A recent news feature in Nature Biotechnology asked some of the most prominent synthetic biologists how they define their field. The diversity and vagueness of the responses highlighted the difficulties the community has had centering itself on a set of focused objectives. Because Synthetic Biology is such a new field with no central discovery to mark its launch point, and because the application of systematic engineering to biology is so fraught with problems, the Synthetic Biology community has had trouble defining itself in concrete terms. This comes despite such efforts as the Synthetic Biology Engineering Research Center (SynBERC), an NSF-funded consortium of faculty across various universities that is intended to facilitate joint research efforts within Synthetic Biology. Some responses in the article suggested that Synthetic Biology had become more of a buzzword meant to garner federal research dollars than a productive field. For those of us in the field at the moment, this hit painfully close to home.

I enrolled in the UCSF/UC-Berkeley Joint Graduate Group in Bioengineering largely because it boasted the largest and most promising Synthetic Biology faculty in the world. Before that, I worked for a year with a prominent member of the field at MIT where I started to get a sense of the field. As a biochemist, I was taken aback at the engineering jargon and oversimplification I felt was being applied to systems I knew were very complex and incompletely studied. But the positive efforts I witnessed far outweighed the negatives. One tremendously successful Synthetic Biology effort has been the International Genetic Engineered Machines (iGEM) competition, which challenges teams of undergraduates, graduates, and even high school students to undertake a genetic engineering project over a summer. Arguably the only “biology competition” in the world, the masterfully executed iGEM competition and jamboree thrills both students and participating faculty with the potential of Synthetic Biology. The iGEM competition relies heavily on the Registry of Standard Biological Parts, a large, open library of genetic engineered parts, largely submitted by iGEM students. The idea behind the Registry is that students and scientists can use the submitted parts in the Registry to build upon other groups’ work and thereby avoid replicating efforts. It was impressive efforts such as iGEM and the Registry, together with excellent work by highly reputable scientists and engineers that convinced me to stay and contribute to synthetic biology.

Though Synthetic Biology is facing increasing criticism, I readily defend it as the most promising approach to engineering biology. Though there are many difficulties with engineering biology, Synthetic Biology has made the most prominent and daring attempt at solving some of these challenges. Having worked in the field for several years now, I am consistently impressed by the dedication with which Synthetic Biology’s proponents approach its challenges on a daily basis. Most are serious scientist and engineers, tackling and slowly solving real problems. Synthetic Biology should tone down its promises and refocus itself on solving key issues with engineering systems, but it should not be dismissed. Harnessing the powers of biology will take more work than even Synthetic Biology’s critics realize, but Synthetic Biology has made the first few steps, and the payoff should be well worth the struggle. We should be patient and let it struggle onward.

This problem is most severe in Bangladesh, where more than 40 million people drink arsenic-laden water. In some places, arsenic levels are more than 100 times the World Health Organization’s recommended upper limit of 10 parts per billion. Already arsenic poisoning is evident among 40,000 Bangladeshis. And without some kind of intervention, it is expected that arsenic poisoning will eventually cause 10% of deaths in this country of 140 million.

100L Electrode Assembly, the assembly of iron sheets that generate rust. This assembly will be used in a prototype that the team will be field testing this summer in West Bengal, India.

Conventional arsenic treatment methods are too expensive for nearly half of the people drinking arsenic-contaminated water. To address this need, the Berkeley Arsenic Alleviation Group (BAAG), of which Case is a part, aims to provide affordable, sustainable technologies that remove arsenic from groundwater. Their goal is to develop a technology that removes arsenic efficiently and cheaply and that can be easily operated and maintained by local communities. One of the two techniques for arsenic removal developed by Professor Ashok Gadgil at Lawrence Berkeley National Laboratory is ElectroChemical Arsenic Remediation or ECAR. In this process, iron is placed in water with high levels of arsenic, then electricity is used to dissolve the iron which produces rust. Arsenic is known to bind very strongly to the surface of rust particles. Consequently, rust — along with the arsenic bound to its surface — can be removed from the water through filtration or settling. ECAR requires only small quantities of iron—iron nails for example are sufficient—and such low amounts of electricity that it can be powered with a car battery or solar cells.

Standard ECAR Batch Test. This is how most of Case's ECAR tests are done, on a much smaller scale and with much smaller electrodes.

