Booting Up A Synthetic Genome (Updated for typos)

The press is all abuzz over the Venter Institute's paper last week demonstrating a functioning synthetic genome.  Here is the Gibson et al paper in Science, and here are takes from the NYT and The Economist (lede, story).  The Economist story has a figure with the cost and productivity data for gene and oligo synthesis, respectively.  Here also are Jamais Cascio and Oliver Morton, who points to this collection of opinions in Nature.

The nuts and bolts (or bases and methylases?) of the story are this: Gibson et al ordered a whole mess of pieces of relatively short, synthetic DNA from Blue Heron and stitched that DNA together into full length genome for Bug B, which they then transplanted into a related microbial species, Bug A.  The transplanted genome B was shown to be fully functional and to change the species from old to new, from A to B.  Cool.

Yet, my general reaction to this is the same as it was the last time the Venter team claimed they were creating artificial life.  (How many times can one make this claim?)  The assembly and boot-up are really fantastic technical achievements.  (If only we all had the reported $40 million to throw at a project like this.)  But creating life, and the even the claim of creating a "synthetic cell"?  Meh.

(See my earlier posts, "Publication of the Venter Institute's synthetic bacterial chromosome", January 2008, and "Updated Longest Synthetic DNA Plot ", December 2007.)

I am going to agree with my friends at The Economist (see main story) that the announcement is "not unexpected", and disagree strongly that "The announcement is momentous."  DNA is DNA.  We have known that for, oh, a long time now.  Synthetic DNA that is biologically indistinguishable from "natural DNA" is, well, biologically indistinguishable from natural DNA.  This result is at least thirty years old, when synthetic DNA was first used to cause an organism to do something new.  There are plenty of other people saying this in print, so I won't belabor the point; see, for example, the comments in the NYT article.

One less-than-interesting outcome of this paper is that we are once again going to read all about the death of vitalism (see the Nature opinion pieces).  Here are the first two paragraphs from Chapter 4 of my book:

"I must tell you that I can prepare urea without requiring a kidney of an animal, either man or dog." With these words, in 1828 Friedrich Wöhler claimed he had irreversibly changed the world. In a letter to his former teacher Joens Jacob Berzelius, Wöhler wrote that he had witnessed "the great tragedy of science, the slaying of a beautiful hypothesis by an ugly fact." The beautiful idea to which he referred was vitalism, the notion that organic matter, exemplified in this case by urea, was animated and created by a vital force and that it could not be synthesized from inorganic components. The ugly fact was a dish of urea crystals on his laboratory bench, produced by heating inorganic salts. Thus, many textbooks announce, was born the field of synthetic organic chemistry.

As is often the case, however, events were somewhat more complicated than the textbook story. Wöhler had used salts prepared from tannery wastes, which adherents to vitalism claimed contaminated his reaction with a vital component. Wöhler's achievement took many years to permeate the mind-set of the day, and nearly two decades passed before a student of his, Hermann Kolbe, first used the word "synthesis" in a paper to describe a set of reactions that produced acetic acid from its inorganic elements.

Care to guess where the nucleotides came from that went into the Gibson et al synthetic genome?  Probably purified and reprocessed from sugarcane.  Less probably salmon sperm.  In other words, the nucleotides came from living systems, and are thus tainted for those who care about such things.  So much for another nail in the vital coffin.

Somewhat more intriguing will be the debate around whether it is the atoms in the genome that are interesting or instead the information conveyed by the arrangement of those atoms that we should care about.  Clearly, if nothing else this paper demonstrates that the informational code determines species.  This isn't really news to anyone who has thought about it (except, perhaps, to IP lawyers -- see my recent post on the breast cancer gene lawsuit) but it might get a broader range of people thinking more about life as information.  What then, does "creating life" mean?  Creating information?  Creating sequence?  And what sort of design tools do we need to truly control these creations?  Are we just talking about much better computer simulations, or is there more physics to learn, or is it all just too complicated?  Will we be forever chasing away ghosts of vitalism?

