December 2008 Archives

Garage Biology Project: Melamine-detection Bugs

Worried about whether your yogurt is safe?  Drop in some of  Meredith Patterson's home-brew bugs and see if they turn green.  The AP has a short story about Patterson and DIYBio: "Amateurs are trying genetic engineering at home".  No surprise that it is a bit short on details.

This story made it as far (temporarily) as the front page of The Huffington Post, which I find interesting.  I wonder whether the editors put it there out of genuine interest or to scare the crap out of their readers.

It's only been eight years since I first speculated about garage biology (PDF), and only three since the topic appeared in Wired (Splice it yourself).  iGEM has only been around since 2004.  Biology, for the most part, remains Open (See, "Thoughts on Open Biology"):

As in 2000, I remain today most interested in maintaining, and enhancing, the ability to innovate.  In particular, I feel that safe and secure innovation is likely to be best achieved through distributed research and through distributed biological manufacturing.  By "Open Biology" I mean access to the tools and skills necessary to participate in that innovation and distributed economy.
I find myself a bit surprised to feel a bit surprised that this is this is all going just as I expected (PDF).  (Aside: if there isn't a name for that, there should be; I predicted X, and not only am I surprised that it is coming true, I am surprised to feel surprised that it is coming true...because I really believed it was going to come true.  I think.)  From the AP story:

[Patterson]  learned about genetic engineering by reading scientific papers and getting tips from online forums. She ordered jellyfish DNA for a green fluorescent protein from a biological supply company for less than $100. And she built her own lab equipment, including a gel electrophoresis chamber, or DNA analyzer, which she constructed for less than $25, versus more than $200 for a low-end off-the-shelf model.
Frankly, I don't know whether to feel relieved or uneasy.  That ambivalence will probably characterize my response to this technology from here on out.  Whether we like it or not, we are about to find out what role garage biology will play in our physical and economic security (Journal article, PDF).
The ongoing American Geophysical Union meeting is full of cheery news.  According to a report in the IHT, more than 2 trillion tons of landlocked ice have melted since 2003 in Greenland, Antarctica, and Alaska.  Of that, more than half occurred in Greenland, and satellite measurements confirm that the melting is accelerating.

The new results follow on James Hansen's earlier work based on data, rather than models, suggesting that both warming and sea level rise are likely happen faster than the IPCC consensus estimates (see "It's time to Invest in Water Wings"), because the IPCC models explicitly exclude the effect of ice sheet movement and landlocked ice melting.

It gets even better.  Reduced sea ice coverage is also now strongly affecting the thermal balance of the poles:

As sea ice melts, the Arctic waters absorb more heat in the summer, having lost the reflective powers of vast packs of ice. That absorbed heat is released into the air in the autumn. That has led to autumn temperatures in the last several years that are 6 degrees Fahrenheit to 10 degrees (3.5 degrees to 6 degrees) warmer than they were in the 1980s.
Warming of the land and sea are coupled: "The loss of sea ice warms the water, which warms the permafrost on nearby land in Alaska, thus producing methane," itself a potent greenhouse gas, according to Julienne Stroeve, a research scientist at the National Snow and Ice Data Center in Boulder, Colorado.  (See my previous posts: "Methane Time Bomb" and "Update".)

With respect to the anomolously high Arctic temperatures, The Independent's Steve Connor wonders "Has the Arctic melt passed the point of no return?":

The phenomenon, known as Arctic amplification, was not expected to be seen for at least another 10 or 15 years and the findings will further raise concerns that the Arctic has already passed the climatic tipping-point towards ice-free summers, beyond which it may not recover.
The coupling of land and sea warming constitute a feedback mechanism that threatens to create runaway warming and increased methane emissions, which will only make things worse.  Only more data will help resolve any remaining uncertainty.  While we gather that data, our time to fiddle is running out.

"Saltwater Crops May Be Key To Solving Earth's Land Crunch"

Wired News is carrying a story by Alexis Madrigal on saltwater agriculture, focusing on a new Perspectives piece in Science by Jelte Rozema and Timothy Flowers.  Here is the opening paragraph from the Science piece, which contains some good numbers:

Currently, humans use about half of the fresh water readily available to them to support a growing world population [expected to be 9.3 billion by 2050]. Agriculture has to compete with domestic and industrial uses for this fresh water. Good-quality water is rapidly becoming a limited and expensive resource. However, although only about 1% of the water on Earth is fresh, there is an equivalent supply of brackish water (1%) and a vast quantity of seawater (98%). It is time to explore the agronomic use of these resources.
The authors go on to explore the many advantages, including 1) local agriculture (near coastal populations), 2) irrigation using seawater (yummy micronutrients as fertilizer), and 3) the utility of combined aquaculture practices.  The usual caveats about land use, local property rights, and environmental effects all apply.  But the numbers, at the depth presented, are impressive.

