Archive for the ‘synthetic biology’ Category

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Plants that glow in the dark; Kickstarter campaign or public relations campaign?

Tuesday, May 7th, 2013

Synthetic biologists have set up a Kickstarter campaign, Glowing Plants: Natural Lighting with no Electricity, designed to raise funds for a specific project and enthusiasm for  synthetic biology in the form of plants that glow in the dark. As of this morning (May 7, 2013, 9:50 am PDT), the campaign has raised $248, 600. They’ve met their initial goal of $60,000 and are now working towards their stretch goal of $400,000 with 30 days left.

Glowing Arabidopsis

Glowing Arabidopsis

Ariel Schwartz in her May 7, 2013 article for Fast Company describes the project this way,

Based on research from the University of Cambridge and the State University of New York, the Glowing Plants campaign promises backers that they’ll receive seeds to grow their own glowing Arabidopsis plants at home. If the campaign reaches its $400,000 stretch goal, glowing rose plants will also become available.

“We wanted to test the idea of whether there is demand for synthetic biology projects,” explains project co-founder Antony Evans. …

…

Kickstarter backers will get seeds created using particle bombardment. Gold nano-particles coated with a DNA construct developed by the team are fired at plant cells at a high-velocity. A small number of those particles make it into the Arabidopsis plant cells, where they’re absorbed into the plant chromosomes.

Arabidopsis was chosen for a number of reasons: it’s not native to the U.S., so there is little risk of cross-pollination; it doesn’t survive well in the wild (again, reducing risk of cross-pollination), it self-pollinates, and up until recently, it was thought to have the shortest genome of any plant. That means the protocols for Arabidopsis plant transformation work are well-established. Roses (the stretch goal plant) have also been studied extensively, and they carry little risk of cross-pollination, according to Evans.

As Schwartz notes, the project has potential for future applications,

In the meantime, Evans and his team plan on spending the next year on the campaign. Eventually, Evans imagines that the Glowing Plants creators will work on bigger glowing plant species, so one day they could even be used for street lighting.

Here’s more about the team behind this Kickstarter campaign (from the project page, click on Antony Evans),

Omri Amirav-Drory, PhD, is the founder and CEO of Genome Compiler, a synthetic biology venture. Prior to starting his company, Omri was a Fulbright postdoctoral research fellow at Stanford University School of Medicine and HHMI, performing neuroscience research using structural and synthetic biology methods. Omri received his PhD in biochemistry from Tel-Aviv University for biochemical and structural studies of membrane protein complexes involved in bio-energetics.

Antony Evans has an MBA with Distinction from INSEAD, an MA in Maths from the University of Cambridge and is a graduate of Singularity University’s GSP program. He is both a Louis Frank and Oppidan scholar and worked for six years as a management consultant and project manager at Oliver Wyman and Bain & Company. Prior to this project he co-founded the world’s first pure mobile microfinance bank in the Philippines and launched a mobile app in partnership with Harvard Medical School.

Kyle Taylor was born and raised in the great state of Kansas, where his love of plants evolved out of an interest in the agriculture all around him. This lead him to major in Agriculture Biochemistry and minor in Agronomy at Iowa State University and then pursue a PhD in Cell and Molecular Biology at Stanford University. Not too bad for a rural country boy! Since a lot of people helped him get to this point, he’s driven to share his passion and excitement by making what he does more accessible. Kyle teaches Introduction to Molecular Cell Biology at Biocurious and is our resident plant expert.

This project reminded me of artist Eduardo Kac (pronounced Katz) and his transgenic bunny, Alba. She glows/ed green in the dark. Here’s more from Kac’s ‘transgenic bunny’ webpage,

My transgenic artwork “GFP Bunny” comprises the creation of a green fluorescent rabbit, the public dialogue generated by the project, and the social integration of the rabbit. GFP stands for green fluorescent protein. “GFP Bunny” was realized in 2000 and first presented publicly in Avignon, France. Transgenic art, I proposed elsewhere [1], is a new art form based on the use of genetic engineering to transfer natural or synthetic genes to an organism, to create unique living beings. This must be done with great care, with acknowledgment of the complex issues thus raised and, above all, with a commitment to respect, nurture, and love the life thus created.

Alba, the fluorescent bunny. Photo: Chrystelle Fontaine

Alba, the fluorescent bunny. Photo: Chrystelle Fontaine

She never looks quite real to me. Under a standard light, she’s a white rabbit but glows when illuminated by a blue  light.  From Kac’s transgenic bunny page,

She was created with EGFP, an enhanced version (i.e., a synthetic mutation) of the original wild-type green fluorescent gene found in the jellyfish Aequorea Victoria. EGFP gives about two orders of magnitude greater fluorescence in mammalian cells (including human cells) than the original jellyfish gene

I don’t know if she still lives but Kac was creating work based on her up until 2011. You can find more here.

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Science, politics, and logic

Friday, April 12th, 2013

I started the week with a posting where I highlighted a presentation about algae, biofuels, policy making, and politics (my Apr. 8, 2013 posting: Algae factories could produce nanocellulose for biofuels and more) and I’m going to end this week with another politics/policy posting, this time focusing on artemisinin and malaria.

