A Few Thoughts on Water

Years ago, I frequently commuted between Los Angeles and Seattle by air.  The contrast between the two cities was always a bit jarring, particularly in July and August -- high summer on the west coast of North America -- when the lawns in Seattle are brown while all the residential yards in Los Angeles are a beautiful emerald green.  Summer rainfall in Seattle is usually about 1.8 inches spread over those two months, while Los Angeles is essentially dry.

A couple of weeks ago I flew into LAX from the east coast and got another perspective on water use there.  My first glimpse of the basin was the smog lapping up against the rim of the San Gabriel Mountains. I managed to snap a quick photo after we had flown over the ridge (the smog is on the lower left, though the contrast was more impressive when we were looking from the east side).

IMG_0477.JPGEven in May it looks a little dry 'round those parts.

A few minutes later, I noticed large green patches covering the sides (usually the west side) of hills.  This continued all the way to downtown LA, and we were high enough for most of that time that I couldn't figure out why the locals were spending so much of their precious water keeping the sunset sides of hills green.  Then, finally, we passed over one low enough that the purpose jumped out at me.

Cemeteries.

Even in death, Los Angelinos maintain their homage to William Mulholland by keeping him eternally damp.  And in death, Los Angelinos continue to contribute to the smog shown above -- the grass covering the land of the dead is trimmed quite short.  Many, many square miles of it.  A cushy life, have those dead people.  And to be fair to Los Angeles (which, admittedly, is hard for me), Seattle, too, uses a great deal of water and hydrocarbons to keep our decaying ancestors covered with a trim layer of green.  It happens everywhere here.  Welcome to America.

Even the way the US irrigates land to feed the living represents a profligate use of water.  According to the USDA, 80% of the water consumed in this country goes to agriculture. (Note that "use" and "consumption" are often confused.  Agriculture and thermoelectric power generation both "use" about 40% of the nation's freshwater, but while almost 100% of the water used for power generation is returned to where it was taken from -- albeit somewhat warmer than when it was taken -- much of the of water put on crops is does not reach the roots or is evaporated and lost to the atmosphere.)  Notice that I did not use the word "waste", because some of the leakage winds up back in groundwater, or otherwise finds its way into the environment in a way that might be classified as "beneficial".

And pondering water use here in the US, and the impact on our economy, my thoughts turn to water use in Asia.  Much ado was made in the last couple of years about the IPCC report of anomalous melting of Asian glaciers, followed by the discovery that there was no actual data behind the assertion.

A recent paper in Science adds some much needed analysis to the story.  Walter Immerzeel and colleagues set out to understand the relative importance of meltwater and rainwater to river flows in Asia.  It is interesting to me that this sort of analysis wasn't done before now: "Earlier studies have addressed the importance of glacial and snow melt and the potential effects of climate change on downstream hydrology, but these are mostly qualitative or local in nature."

For five large river basins the authors used a combination of precipitation data, snow melt models, and evaporation rates, to calculate the Normalized Melt Index (NMI).  The NMI is the ratio of snow and glacier discharge to downstream discharge.  If all the water in a river downstream is from melting, then this ratio is obviously one; if the ratio is less than one, rainfall contributes more than meltwater, and if it larger than one, more water is lost through evaporation or other processes (like agriculture) and meltwater is more important for total flow.

Here are the results.  For each of the rivers, the authors calculated the percentage of the total discharge generated by snow and glacial melt:
 

Indus

151%

Brahmaputra

27%

Ganges

10%

Yangtze

8%

Yellow

8%

In other words, water supplies in the Indus river valley are largely dependent on meltwater, whereas the large river systems in China appear to be less dependent on meltwater.  That is a very interesting result, because the story told by lots of people (including myself) about the future of water in China is that they are in big trouble due to glacial melting in the Himalayas.  Assuming this result holds up, China may be better off in a warmer world that I had anticipated.

The authors also used various projections of snow and rainfall to estimate what water supplies would look like in these rivers in 2050.  As you might expect, a warmer world leads to less snowfall, more melting, and lower river flows.  But as the warmer world brings increased rainfall, the impact is smaller than has been widely assumed.  I am not going to bother putting any of the numbers in here, because, as the authors note, "Results should be treated with caution, because most climate models have difficulty simulating mean monsoon and the interannual precipitation variation, despite recent progress in improving the resolution of anticipated spatial and temporal changes in precipitation."