The goal of Case’s research is to understand ECAR’s reaction products; in other words, the formation of rust and its interaction with arsenic. The information he generates will reveal the mechanism for arsenic removal on rust and enable members of BAAG to determine the long-term stability of the waste generated through ECAR. To assess the arsenic-laden particles made in ECAR, Case uses Scanning Electron Microscopy and X-Ray Absorption Spectroscopy, which provide information on particle morphology, structure, and composition. Case’s research is driven by concern for the millions of people lacking access to safe drinking water and basic sanitation as well as a fascination with the chemistry of metals in aqueous systems. Fortunately, he’s found a project that satisfies both these interests.

This project has proved fortuitous in other ways too. An accidental discovery in the lab has added a promising new dimension to Case’s research. Although we’re most familiar with common orange rust, there are actually several different kinds of rust.  When he began the project, Case’s focus was on orange rust. But one day in the lab, he noticed that instead of the typical orange rust his experiment was producing a rust so dark green it appeared almost black. His fear that he’d damaged the power supply wiring soon turned to curiosity when he saw that this new particle settled much faster than orange rust. Further testing revealed that Green Rust, which has a much larger particle size, settles in under an hour, a huge improvement over orange rust which takes several days to settle out.  If this discovery pans out, it could eliminate the need for a filter or coagulant in future ECAR prototype designs, further reducing costs for this potentially life-saving technology.

Related:

• Berkeley Arsenic Alleviation Group
• Water research pt. 1: The Water Resources Center Archives
• Research highlights: water

The Whitney Siphon, Saugus Division, 1909, from the WRCA's Lippincott Collection

WRCA pulls together a wide array of water-related materials that are difficult to find elsewhere, let alone all in one place. Their ongoing efforts to collect and preserve water-related information have recently focused on capturing electronic data, as more reports, meeting minutes, and information appear only online.  Using web archiving tools, librarians are able to save and make searchable otherwise ephemeral data from websites, for example those run by water and irrigation districts, or federal, state, and local water agencies.

For those interested in exploring further, WRCA’s collection can be accessed through both Melvyl and Oskicat. One element of this collection that Head Librarian Linda Vida suspects is underutilized by graduate students are WRCA’s archival materials, which must be searched with finding aids.  Fortunately, these finding aids are now available online. WRCA also participates in the eScholarship Publishing program, which makes the full-text of scholarly publications available online for free. The recordings of the California Colloquium on Water lectures are another online resource that students may find useful. WRCA also sends one student each semester on a Water Education Foundation tour. During these 2-3 day tours, you will learn more about state water issues and meet other water professionals. Join WRCA’s mailing list to find out how to be considered for this opportunity by sending an email to waterarc@library.berkeley.edu. To keep up-to-date on the latest WRCA news you can also follow them on Facebook.

Men working with water jets, 1912 from the Lippincott Collection

Sadly, the future of the WRCA on Berkeley’s campus is in jeopardy. Although WRCA is located at Berkeley, it is funded by the Office of the President for the benefit of the UC system as a whole. In October, Dan Dooley, the Vice President of the Division of Agriculture and Natural Resources (ANR) announced that to save money ANR would seek a UC campus to adopt the library and its $230,000 annual cost.  Berkeley risks losing this unique resource. This would be a serious loss to the campus community and water professionals who regularly consult WRCA in their work. WRCA is truly a public resource; a UC library card is not needed to check out or use their materials, and the library would like to maintain its liberal lending policy. For now, the library will remain open in its current location (410 O’Brien Hall) until June 30, 2010. If you’re interested in supporting WRCA’s bid to stay at Berkeley, you can send an email to Linda Vida (lvida@library.berkeley.edu) expressing your interest in helping their cause. WRCA librarians are compiling a list of people who are willing to take part in a letter writing campaign and will send out an email to the group once they’ve decided on a course of action. However things end up – and WRCA is definitely a campus resource worth fighting for – I highly recommend that you stop by WRCA, either to become acquainted with their collection or to enjoy a peaceful place to study.

Related:

Research highlights: Water

Photo by Lee Otis

This week we launch our second installment in “research highlights.” In October, we featured fire. Now, in December, as we wait for the next winter storm to sweep across the Bay Area, we turn our attention to water.

Water makes a compelling research topic because it is fundamental to life and so central to the way we live. Many believe that the management and distribution of the world’s water supply will be the critical environmental challenge of the twenty-first century. Already more than a billion people lack clean water to drink and for basic sanitation. And because many of climate change’s impacts will be related to water—e.g., melting glaciers and more severe droughts—additional changes to the availability and quality of the earth’s water resources are expected. While some of these concerns may seem abstract from the relative security of Berkeley’s campus, floods, droughts, tsunamis, and hurricanes, repeatedly remind of us water’s tremendous power to reshape human lives and challenge human institutions. Not surprisingly, water has gripped the imaginations of authors, artists, chemists, designers, historians, lawyers, and policy makers to name just a few.

