Monthly Archives: May 2010

At last, Fast Company and IEEE’s Nanoclast brought together—by quantum computing

Addy Dugdale at Fast Company has written an article about one of the latest advances toward quantum computing,

Quantum computing just got a little bit closer, after an Australian team of researchers unveiled a seven-atom transistor. Measuring just four billionths of a meter and embedded in a single silicon crystal, it acts as a switch on a chip and paves the way for faster processing in an even smaller package. The team, from the Centre of Quantum Technology at the University of New South Wales, did the tricky stuff by hand, which means that commercial versions of their breakthrough will be at least five years away.

The research is pretty exciting stuff and Dexter Johnson (Nanoclast at the IEEE [Institute of Electrical and Electronics Engineers]) helps put the feat into perspective,

The quantum computer is one of those technologies that gets held out as some sort of Holy Grail and remains just as elusive with those who have claimed to have achieved it being regarded with a high degree of skepticism.

One avenue that has been pursued in realizing a solid-state quantum computer has been the use of quantum dots as the building block.

Quantum dots are a strange phenomenon. Spectrum [an IEEE publication] Editor, Eric Guizzo, described them nicely in the quantum computer application as …

So as not to copy Dexter’s entire post here, let’s just say quantum dots can make the process of calculating much faster. But there are problems with using quantum dots as was noted in my May 12, 2010 posting about research at McGill University,

Dr. Peter Grütter, McGill’s Associate Dean of Research and Graduate Education, Faculty of Science, explains that his research team has developed a cantilever force sensor that enables individual electrons to be removed and added to a quantum dot and the energy involved in the operation to be measured.

Being able to measure the energy at such infinitesimal levels is an important step in being able to develop an eventual replacement for the silicon chip in computers – the next generation of computing. Computers currently work with processors that contain transistors that are either in an on or off position – conductors and semi-conductors – while quantum computing would allow processors to work with multiple states, vastly increasing their speed while reducing their size even more.

One other important feature noted in the research from McGill is that several dots may be piled on top of each other in such a way that there appears to be only one dot. Measuring the energy would allow researchers to recognize that situation. Maybe the folks in Australia and at McGill could work together? Of course that won’t fix everything as Dexter points out after the lead Australian researcher, Michelle Y. Simmonds, notes the importance of her team’s work,

The research, which was initially published in the journal Nature Nanotechnology, marks the first time that it has been possible to dictate the placement and behavior of single atoms within a transistor, according to Simmons.

“We’re basically controlling nature at the atomic scale,” Simmons is quoted as saying. “This is one of the key milestones in building a quantum computer.”

[back to Dexter]

Well, there are issues such as entanglement, the coupling between quibits, to be addressed, but it is a step towards quantum computers.

Nano, Edvard Munch’s The Scream, and some more about oil

Striking resemblance isn’t there? I gather this was found by accident as scientists were examining oil shale under a scanning electron microscope (SEM) manufactured by JEOL USA. From the news item on Nanowerk,

The clear details shown in the picture (micrograph) from the SEM is due to not only the optics of the microscope, but the way in which the sample was prepared and precisely cross sectioned from a larger chunk of shale through the use of a special ion-beam cross section polisher. This tool has become indispensable for oil shale analysis.

One of today’s hottest areas of potential under-utilized energy resources is shale. Abundant in specific regions of the United States, oil shale is a fine-grained, sedimentary rock composed of flakes of clay minerals and tiny fragments of other minerals, especially quartz and calcite. Shale also has a complex network of soft veins of an organic substance, kerogen and accessory opaque minerals such as pyrite.

When heated, kerogen can release hydrocarbons, or fossil fuel. By studying the internal composition of the shale and the network of kerogen filled veins, scientists can determine the abundance and ease of extraction of oil.

It seems timely to discuss alternative methods of accessing oil in light of the situation in the Gulf of Mexico and the leak. As for BP, the company at the centre of the controversy, its logo, in the day and age of branding, is under assault as Suzanne Labarre in her article (BP Logo Gets Oily, Gruesome Redesigns Courtesy of Greenpeace Followers) on Fast Company notes,

Greenpeace asks you, gentle public, to redesign BP’s logo to more aptly convey its dirty ways. Skulls and crossbones welcome.

You’ve seen BP’s green-and-yellow sunburst logo, right? Seems completely out of place now that the defining image of the company is a dark blob spreading across the Gulf. With that in mind, Greenpeace has put up the Bat-Signal for a fresh logo that better conveys the oil company’s miraculous ability to ruin the world.