That's all I have for deep meaning at the moment.  I've hardly just got off one set of airplanes (New York-DC-LA) and have to get on another for Brazil in the morning. 

I would, however, point out that the recent paper describes what may be a species-specific processing hack.  From the paper:

...Initial attempts toextract the M. mycoides genome from yeast and transplant it into M. capricolum failed. We discovered that the donor and recipient mycoplasmas share a common restriction system. The donor genome was methylated in the native M. mycoides cells and was therefore protected against restriction during the transplantation from a native donor cell. However, the bacterial genomes grown in yeast are unmethylated and so are not protected from the single restriction system of the recipient cell. We were able to overcome this restriction barrier by methylating the donor DNA with purified methylases or crude M. mycoides or M. capricolum extracts, or by simply disrupting the recipient cell's restriction system.

This methylation trick will probably -- probably -- work just fine for other microbes, but I just want to point out that it isn't necessarily generalizable and that the JVCI team didn't demonstrate any such thing.  The team got this one bug working, and who knows what surprises wait in store for the next team working on the next bug.

Since Gibson et al have in fact built an impressive bit of DNA, here is an updated "Longest Synthetic DNA Plot" (here is the previous version with refs.); alas, the one I published just a few months ago in Nature Biotech is already obsolete (hmph, they have evidently now stuck it behind a pay wall).

A couple of thoughts:  As I noted in DNA Synthesis "Learning Curve": Thoughts on the Future of Building Genes and Organisms (July 2008), it isn't really clear to me that this game can go on for much longer.  Once you hit a MegaBase (1,000,000 bases, or 1 MB) in length, you are basically at a medium-long microbial genome.  Another order of magnitude or so gets you to eukaryotic chromosomes, and why would anyone bother building a contiguous chuck of DNA longer than that?  Eventually you get into all the same problems that the artificial chromosome community has been dealing with for decades -- namely that chromatin structure is complex and nobody really knows how to build something like it from scratch.  There is progress, yes, and as soon as we get a real mammalian artificial chromosome all sorts of interesting therapies should become possible (note to self: dig into the state of the art here -- it has been a few years since I looked into artificial chromosomes).  But with the 1 MB milestone I suspect people will begin to look elsewhere and the typical technology development S-curve kicks in.  Maybe the curve has already started to roll over, as I predicted (sketched in) with the Learning Curve. 

Finally, I have to point out that the ~1000 genes in the synthetic genome are vastly more than anybody knows how to deal with in a design framework.  I doubt very much that the JCVI team, or the team at Synthetic Genomics, will be using this or any other genome in any economically interesting bug any time soon.  As I note in Chapter 8 of Biology is Technology, Jay Keasling's lab and the folks at Amyris are playing with only about 15 genes.  And getting the isoprenoid pathway working (small by the Gibson et al standard but big by the everyone-else standard) took tens of person years and about as much investment (roughly ~$50 million in total by the Gates Foundation and investors) as Venter spent on synthetic DNA alone.  And then is Synthetic Genomics going to start doing metabolic engineering in a microbe that they only just sequenced and about which relatively little is known (at least compared with E. coli, yeast, and other favorite lab animals)?  Or they are going to redo this same genome synthesis project in a bug that is better understood and will serve as a platform or chassis?  Either way, really?  The company has hundreds of millions of dollars in the bank to spend on this sort of thing, but I simply don't understand what the present publication has to do with making any money.

So, in summary: very cool big chuck of synthetic DNA being used to run a cell.  Not artificial life, and neither artificial cell nor synthetic cell.  Probably not going to show up in a product, or be used to make a product, for many years.  If ever.  Confusing from the standpoint of project management, profit, and economic viability.

But I rather hope somebody proves me wrong about that and surprises me soon with something large, synthetic, and valuable.  That way lies truly world changing biological technologies.

Book Talk at Reiter's in Washington DC, May 19

Tomorrow evening, May 19th, I will give a short talk about my recent book Biology is Technology at Reiter's Books  in Washington DC, followed by discussion and refreshments.  Among other issues, I will discuss updated figures for the impact of biotech and bioengineering on the US and world economies, the impact of the recent BRCA 1/2 gene patent decision, garage biotech, biosecurity, and regulation.