With just two weeks left in the semester, it has been hard to find people with the free time to talk about their research. Nevertheless, until the end of the semester, we’ll be featuring Berkeley graduate students’ water-related research projects along with relevant campus resources. Up first, the Water Resources Center Archives.

Related:

Water research pt. 1: The Water Resources Center Archives

Photo by Lee Otis

Quiroste Valley, Año Nuevo State Reserve

Through their use of fire, Native Californians once played a pivotal role in maintaining a patchwork of diverse habitats throughout the state.  Some of California’s most iconic landscapes, including the open meadows of Yosemite Valley and the rolling coastal prairie surrounding the Golden Gate, are attributed to the land management practices of local tribal people. Fire was the most important of the many tools Native Californians used to manage local ecosystems for food, medicine, and raw materials. Recently there’s been a surge of scholarly interest in the significance of Indian burning in order to reconstruct particular burning practices Native people employed, practices largely disrupted by European colonization. As early as 1793, colonial officials set out to eliminate Indian fires at the same time exotic plants and animals changed California’s fire environment. Taken together the drastic social and environmental changes of the last two centuries have clouded our understanding of the role that Indian burning played in California.

Members of the research team meet in the field

An exciting collaborative research project at Año Nuevo State Reserve is using an interdisciplinary ecological and archaeological approach to piece together the most complete picture of indigenous land management and its effects in California to date. This research is the joint effort of the Amah Mutsun Ohlone, the California Department of Parks and Recreation, the San Francisco Estuary Institute, and researchers at UC Berkeley and UC Santa Cruz.

Nicole Vaillant samples a fire scar

As part of this project, Chuck Striplen, a graduate student in Environmental Science, Policy & Management and an Amah Mutsun tribal member, is using fire scars to reconstruct the fire history of a prominent historic Ohlone village site and the surrounding watershed. Fire scars indicate when fires occurred, and can often reveal information about the seasonality of fires. By analyzing fire scars from trees throughout this watershed, Chuck can put together the fire regime for this area over time. Chuck’s research is being conducted in conjunction with the Fire Science Laboratory at UC Berkeley and his findings will address the seasonality, extent, severity, and frequency of fires in the Quiroste Valley. Combined with archaeological information about what food and materials the Amah Mutsun Ohlone tribe used in the past and historical landscape data from maps and photographs, Chuck’s research will shed new light on how California Indians managed and shaped their environment. In addition to its academic significance, this research will be useful to land managers throughout the state. One positive outcome of this collaboration has been the creation of California’s newest State Cultural Preserve – Quiroste Valley, encompassing the entire viewshed of the historic village – which also includes mechanisms by which the Tribe can eventually co-manage the Preserve with State Parks.

Related:

• Fire research pt. 3: Fire in space
• Fire research pt. 2: Ghanaian cookstoves
• Fire research pt. 1: Embers & ignition
• Announcing a new feature: research highlights
• A series of articles on this project are being published in News from Native California
• Visit the Amah Mutsun Tribal Band’s website
• More historical ecology of the Bay Area

The Ares rocket which will launch the Orion crew exploration vehicle into orbit. Image credit: NASA via nasa1fan/MFSC on Flickr.

Fittingly on a day when NASA successfully fired a rocket into the moon, we turn our attention to space. More specifically, we’ll be looking at fire safety in space, which is the focus of Sonia Fereres’s research. NASA’s Constellation Program aims to send people back to the moon, then to Mars and beyond. Part of this program involves the creation of a new generation of spacecraft like the Orion crew exploration vehicle. Unlike the Space Shuttles currently in operation, whose cabin environment mimics the atmospheric pressure and oxygen concentration of earth at sea level, the new vehicles are designed to have lower pressure cabin environments with increased oxygen concentrations. Raising oxygen concentrations increases the risk of fire, a phenomenon that poses unique challenges and dangers on board spacecraft.

That’s where Sonia’s research comes in. For her Ph.D. in Mechanical Engineering, she’s studying the flammability of different materials under these low pressure, high oxygen conditions. Flammability can be characterized several ways: ease of ignition, flame spread, and heat release rate, to name a few. Sonia studies the ease of ignition because the other dimensions of flammability only come into play once ignition has occurred, making it of paramount importance for fire safety.