Malaria is a serious, serious problem in many parts of the world as Brendan Borrell notes in his Apr. 4, 2013 article, The WHO vs. the Tea Doctor, about an herbal tea that contains artemisinin, for Slate.com,

Of all the illnesses that have afflicted humanity over millennia, few have left their mark quite like malaria, which infects 200 million people each year and kills at least 655,000, most of whom are children. [emphasis mine] Falciparum malaria—the most common type in sub-Saharan Africa—starts as a debilitating fever, which can progress in severe cases to convulsions, brain damage, and death. In this part of the world, it’s almost impossible to stay completely free of the parasites for long. Adults often display a low level of immunity, which makes each subsequent infection painful and unpleasant but usually not fatal.

As I’m about to contrast the information in Borrell’s article with the information in an Apr. 11, 2013 news release from the University of California Berkeley on EurekAlert, about the development of a synthetic artemisinin, I’m going to highlight their ‘agreement’ as the seriousness of the malaria problem,

… a lifesaver for the hundreds of millions of people in developing countries who each year contract malaria and more than 650,000, most of them children, who die of the disease. [emphasis mine]

Borrell sets the discussion for his take on the artemisinin situation with a little history (Note: Links have been removed),

The story of artemisinin demonstrates that even the best malaria drugs are worthless if they are not getting to the people who need them. In the late 1990s, African malaria parasites had become resistant to standard treatments such as chloroquine, and malaria deaths in Uganda doubled in a decade. By the early 2000s, there was a proven alternative: artemisinin combination therapies [ACTs]. Nevertheless, the Global Fund for AIDS, Tuberculosis, and Malaria repeatedly rejected countries’ requests for money for ACTs, funding failing treatments over ACTs at a rate of 10-to-1. In 2004, a group of fed-up scientists writing in the Lancet called these decisions “medical malpractice.” Today, although ACTs are heavily subsidized by the international aid community, local clinics frequently run out of stock, and Africans often end up with substandard, ineffective, and sometimes counterfeit medications.

Borrell goes on to recount the story of a  Chinese plant, sweet wormwood ((Artemisia annua), which is the source for both a class of anti-malarial drugs and a tea (Note: A link has been removed),

It [sweet wormwood] can also be grown in wetter parts of Africa, and a year’s supply costs no more than a few dollars. Although the tea itself has traditionally been used in treatment, not prevention, in China, a randomized controlled trial on this farm showed that workers who drank it regularly reduced their risk of suffering from multiple episodes of malaria by one-third. For a group of people who were once waylaid by this mosquito-borne disease four or more times per year, the tea is a godsend.

According to the article, WHO (World Health Organization) and most malaria researchers are opposed to the tea’s use. Reasons given include the claim that herbal concoctions are more dangerous and less effective than pharmaceuticals and that use of the tea could lead to the malaria parasite developing resistance to the drugs.

There are two issues I have with the first claim about herbal concoctions. Having perused the Compendium of Pharmaceuticals (CPS), I can tell you the last I looked it was huge and listed thousands and thousands of drugs and their side effects (did you know that death is considered a side effect?). Fabrication in a laboratory does not equal safety any more that chopping something off a plant and brewing it as a tea equals safety. Personally, I don’t understand why they aren’t testing the tea, which is derived from sweet wormwood and successfully passed one randomized clinical trial, to see if the result can be repeated and also to test it against the drugs in human clinical trials.

As for the second claim that use of the tea could lead to the malaria parasite developing resistance to the drugs, isn’t that what happened to anti-malarial drugs in the late 1990s? Using chloroquine led to resistance against chloroquine. Following this claim to its logical end, we should never use any drug or herbal concoction as either might lead to resistance.

As for the tea’s successful clinical trial, the researcher experienced difficulty getting his study published (from the article; Note: A link has been removed),

While the workers are effusive about the tea, malaria experts have taken less kindly to it. When Ogwang [Patrick Ogwang of the Ugandan Ministry of Health] tried to publish the results in Malaria Journal, a reviewer largely praised the quality of the science but nixed publication out of concern that use of the tea could render ACTs ineffective. It’s a remarkably patronizing recommendation: that a scientific journal should keep the latest evidence out of the hands of Africans, lest they begin treating themselves. Marcel Hommel, editor in chief of the journal, defends the decision, saying, “It is the responsibility of an editor to avoid publishing papers that promote interventions which could potentially put patients at risk.” Ogwang eventually published his results in a less prestigious journal.

Borrell expresses reservations about herbal medicines/concoctions and he supports having the drugs for special cases but he also notes a study which suggests that a tea made from the plant might be more effective for adults and for less severe cases. From the article (Note: Links have been removed),

In the case of malaria, Anamed and others also argue that it makes sense to preserve stocks of conventional drugs for children and severe cases. One reason ACTs have been so expensive is the cost of isolating artemisinin, but there have long been indications that using a cruder, cheaper whole-plant extract could potentially be more effective and cheaper. In a study conducted in rats last year, University of Massachusetts researchers compared a single dose of pure artemisinin to dried whole leaves, and found that the whole plant was better at killing malaria parasites. And while millions have been spent bioengineering bacteria to crank out pure artemisinin on a budget, you still have to get it to the people who need it.

The resistance that the experts fear has been proved true, according to Borrell’s article, in areas where artemisinin drugs have been distributed and used with abandon.

Coincidentally or not, the University of California Berekeley announced a the development of semi-synthetic artemisinin in the Apr. 11, 2013 news release mentioned earlier,

Twelve years after a breakthrough discovery in his University of California, Berkeley, laboratory, professor of chemical engineering Jay Keasling is seeing his dream come true.

On April 11 [2013], the pharmaceutical company Sanofi will launch the large-scale production of a partially synthetic version of artemisinin, a chemical critical to making today’s front-line antimalaria drug, based on Keasling’s discovery.