Here’s one sample logo (there are more at Fast Company),

An alternate BP logo

The Scientist opens its archives for a limited period of time

I received an email from The Scientist magazine website alerting me to their special open access at almost the same time I came across a posting by Dave Bruggeman at Pasco Phronesis about a recent synbio and the FBI article in the very same magazine.

The original article by Jill Frommer titled, SYNTHETIC BIO MEET “Fbio”; You may soon be visited by an FBI agent, or a scientist acting on behalf of one. Here’s why, provides an overview of the current situation with regard to law enforcement agencies and practitioners in the life sciences field (note: The Scientist is primarily a life sciences magazine).

From Dave’s posting,

The Scientist has a long, detailed article outlining the Federal Bureau of Investigation’s relationship with the biological sciences community. Unfortunately, recent cases such as those of Thomas Butler and Steve Kurtz have established a more adversarial relationship between the FBI and the biological sciences than would be beneficial – for both sides. …

I think some history could help understand why there are challenges in this area, where the nuclear science/weapons research areas didn’t quite have the combination of ambivalence and distrust that come through in the Scientist piece.

It’s well worth looking at both pieces, now especially if you are loathe to register at The Scientist for the privilege of reading an article. Note: I registered a while back and they send a monthly notice about the latest issue but have never bothered me otherwise.

Drawing pictures with your eyes at FutureEverything digital celebration

The title is meant literally, i.e., drawing pictures using your eyes only. What makes the feat even more extraordinary is that the designers hacked a Playstation 3 webcam to create the Eyewriter and (from the BBC article by Zoe Kleinman) “You could put it together at home without a soldering iron for about £30.”

The project won first prize at the FutureEverything festival in Manchester, England. From the BBC article,

Artists, musicians, engineers and hackers from around the world recently descended on Manchester for a three day celebration of digital culture.

Now in its 15th year, FutureEverything (previously called Futuresonic) has quietly established itself as an annual gathering for the technology avant garde.

With a £10,000 prize up for grabs for the best innovation, the stakes were high for the exhibitors at a local pop-up art gallery called The Hive.

The first prize went to Eyewriter, a team who developed a pair of glasses designed to track and record eye movement, enabling people to draw pictures using their eyes.

It was designed for Californian graffiti artist Tony Quan, who has ALS, a form of motor neurone disease. His eyes are the only part of his body that he can move.

Kleinman’s article features details about other projects that were shown at the festival as well as a video which features the artist, Tony Quan, putting the Eyewriter to the test, and an interview with the festival founder and organizer.

Something like the Eyewriter points to exciting possibilities for leveling the playground so everyone (no matter what physical limitations they may have) can participate. It also points to the benefits of hacking.

Synthetic biology: commercialization, Canadian farmers, and public discourse

You may see synthetic biology (or more properly a synthetic organism) referred to as ‘Synthia’. The term was coined (or, for some word play, created) by the ETC Group as they note in their May 20, 2010 news release about J. Craig Venter’s latest accomplishment (noted on this blog here and here),

The construction of this synthetic organism, anticipated and dubbed “Synthia” by the ETC Group three years ago, will stir a firestorm of controversy over the ethics of building artificial life and the implications of the largely unknown field of synthetic biology.

Clearly the ETC Group, which is based in Canada, has been gearing up for a campaign. It’ll be interesting to note whether or not they are successful at making ‘Synthia’ stick. I gather the group was able to capitalize on ‘frankenfoods’ for the campaign on genetically modified foods but someone else coined that phrase for them. (You can read about who coined the phrase in Susan Tyler Hitchcock’s book, Frankenstein; a cultural history.)

The advantage with ‘frankenfoods’ is the reference to an internationally recognized cultural icon, Frankenstein, and all of the associations that naturally follow. With ‘Synthia’, the ETC Group will have to build (link? graft?) the references to/onto the term.

I shouldn’t forget that the ETC Group does make an important point with this,

The team behind today’s announcement, led by controversial scientist and entrepreneur Craig Venter, is associated with a private company, Synthetic Genomics Inc, bankrolled by the US government and energy behemoths BP and Exxon. Synthetic Genomics recently announced a $600 million research and investment deal with Exxon Mobil in addition to a 2007 investment from BP for an undisclosed amount. Venter, who led the private sector part of the human genome project ten years ago, has already applied for patents related to Synthia’s technology.

In a possibly related (to the ETC Group) statement, the National Farmers Union (NFU) had this to say (from the May 22, 2010 news item on CBC News),

The National Farmers Union says the development of a synthetic cell could lead to worrisome, long-term consequences.

