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
Disaggregation among natural and social scientific communities can lead to misunderstandings about the different components of disaster management and socio-ecological systems. Terms like resilient, adaptive, robust are often used to describe systems and their processes and come up in the literature, policy, and the media very frequently. They have catch my attention because they have different use patterns in the field I know a little about: biology.
Adaptation, coping, resilience, and robustness have similar definitions, but they sometimes have different technical definitions across disciplines. Their different meanings contribute to their value, and they highlight the differences in perspectives that each scientific community contributes. However, the details matter for distinguishing important components of systems and what aspects might be suggestive for new insights or that might be responsive to intervention or assessment. It’s also important to establish common ground meanings when communities get together and work towards common goals.
The following represents some of my notes and thinking as I try to sort out the definitions on my own. For me, it means asking how different perspectives contribute to the ways in which we interact in socio-ecological systems.
Adaptation
The Intergovernmental Panel on Climate Change (IPCC) 4th Assessment Report defines adaptation as:
Initiatives and measures to reduce the vulnerability of natural and human systems against actual or expected climate change effects. Various types of adaptation exist, e.g. anticipatory and reactive, private and public, and autonomous and planned. Examples are raising river or coastal dikes, the substitution of more temperature-shock resistant plants for sensitive ones, etc.
This definition takes its function from the ability of humans to manipulate their environment, making it better suited to human-identified goals and interests, even if acting on behalf of other organisms. Some synonyms include alteration, modification, redesign, remodeling, revamping, reworking, reconstruction, conversion, adjustment, acclimatization, acclimation, accommodations, habituation, acculturation, assimilation, and integration.
Adaptation is also used to describe genetically-accumulated evolutionary change over time in organisms as a response to natural selection. This is different from the case where manipulating the environment substitutes in the short-term replaces the pressure of genetic adaptation over the long term.
So I suppose this is why it calls to mind a version of evolution based on characters acquired in its lifetime (commonly known as Lamarckian inheritance)–if only for the appropriation of the term adaptation to refer to intra (within) generational processes and not inter (between) generational processes.
Adaptation for evolutionary biologists typically means processes through which a population becomes better suited to its environment over the course of many generations, often through natural selection. A great deal of debate and research has been directed at how we recognize adaptation in hindsight. This is because it can be difficult to state the causes for the evolution of a trait when we do not have direct observation and only historical signatures to learn from. Most notably this was discussed in “The Spandrels of San Marco”, a paper by Stephen Gould and Richard Lewontin (1979) that uses an analogy from architecture for the evolution of organismal form and function.
I agree that changing the environment in the ways mentioned in the IPCC definition will likely limit vulnerabilities for humans and other populations. However, there is an implicit assumption here that the goal should be for humans NOT to have to adapt over a course of generations–despite the inevitability of genetic change over time. It presupposes an assumption of stasis – and a very western one when compared to eastern notions of change and mutability. Richard Nisbett catalogues how some of these assumptions about change and stasis in his book The Geography of Thought. For me, it depends on what time scale one is looking to understand if stasis or change is more relevant. Still, I think its difficult to argue anymore that stasis is more relevant than change.
The necessary question should not be IF we should adapt (genetically or by manipulating the environment). Instead we should ask, “What are we adapting to and how are we getting there?” Will humans and other populations be adapting to artificially-supported ‘vulnerability balloons’ as we are almost surely doing now through our uses of technology and fossil fuels?
This question of adaptive goal is important because the IPCC definitions include definitions of costs and benefits with its description of adaptation. To what goal are these costs and benefits applied? Within the frame of a generation or an organism’s lifetime, explicating goals may make sense, but ascribing goals to a ecosystem – much less whole populations – gets very very slippery. You start to need some way to implicate who or what is writing that mission statement.
Similarly the IPCC includes adaptive capacity in its glossary as the ability, institutions, and resources that can be used to implement adaptation measures.