The drug is the first triumph of the nascent field of synthetic biology and will be, Keasling hopes, a lifesaver ….

Keasling and colleagues at Amyris, a company he cofounded in 2003 to bring the lab-bench discovery to the marketplace, will publish in the April 25 issue of Nature the sequence of genes they introduced into yeast that allowed Sanofi to make the chemical precursor of artemisinin. The paper will be available online April 10.

“It is incredible,” said Keasling, who also serves as associate director for biosciences at Lawrence Berkeley National Laboratory and as CEO of the Joint Bioenergy Institute in Emeryville, Calif. “The time scale hasn’t been that long, it just seems like a long time. There were many places along the way where it could have failed.”

The yeast strain developed by Amyris based on Keasling’s initial research and now used by Sanofi produces a chemical precursor of artemisinin, a compound that until now has been extracted from the sweet wormwood plant, Artemsia annua. Artemisinin from either sweet wormwood or the engineered yeast is then turned into the active antimalarial drug , and typically mixed with another antimalarial drug in what is called arteminsinin combination therapy, or ACT.

Global demand for artemisinin has increased since 2005, when the World Health Organization identified ACTs as the most effective malaria treatment available. Sanofi said that it is committed to producing semisynthetic artemisinin using a no-profit, no-loss production model, which will help to maintain a low price for developing countries. Though the price of ACTs will vary from product to product, the new source for its key ingredient, in addition to the plant-derived supply, should lead to a stable cost and steady supply, Keasling said.

Unfortunately, no details about Sanofi’s no-profit, no-loss production model are offered. Perhaps a reader could ease my ignorance? I am interpreting this model to mean that while Sanofi won’t make money from the project, it does expect to recoup its costs (no-loss). (I most recently mentioned Sanofi, a French multinational, in an Apr. 9, 2013 posting about the winners of its 2013 competition for Canadian students.)

The backers of the research do provide some reasoning for this synthetic biology artemisinin project (from the news release),

“The production of semisynthetic artemisinin will help secure part of the world’s supply and maintain the cost of this raw material at acceptable levels for public health authorities around the world and ultimately benefit patients,” said Dr. Robert Sebbag, vice-president of Access to Medicines at Sanofi. “This is a pivotal milestone in the fight against malaria.” [emphasis mine]

I wonder what constitutes an ‘acceptable’ level of costs to public health authorities and, for that matter, to Sanofi. After all, I was under the impression after reading Borrell’s article that all one needed to do was to cultivate the plant and harvest it for materials to make tea.  There was no mention of difficulties cultivating the plant in countries outside of China where it originated nor was there any mention that it was expensive to cultivate.

There are some fairly big names, in addition to Sanofi, involved in this synthetic biology project,

The success is due in large part to two grants totaling $53.3 million from the Bill & Melinda Gates Foundation to OneWorld Health, the drug development program for PATH, an international nonprofit organization aiming to transform global health through innovation. [emphasis mine] OneWorld Health shepherded the drug’s development out of Keasling’s UC Berkeley lab to Amyris for scale-up and then to pharmaceutical firm Sanofi, based in France, for production.

I am pointing out some interesting relationships with the intention of providing a view of a complex situation with many well-intentioned players, where lines of opposition have been drawn and the people most at risk seemingly forgotten. If the tea hasn’t caused resistance in over 1,500 years of use in China while the drugs have already done so on the Thai-Cambodian border as per Borrell’s article, why isn’t it being accepted and used? While some might point at corporate profit requirements (and I’m not discounting that motive regardless of what Sanofi’s company executives say), there are also issues of institutionalized opposition to any developments made outside of the medical establishment, and the fetishization of the laboratory environment where drugs are made pure in a pure environment while herbs come from the ‘dirty’ earth.

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Synthetic biology project map

Tuesday, April 9th, 2013

The Synthetic Biology Project (an initiative of the Woodrow Wilson International Center for Scholars) has updated an international map of synthetic biology research labs originally launched in 2009. From their Apr. 8, 2013 announcement,

Updated Map Tracks Global Growth of Synthetic Biology

As research into synthetic biology increases, this map identifies companies, universities, research institutions, laboratories and other centers across the globe that are active in this emerging field.

In 2009, the Synthetic Biology Project began mapping the increased research in the field of synthetic biology. Today, we are launching an updated version of this map, which can be found at http://www.synbioproject.org/library/inventories/map/.

The updated map can be used to examine the locations of companies, universities, research institutions, government and military laboratories and policy centers that are active in this emerging field. In addition to expanded listings, the updated map features improved functionality, more detailed information and additional categories and subcategories. The map can also be accessed on Android and Apple mobile devices.

This map is based on publicly available data from official websites, scientific literature, government reports and records, and newspaper and journal articles, but this field is dynamic, and the map is a work in progress. We welcome your input. A form to submit information can be found at http://www.synbioproject.org/sbmap/add-item/. Comments can also be sent to synbio@wilsoncenter.org.

Thank you for your submissions: All suggestions will be reviewed and incorporated into the map.

A detailed analysis of the current landscape will be released in the coming weeks. More information about the methodology and sources for the update can be found here. The data behind the map can be found here.

As it turns out, there are some Canadian cities listed on the map and upon checking I found addresses and localized maps. Until now, I had been unaware that my local British Columbia (Canada) Cancer Control Agency laboratories pursue research into synthetic biology.

