Tag Archives: synthetic biology

Entanglement issues and open source synthetic biology

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According to current thought, entanglement makes quantum computing possible and the more of it you have, the more powerful the quantum computing. Scientists, David Goss at the Institute of Mathematical Physics in Braunschweig, Germany; S. T. Flammia at the Perimter Institute in Waterloo, Canada; and Jens Eisert at the University of Postdam, Germany) have recently published findings which suggest that there is such a thing as too much entanglement. There’s more in the article on physorg.com including this description of entanglement,

Entanglement, explains both Eisert and Gross, represents correlations in behavior. One system is related to another on a global scale, each affecting the other. In quantum computing, the way systems are entangled – correlated – can help scientists perform powerful computational tasks. However, entanglement is about more than just correlations. “Entanglement introduces a certain randomness into the system,” Gross says. “This randomness appears in the measurement outcomes. However, as the entanglement goes up, so does the randomness. When entanglement increases to a certain point, there is so much randomness that the system ends up being about as useful as coins tossed into the air. You don’t get any useful information.”

Now onto synthetic biology. The Project on Emerging Nanotechnologies (PEN) has a June 17, 2009 event (9:30 am to 10:30 am PST) titled, Synthetic Biology: Feasibility of the Open Source Movement.

According to the website description, this event is about IP issues and synthetic biology. From the website,

Will this open source movement succeed? Are life sciences companies ready for open source? What level of intellectual property (IP) protection is necessary to secure industry and venture capital involvement and promote innovation? And does open source raise broader social issues? On June 17, a panel of representatives from various sectors will discuss the major challenges to future IP developments related to synthetic biology, identify key steps to addressing these challenges, and examine a number of current tensions surrounding issues of use and ownership.

The focus will be on US law, which is significantly different than Canadian law but if you’re interested, there will likely be a webcast posted on their site afterward or if you’re in Washington, DC, you can RSVP here to attend.

Canadian attosecond researcher wins medal

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The Natural Sciences and Engineering Research Council (NSERC)  awarded Dr. Paul Corkum at the University of Ottawa with $1M in funding and the Gerhard Herzberg Canada Gold Medal for Science and Engineering. Corkum’s work is in the field of attosecond science.

I looked up attosecond to find out that it is one quintillionth of a second or one thousandth of a femtosecond. I found the description of the work a little more helpful (from Attosecond science researcher wins Gerhard Herzberg Canada Gold Medal),

Dr. Paul Corkum and his team at NRC used the world’s fastest laser light pulses to capture the first image of an electron, one of the smallest bits of matter in the universe.

And this helped too,

Dr. Paul Corkum and his team … used the world’s fastest laser light pulses to capture the first image of an electron, one of the smallest bits of matter in the universe. This manipulation of electrons could lead to breakthroughs in fields as diverse as computing, engineering and medicine.

I’m still trying to find ways to describe nanotechnology and now there’s attosecond science. Not to mention synthetic biology (I’m still not sure I can define the difference between that and biotechnology). Btw, there’s a Project on Emerging Nanotechnologies event, Synthetic Biology: The Next Biotech Revolution Is Brewing on Wednesday, March 25, 2009 from 9:30 am to 10:30 am PST. It will be webcast live and posted on their website a few days later. If you’re in the Washington, DC area and want to attend please RSVP by clicking on the event title link. The event features Michael Rodemeyer from the University of Virginia. He’s the author of a report titled New Life, Old Bottles: Regulating First-Generation Products of Synthetic Biology and will be discussing the US regulatory framework for biotechnology and whether synthetic biology can be contained within that framework.

Quantum dots possibly toxic? And a followup to the Canadian 2009 budget and Genome Canada

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After last week’s (and continuing into this week) excitement over Canadian scientists creating the smallest quantum dot ever, there’s an article about possible toxicity in Science Daily here. The gist of the article is that quantum dots which are used in solar cells, medical imaging devices, and elsewhere could decompose during use or after they’re disposed. In any event, the decomposed dots could release metals that are toxic when they are exposed to acidic and/or alkaline environments. According to the article, there’s no need to sound an alarm yet but it’s a good idea to keep an eye on the situation.

I made a comment abut mapping genomes when discussing the science funding cuts in the Canadian budget which featured Genome Canada’s complete disappearance [from the budget].  I referred to a comment by Denise Caruso (she was featured in a Project on Emerging Nanotechnologies webcast discussing synthetic biology here). I’ve reviewed the webcast and found that she wasn’t referring to genome mapping per se but was discussing something called the Encode Study which was four years long and funded by the Human Genome Project. It featured an international consortium of 80 organizations that were working together to create an encyclopedia of DNA elements. Here’s a rough transcription of her comments,

We have no idea what we’re talking about here. The genes don’t operate the way we thought they did. The genome is not a tidy collection of independent genes where the sequence of DNA does this [action] and always does this so we can put it on a shelf [and have it on a] parts inventory list. [The genes] operate within networks. What they [study participants] said was almost 180 degrees opposite to what we have believed for quite some time.