I look forward to seeing you there -- please bring hard questions.

Biology is Technology: The Promise, Peril, and New Business of Engineering Life
Robert Carlson
Harvard University Press, 2010
www.biologyistechnology.com

Where:

(Note that Reiter's has recently moved.)
Reiter's Books
1900 G St. NW
Washington DC 20006
www.reiters.com

When:

May 19, 2010
6:30 PM

The Economist Ideas Economy: Human Potential

I've just signed on to The Economist's next event in the Ideas Economy series, "Human Potential".  15-16 September, 2010 in NYC.  See you there.

DIYBio and Making at the BBC

This morning's biosecurity update from the Partnership for Global Security carried a mess of links I hadn't seen, including a story at the BBC entitled "Tech Know: Life hacking with 3D printing and DIY DNA kits".  The embedded video has an interesting clip on a printed stainless steel Mobius strip with freely moving rings that can run around the perimeter -- interlinked complex shapes.  Neat.  (Not a new thing in plastics, but I hadn't seen it in metal before.)

Cambridge's James Brown gets the honor of introducing the Beeb's audience to synthetic biology, biobricks, and engineering methods for biological systems.  The 3D-printed DremelFuge gets a photo and a significant mention.  I explicitly pointed to this sort of application of 3D printing in my book, though it is happening even faster than I had imagined.  Shapeways is now printing all sorts of interesting materials, though the resolution of most 3D printers and processes still doesn't make them useful for the sorts of objects I want to print.  That said, there is clear improvement over time.

It will be interesting to see how long it takes before you can print mixed media functional objects, say something like a zero-dead volume, positive displacement membrane pump.  Or better yet an entire pump block.  (Which is usually milled from a piece of stainless steel -- see where this is going?)  That gets you the most annoying bit of kit needed for a DNA synthesizer.  At which point you can forget any regulations limiting access to DNA of any sequence. 

"National Strategy for Countering Biological Threats"

I recently had cause to re-read the National Strategy for Countering Biological Threats (Full PDF), released last fall by the National Security Council and signed by the President. I think there is a lot to like, and it demonstrates a welcome change in the mindset I encounter in Washington DC.

When the document came out, there was just a little bit of coverage in the press. Notably, Wired's Threat Level, which usually does a commendable job on security issues, gave the document a haphazard swipe, asserting that "Obama's Biodefense Strategy is a Lot Like Bush's".  As described in that post, various commentators were unhappy with the language that Under Secretary of State Ellen Tauscher used when announcing the Strategy at a BWC meeting in Geneva. According to Threat Level, "Sources tell this reporter that the National Security Council had some Bush administration holdovers in charge of editing the National Strategy and preparing Ms. Tauscher's script, and these individuals basically bulldozed the final draft through Defense and State officials with very little interagency input and with a very short suspense." Threat Level also asserts that "Most are disappointed in the language, which doesn't appear to be significantly different than the previous administration." It is unclear who "Most" are.

In contrast to all of this, in my view the Strategy is a clear departure from the muddled thinking that dominated earlier discussions. By muddled, I mean security discussions and policy that, paraphrasing just a little, went like this: "Biology Bad! Hacking Bad! Must Contain!" 

The new National Strategy document takes a very different line. Sources tell this reporter, if you will, that the document resulted from a careful review that involved multiple agencies, over many months, with an aim to develop the future biosecurity strategy of the United States in a realistic context of rapidly spreading infectious diseases and international technological proliferation driven by economic and technical needs. To wit, here are the first two paragraphs from the first page (emphasis added, of course):

We are experiencing an unparalleled period of advancement and innovation in the life sciences globally that continues to transform our way of life. Whether augmenting our ability to provide health care and protect the environment, or expanding our capacity for energy and agricultural production towards global sustainability, continued research and development in the life sciences is essential to a brighter future for all people.