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Algae factories could produce nanocellulose for biofuels and more

Monday, April 8th, 2013

The American Chemical Society (ACS) is holding its 245th meeting April 7 – 11, 2013 and its first International Symposium on Bacterial Nanocellulose simultaneously. I have written about nanocellulose previously but it’s always been concerned with the type derived from plant matter; bacterial nanocellulose is new to me but not the scientific community as the Apr. 8, 2013 news item on Azonano notes,

In the 1800s, French scientist Louis Pasteur first discovered that vinegar-making [and Kombucha tea and nata de coco] bacteria make “a sort of moist skin, swollen, gelatinous and slippery” — a “skin” now known as bacterial nanocellulose. Nanocellulose made by bacteria has advantages, including ease of production and high purity that fostered the kind of scientific excitement reflected in the first international symposium on the topic, Brown [R. Malcolm Brown, Jr., Ph.D.] pointed out.

Before going on to this latest research, here’s a description of cellulose and nanocellulose as per its presence in plant material (from the news item),

Cellulose is the most abundant organic polymer on Earth, a material, like plastics, consisting of molecules linked together into long chains. Cellulose makes up tree trunks and branches, corn stalks and cotton fibers, and it is the main component of paper and cardboard. People eat cellulose in “dietary fiber,” the indigestible material in fruits and vegetables. Cows, horses and termites can digest the cellulose in grass, hay and wood.

Most cellulose consists of wood fibers and cell wall remains. Very few living organisms can actually synthesize and secrete cellulose in its native nanostructure form of microfibrils. At this level, nanometer-scale fibrils are very hydrophilic and look like jelly. A nanometer is one-millionth the thickness of a U.S. dime. Nevertheless, cellulose shares the unique properties of other nanometer-sized materials — properties much different from large quantities of the same material. Nanocellulose-based materials can be stronger than steel and stiffer than Kevlar. Great strength, light weight and other advantages has fostered interest in using it in everything from lightweight armor and ballistic glass to wound dressings and scaffolds for growing replacement organs for transplantation.

A new kind of bacteria actively entered the nanocellulose picture in 2001 (from the news item) allowing Brown to exploit research he had been pursuing since the 1970s (from the news item),

Brown recalled that in 2001, a discovery by David Nobles, Ph.D., a member of the research team at the University of Texas at Austin, refocused their research on nanocellulose, but with a different microbe. Nobles established that several kinds of blue-green algae, which are mainly photosynthetic bacteria much like the vinegar-making bacteria in basic structure; however, these blue-green algae, or cyanobacteria, as they are called, can produce nanocellulose. One of the largest problems with cyanobacterial nanocellulose is that it is not made in abundant amounts in nature. If it could be scaled up, Brown describes this as “one of the most important discoveries in plant biology.”

While I find the science interesting, it’s Brown’s comments about the policy and politics of commercializing nanocellulose-based fuels that intrigue me (from the news item),

In his report at the ACS meeting, Brown described how his team already has genetically engineered the cyanobacteria to produce one form of nanocellulose, the long-chain, or polymer, form of the material. And they are moving ahead with the next step, engineering the cyanobacteria to synthesize a more complete form of nanocellulose, one that is a polymer with a crystalline architecture. He also said that operations are being scaled up, with research moving from laboratory-sized tests to larger outdoor facilities.

Brown expressly pointed out that one of the major barriers to commercializing nanocellulose fuels involves national policy and politics, rather than science. Biofuels, he said, will face a difficult time for decades into the future in competing with the less-expensive natural gas now available with hydraulic fracturing, or “fracking.”  [emphasis mine] In the long run, the United States will need sustainable biofuels, he said, citing the importance of national energy policies that foster parallel development and commercialization of biofuels.

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Public domain biotechnology: biological transistors from Stanford University

Friday, March 29th, 2013

Andrew Myers’ Mar. 28, 2013 article for the Stanford School of Medicine’s magazine (Inside Stanford Medicine) profiles some research which stands as a bridge between electronics and biology and could lead to biological computing,

… now a team of Stanford University bioengineers has taken computing beyond mechanics and electronics into the living realm of biology. In a paper published March 28 in Science, the team details a biological transistor made from genetic material — DNA and RNA — in place of gears or electrons. The team calls its biological transistor the “transcriptor.”

“Transcriptors are the key component behind amplifying genetic logic — akin to the transistor and electronics,” said Jerome Bonnet, PhD, a postdoctoral scholar in bioengineering and the paper’s lead author.

Here’s a description of the transcriptor (biological transistor) and biological computers (from the article),

In electronics, a transistor controls the flow of electrons along a circuit. Similarly, in biologics, a transcriptor controls the flow of a specific protein, RNA polymerase, as it travels along a strand of DNA.

“We have repurposed a group of natural proteins, called integrases, to realize digital control over the flow of RNA polymerase along DNA, which in turn allowed us to engineer amplifying genetic logic,” said Endy [Drew Endy, PhD, assistant professor of bioengineering and the paper’s senior author].

Using transcriptors, the team has created what are known in electrical engineering as logic gates that can derive true-false answers to virtually any biochemical question that might be posed within a cell.

They refer to their transcriptor-based logic gates as “Boolean Integrase Logic,” or “BIL gates” for short.

Transcriptor-based gates alone do not constitute a computer, but they are the third and final component of a biological computer that could operate within individual living cells.

The article also offers a description of Boolean logic and the workings of standard computers,

Digital logic is often referred to as “Boolean logic,” after George Boole, the mathematician who proposed the system in 1854. Today, Boolean logic typically takes the form of 1s and 0s within a computer. Answer true, gate open; answer false, gate closed. Open. Closed. On. Off. 1. 0. It’s that basic. But it turns out that with just these simple tools and ways of thinking you can accomplish quite a lot.