Here is a nice bit from Madrigal's story:

After taking into account environmental protections and other factors, [Robert] Glenn's report estimates that 480,000 square miles of unused land around the world could be used to grow a special set of salt-tolerant plants -- halophytes. Glenn's team calculated that this could produce 1.5 billion barrels of oil equivalent per year. That's 35 percent of the United States' liquid fuel needs.
Why aren't we already employing salt-tolerant plants to produce food and fuel?  Back to Rozema and Flowers:

...Although between 1996 and 2006 there were more than 30 reports of transformation of rice with different genes aimed at increasing salt tolerance, transgenic salt-tolerant rice is not close to release. The likely explanation is that salt tolerance is a complex trait determined by many different genes, so that transformation of multiple genes into a plant is required.
Wandering down this road a bit led me to Pamela Ronald's blog "Tomorrow's Table", one entry of which is up at the Nature Network and mentions local research in Bangladesh to create GM, salt-tolerant rice.  On a visit to Dhaka university, she explains the local imperative:

...Salinity is a problem for rice farmers here. Not only is the sea water rising, but fresh water supplies are under pressure partly because farmers are pumping more every year and also because Bangladesh is downstream from India, who gets first dibs on the fresh water through a network of dams. The result is that every year the saline lands encroach north, hurting rice yields, a serious problem here where the average Bengali receives 2/3 of their diet from rice.
The local research effort is proceeding both via breeding and genetic engineering.  Ronald writes of seeing "...Newly developed transgenic lines thriving under high salt concentrations that kill the conventional variety".  This is interesting both because the Bangladeshi team may be making progress and because a local team has taken on the task -- the country isn't going to be on any conventional list of biotech leaders.  So kudos to the local team.

What could we do to make this all go faster?  The story on salt-tolerance appears to be that it isn't yet a very well understood trait.  This means anyone interested in hacking plants to that end needs to have all the relevant genes and also a good way to get them into any given plant.

My guess is that this is going to start going a lot faster in systems where minichromosomes are up and running in plants of interest.  This will dramatically facilitate the insertion of genes into plants, without worrying about disrupting the endogenous genetic structure. I mentioned this in my post on SB 4.0, and just as a pointer here is the PLoS Genetics describing the creation of stably inheritable minichromosomes in Maize: "Meiotic Transmission of an In Vitro-Assembled Autonomous Maize Minichromosome".  Chromatin appears to have this technology working pretty well.  Recapitulating the work in rice and other crops will take time, of course, but my scrawled notes from Daphne Preuss' talk in Hong Kong suggest it went pretty fast in Maize once they figured out what they were doing.  I'll have more on this when I understand it better.
In case you haven't seen the headlines the lase couple of days, Bob Graham and Jim Talent say we are doomed.  Mostly.  Sort of.  Maybe?

Here is the page to download the report.  In summary, the commission predicts an attack using a weapon of mass destruction with in the next five years.  They are more worried about biological weapons than nuclear ones.

Despite the grim tone of most of the text, here is something useful to squawk back at Chicken Little:

...One should not oversimplify or exaggerate the threat of bioterrorism. Developing a biological weapon that can inflict mass casualties is an intricate undertaking, both technically and operationally complex. 
That is among the more optimistic statements in the entire document.

I caught Bob Graham on the Colbert Report last night, and the interview helped me figure out what has been bugging me about the language used by the report and its authors as they talk to the press.  No, not the part where Graham and Colbert -- two grown men in suit and tie -- used copies of the report like GI Joe figures in desktop combat (see 2:30 -- that brief interlude was enlightening in a different way):

The lightbulb went off when Graham said "The most important thing we can do is make sure that we, and the rest of the world, are locking down all the nuclear and biological material so that it is not capable of leaking into the hands of terrorists."

That sounds great, and the report goes on at length about securing BSL-3 and -4 facilities here in the US so that nasty bugs are kept behind locked doors, doors that are guarded by guys with visible guns.  That constitutes a particular kind of deterrence, which is fine.  As I have spent far too much of my life working in clean rooms trussed up in bunny suits, I can only feel sympathy for the folks who will have to deal with that security and suit up to work in the lab every day.  But those bugs are dangerous, and biosafety in those facilities is no joke.  The near-term threat is undoubtedly from bugs that already exist in labs.

But this is where things start to go off the rails for me.  Graham didn't have a lot of time with Colbert, but his language was disturbingly absolute.  I am concerned the Commission's views on biological technologies are dysfunctionally bipolar.  Here is what I mean: Even though the text of report reassures me that the people who actually put words on the page have a sense of how far and how fast biological technologies are proliferating (which I get to below), the language used by the official spokesman involves "locking down all the biological materials".  I worry that "locking down" anything might be construed in Washington DC, or by the populace, as constituting sufficient security measures.  See my article from last year "Laying the foundations for a bio-economy" for an update on what has happened as a result trying to "lock down" methamphetamine production in the US.  Short summary: There is more meth available on the streets, and the DEA acknowledges that its efforts have created an environment in which it actually has worse intelligence about who is making the drug and how it gets distributed.