The beneficial nature of life science research is reflected in the widespread manner in which it occurs. From cutting-edge academic institutes, to industrial research centers, to private laboratories in base­ments and garages, progress is increasingly driven by innovation and open access to the insights and materials needed to advance individual initiatives.

Recall that this document carries the signature of the President of the United States.  I'll pause to let that sink in for a moment.

And now to drive home the point: the new Strategy for Countering Biological Threats explicitly points to garage biotech innovation and open access as crucial components of our physical and economic security. I will note that this is a definite change in perspective, and one that has not fully permeated all levels of the Federal bureaucracy and contractor-aucracy. Recently, during a conversation about locked doors, buddy systems, security cameras, and armed guards, I found myself reminding a room full of biosecurity professionals of the phrase emphasized above. I also found myself reminding them -- with sincere apologies to all who might take offense -- that not all the brains, not all the money, and not all the ideas in the United States are found within Beltway. Fortunately, the assembled great minds took this as intended and some laughter ensued, because they realized this was the point of including garage labs in the National Strategy, even if not everyone is comfortable with it. And there are definitely very influential people who are not comfortable with it. But, hey, the President signed it (forgive me, did I mention that part already?), so everyone is on board, right?

Anyway, I think the new National Strategy is a big step forward in that it also acknowledges that improving public health infrastructure and countering infectious diseases are explicitly part of countering artificial threats. Additionally, the Strategy is clear on the need to establish networks that both promulgate behavioral norms and that help disseminate information. And the new document clearly recognizes that these are international challenges (p.3):

Our Strategy is targeted to reduce biological threats by: (1) improving global access to the life sciences to combat infectious disease regardless of its cause; (2) establishing and reinforcing norms against the misuse of the life sciences; and (3) instituting a suite of coordinated activities that collectively will help influence, identify, inhibit, and/or interdict those who seek to misuse the life sciences.

...This Strategy reflects the fact that the challenges presented by biological threats cannot be addressed by the Federal Government alone, and that planning and participation must include the full range of domestic and international partners.

Norms, open biology, better technology, better public health infrastructure, and better intelligence: all are themes I have been pushing for a decade now. So, 'nuff said on those points, I suppose.

Implementation is, of course, another matter entirely. The Strategy leaves much up to federal, state, and local agencies, not all of whom have the funding, expertise, or inclination to follow along. I don't have much to say about that part of the Strategy, for now. But I am definitely not disappointed with the rest of it. It is, you might say, the least bad thing I have read out of DC in a long time.

Chinese Real Estate Bubble Confusion (Or "On The Frailty of Selective Information")

(Updated to include the overall local-national GDP discrepancy of at least ~2.5%.)

We often see headlines loudly proclaiming certain things to be true about China.  They are taking over!  No, wait, they are collapsing!  It's raining!  No, it's a drought!  How is one supposed to make sense of any of this?

One small part of the answer is that even the Chinese don't have a great idea of what is going on.  As a result, last Thursday (March 11), based on Chinese government data, the Financial Times and the Wall Street Journal carried stories on the state of the Chinese real-estate market that came to completely opposite conclusions.  Here's the WSJ headline: "China's Real-Estate Boom Appears to Cool."  And here is the FT: "Fears grow over China property bubble despite efforts at cooling."  Both stories cite identical statistics about price increases over the last year, though the WSJ leans on reduced sales volumes reported by the Government and by a consultancy that tracks sales.  (Imagine this, if you can -- a reduction from 50% to 37% in the annual increase in sales is seen as a "cooling" of the market!)

The main problem with this reporting is that there is very little reason to believe the underlying data is accurate.  See, for example, this story from Xinhua a few weeks ago: "China statistics chief admits errors in property data calculation".

Dueto staff shortages, housing price data mainly stemmed from reports by real estate developers, said [Ma Jiantang, director of the National Bureau of Statistics (NBS)], who cited Beijing as an example where only one or two officials were responsible for collecting data from hundreds of real estate companies.