“AND” and “OR” are just two of the most basic Boolean logic gates. An “AND” gate, for instance, is “true” when both of its inputs are true — when “a” and “b” are true. An “OR” gate, on the other hand, is true when either or both of its inputs are true.

In a biological setting, the possibilities for logic are as limitless as in electronics, Bonnet explained. “You could test whether a given cell had been exposed to any number of external stimuli — the presence of glucose and caffeine, for instance. BIL gates would allow you to make that determination and to store that information so you could easily identify those which had been exposed and which had not,” he said.

Here’s how they created a transcriptor (from the article),

To create transcriptors and logic gates, the team used carefully calibrated combinations of enzymes — the integrases mentioned earlier — that control the flow of RNA polymerase along strands of DNA. If this were electronics, DNA is the wire and RNA polymerase is the electron.

“The choice of enzymes is important,” Bonnet said. “We have been careful to select enzymes that function in bacteria, fungi, plants and animals, so that bio-computers can be engineered within a variety of organisms.”

On the technical side, the transcriptor achieves a key similarity between the biological transistor and its semiconducting cousin: signal amplification.

Refreshingly the team made this decision (from the article),

To bring the age of the biological computer to a much speedier reality, Endy and his team have contributed all of BIL gates to the public domain so that others can immediately harness and improve upon the tools.

“Most of biotechnology has not yet been imagined, let alone made true. By freely sharing important basic tools everyone can work better together,” Bonnet said.

Here’s a citation and a link to the researchers’ paper in Science,

Amplifying Genetic Logic Gates by Jerome Bonnet, Peter Yin, Monica E. Ortiz, Pakpoom Subsoontorn, and Drew Endy. Science 1232758 Published online 28 March 2013 [DOI:10.1126/science.1232758]

This paper is behind a paywall. As for Myers’ article, it’s well worth reading for its clear explanations and forays into computing history.

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Mar. 20, 2013 live webcast about synthetic biology and nanotechnology poll

Tuesday, March 19th, 2013

The Woodrow Wilson International Center for Scholars has an event which you can attend in person if you’re in Washington, DC or can attend from elsewhere via a webcast. Here’s why you might want to attend,

Beginning in 2006, the Science and Technology Innovation Program at the Woodrow Wilson International Center for Scholars and Peter D. Hart Research Associates have conducted periodic national telephone surveys to gauge the public awareness of and attitudes towards synthetic biology and nanotechnology.

In our latest survey, conducted in January 2013, three-fourths of respondents say they have heard little or nothing about synthetic biology, a level consistent with that measured in 2010. While initial impressions about the science are largely undefined, these feelings do not necessarily become more positive as respondents learn more. The public has mixed reactions to specific synthetic biology applications, and almost one-third of respondents favor a ban “on synthetic biology research until we better understand its implications and risks,” while 61 percent think the science should move forward.

The survey also found that, despite outreach efforts, 68 percent of respondents have heard little or nothing about nanotechnology, which indicates no change in awareness since 2009.

Please join us Wednesday,March 20, 2013, at noon to discuss the complete results from the latest poll.

Here are the specifics,

What:

Results of the 2013 national public opinion poll on synthetic biology and nanotechnology

When:

Wednesday, March 20, 2013, Noon– 1:30 PM (Light lunch available at 11:30 am) [The times listed are EDT, for those of us on the West Coast of North America,  the webcast starts at 9 am]

 Who:

David Rejeski, Director, Science and Technology Innovation Program

Abigail Davenport, Senior Vice President, Peter D. Hart Research Associates

 Where:

Woodrow Wilson International Center for Scholars,
5th Floor Conference Room,
1300 Pennsylvania Ave. NW
Washington, DC

RSVPs and miscellaneous,

A light lunch will be served beginning at 11:30 am.

You must register to attend the event. To RSVP, please visit:

http://www.wilsoncenter.org/event/rsvp?eid=26431&pid=116

This event will be Webcast LIVE at

http://www.wilsoncenter.org/event/awareness-and-impressions-synthetic-biology-results-the-2013-poll

There is no RSVP required to view the webcast.

For directions, please visit: http://www.wilsoncenter.org/directions

Media planning to cover the event should contact Aaron Lovell at (202) 691-4320 or at aaron.lovell@wilsoncenter.org

To learn more about the Synthetic Biology Project, please visit: http://www.synbioproject.org

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Phytoremediation, clearing pollutants from industrial lands, could also be called phyto-mining

Tuesday, March 5th, 2013

The University of Edinburgh (along with the Universities of Warwick and Birmingham, Newcastle University and Cranfield University) according to its Mar. 4, 2013 news release on EurekAlert is involved in a phytoremediation project,

Common garden plants are to be used to clean polluted land, with the extracted poisons being used to produce car parts and aid medical research.

Scientists will use plants such as alyssum, pteridaceae and a type of mustard called sinapi to soak up metals from land previously occupied by factories, mines and landfill sites.

Dangerous levels of metals such as arsenic and platinum, which can lurk in the ground and can cause harm to people and animals, will be extracted using a natural process known as phytoremediation.

A Mar. 4, 2013 news item on the BBC News Edinburgh, Fife and East Scotland site offers more details about the project and the technology,

A team of researchers from the Universities of Edinburgh, Warwick, Birmingham, Newcastle and Cranfield has developed a way of extracting the chemicals through a process called phytoremediation, and are testing its effectiveness.