“This new technology raises serious concerns about who controls it, what it will be used for, and its potential impact,” [Terry] Boehm [president, NFU] said.

There are two things I want to note. First, the concerns raised by the ETC Group, the NFU, and others in Canada and across the globe are important and require discussion. Second, all of the parties involved business interests, civil society groups, scientists, government agencies, etc. work independently and together (formally and informally) to promote their interests.

In a related note: In a May 23, 2010 CBC news item (published on Sunday during a long weekend),

The government is looking for ways to monitor online chatter about political issues and correct what it perceives as misinformation.

The move started recently with a pilot project on the East Coast seal hunt. A Toronto-based company called Social Media Group has been hired to help counter some information put forward by the anti-sealing movement.

The Department of Foreign Affairs and International Trade has paid the firm $75,000 “to monitor social activity and help identify … areas where misinformation is being presented and repeated as fact,” Simone MacAndrew, a department spokesperson, said in an email.

The firm alerts the government to questionable online comments and then employees in Foreign Affairs or the Department of Fisheries and Oceans, who have recently been trained in online posting, point the authors to information the government considers more accurate.

It appears to be just the beginning. [emphases mine]

(Digression alert! Does this mean I’ll be able to easily get more information about nanotechnology research in Canada, about the national institute, about nanomaterials, about proposed regulatory frameworks, etc.?)

I have to admit to being suspicious about this ‘information initiative’ when the announcement appears to have been made in an email during a holiday weekend. As well, it seems a bit schizoid given the government’s ban (I’ve commented about that here) on direct communication between journalists and scientists working for Environment Canada. So, the government will contact us if they think we have it wrong but a journalist can’t directly approach one of their scientists to ask a question.

Returning to my main focus, the impact that all these groups with their interests, by turns competitive and collegial, will have on the synthetic biology debate is impossible to evaluate at this time. It does seem that much of the framing for the discussion has been predetermined by various interest groups while the rest of us have remained in relative ignorance. I think the ‘pre-framing’ is inevitable given that most of us would not be interested in engaging in a discussion about developments which were largely theoretical, until recently.

For those who are interested in learning about the science and the debates, check out the Oscillator here. She notes that we’ve had some parts of this discussion as early as the 19th century,

My ScienceBlogs colleague PZ Myers compares the synthetic genome to Wöhler’s chemical synthesis of urea in 1828. In the 19th century, scientists debated whether or not the chemicals that make up living cells–organic chemistry–had to be made by a cell possessing a “vital spark” or could be made by humans in a test tube. By synthesizing urea from ammonium cyanate, Wöhler broke down some of the mysticism associated with living cells. From that point on, organic chemistry stopped being magic and became a science.

Does the Venter Institute’s achievement show that life is just chemicals? I don’t think so …

Canada and synthetic biology in the wake of the first ‘synthetic’ bacteria

Margaret Munro’s excellent article on Craig Venter’s recently published synthetic biology achievement provides some Canadian perspective on the field as a whole. Titled as Synthetic genome inspires both awe and apprehension in the Vancouver Sun’s (it was titled elsewise in other CanWest publications), May 21, 2010 edition, the article offers,

“It is a remarkable technological feat,” said University of Toronto bioengineer Elizabeth Edwards.

“It’s paradigm-shifting,” said University of Calgary bioethicist and biochemist Gregor Wolbring, adding the fast-moving field of synthetic biology is ushering in “cyber” cells and life.

It could be as “transformative” as the computer revolution, said Andrew Hessel, of the Pink Army Cooperative, an Albertabased initiative promoting doit-yourself bioengineering.

Hessel said Venter deserves the Nobel Prize for his pioneering work in creating “a new branch on the evolutionary tree” — one where humans shape and control new species.

Munro also provides a strongly cautionary position from Pat Roy Mooney of the ETC Group (a civil society or, as I sometimes say, activist group) as well as a good explanation for what all the excitement is about.

Wolbring (quoted in Munro’s article) has long commented on issues around nanotechnology, human enhancement, synthetic biology and more. His blog is here and his Twitter feed is here.

Andrew Hessel’s Pink Army Cooperative can be found here. If you go, you will find that the organization’s aim is,

A new approach to developing breast cancer treatments. Pink Army is a community-driven, member owned Cooperative operating by open source principles. Using synthetic biology and virotherapy to bring individualized treatments tailored to each patient’s DNA and cancer, faster and cheaper than ever before.

The ETC Group has written a news release on this latest synthetic biology event,

As Craig Venter announces lab-made life, ETC Group calls for Global Moratorium on Synthetic Biology.