Frankly, I haven't quite sorted out all of the things that bother me about the report, the way we talk about security in this country, and the inevitable spread of powerful biological technologies.  What follows are some additional notes and ruminations on the matter.   

Here is what the text of the report has to say about the threat from DNA synthesis technologies:

The only way to rule out the harmful use of advances in biotechnology would be to stifle their beneficial applications as well--and that is not a realistic option. Instead, the dual-use dilemma associated with the revolution in biology must be managed on an ongoing basis. As long as rapid innovations in biological science and the malevolent intentions of terrorists and proliferators continue on trajectories that are likely to intersect sooner or later, the risk that biological weapons pose to humanity must not be minimized or ignored.
Hmm...well, yes.  I'm glad they acknowledge the fact that in order to benefit from the technology it must be developed further, and that security through proscription will retard that innovation.  I am relieved that this part of the report's recommendations do not include measures I believe would be immediately counterproductive.  The authors later write:

The more that sophisticated capabilities, including genetic engineering and gene synthesis, spread around the globe, the greater the potential that terrorists will use them to develop biological weapons. The challenge for U.S. policymakers is to prevent that potential from becoming a reality by keeping dangerous pathogens--and the equipment, technology, and know-how needed to weaponize them--out of the hands of criminals, terrorists, and proliferant states. 
The charge in the last sentence sounds rather infeasible to me.  Anyway, the Commission then puts responsibility for security on the heads of scientists and engineers working in the life sciences: 

The choice is stark. The life sciences community can wait until a catastrophic biological attack occurs before it steps up to its security responsibilities. Or it can act proactively in its own enlightened self-interest, aware that the reaction of the political system to a major bioterrorist event would likely be extreme and even draconian, resulting in significant harm to the scientific enterprise.

...ACTION: The Department of Health and Human Services and Congress should promote a culture of security awareness in the life sciences community.

Members of the life sciences community--universities, medical and veterinary schools, nongovernmental biomedical research institutes, trade associations, and biotechnology and pharmaceutical companies--must foster a bottom-up effort to sensitize researchers to biosecurity issues and concerns. Scientists should understand the ethical imperative to "do no harm," strive to anticipate the potential consequences of their research, and design and conduct experiments in a way that minimizes safety and security risks.
(This bit sounds like the Commission heard from Drew Endy.)

...The currently separate concepts of biosafety and biosecurity should be combined into a unified conceptual framework of laboratory risk management. This framework should be integrated into a program of mandatory education and training for scientists and technicians in the life sciences field, whether they are working in the academy or in industry. Such training should begin with advanced college and graduate students andextend to career scientists. The U.S. government should also fund the development of educational materials and reference manuals on biosafety and biosecurity issues. At the same time, the responsibilities of laboratory biosafety officers should be expanded to include laboratory security and oversight of select agents, and all biosafety officers should be tested and certified by a competent government authority.
The phrase "culture of security awareness" appears frequently.  This creeps me out more than a bit, particularly given our government's recent exhortations to keep an eye on our neighbors.  You never know who might be a sleeper.  Or a sleep-walking bioterrorist.  I make this point not entirely in jest.  Who wants to live in such a paranoid culture?  Particularly when it is not at all clear that such paranoia makes us safer.

To be fair, I called for something not too dissimilar in 2003 in The Pace and Proliferation of Biological Technologies.  It only makes sense to keep an eye out for potential bioterror and bioerror, and we should have some sort of educational framework to make sure that people are aware of the potential hazards as they hack DNA.  But seeing that language in a report from a legislatively-established body makes me start imagining Orwellian propaganda posters on the walls of labs around the country.  Ick.  That is no way to foster communication and innovation.

On a different topic, here is something that opened my eyes. The report contains a story about a Russian -- someone in charge of weighing out uranium for his coworkers -- who was able to continuously steal small amounts of fissile materiel because the scales were officially recognized to be calibrated only to within 3%.  By withholding a little each time, he amassed a stash of 1.6 kg of "90 percent enriched uranium", while the official books showed no missing materiel.  Fortunately the fellow was caught, because while he was a clever thief he was a not-so-clever salesman.  As part of subsequent non-proliferation efforts, the US government paid for more accurate scales in order to prevent another incident of stealing "a bomb's worth of uranium, bit by bit".  Holy shit.

It is nice to hear that this sort of leak has been plugged for the nuclear threat.  I hope our government clearly understands that such plugs are few and far between for biological threats.