Rick Weiss who was interviewing her went on to describe how a genes that are seemingly unrelated signal each other in ways that we had not expected. Who knows how it all works in the environment i.e. when you get out of the lab?

So getting back to my original point, mapping is fine but it’s not the most primary goal. As per the webcast, it’s the relationships or networks that are important.

A quick note: the University of Virginia has a virtual lab that features information and podcasts about nano. You can go here to see it.

Synthetic biology, ethics, and IT

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I watched the Project on Emerging Nanotechnologies (PEN) live webcast yesterday (Jan.8.09) with Arthur Caplan, an ethicist, discussing ethical implications associated with synthetic biology. If you’re interested the webcast will be compressed and made available on their site in about five or six days. (I’ll put up a link when I see it there.)

There ware a couple of interesting bits. Caplan pointed out that emerging technology and science is often represented as appearing magically overnight  when in fact it’s the result of years of incremental work which was being discussed not only by scientists but also social scientists, ethicists, and policy makers.  I think that happens because it makes a better story and/or because a lot of reporters have no context. Reporters don’t necessarily spend much time on any particular beat and today’s science reporter might be yesterday’s sports reporter.

Caplan also mentioned Craig Venter who is determined to prove that there is no difference between life and nonlife. ie. That you can create a living organism by putting together ingredients such as synthesized DNA that you can purchase via the internet. Denise Caruso (blog posting Jan.7.09) alluded to that perspective in her PEN webcast on synthetic biology. She ascribed to the fact that a lot of the people involved in developing synthetic biology have engineering and/or IT backgrounds. As she pointed out, organismic biologists do not share the opinion and in fact use different language and, for the most part, are not involved in the synthetic biology discussions.

Synthetic conversation between Rick Weiss and Denise Caruso

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The conversation took place under the auspices of the Project on Emerging Nanotechnologies (PEN) in November 2008 and thank goodness for webcasting since that means there’s a copy free for the viewing here [ETA Sept. 30, 2011: I have replaced the link as it points to the wrong page with this URL http://www.synbioproject.org/events/archive/synthetic_biology_coming_up_fast/]. The discussion is absorbing and I highly recommend it. However, it’s disturbing. They discuss bio error and bio terror along with mentioning how easy it would be to create synthetic life (this leads to a brief discussion about how we define life).  It’s provocative in a thoughtful way. Weiss was a science reporter who is now a fellow at the Center for American Progress. Caruso (former journalist) is the executive director of the Hybrid Vigor Institute which she founded in 2000.

There is an ethics discussion about synthetic biology tomorrow at PEN 9:30 – 10:30 am PST. Go here to enjoy the live webcast or to view it later.

Nano events

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The Project on Emerging Nanotechnologies (PEN) has a couple of events coming up later this month. The first one is this coming Thurs., Jan. 8, 2009 ‘Synthetic Biology: Is Ethics A Showstopper? from 12:30 pm to 1:30 pm EST. The event features two speakers, Arthur Caplan, an ethicist from the University of Pennsylvania, and Andrew Maynard, the chief science advisor for PEN. They request an RSVP, if you are attending in person. Go here for more details and/or to RSVP. Or you can view the webcast live or later. Their other event is on Weds.,  Jan. 14, 2009 and is called ‘Nanotech and Your Daily Vitamins’. The time for this event is 9:30 am – 10:30 am EST. The featured speakers, William B. Schultz and Lisa Barclay, are the authors of a report for PEN about the FDA and how it can address issues surrounding dietary supplements that use nanomaterials. For more details about the event and/or to RSVP, go here. There is also the webcast option. There is a link to the report from the event page but you have to log in to view it (as of Jan.6.09).

Nanotech BC is cancelling its Jan. 15, 2009 breakfast speaker event. Meanwhile, Nanotech BC organizers are preparing for the second Cascadia Symposium on April 20 – 21, 2009 at the Bayshore. They’ve gone for a larger venue (250 people) than last year’s. No other details are available yet.

Inspiration for a new approach to risk regulation for nanotechnology

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I’m getting into the home stretch now regarding the ‘Risk Management Principle for Nanotechnology’ article. After dealing with the ‘classic’ risk principles and the newer precautionary principles, the authors (Marchant, Sylvester, and Abbott) unveil a theory for their proposed ‘new principles’. The theory is based on work by I. Ayres and J. Braithwaite on something they call, ‘Responsive Regulation’. Briefly, they suggest avoiding the regulation/deregulation debate in favour of a flexible regulatory approach where a range of strategies are employed.