"Under the circumstance, we have to rely on the employees of property companies after giving them short-term training," Ma said. "And some of the employees lack professionalism and a sense of responsibility."

And of course the real-estate developers have every reason to want the government (and the public) to conclude that prices are not out of control.  Beijing is attempting to put the breaks on a housing bubble, but the developers are making out like bandits.  There does not appear to by any reason for them to report accurately on pricing and volume.

Beyond the real estate market, even assessing the overall economic activity of the country is somewhat opaque for Beijing.  See this recent story from Xinhua, "China mulls unified GDP calculation":

China's top economic planning body has confirmed that China is considering bring local GDP under unified calculation in an effort to prevent local officials from cooking economic growth figures for political benefits.

...In the first half of 2009, the sum of provincial GDP figures was 1.4 trillion yuan more than the national figure, calculated by the NBS independently. Almost half of the provincial governments reported a double-digit GDP growth whereas the national growth figure was only 7.1 percent.

Leaving aside the cumulative difference in growth rate, that 1.4 trillion yuan imbalance amounts to an absolute yearly discrepancy of ~2.5% just for the first six months of 2009, which would severely complicate sorting out domestic economic policy.  It would also make strategic judgments by other countries rather problematic.
 
For what it is worth, my man on the ground is an architect who has been working in China for more than a decade now, building everything from government offices, to residential towers, to subdivisions, and beyond.  His latest big project under construction is a kilometer-long building containing housing, offices, performing arts spaces, sports fields along the "ridgeline" on top, and an interior train running the length of the entire structure.  It sounds like a fantasy land.  Perhaps it is.

In other news, the architect reports his firm just completely sold out a mid-range 40 story condo tower to individual purchasers in two days, as fast as the paperwork could get signed.  When asked if he thought this indicated a healthy market and real economy: "No way!" 

Shame On You, Portland!

What Happened to March?  I got on a plane this morning headed for New York, but somehow arrived on April 1st.  It's the only explanation for this:

Portland hurts Tibetans
(China Daily)
Updated: 2010-03-11 07:51

While many in the international community are watching with anxiety to see if Washington moves to repair its ties with Beijing, a reckless decision by an American city is rubbing salt into the unhealed wound of the world's most important bilateral relations.

The city of Portland, Oregon, proclaimed Wednesday, March 10, their "Tibet Awareness Day" despite strong opposition from the Chinese government.

While most people and most countries in the world recognize Tibet as part of China, the decision by the American city interferes in China's internal affairs and is an open defiance of China's state sovereignty.

It could have an adverse effect on Sino-US relations, which has yet to recover from major deterioration following Washington's $6.4-billion arms sale to Taiwan and US President Barack Obama's meeting with the Dalai Lama.

The designation of the "Tibet Awareness Day" was apparently orchestrated by the Dalai Lama clique, which has been engaged in activities aimed to separate China and undermine Tibet's stability in the guise of religion.

It is still beyond our belief that politicians in Portland have chosen to celebrate a handful of fanatics trumpeting Tibet independence while turning a blind eye to either history or the status quo of present-day Tibet. History has told us that Tibet has always been a part of China, and there is ample evidence proving the fact that Tibetan people now enjoy a much better life and enjoy the full freedom of religion.

Americans are well-known for putting individual freedom above everything. While the city of Portland entertains a few Tibet separatists, has it ever occurred to its decision-makers that their move are infringing on the interest of 2.8-million Tibetans here in China?

Garage Biology in Silicon Valley

A couple of weeks ago I made a whirlwind trip to San Francisco that turned out to be all about garage biology.  I started off with a talk to the California Assembly Select Committee on Biotechnology.  Here are my slides (Carlson_CA_Assembly_February_2010.pdf), which focus on the role of small business and garage hackers in creating innovation in the Bioeconomy, and here is the agenda (PDF).  See my recent post on "Micro-Brewing the Bioeconomy" for the details of craft brewing as an example of distributed biological manufacturing.  I also did an event at the GBN for the book, and I'll post a link to the recording when it goes live.