But they went one step further and tried to estimate the effects of potential decreased water supply on local food supplies.  Couched in terms of crop yields, etc., Immerzeel et al estimate that the Brahmaputra will support about 35 million fewer people, the Indus will support about 26 million fewer people -- that's food for 60 million fewer people in India and Pakistan, if you are counting -- and the Yellow about 3 million more people.  Finishing up, they write:

We conclude that Asia's water towers are threatened by climate change, but that the effects of climate change on water availability and food security in Asia differ substantially among basins and cannot be generalized. The effects in the Indus and Brahmaputra basins are likely to be severe owing to the large population and the high dependence on irrigated agriculture and meltwater. In the Yellow River, climate change may even yield a positive effect as the dependence on meltwater is low and a projected increased upstream precipitation, when retained in reservoirs, would enhance water availability for irrigated agriculture and food security.

I am perplexed by the take on these results over at Nature News by Richard Lovett.  His piece carries the title, "Global warming's impact on Asia's rivers overblown".  I'll give Lovett the out that he may not have written the actual headline (Editors!), but nonetheless he sets up the Immerzeel paper as a big blow to some unnamed group of doomsayers.  Perhaps he imagines that Immerzeel completely undermines the IPCC report?  This is hardly the case.  As I wrote last January, sorting out the mistake over Himalayan melting rates is an example of science working through a blunder.  Instead overturning some sort of vague conspiracy, as best I can tell Immerzeel is simply the first real effort to make quantitative assessments of something to which much more attention should have been paid, much earlier than it was.

And even Lovett appears to acknowledge that reducing the human carrying capacity of the Brahmaputra and Indus river valleys by 60 million people is something to be concerned about.  From Lovett: 

The findings are important for policy-makers, says Jeffrey Kargel, a glaciologist at the University of Arizona in Tucson. "This paper adds to mounting evidence that the Indus Basin [between India and Pakistan] is particularly vulnerable to climate change," says Kargel. "This is a matter that obviously concerns India and Pakistan very much."

Indeed.  As they should concern us all.

Yummy, Corrosive Biodiesel

Yummy for microbes, that is.  Who turn the methyl esters in biodiesel -- with some intermediate steps -- into hydrogen sulfide that corrodes carbon steel.

This according to a paper last month in Energy & Fuels, Aktas et al explore "Anaerobic Metabolism of Biodiesel and Its Impact on Metal Corrosion".  The authors observe that "Despite the global acceptance of biodiesel, the impact of integrating this alternate fuel with the existing infrastructure has not been fully explored."

Here is a paragraph from the paper, full of interesting tidbits:

The chemical stability characteristics of biodiesel are well-documented,(3, 4) but the susceptibility of this fuel to biodegradation is not well-known. Biodiesel methyl esters are sparingly soluble in seawater, with a saturation concentration of 7 ppm at 17 °C.(5) Several studies showed that aerobic microorganisms readily degrade biodiesel.(6-8) The half-life for the biodegradation of the vegetable methyl esters in agitated San Francisco Bay water was less than 4 days at 17 °C.(9) However, anaerobic conditions prevail whenever heterotrophic microbial respiration consumes oxygen at a rate that exceeds diffusion. This is typically the case in subsurface environments, including oil reservoirs,(10-12) oil-contaminated habitats,(13) refineries, storage vessels, pipelines, oil−water separators, and ballast tanks.

In particular, it is interesting that biodiesel spills might be metabolized by bugs in the environment at a much greater rate than petrodiesel.  Next, it is interesting that our steel infrastructure might be susceptible to more rapid degradation with the inclusion of bio-products.  Plastics, anyone?

The paper concludes:

Our studies suggest that biodiesel can be quite easily hydrolyzed and converted to a variety of fatty acid intermediates by anaerobic microorganisms, regardless of their previous hydrocarbon- or biodiesel-exposure history. The acidic nature of these intermediates accelerates the pitting corrosion process of the most common metal alloy used throughout the fuel infrastructure.(39) The corrosion of pipelines, tanks, storage units, and associated equipment increases the risk of the release of hazardous materials to the environment, with concomitant pollution issues. With the widespread use of biodiesel as an additive to fuel supplies, it is at least prudent to consider how best to avoid the negative consequences associated with the microbial metabolism of these labile fuel components.

Something to watch, obviously.

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).