I think this is all a bit confusing, and I feel it makes more sense to reserve the definition of adaptation for genetic, phenotypic, and behavioral attenuation of organisms or systems to their environment across generations. To describe the processes that organisms and systems use during their lifetimes I think we need a term that encompasses more variability, one that is less blatantly anthropocentric and functionalist in its approach to socio-ecological coevolution. We also need a long view on systems not ones that are limited to single generations only – something that the biological definition of adaptation retains but that the socio-technical one does not.
Borrowing from the literature of evolutionary biology, behavior, and developmental biology, plasticity seems far better suited to the processes of environmental manipulation being described by the IPCC. This is because it references a material (plastic) that maintains its basic molecular structure while having variable capacity to take on any number of manipulations or forms.
Coping and Plasticity
The terms coping and adaptation are sometimes used interchangeably leading to confusion. Here I think there is some opportunity to disentangle the two. A compilation of brainstorming sessions by groups of development practitioners in Ghana, Niger and Nepal described some differences which were then documented in the Climate Vulnerability and Capacity Analysis Handbook. The results of the group’s sessions were pointing to what I think was a difference between 1) consistent and conscious actions to reduce vulnerability (adaptation) versus 2) ad hoc solutions (coping).
It’s worthwhile to differentiate coping and adaptation as within and between generation processes, respectively. Biologists use plasticity to describe the ability of an organism or group to adjust within its lifetime via behavioral or developmental responses to the environment. This may indeed include manipulation of the environment to decrease vulnerability. Phenotypic plasticity is a description that could easily encompass artifacts, behaviors, institutions, and aggregations of resources as extensions of an organism’s phenotype. It invokes important concepts from evolutionary biology including the role of cooperation in building and maintaining extended phenotypes (such as aggregations of useful materials like insurance, band-aids, and water) or how phenotypic reaction norms can change in response to different environments–shedding light on why a strategy in one environment may not be as successful in another. There is further correspondence here with plasticity and the concept of developmental canalization (that organismal systems can get locked in to specific trajectories) and with the concept of path dependence in the development of economic and institutional systems.
So a better definition of plasticity might re-appropriate the IPCC’s definition of adaptation and rework it as:
An adjustment in natural or human systems in response to actual or expected climatic stimuli or their effects, which moderates harm or exploits beneficial opportunities. Plasticity operates through cognitive (sensing), social (interactional), physiological, and other mechanisms that can adjust to a wide range of variability. Plasticity is the ability to respond to variability and a range of realized and possible futures continuously and in a sustained approach. Plasticity or coping strategies attenuate the use of resources to local needs and involve planning that hybridizes old and new knowledge and strategies in an exploratory process.
Here I think this definition makes it much easier to bridge what may be happening at a physiological level (cellular temperature variation, sweating) with responses at an artifact level (clothing, ventilation) and an institutional (e.g. policies towards what it means to be cool).
This is because the term plasticity explicitly invokes a connotation of variability, while adaptation feels more like a description of how well two things (in this case organism or population and environment) fit together. Clearly, if the environment is highly variable we need variability in our systems, not assumptions and values of how well we already fit and work within it.
Coping, on the other hand, seems pretty straightforward. Survive. It makes sense to leave a lot of variability open for this one, because when it comes time for coping strategies, any and all tactics may be appropriate. But then again, there can be ways to cope that are more responsive than others. But I think this starts to dig into a definition of resilience or robustness, where the system properties begin to matter more than than how they manifest themselves in practice. What I mean by this is that as people, organisms, and ecosystems attempt to cope with change, their ability to draw on networks or strategies for coping is itself embedded in the system. Some systems, as a function of their structure, cope better than others. Consequently the adapt better than other too.
Resilience
The Climate Vulnerability and Capacity Analysis Handbook adapts its definition from UNISDR (2009) defining resilience as “the ability of a system to resist, absorb, and recover from the effects of hazards in a timely and efficient manner, preserving or restoring its essential basic structures, functions, and identity.”