With this tool kit [range of strategies] in hand, regulators can play a tit-for-tat strategy: they allow firms to self-regulate so long as the firms reciprocate with responsible action; if instead some firms act opportunistically, regulators respond to the defectors with appropriate penalties and more stringent regulation. p. 52 (Nanoethics, 2008, vol. 2 pp. 43-60

There are some difficulties associated with this approach but that is being saved for my next posting in this series.

The Project on Emerging Nanotechnologies has two events coming up. ‘Synthetic Biology: Is Ethics a Showstopper?’ on Thursday, January 8, 2009 from 12:30 pm – 1:30 pm (EST). For information on location (you have to RSVP) or how to attend via webcast (no RSVP required), check here. The other event is called, ‘Nanotech and Your Daily Vitamins; Barriers to Effective FDA Regulation of Nanotechnology-Based Dietary Supplements’ and will be held on Thursday, January 15 (?) from 9:30 am – 10:30 am (EST). The date listed on their website and in their invitation is January 14, which is incorrect. I imagine they’ll correct either the date or date soon. For more details about the event itself, the physical location (If you’re planning to go, please RSVP), or the webcast directions (RSVP) not required) please check here.

UK Royal Commission concludes that nano should be regulated and synthetic bio event reminder

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According to the online BBC News, the Royal Commission on Environmental Pollution has suggested that reporting the use of nanomaterials in industrial applications become mandatory and that establishing tests for danger and regulatory insight be undertaken cooperatively and internationally. The Commission advised against a blanket moratorium or ban on the development of nanomaterials because there are so many potential benefits. The members of the commission focused their efforts on how nanomaterials function rather than their size or dimension. There’s more from the article here.

On a personal basis, this is rather timely as I’m trying to write up a PhD research proposal and I’ve remarked on this obsession with ‘nano numbers’ as it were. There’s a group of people at Cornell University who are trying to find ways to convey size as a means of educating the public about nanotechnology. I don’t think that’s a good idea after having tried that strategy a few times in conference presentations and watching my audiences’ eyes glaze over. Most of us don’t have any sense of how big a germ is but we can imagine it and I think that’s what will happen with nanomaterials — we will be able to imagine them. Or for another example, what about electricity? We don’t see it but we take it for granted and we have a pretty good sense that certain activities could kill or severely harm us, i. e. “Don’t touch a live wire” or “Don’t stick a knife into your toaster when it’s plugged in and switched on.”

The Synthetic Bio: Coming Up Fast! event organized by the Project on Emerging Nanotechnolgies is taking place on Nov. 14, 2008. (The first notice for this event was in my Oct. 28, 2008 posting.) The webcast has been delayed to 1:45 pm ET or, as I think of it, 10:45 am PT.  If you’re planning to attend the live event, check out the details here.

Synthetic Biology webcast

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Just got an invite to: Synthetic Biology: Coming Up Fast! the latest webcast/live event from the Project on Emerging Nanotechnologies (PEN). It will take place Friday, November 14, 2008 12:30 pm – 1:30 pm ET. According to the press release,

Synthetic biology is being touted by scientists and venture capitalists as “the next big thing.”  Researchers claim to be on the brink of creating artificial life in a laboratory and making the world’s first synthetic microbes.  The first blockbuster synbio drug–an affordable cure for malaria–is expected on the market by 2010.  And a whole new biofuels industry spawned by synthetic biologists that promises to conquer the globe’s energy problems seems just around the corner.

The speakers are,

Denise Caruso, former New York Times columnist and longtime analyst of technology-based issues and industries, will explore this question with the Center for American Progress’s Rick Weiss.  Caruso is the author of Intervention: Confronting the Real Risks of Genetic Engineering and Life on a Biotech Planet (2006).  Weiss recently left The Washington Post after a distinguished career as one of the country’s foremost science journalists.

David Rejeski, PEN executive director, will be moderating. If you’re in the Washington, DC area you can attend but you do need to rsvp otherwise there’s the live webcast (or if the timing is bad, they will make post it later but it can take a few days). For more information, check here.

More about synthetic biology

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There is a report detailing the research on public awareness of nanotechnology and synthetic biology mentioned in yesterday’s posting. You can find it here.

One of these days I’m going to figure out how to make the comments immediately visible until then I’ll write up comments in the postings which is why I’m mentioning Andrew Maynard (Chief Science Advisor for the Project on Emerging Nanotechnologies). He dropped a line pointing out that the October 2008 issue of Esquire magazine features five scientists amongst their 75 most influential people of the 21st century. Three of  the five scientists are synthetic biologists. That’s pretty amazing when you think that most of Esquire’s readers have never heard of it (as per almost 90% of the US population according to the research data). Here‘s more about Andrew Maynard and Esquire’s October 2008 issue.