In a paper published today in the journal Science, the J. Craig Venter Institute and Synthetic Genomics Inc announced the laboratory creation of the world’s first self-reproducing organism whose entire genome was built from scratch by a machine.(1) The construction of this synthetic organism, anticipated and dubbed “Synthia” by the ETC Group three years ago, will stir a firestorm of controversy over the ethics of building artificial life and the implications of the largely unknown field of synthetic biology.

As for the state of synthetic biology research in Canada, that might be available in an international agency’s publication. As far as I’m aware, there is no national research agency although I did (recently) find this mention on the National Institute of Nanotechnology’s Nano Life Sciences page,

The Nano Life Sciences researchers investigate the fields of synthetic biology, computational biology, protein structure, intermolecular membrane dynamics and microfluidics devices for biological analysis. [emphasis mine]

I will continue digging and come back to this topic (synthetic biology in Canada) as I find out more.

Bio: fiction, etc. festival in Europe

I believe that it truly was a coincidence when this information hit my mailbox in the same week that Craig Venter made his big synthetic biology announcement (noted on this blog here),

The 1st Bio:Fiction Science, Art & Filmfestival aims at attracting public awareness to synthetic biology and its ramifications for our daily life in the future. Synthetic biology is the design and construction of new biological systems not found in nature. Synthetic biology aims at creating new forms of life for practical purposes. By applying engineering principles to biology scientists will be able to design life forms much different from breeding or traditional genetic engineering. Filmmakers are encouraged to share their cinematic visions of a present or future society shaped by synthetic biology. Prizes will be awarded in the following categories: Short Fiction;Documentary Film; Animation; Online-Audience Award, Special Award of the Jury.

The festival will be held in Vienna, Austria in May 2011 and the deadline for entries is July 15, 2010. The festival website is here.

Synbio (synthetic biology) hits the big time: Venter, media storm, and synbio collaboration webcast

Craig Venter’s and his team’s achievement is being touted widely right now. From the news item (Researchers create first self-replicating, synthetic bacterial cell) on Nanowerk,

The team synthesized the 1.08 million base pair chromosome of a modified Mycoplasma mycoides genome. The synthetic cell is called Mycoplasma mycoides JCVI-syn1.0 and is the proof of principle that genomes can be designed in the computer, chemically made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by the synthetic genome.

This research will be published by Daniel Gibson et al in the May 20th edition of Science Express and will appear in an upcoming print issue of Science.

This has, of course, roused a discussion which is taking place in the blogosphere, in science journals, and elsewhere. Dave Bruggeman at his Pasco Phronesis blog offers a few thoughts about the achievement,

While many are hailing the replication as a significant breakthrough, others are not as impressed. For one thing, while it is described in some circles as synthetic life, the new life has a synthetic inside housed within a pre-existing bacterium shell. For another, there are related projects involving higher lifeforms that may deserve greater attention from a policy perspective.

His comments provide a bracing contrast to some of the hyperbole as per this news item (Life after the synthetic cell – opinions from eight leading synthetic-biology pundits) on Nanowerk,

In the Opinion section of Nature, eight leading synthetic-biology pundits reflect on what effect Craig Venter’s latest achievement could have on science and society.

All the commentators hail the work as highly significant — Arthur Caplan going so far as to describe it as “one of the most important scientific achievements in the history of mankind”. Beyond that they have mixed feelings about what the Mycoplasma bacterium represents.

Coincidentally (or not), the Hudson Institute is hosting its third meeting about moral issues and synthetic biology. From this news item (Moral issues raised by synthetic biology subject of Hastings Center Project) on Nanowerk,

The Hastings Center has been at the forefront of interdisciplinary research into ethical issues in emerging technology. The synthetic biology project is funded by a grant from the Alfred P. Sloan Foundation . Project participants include synthetic biologists, bioethicists, philosophers, and public policy experts. The Center’s work is part of a comprehensive look at synthetic biology by the Alfred P. Sloan Foundation. Other participants in the initiative are the J. Craig Venter Institute and the Woodrow Wilson International Center for Scholars. [emphasis mine]

Intriguingly, the Woodrow Wilson Center hosts the Synthetic Biology Project (a spinoff from their Project on Emerging Technologies [PEN]).