Once the plants have drawn contaminated material out of the soil, they will be harvested and processed in a bio-refinery.

…

A specially designed bacteria will be added to the waste to transform the toxic metal ions into metallic nanoparticles.

The team said these tiny particles could then be used to develop cancer treatments, and could also be used to make catalytic converters for cars.

Dr Louise Horsfall, of Edinburgh’s University’s school of biological sciences, said: “Land is a finite resource. As the world’s population grows along with the associated demand for food and shelter, we believe that it is worth decontaminating land to unlock vast areas for better food security and housing.

“I hope to use synthetic biology to enable bacteria to produce high value nanoparticles and thereby help make land decontamination financially viable.”

The research team said the land where phytoremediation was used would also be cleared of chemicals, meaning it could be reused for new building projects.

In my Sept. 28, 2012 posting I featured an international collaboration between universities in the UK, US, Canada, and New Zealand in a ‘phyto-mining’ project bearing some resemblance to this newly announced project. In that project, announced in Fall 2012, scientists were studying how they might remove platinum for reuse from plants near the tailings of mines.

I do have one other posting about phytoremediation. I featured a previously published piece by Joe Martin in a two-part series on the topic plant (phyto) and nano soil remediation. The March 30, 2012 posting is part one, which focuses on the role of plants in soil remediation.

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A tooth and art installation in Vancouver (Canada) and bodyhacking and DIY (do-it-yourself) culture in the US

Friday, September 21st, 2012

After a chat with artist David Khang, about various mergings of flesh and nonliving entities, I saw his installation, Amelogenesis Imperfecta (How Deep is the Skin of Teeth)  at Vancouver’s grunt gallery with  an enhanced appreciation for the shadowy demarcation between living entities (human and nonhuman) and between living and nonliving entities (this was à propos the work being done at the SymbioticA Centre in Australia, which is mentioned in the following excerpt) and some of the social and ethical questions that arise. Robin Laurence in her Sept. 13, 2012 article for the Georgia Straight newspaper/website describes both the installation and its influences,

With Khang’s newly launched works, Amelogenesis Imperfecta (How Deep Is the Skin of Teeth), on view at the grunt gallery until September 22, and Beautox Me, at CSA Space [#5–2414 Main Street] through October 7, he has again found formally and intellectually complex ways to meld his seemingly disparate professions. The grunt gallery installation includes microscopic laser drawings on epithelial cells and an animated short of a human tooth evolving into a fearsome, all-devouring shark. This work developed out of experiments Khang conducted during his 2010 residency at SymbioticA Centre for Biological Arts in Perth, Australia. “It began as a goal-oriented project to manufacture enamel,” he says, “but ended up being a meditation on ethical interspecies relations.” Fetal calf serum, he explains, is used “to fuel” all stem-cell research.

In our far ranging discussion, Khang (whose show at the Grunt [350 E. 2nd Avenue, Vancouver, ends on Saturday, Sept. 22, 2012) and I discussed not only interspecies relations but also the integration of flesh with machine/technology,which is being explored and discussed at SymbioticA and elsewhere.

Coincidentally, one day after my chat with Khang I found this Sept. 19, 2012 article (Biohackers And DIY Cyborgs Clone Silicon Valley Innovation) by Neal Ungerleider for Fast Company (Note: I have removed links),

The grinders (DIY cybernetics enthusiasts) and their comrades in arms--biohackers working on improving human source code, quantified self enthusiasts who arm themselves with constant bodily data feeds, and independent DIY biotechnology enthusiasts--are moonlighting for now in basements, shared spaces, and makeshift labs. But they’re ultimately aiming to change the world. Think of how bionic [sic] legs like those belonging to Oscar Pistorius and cochlear implants that let the deaf hear have changed everyday life for so many people. Then multiply that by a million. A million people. And millions of dollars.

Not only has the new wave of do-it-yourself (DIY) cybernetics moved well beyond science fiction, it’s going to cause a business boom in the not-too-distant future.

I have two comments. (1) Pistorius does not have bionic legs but he does use some very high tech racing prosthetics, which I describe briefly in my July 27, 2009 posting in part 4 of a series on human enhancement. On the basis of this error, you may want to apply a little caution when reading the rest of Ungerleider’s  article. (2) Prior to this article, I hadn’t considered machine/flesh integration as a business opportunity but clearly I’ve been shortsighted.

I was particularly interested in this following passage where Ungerleider mentions the fusion of the living and of the electronic.

In Brooklyn, a small “community biolab” called Genspace is home to approximately a dozen DIY biology experimenters whose work often involves the fusion of the living and the electronic. Classes are offered to the public in synthetic biology, which engineers living organisms as if they were biological machines.

A workshop recently held at Genspace, Crude Control, showed how in-vitro meat and leather could be created via tissue engineering, and it explored the possibility of creating semi-living “products” from them. Although the Genspace workshop was for educational purposes, similar technologies are already being monetized elsewhere–Peter Thiel recently sank six figures into a startup that will make 3-D printed in vitro meat commercially available.