FIST chamber

To determine the fire risk posed by these extraterrestrial conditions while remaining firmly grounded in a Berkeley laboratory, Sonia runs experiments inside a special containment chamber, the Forced Ignition and Spread Test (FIST). There, she can manipulate ambient pressure and oxygen concentration in order to compare time to ignition and sample mass loss until ignition under various conditions. This research will help establish whether reduced pressure and enriched oxygen environments pose a higher fire risk than normal atmospheric conditions, a subject of considerable interest to NASA as it develops a space program for the twenty-first century.

Related:

• Announcing  a new feature: Research highlights
• Fire research pt. 1: Embers & Ignition
• Fire research pt. 2: Ghanaian cookstoves
• Fire research pt. 4: Indigenous land management

Hawa Issifu cooking on an improved stove

The wood-burning cookstoves used in northern Ghana are crucial elements in local food production and culture, but they also have health and environmental impacts that make them the target for international development interventions. Wood-burning stoves contribute to greenhouse gas emissions and release particulate matter that is harmful to human health. Globally, exposure to indoor air pollution is one of the leading environmental causes of disease and one that disproportionately affects women and children. Jason was drawn to working on cookstoves because they sit at the nexus of so many different development issues: energy, environment, health, poverty, and gender. More generally, cookstoves have attracted the attention of researchers and practitioners alike because small improvements in cookstove technology and use promise to have meaningful impacts on people’s lives.

A training on stove construction in Gorima

Jason’s research is part of a collaboration between UC Berkeley, the Ghanaian Council for Scientific and Industrial Research, and Plan Ghana that aims to share both technology and knowledge with the women in these rural communities. Together they’re distributing improved cookstoves and providing training on how to build and use these stoves. The new stoves are designed to make a better fire and to vent smoke away from the user. In a better fire the combustion of the wood is more complete, which results in a more efficient use of the energy stored in the wood and the release of less particulate matter.

Within this context, Jason is evaluating the impacts of the improved cookstoves by quantifying their health and environmental impacts using a randomized-control field trial. In the field, he measured how much wood was burned and how much carbon monoxide women were exposed to while cooking a traditional meal. He is also using temperature sensors to record stove usage patterns. With this information and data from household surveys, Jason hopes to estimate the longitudinal impact of improved stoves on women and children’s health as well as their impact on the environment. At a larger scale, Jason is interested in the fate of wood in this system that does not get burned for cooking and what role training and education plays in the adoption of new technology.  While he and his fantastic undergraduate research assistant, Richard Tam, begin the work of assembling and analyzing a substantial data set on stove and fuel usage, Jason is still appreciating the practical education in international development he gained through his experience implementing trainings in stove construction and use for hundreds of women across several north Ghanaian villages.

Related:

• A video on stove making
• Berkeley’s International Public Policy Group
• Announcing a new feature: Research highlights
• Fire research pt. 1: Embers & ignition
• Fire research pt. 3: Fire in space
• Fire research pt. 4: Indigenous land management

Ember tunnel

Sarah’s research examines how an ember or hot particle ignites pine needles, grasses, and other materials common in wildlands. Using a specialized small-scale wind tunnel, she tests how the size and temperature of embers and hot particles, the type of fuel bed, and wind velocity affect ignition. Above the wind tunnel, an automated lighter heats particles with a flame before dropping them onto the sample fuel material (e.g., pine needles) below. A video camera captures the interaction between these heated particles and the fuel bed, while thermocouples record its temperature.

Ultimately, the information Sarah’s research generates can be incorporated into models for predicting fire development and spread at the landscape scale. Research that begins with the interaction between a single ember and a bed of grass may someday influence the how residential developments interface with the forests, shrublands, and grasslands next door.

Related:

• Introducing a new feature: Research highlights
• Fire research pt. 2: Ghanaian cookstoves
• Fire research pt. 3: Fire in space
• Fire research pt. 4: Indigenous land management
• Combustion and Fire Processes Lab

The first theme is fire, which seems fitting for a California fall.

Each year as the summer draws to a close, thousands of Californians flock to the Black Rock Desert for Burning Man, an event that always culminates in flames. At the same time,  after months with no rain, fire danger is high across the state and wildfires are a common occurrence. These events hint at the potential scope of fire-related research agendas, which might include fire as art,  fire as ecological process, or the tools for managing fire on the ground or in the halls of government. As an introduction to the various ways Berkeley graduate students have chosen to investigate fire, the blog will present four graduate student research projects over the next four days. Tomorrow, forest fires!