Last week (May 12, 2010), the SynBio Project webcast (access here) an event titled, Synbio in Society: Toward New Forms of Collaboration? which featured,

One response to society’s concerns about synthetic biology has been to institutionalize the involve­ment of social scientists in the field. There have been a series of initiatives in which ethics and biosafety approaches have been purposely incorporated into synthetic biology research and development. [emphasis mine] The collaborative Human Practices model within the NSF-funded SynBERC project was the first initiative in which social scientists were explicitly integrated into a synthetic biology research program. But these new collaborations have also flourished in the UK where four research councils have funded seven scientific networks in synthetic biology that require consideration of ethical, legal and social issues. Another example is the US-UK Synthetic Aesthetics Project, which brings together synthetic biologists, social scientists, designers and artists to explore collaborations between synthetic biology and the creative professions.

Similarly, the European Commission’s Seventh Framework Program funds a project called Synth-ethics, which “aims at discerning relevant ethical issues in close collaboration with the synthetic biology community.

I watched the webcast as it was being streamed live unaware that a big announcement would be made this week. The science community did not share my ignorance so this work has been discussed for months (Science is a peer-reviewed journal and peer review, even if expedited, is going to take more than a month).

I’m willing to bet that the webcast and the Hudson Institute meeting were timed to coincide with the announcement and that the journal Nature was given lots of time to solicit opinions from eight experts.

I have one more item of note. Science Channel will be presenting a special programme on Venter’s work,”Creating Synthetic Life, premiering Thursday, June 3, 2010, at 8PM e/p.” More from their press announcement,

Over the course of five years, only Science Channel cameras captured the failures, successes and breakthrough moments of Dr. Venter, Nobel Laureate Hamilton Smith, Dr. Clyde Hutchison and JCVI [J. Craig Venter Institute] researchers as they meticulously sought to create a synthetic single-celled organism.

What exactly does today’s news mean for the human race? Where exactly will it take us? Could the technology be used for negative purposes? What are the ethical concerns we must weigh before using it?… This one-hour special is an open forum discussion featuring Dr. Venter, leading bioethicists, top scientists and other members of the scientific community discussing the breakthrough’s ramifications and how it may change our world and the future.

Your Questions Answered allows viewers to ask the experts about how this technology will affect their lives. From now through May 26, submit your questions via Facebook, and they could be asked during the show.

Clearly, Science Channel took a calculated risk (see Venter’s bio page to understand why it was a calculated risk) when they started following Venter’s work.

In looking at all this, it’s fascinating to consider the combination of planning, calculated risk-taking, and luck that have come together to create this ‘synthetic biology moment’.

Of special interest to me, is the way that social scientists and ethicists and others have been integrated into the larger synthetic biology initiative. In my more cynical moments, I view this integration as a means of trying to allay concerns before a ‘stem cell’ or GM (genetically modified) food (aka Frankenfoods) controversy erupts. In less cynical moments, I like to think that lessons were learned and that the concerns will be heard and heeded.

Québec City hosts LB 13 conference on organized molecular films

July 18 – 21, 2010 are the dates when Québec City will welcome a conference that feature nanotechnology-related subjects, from the conference website,

LB13 is an international conference which originally focussed on Langmuir- Blodgett films and their applications. With the ongoing evolution and expansion of interfacial chemistry and physics into other research and technological fields, the scope of the LB conferences now includes interdisciplinary topics related to organized molecular films and nanostructures in general. The LB conferences started in 1983 and since then have been hosted by many different countries. The meetings provide a forum for the exchange of concepts and ideas between scientists from Asia, Europe and North America. …

LB13 will focus on supramolecular assemblies, molecular devices, and biological interfaces including cell-surface interactions. The related nano-science aspects and nano-technologies will be also extensively discussed.

Thanks to Azonano for pointing me to this news.

Kick my nano?

A new website, Kick My Nano features feeds from various nanotechnology blogs (including this one). It seems to be part of a larger entity, the Canada Byte Com Series websites which is affiliated with something called, Progressive Bloggers. My haziness about the relationships between these websites is that while there are acknowledgments, the relationships are not clarified since the About pages for the ‘Kick’ and ‘Canada Byte’ sites were not operational when I checked them. I did find this essay about Progressive Bloggers on Wikipedia,

Progressive Bloggers is the name of an affiated group of Canadian bloggers who come from the centre, centre-left and left-wing of the political spectrum. Progressive Bloggers primarily maintain their own blogs, whose content is then aggregated on the main Progressive Bloggers website.

Progressive Bloggers was created in May, 2005 by Wayne Chu from the Canadian political website freethought.ca.

The essay goes on to note that as of 2009, there are over 400 blogs being aggregated through Progressive Bloggers. Thank you, it’s nice to be on an aggregator.