The teacher at the Crude Control workshop, Oron Catts, [emphasis mine] walked participants through “basic tissue culture and tissue engineering protocols, including developing some DIY tools and isolating cells from a bone we got from a local butcher.” Some of Catts’ previous projects include bioengineering a steak from pre-natal sheep cells (in his words, “steak grown from an animal that was not yet born“) and victimless leather grown from cell lines. [emphases mine]
 

I emphasized Oron Catts because he is SymbioticA Centre’s director.From his biographical page on the SynbioticA Centre website,

Oron Catts is an artist, researcher and curator whose work with the Tissue Culture and Art Project (which he founded in 1996 with Ionat Zurr) is part of the NY MoMA design collection and has been exhibited and presented internationally. In 2000 he co-founded SymbioticA, an artistic research laboratory housed within the School of Anatomy and Human Biology, The University of Western Australia. Under Oron’s leadership, SymbioticA has gone on to win the Prix Ars Electronica Golden Nica in Hybrid Art (2007) and became a Centre for Excellence in 2008.

…

Oron has been a researcher at The University of Western Australia since 1996 and was a Research Fellow at the Tissue Engineering and Organ Fabrication Laboratory, Harvard Medical School, Massachusetts General Hospital, Boston from 2000-2001. He worked with numerous other bio-medical laboratories around the world. In 2007 he was a visiting Scholar at the Department of Art and Art History, Stanford University. He is currently undertaking a “Synthetic Atheistic” residency which is jointly funded by the National Science Foundation (USA) and the Engineering and Physical Sciences Research Council (UK) to exploring the impactions of synthetic Biology; and is a Visiting Professor of Design Interaction, Royal College of Arts, London.

You can find out more about the SymbioticA Centre here.

As for the “steak grown from an animal that was not yet born” and “victimless leather,” the terminology hints   while the description of the work demonstrates how close we are to a new reality in our relationships with nonhumans. Some readers may find the rest of Ungerleider’s article even more eyebrow-raising/disturbing/exciting.

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DARPA’s Living Foundries and advanced nanotechnology via synthetic biology

Thursday, May 31st, 2012

This is not a comfortable topic for a lot of people, but James Lewis in a May 26, 2012 posting on the Foresight Institute blog, comments on some developments in the DARPA (US Defense Advanced Research Projeect Agency) Living Foundries program (Note: I have removed a link),

Synthetic biology promises near-term breakthroughs in medicine, materials, and energy, and is also one promising development pathway leading to advanced nanotechnology and a general capability for programmable, atomically-precise manufacturing. Darpa (US Defense Advanced Research Projects Agency) has launched a new program [Living Foundries] that could greatly accelerate progress in synthetic biology by creating a library of standardized, modular biological units that could be used to build new devices and circuits.

…

If Darpa’s Living Foundries program achieves its ambitious goals, it should create a methodology, toolbox, and a large group of practitioners ready to pursue a synthetic biology pathway to building complex molecular machine systems, and eventually, atomically precise manufacturing systems.

DARPA opened solicitations for this program Sept. 2, 2011 and made a series of award notices starting May 17, 2012 stretching to May 31,2012. Here’s a description of the program from the DARPA Living Foundries project webpage,

The Living Foundries Program seeks to create the engineering framework for biology, speeding the biological design-build-test cycle and expanding the complexity of systems that can be engineered. The Program aims to develop new tools, technologies and methodologies to decouple biological design from fabrication, yield design rules and tools, and manage biological complexity through abstraction and standardization.  These foundational tools would enable the rapid development of previously unattainable technologies and products, leveraging biology to solve challenges associated with production of new materials, novel capabilities, fuel and medicines. For example, one motivating, widespread and currently intractable problem is that of corrosion/materials degradation. The DoD must operate in all environments, including some of the most corrosively aggressive on Earth, and do so with increasingly complex heterogeneous materials systems. This multifaceted and ubiquitous problem costs the DoD approximately $23 Billion per year. The ability to truly program and engineer biology, would enable the capability to design and engineer systems to rapidly and dynamically prevent, seek out, identify and repair corrosion/materials degradation.

Accomplishing this vision requires an approach that is more than multidisciplinary – it requires a new engineering discipline built upon the integration of new ideas, approaches and tools from fields spanning computer science and electrical engineering to chemistry and the biological sciences.  The best innovations will introduce new architectures and tools into an open technology platform to rapidly move new designs from conception to execution.

Performers must ensure and demonstrate throughout the program that all methods and demonstrations of capability comply with national guidance for manipulation of genes and organisms and follow all guidance for biological safety and Biosecurity.

Katie Drummond in her May 22, 2012 posting on the Wired website’s Danger Room blog makes note of the awarded contracts (Note: I have removed the links),

Now, Darpa’s handed out seven research awards worth $15.5 million to six different companies and institutions. Among them are several Darpa favorites, including the University of Texas at Austin and the California Institute of Technology. Two contracts were also issued to the J. Craig Venter Institute. Dr. Venter is something of a biology superstar: He was among the first scientists to sequence a human genome, and his institute was, in 2010, the first to create a cell with entirely synthetic genome.

In total, nine contracts were awarded as of May 31, 2012. MIT (Massachusetts Institute of Technology) was awarded two, while  Stanford University, Harvard University, and the Foundation for Applied Molecular Evolution were each awarded one.

The J. Craig Venter Institute received a total of almost $4M for two separate contracts ($964,572 and $3,007, 321). Interestingly, Venter has just been profiled in the New York Times magazine in a May 30, 2012 article by Wil S. Hylton with nary a mention of this new project (I realize the print version couldn’t be revised but surely they could have managed a note online).  The opening paragraphs sound like a description of the Living Foundries project for people who don’t specialize in reading government documents,

In the menagerie of Craig Venter’s imagination, tiny bugs will save the world. They will be custom bugs, designer bugs — bugs that only Venter can create. He will mix them up in his private laboratory from bits and pieces of DNA, and then he will release them into the air and the water, into smokestacks and oil spills, hospitals and factories and your house.