The IPCC defines resilience as “the ability of a social or ecological system to absorb disturbances while retaining the same basic structure and ways of functioning, the capacity for self-organisation, and the capacity to adapt to stress and change.”
While Walker et al (2004) define resilience as “the capacity of a system to absorb disturbance and reorganize while undergoing change so as to still retain essentially the same function, structure, identity, and feedbacks.”
In these cases resilience emphasizes a system’s ability to maintain or return to specific structural or functional features–i.e. to maintain its identity, its durability, its persistence. But as noted by Erica Jen in her article “Stable or Robust? What’s the Difference?” (2005), the choices of features or structural elements that we attend to are important for assessing both the capacity and quality of that responsiveness to change.
So what is the function, what is functional, and for whom? Definitions matter.
One way to think about resilience is to imagine a couple of different water balloons. One balloon is filled halfway full. Another is filled so that the latex rubber that composes its surface and membrane is stretched tightly to hold the water in. Now you can throw both balloons back and forth between each other, and neither may pop. But what do you think will happen when the balloons are stretched, twisted, or allowed to drop on the ground where a twig might be a hazard to the already tense surface of the overfilled balloon? It will probably pop and spill the water out.
A system’s resilience is a lot like a water balloon, and the degree of resilience is determined by how much water is forced into the balloon, the size of the balloon, and how much it is pushed to its limits. We might think of the balloons shape, its ‘throwability’ or the thickness of its membrane as examples of functional or structural elements. In most cases, we are looking at how well the balloon is able to maintain it shape and its continuity despite being stressed – i.e. it is functionally a ‘water balloon’, it has a round shape, and responds to the exterior and interior pressures of air and water.
Rarely do we think that a water balloon might reconfigure itself, rearranging the organization of its functions, structural elements, or features to be able to accomplish the same task differently. What would happen if the water and the balloon separated or if the water balloon system was able to draw on other systems (e.g. refrigeration) to change the relationships between its functional elements? What if we no longer simply considered only the water inside of the balloon as the system responding to the task of throwing? What if the throwing and catching movements were also included? Would we still think of a resilient system, or would we start to walk a path of robustness–of being able to adjust the definitions and constraints of the systems themselves in pursuit of coevolutionary relationships between them?
Robustness
Robustness is a different beast altogether – literally. While resilience is focused on maintaining a system, we can describe robustness as the ability of a system to change and in doing so to respond to environment and to develop entirely new functions as a result.
Some argue that robustness describes the ability of a system to withstand mutations and maintain its phenotype or “shape” as a result (Wagner, 2005). Instead I think there is a greater correspondence of robustness with transformation as used by Walker et al (2004). Transformability is “the capacity to create a fundamentally new system when ecological, economic, or social (including political) conditions make the existing system untenable.” I’m less sure about the “untenable” part of Walker et al’s definition.
Robustness is the ability of a system to evolve system functions, not simply maintain those that already exist. In this way, an analogy can be drawn between adaptation/robustness and plasticity/resilience. Similarly, I think robustness has a quality of being parametric. Parametric architecture has the quality of being built from common construction principles, but by varying the parameter values of those rules of construction, endless forms become possible.
References
Walker, B., C. S. Holling, S. R. Carpenter, and A. Kinzig. 2004. Resilience, adaptability and transformability in social–ecological systems. Ecology and Society 9(2): 5. [online] URL: http://www.ecologyandsociety.org/vol9/iss2/art5
UNISDR, 2009. Terminology: Basic terms of disaster risk reduction and IISD et al, 2007. Community-based Risk Screening – Adaptation and Livelihoods (CRiSTAL) User’s Manual, Version 3.0.
Climate Vulnerability and Capacity Analysis Handbook
IPCC, 2007: Climate Change 2007: Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, Annex I., M.L. Parry, O.F. Canziani, J.P. Palutikof, P.J. van der Linden and C.E. Hanson, Eds., Cambridge University Press, Cambridge, UK, 976pp.