I spent most of one Saturday hanging out at a garage biology lab in Silicon Valley.  When I walked in the door, I was impressed by the sophistication of the set-up.  The main project is screening for anti-cancer compounds (though it wasn't clear to me whether this meant small molecules or biologics), and the people involved have skillzzz and an accumulation of used/surplus equipment to accomplish whatever they want; two clean/cell-culture hoods, two biorobots (one of which is being reverse engineered), incubators, plate readers, and all the other doodads you might need.  They aren't messing around.  I didn't get into the details of the project, but the combination of equipment, pedigree, and short conversations with the participants told me all I needed to know.  That doesn't mean they will be successful, of course, just that I believe they are yet another example of what can be attempted in a garage.  This sort of effort is where new jobs, new economic growth, and, most importantly, desperately needed new technologies come from.  Garage innovation is at the heart of the way Silicon Valley works, and it is envied around the world.

I continue to get push back from people who assert that "it is really too hard" to hack biology in a garage, or too expensive, or that garage labs just can't be up to snuff.  This sort of dissent usually comes out of National Labs, Ivy League professors, or denizens of the beltway.  All I can say to this is -- Doodz, you need to get out more.

So why am I not telling you the who and the where for the photos above?  Because, like many garage biology hackers, they are a little skittish given the way the Uncle Sam has been off his rocker for the last few years when it comes to mis-perceived biothreats (Shoot first, Google later).  The people who built the lab pictured above are pursuing a project that is technically well beyond anything discussed on the DIYBio list, and while they may be watching the DIYBio conversation they don't advertise what they are up to.  It would be better for all of us if we could rest assured that conversations about this sort of work could proceed in the open without guys showing up in biohazard suits with weapons drawn -- Youtube, at the 00:00:48 mark.  Words fail to describe this video.  Or, rather, I have plenty of choice words to describe the quality of the investigation and planning that went into an armed assault on the residence of an art professor whose many previous public shows and events included biological technologies including hacked bacteria -- and indeed I have shared those words with the appropriate individuals in DC, and will do so again -- but it won't do my blood pressure any good to go further down that road here.

While the innocuous art professor may be back at work, and while some may view this as water under the bridge, it is not my impression that Federal law enforcement officials truly understand the impact of their behavior.  (Here, I will try again: Dear Feds, You are making us less safe.)  The response to errant "enforcement"efforts (or "career enhancement", depending on your perspective) is exactly what you would expect -- people stop talking about what they are doing, making the job of sorting out potential threats all that much harder.  I recall giving a talk in DC in 2003 or so wherein I made this point to a room full of intelligence types (domestic and foreign), and only about half of them -- predominantly the younger ones -- understood that information was their only tool in this game.  The notion that you could effectively produce safety through prohibiting garage biology and related efforts is the height of folly.  See, for example, "And the Innovation Continues...Starting with Shake andBake Meth!" for the latest on the effectiveness of domestic prohibition of methamphetamine production.  The effect is -- surprise!!! -- more innovation.  Just like it always is.  However much garage biology we wind up with, we will be much safer if practitioners are willing to discuss what they are up to without worrying about misdirected badges, search warrants, and guns. 

To be sure, I don't have reason to suspect anything but good intentions and productive work originating from the garage lab shown above.  Nor is a drug screening project likely to result in something scary.  But I certainly can't know they won't make a mistake.  I would feel more comfortable if they, in turn, didn't feel like they had to keep a low profile so that there could be open discussion of potential missteps.  This applies to individuals and governments alike: "Above all else, let us insist that this work happens in the light, subject to the scrutiny of all who choose to examine it." (PDF)  And I am waaay more concerned about what the government might get up to behind closed doors than I am about activities of individuals.  