Each of the bugs will have a mission. Some will be designed to devour things, like pollution. Others will generate food and fuel. There will be bugs to fight global warming, bugs to clean up toxic waste, bugs to manufacture medicine and diagnose disease, and they will all be driven to complete these tasks by the very fibers of their synthetic DNA.

This is is not a critical or academic  analysis of Venter’s approach to biology, synthetic or otherwise, but it does offer an in-depth profile and, given Venter’s prominence in the field of synthetic biology, it’s a worthwhile read.

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An art to synthetic biology governance?

Friday, March 23rd, 2012

The Woodrow Wilson Center for International Scholars will be hosting, courtesy of its Synthetic Biology Project (SynBio Project), an event on March 27, 2012 titled (from the March 21, 2012 event announcement),

The Art of Synthetic Biology Governance: Considering the Concepts of Scientific Uncertainty and Cross-Borderness

When: March 27, 2012 from 12:30 p.m. – 2:00 p.m. (Light lunch available at noon.)

Who: Dr. Claire Marris, [senior research fellow at] King’s College London [and one of the report’s authors]

David Rejeski, Director, Science and Technology Innovation Program, will moderate the session

Where: Woodrow Wilson International Center for Scholars

5th Floor Conference Room
Ronald Reagan Building
1300 Pennsylvania Ave NW
Washington, D.C.

Sadly, it seems that there will not be a webcast, livestreamed or otherwise so the only option is to attend in person. If you can attend in person, here’s the registration link.

This event marks the release of a new working paper from the London School Economics (LSE), “BIOS working paper no. 4, The Transnational Governance of Synthetic Biology: Scientific uncertainty, cross-borderness and the ‘art’ of governance.” BTW, BIOS is the LSE’s Centre for the Study of Bioscience, Biomedicine, Biotechnology and Society.

There’s more about the report here, as well as, a PDF of the report on the Synbio Project website. I’ve only read about 1/4 of the report and can only comment on their general approach which I find quite interesting. From the executive summary of the working report, The Transnational Governance of Synthetic Biology: Scientific uncertainty, cross-borderness and the ‘art’ of governance,

The paper goes beyond proposals to mitigate specific risks of synthetic biology to investigate the root causes of such concerns, and address the challenges at an overarching level.

…Effective governance seeks to foster good science, not to hamper it, but recognises that good science goes hand in hand with open, clear, transparent regulation to ensure both trust and accountability.

• Such an ‘art of governance’ seeks to facilitate effective interactions between the range of current and emerging social actors involved in or affected by scientific and technological developments, to ensure that all parties have the opportunity to express their perspectives and interests at all stages in the pathways of research and development, through transparent and democratic processes. The art of governance recognises that no decisions will suit all actors, but effective compromise depends on ensuring openness and transparency in the process by which decisions are reached, demonstrating genuine consideration of all perspectives.

We highlight three crucial challenges for the effective national and international governance of synthetic biology:

• FIRST, governance of science is not just a matter of governing the production and application of knowledge, but must also recognise that scientific uncertainty is not merely temporary but endemic: not merely calculable risks, but provisional unknowns, unknown unknowns, and even wilful ignorance or a conscious inability-to-know. Such ‘non-knowing’ cannot be overcome simply by acquiring more knowledge: increasing knowledge often leads to increasing uncertainty. [emphasis mine] Effective governance of synthetic biology must give explicit and attention to both knowledge and non-knowing.

• SECOND, synthetic biology relies on collaborative contributions from distinct disciplines and professions, and this requires accountability beyond that internal to each field. While good governance of synthetic biology demands proper accountability within scientific disciplines and professional bodies, it also requires the cultivation of external accountability, not only across and between such fields, but beyond, to all those who may be affected. Such networks of accountability accommodate change over time, facilitate mutual trust and responsiveness among various groups and constituencies, encourage good practice and robust science, and enhance openness and transparency. [emphasis mine]

• THIRD, the combination of scientific uncertainty and cross-borderness ensures that no single group, organization, constituency or regulatory body will have the capacity to oversee, let alone to control, the development of synthetic biology. An art of governance is required to accept the constitutive fragmentation of social authorities, and to work with such diversity, not as a hindrance, but as a condition of, and advantage for, effective governance. [emphasis mine]

In the light of these three challenges, we argue that scientifically informed, evidence-based approaches to policy-making, while essential, are insufficient. It is time to bring back a sense of the ‘art’ to the governance of biotechnology: an approach which employs proactive, open-ended regulatory styles able to work with uncertainty and change, to make links across borders, and to adapt to evolving relations among changing stakeholders, including researchers, research funders, industry, and multiple publics. (pp. 3-4)

I quite appreciate the descriptions of uncertainty and unknowingness as I’ve been coming to that conclusion for some time but they’ve said more elegantly than I can. As for the art of governance as a means of dealing with the cross-borderness (similar terms in academia include: transdisciplinary, crossdisciplinary, and multidisciplinary), as well as the uncertainty  inherent to synthetic biology (and the other emerging technologies) I like the proposed metaphor and scope of this approach to governance.  They may seem unattainable but it’s important to set one’s sights as high as possible in these types of efforts because inevitably the grand ideas will be chopped down to size in practice, in much the same way that one uses a large piece of marble to sculpt a statue which will have significantly less mass.

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