Stephen Jay Gould and Richard C. Lewontin. “The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme” Proc. Roy. Soc. London B 205 (1979) pp. 581-598
Wagner, Andreas. 2005. Robustness and Evolvability in Living Systems (Princeton Studies in Complexity). Princeton University Press.
Nisbett, R. E. (2004). The Geography of Thought: How Asians and Westerners Think Differently…and Why. Simon and Schuster.
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.
I ran across this today while searching for some mitochondrial gene information. It’s the MitoWheel (re:blogged via pimm). Gábor Zsurka, a mitochondrial geneticist, produced it in flash with actionscript.
“Genetics Just Got Personal” is the new tagline for 23andme, a new start-up that aims to take people’s saliva samples, genotype them, and make their genetic “plot points” accessible and searchable. Individuals can compare their single-nucleotide polymorphisms (SNPs) to identify ancestral locations, compare them with celebrities, and see what diseases are associated with these SNPs. If an entire family submits their samples for testing, each of them can compare themselves to each of their family members. In 23andme’s letter to the medical community, they state that “the information [23andme service] provides is tailored to genotypes, not to individuals”.
It’s surprising then, given the history of genetics, that 23andme decided to use the “Genetics Just Got Personal” tagline. When someone says that something just got personal, it usually points to conflict, and that a specific individual, rather than a group, stands to loose as a result. Likewise, when someone says it’s not personal, it often refers to some effect that has had an asymmetrical effect on an individual even though it was not directly intended for them. The 23andme tagline sounds like something Arnold Shartzeneggar would say. It does sound tough and too the point, but it also raises suspicions about what getting personal means. Does this mean that my SNPs, which were previously unknown to me, will enter the forefront of my individual decision-making and social interactions? Will it become a part of the design ecology that other will consider when making medicines, devices, or services?
If genetic information does enter our everyday decision-making processes, a central concern is how that information is conveyed and how the information design biases or constrains the decisions we make. Given that 23andme is providing incomplete information, should I make a health decision based on what’s available? I don’t think they’re advocating that anyone make health or reproductive decisions based on the information they provide. They do, after all, provide suggestions for a range of resources (including genetic counseling) for contextualizing the costs and benefits of these kinds of decisions.
Still, I’m left with questions about how the visual design of bioinformatic resources like 23andme creates and constrains different ways of thinking about and engaging with the information.
23andme’s stated goals include advancing research and being world’s most trusted source of genetic information. Can we imaging any scenarios where these goals would come into conflict?
Given that the value of the resource increases with each additional genotype, are those that contribute to the resource entitled to any of the database’s value over time?
Well, it looks like 23andMe finally went online. It’s been over a year since I did this sketch (left) and less than that since Google invested heavily in their startup costs. So when I opened up the New York Times today and saw their article on 23andMe’s launch (that’s effective PR), I still couldn’t help but be surprised that they had gotten going so quickly.
The key question for me is about their interface and interaction design. Will it compare to the same old bioinformatic machine style gene representations (square genes; primary colors), or will there be evidence of a concerted effort to push the visual language of the genome into something that connects with the wide array of meaning associated with genes? After I’ve had a chance to browse their site a bit, I’ll report back with some visual analysis. One thing is certain; they’ve definitely internalized the web 2.0 visual style of rounded corners and big type!
August 6, 2007 at 7:40 am · Filed under art, genomics
Announcing the launch of a new genomic art website curated by Holly Longstaff and Jordan Miller. The gallery is graciously supported by Genome British Columbia. The purpose of this project is to spark public dialogue and debate about genetic and genomic science.
The site describes the “Allegories of the Genome” project, which also included an exhibition that was held in Winnipeg, Manitoba at outworks Gallery in February, 2007. The online gallery expands beyond the February show to showcase the work of 14 international artists working in a variety of mediums.
We hope you all will take a few minutes to view the artists’ work and read what they have to say about novel technologies.