Next week I am headed to DC for another biosecurity/bioterrorism discussion, which will be interesting in light of the recent "F" grade given to US biopreparedness by the President's Commission on the Prevention of Weapons of Mass Destruction Proliferation and Terrorism.  See also my earlier analysis of the report.  I mention this here because the US Government still doesn't get the role of garage biology in much needed innovation (see the slides above from the talk to the CA Assembly Committee for a list of important technical advances from small businesses and individuals -- this discussion is also in the book).  Nor has the US Government clued into the PR job they have ahead of them with students who are gaining skills and who want to practice them in the garage.  Both the FBI and the Biological Weapons Commission Convention (sorry, Piers!) had a presence at iGEM in 2009 -- as liasons to students the FBI sent Agents whose cards read "Weapons of Mass Destruction Coordinator".  !!!Calling Chiat\Day!!!

There continues to be a prominent thread of conversation in Washington DC that "biohacking" is somehow aberrant and strange.  But apparently DIYBio, you'll be happy to hear, is a group composed of the Good Guys.  Everyone should feel happy and safe, I guess.  Or maybe not so much, but not for the reasons you might think.

The creation of a false dichotomy between "DIY Biotech" (good guys) and "Biohacking" (bad guys) lends unfortunate credence to the notion that there is an easily identifiable group of well-meaning souls who embrace openness and who are eager to work with the government.  On the contrary, in my experience there are a number of people who are actively hacking biology in their garages who intentionally keep a low profile (I am not certain how many and know of no existing measure, but see discussion above).  This tally included me until a little over a year ago, though now my garage houses a boat under restoration.  These people often consider themselves "hackers", in the same vein as people who hack computers, boats (!), cars, and their own houses.  Yes, it is all hacking, or Making, or whatever you want to call it, and not only is it generally innocuous but it is also the core of technological innovation that drives our economy.  And without direct interaction, I do not believe it is practical to ascribe motivation or intent to an individual - including and especially an incorporated individual - operating in a garage.  Thus, I strongly object to the establishment of a conversation related to biosecurity in which the term "biohacker" has any pejorative connotations precisely because it perpetuates the misconception that i) this group is quantifiable; ii) that the group has any unified motivations or identifiable ethical norms (or anti-norms); iii) that it can realistically be currently addressed (or assessed) as a "group".

Hmm...with that, I have run out of steam for the moment, and have real work to do.  More later.

GM Potatoes Approved in Europe for Industrial Starch Production

Not everyone is happy in Europe today.  Evil Genetically Modified (GM) crops are on the march.  After 12 years of deliberations, the EC approved the cultivation of BASF's Amflora potato for industrial uses or animal feed.  Amflora is only the second GM crop approved for cultivation in Europe.  Before getting into this too far, I want to make clear that such decisions should be based on science, and if the science says there are safety or health concerns then we should be cautious.  But the science, all the science I am aware of, says GM crops are safe, at least from a health perspective.  Non-peer reviewed yelping doesn't count.  (Leakage of transgenes is another matter, which I get to below, lest the reader think I am wholly uncritical of GM crops.)

According to the NYT, the EC's Health Commissioner John Dalli described the decision this way:

Responsible innovation will be my guiding principle when dealing with innovative technologies. After an extensive and thorough review ... it became clear to me that there were no new scientific issues that merited further assessment. ...All scientific issues, particularly those concerning safety, had been fully addressed. Any delay would have simply been unjustified.

Digging into this a bit, I found on the European Commission's site quite a long list of GM crops that are approved for various uses in Europe.  Not cultivation, mind you, but use.  Six member states presently "prohibit the use and/or sale of the GM product on its territory". 

The primary complaint by critics appears to be that Amflora contains antibiotic resistance genes, which is not the change that makes them useful in the field, but rather an old technology used to produce the plants in the first place.  That this very old technology is now being deployed in the field is the result of the slow approval process in Europe.  No new GM crop in the US would contain antibiotic resistance genes.  Why is this important?  Because those genes may leak out of the crop into other organisms.