Thumbnail image for carlson_longest_sDNA_2010.pngA 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

A Few Biosecurity Notes

  • Last January, the UPMC Center for Biosecurity published "U.S. Government Judgments on the Threat of Biological Weapons: Official Assessments, 2004-2009".  If you are interested in bioterrorism, you should have a look.
  • Also in January, the Belfer Center for Science and International Affairs at Harvard's Kenney School of Government released "Al Qaeda Weapons of Mass Destruction Threat: Hype or Reality?" (PDF) By Rolf Mowatt-Larssen.  The document gathers together open source information regarding Al Qaeda's interest in WMD.  Mowatt-Larssen is formerly the Director of Intelligence and Counterintelligence at the U.S. Department of Energy, and spent 23 years at the CIA.  The introduction sets out the purpose of the document as dispelling the doubts of those skeptical there is a real threat.
  • Former Senate Intelligence Committee chairman Bob Graham recently told the Washington Post that "India and Pakistan, as well as Syria and Israel, may have manufactured biological weapons."  Graham said: "The extent to which they may have done it is classified, but it is a serious threat. ...A couple of weeks in the Middle East has given me a greater sense of urgency."  Graham called out the lack of progress here at home in establishing "a response capability".  In an update to the story, the Post then pointed to a description of a new "biosecurity" bill introduced in the House, which from the article sounds to be all about securing national labs rather than standing up any sort of real biodefense response capability.

Sweet dreams.

A Few Notes on China

  • China Daily recently carried an Op--Ed asserting that "Giant leap" in education spurs nasty slump in academics.  (Oddly, the piece appears to be badged as an article, but the URL suggests it is an opinion piece.)  The piece asserts that "According to the education bureau, the number of university applicants in Beijing this year has decreased by 20%, and Shanghai has failed to meet its recruitment demand for three consecutive years."  Those are numbers I will have to dig into.  Another story from China Daily reports that, due to reduced enrollments and accumulated debt, "Universities face bankruptcy".
  • Slashdot has a brief blurb on how "China's Research Ambitions Hurt By Faked Results".  For those who haven't been following this story, while China has been climbing the world rankings of published scientific papers, so has the number of fraudulent papers.  I have to wonder what the real numbers are, though.  The Slashdot story links to a specific example of 70 crystal structures shown last year to be completely fabricated, but other accounts are mostly "just so" stories.
  • China's economic growth jumped to 11.9% in the first quarter of 2010.  The NYT also reports that Beijing raised fuel prices to help keep inflation in check.  Exports rose 46% in March, year on year, while imports rose 45%.
  • According to the NYT, China's Premier Wen Jiabao recently said that "China would pour money into strategic industries, boosting research and development and infrastructure spending to "capture the economic, scientific and technological high ground." Among the areas he singled out were biomedicine, energy conservation, information technology and high-end manufacturing."
  • Earlier this year, for the first time, Chinese oil imports from Saudi Arabia surpassed US imports.  As a result, China ran a trade deficit in March for the first time in years, and is buying up oil production in Canada.  Re-reporting a story from the China Securities Journal, China Daily asserts the sudden drop in the trade deficit is "a result of China's strive for a trade balance by taking measures to encourage imports and stabilize exports".
  • Here is the full text of China's recently published "Report on the Implementation of the 2009 Plan for National Economic and Social Development and on the 2010 Draft Plan for National Economic and Social Development" (via Xinhua).
  • Xinhua asserts that "China's trade surplus with US misread".  Among other revelations, it is apparently all our fault for refusing to export high tech items to China.
  • China has been blocking release of monetary data to the IMF since 2007, which makes it hard for the international organization to make any judgements about currency manipulation: "China allowed the release of its reports until the monetary fund's executive board decided in June 2007 that reports should pay more attention to currency policies. China has quietly blocked release of reports on its policies ever since, without providing its specific reasons to the I.M.F.

    A person who has seen copies of the most recent report last summer said that the monetary fund staff concluded the renminbi was "substantially undervalued."

    The monetary fund regards a currency as substantially undervalued if it is more than 20 percent below its fair market value."

  • Genetically Modified rice has been given a safety certificate by the Chinese Ministry of Agriculture, but the strain has to clear further hurdles before hitting the shelves.  Here are some interesting numbers: "China now yields around 500 million tons of grain annually. With the population expected to increase to 1.6 billion by 2020, 630 million tons of grain will be needed, experts said."  Wow -- that's a 25% increase in 10 years.
  • China has announced "A big plan to wipe out overcapacity".  According to China Daily, "The China Banking Regulatory Commission, China's watchdog on banks, has asked banks to retain strict controls on loans to industries with high energy consumption, high emissions or overcapacity. For instance, no loans are now allowed for any new projects in six industries with overcapacity and ship making unless these projects have approval from the National Development and Reform Commission, China's top economic planner. The six industries are steel and iron, cement, glass sheet, chemical processing of coal, polysilicon and wind power equipment."  Hmmm...the government of a centrally-planned economy proclaiming a drive for efficiency.  Best of luck with that.