informations service under construction. But ultimately, the best marketing will be the effectiveness of the adaptation process.

Is this a one-time experiment or do you think it will continue after the grant? If it is to be self-sustainable, what’s the plan for making that happen?

Envirocasting is the application of a process to translate meaning across cultural contexts with relevance for local concerns. We do not view it as an experimental process so much and an underutilized one. Luckily, there are many resources, case studies, and additional expertise to draw from in the process. Our goal is to assemble them and to draw the pieces together into relevant platforms and prototypes for weather information services.

The project will accomplish this goal as a one-time research project that will publicly document its methods and outcomes as guides so that they can be applied in new use-contexts and for wider information arrays. We fully expect that the different project partners will continue to apply the work and experience in varied ways after the initial project, although they may carry it out to their own ends.

Our method for fostering rhizomatic-like dissemination of the results (and thus, sustainability) is to link with additional strategic partners whose networks span varied social groups, languages, use-contexts, and concerns. Furthermore, the acquisition and integration of the research (as well as the information services it supports) can be broadly advocated from a policy perspective because successes arise from its application and benefit in specific, local communities. The overall plan for sustainability is to demonstrate that these information service platforms reduce risk by enabling decisive action before pending hazards become disasters. If this is demonstrated, sustainability will ensue, even if not in the form described in this proposal.

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.

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

environmental camera from Gabriel Harp on Vimeo.

Sounds fun.

Addendum:  you can also view an explanatory video about Mapping Controversies, narrated by Bruno Latour

Yeast Cell Cycle

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.

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.