According to the NYT, this risk was evaluated as being very low for the Amflora potato.  Fine.  But it is a real risk in general, one that has been observed in other GM crops.  Here is the relevant passage from of my book, in the context of using GM crops as industrial feedstocks (p165 -- refs are at bottom of this post):

Leakage of genes from GM crops into their unmodified cousins is potentially a threat if herbicide-resistance genes are transferred into weeds. Gene flow into close relatives has been observed in tests plot of Kentucky bluegrass and creeping bentgrass, which provided "the first evidence for escape of transgenes into wild plant populations within the USA."[47]  A similar result has now been demonstrated for a stable and persistent transfer of an herbicide-resistance gene from the widely cultivated Brassica napus, commonly known as rape or rapeseed, to its wild relative Brassica rapa.[48]  Within the confines of a laboratory, herbicide-resistance genes can be transferred with relative ease via pollen exchange between common weed species.[49]  These demonstrations may give pause to both policy makers and commercial interests. Any gene transfer in open cultivation that results in unintentional propagation of a new herbicide-resistant weed strain has the potential to cause substantial economic and physical damage.

The resulting potential threat to agricultural systems raises significant questions about the wisdom of relying on genetically modified crops for feedstock production.

If gene leakage can be minimized, then GM crops hold sufficient promise that they should be used.  The EC appears to believe that this is the case for Amflora potatoes.  Critics in Europe aren't satisfied.  But here is the truly nutty bit about criticism from Greenpeace and Friends of the Earth -- it is through their efforts that technological progress in Europe is so damn slow.  Why would any company want to go through the pain and expense of trying to get new technology (i.e., a GM crop that doesn't contain antibiotic resistance genes) into Europe when the only test case took 12 years to make it into the field?

At any rate, the Amflora decision may indicate the mood has changed at the EC level.  Not that the floodgates are likely to open, but perhaps GM crops will now be seen in a different light in Europe.

Refs from Biology is Technology excerpt:

47.  P. G. Johnson et al., Pollen-mediated gene flow from Kentucky bluegrass under cultivated field conditions,Crop Science 46, no. 5(2006): 1990; L. S. Watrud et al., From the cover: Evidence for landscape-level, pollen-mediated gene flow from genetically modified creeping bentgrass with CP4EPSPS as a marker, PNAS 101, no. 40(2004): 14533; J. R. Reichman et al., Establishment of transgenic herbicide-resistant creeping bentgrass (Agrostis stolonifera L.) in nonagronomic habitats, Molecular Ecology 15, no. 13(2006): 4243.

48.  S. I. Warwick et al., Do escaped transgenes persist in nature? The case of an herbicide resistance transgene in a weedy Brassica rapa population, Molecular Ecology 17, no. 5(2007): 1387-1395.

49.  I. A. Zelaya, M. D. K. Owen, and M. J. VanGessel, Transfer of glyphosate resistance: Evidence of hybridization in Conyza (Asteraceae), American Journal of Botany 94, no. 4(2007): 660.

25% of US Grain Crop Used for Biofuel

The Guardian UK reported today that 2009 USDA figures show 25% of grains grown in the US were used to produce liquid biofuels.  The typical food vs fuel story follows.  And it is mostly on point, if tinted by The Guardian's usual populist tone.  Yes, all the grain could in principle be used to feed people.  No, it isn't clear that grain-based ethanol is in fact better than burning petroleum when it comes to total greenhouse gas emissions or energy content.

The story ends with a nod toward "continued innovation in ethanol product" that supposedly is increasing yields and reducing costs.  Huh.  No mention, though, of the fact that any starch crop used to make fuel starts at a major disadvantage with respect to sugar crops, nor that there is an ethanol glut in the US due to construction of too many ethanol production plants.  Neither does the story get into why ethanol isn't a very good fuel to begin with (wrong solvent properties, low energy content, water soluble).

I go into detail about this in my forthcoming book, but the upshot of the argument is that the US is investing quite a lot of money in ethanol production technology and infrastructure that will never be competitive with sugar derived fuels.  And then relatively soon we will get butanol, longer chain alcohols, and true drop-in petroleum replacements made using modified organisms.  In the meantime, I suppose we will just have to suffer through the impact of decisions made more for political reasons than for competitive or national security reasons.  But grain to ethanol isn't really good for anybody except US Senators from farm states.