Recently in Science Category

This week brings news of 1) a dramatic improvement in the estimates of how soil carbon content is related to atmospheric carbon concentration and 2) the exposure of some really crappy work on the rate of melting of Himalayan glaciers by the International Panel on Climate Change (IPCC).  The soil carbon work is Good Data, but Bad News if you care about the effects of high atmospheric carbon concentrations, while the Himalayan glacier story is all about terrible peer review and Bad Data (non-existent data, actually), which doesn't help anybody figure out the real story on water supplies in Asia.

First up, a paper from this week's PNAS by Breeker et al at UT Austin, "Atmospheric CO2 concentrations during ancient greenhouse climates were similar to those predicted for A.D. 2100".  Already from the title you can see where this is going.

The problem Breeker and colleagues address is the following: how do you correlate the carbon content of fossil soils with prevailing atmospheric carbon dioxide concentrations?  Well established methods exist for measuring the carbon content of compounds in fossil soil, but less certain were conditions under which chemical reactions produce those particular compounds.  It turns out that model used to infer atmospheric CO2 contained an error.  Breeker determined that the primary compound assayed when determining soil carbon content forms at much lower atmospheric CO2 concentrations than had been assumed.

Prior attempts to correlate soil carbon (and by proxy atmospheric CO2) with greenhouse periods in Earth's climate had concluded that warm periods experienced CO2 concentrations of much greater than ~1000 parts per million (ppm).  Therefore, one might conclude that only when average atmospheric CO2 spiked above this level would we be in danger of experiencing greenhouse gas warming that threatened glaciers.  The correction supplied by Breeker substantially lowers estimates of the average CO2 concentration that is correlated with continental glacial melting.  Eyeballing the main figure in the paper, it looks to me like we could be in real trouble above 450 ppm -- today we are at just shy of 390 ppm and there is no sign we will be slowing down anytime soon, particularly if India and China keep up their pace of development and emissions.

Looking forward to 2100, things get a touch squiffy because Breeker relies on an estimate of CO2 concentrations that come out of model of global economic activity.  So the title of the paper might be a tad alarmist, simply because 2100 is a long way out for any model to be taken too seriously.  But the correction of the paleodata is a big story because at minimum it reduces the uncertainty of atmospheric CO2 levels, and it appears to clarify the connection between CO2 levels and continental glaciation.  More work is needed on the later point, obviously, or this paper would have been on the cover of Science or Nature.

Now on to a serious screw-up at the IPCC.  Elisabeth Rosenthal at the NYT is reporting that "A much-publicized estimate from a United Nations panel about the rapid melting of Himalayan glaciers from climate change is coming under fire as a gross exaggeration."  Here is Andrew Revkin's take on DotEarth, and anyone interested in this story should read through his post.  The comments are worth perusing because some of the contributors actually seem to have additional useful knowledge, though, of course, nut jobs aplenty show up from both sides of the debate over climate change.

In a nutshell, the issue is that the most recent IPCC chapter on glaciers contained a conclusion, advertised as real analysis, that was in fact a speculation by one scientist promulgated through the popular press.  The authors of that section of the IPCC report may have been warned about the unsubstantiated claim.  Contradictory data and analysis seems to have been ignored.

So, to be frank, this is a giant, inexcusable fuck-up.  The IPCC is composed of so many factions and interest groups that this may be a case of simple blundering or of blatant politicization of science.  But here is the beautiful thing about science -- it is self-correcting.  It may take a while, but science always wins.  (See also my post of a couple of years ago, Dispelling a Climate Change Skeptic's "Deception".)  Every newspaper story I have seen about this particular IPCC screw-up notes that it was brought to light by...wait for it...a climate scientist.  It is an excellent public airing of dirty laundry by the community of science.  So while this episode demonstrates that the last official IPCC report on glacial melting in the Himalayas should not be used for any sort of scientific policy recommendation or economic forecast, you can bet that the next report will do a damn fine job on this topic. 

Finally, whether or not the IPCC gets its act together, there are plenty of good data out there on the state of the planet.  Eventually, Science -- with a capital S -- will get the right answer.  The same methodical process that has resulted in computers, airplanes, and non-stick fry pans will inevitably explain what is really going on with our climate.  And if you use computers, fly on airplanes, or eat scrambled eggs then you are implicitly acknowledging, whatever your political or religious persuasion, that you believe in science.  And you better, 'cause science always wins.

The Economist has posted video from the World in 2010 Festival, held in Washington DC in early December.  The Innovation panel is below, with me (Biodesic), Dean Kamen (DEKA Research), Dwayne Spradlin (Innocentive), and Kai Huang (Guitar Hero), moderated by Mathew Bishop (The Economist).  (Here is a link to video selections from the rest of the event.)  I was chatting with a reporter a few days ago who observed that everyone else on the panel is quite wealthy -- hopefully that bodes well for me in 2010.  But maybe I am destined always to be the odd man out.  C-Span is re-running the video periodically on cable if you want to watch it on a bigger screen, but I can't seem to find an actual schedule.  (Here is their web version: Innovation in 2010.)


I have a couple of general thoughts about the event, colored by another meeting full of economists, bankers, and traders that I attended in the last week of December.  I met a number of fantastically accomplished and interesting people in just a few hours, many of whom I hope will remain lifelong friends. 

First, I have to extend my thanks to The Economist -- they have been very good to me over the last 10 years, beginning in 2000 by co-sponsoring (with Shell) the inaugural World in 2050 writing competition.  (Here is my essay from the competition (PDF).  It seems to be holding up pretty well, these 10 years later, save the part about building a heart.  But at least I wasn't the only one who got that wrong.)

Here is a paraphrased conversation over drinks between myself and Daniel Franklin, the Executive Editor of the newspaper.

Me:  I wanted to thank you for including me.  The Economist has been very kind to me over the past decade.
Franklin: Well, keep doing interesting things.
Me:  Umm, right.  (And then to myself: Shit, I have a lot of work to do.)

On to the World in 2010 Festival.  The professional economists and journalists present all seem to agree that we have seen the worst of the downturn, that the stimulus package clipped the bottom off of whatever we were falling into, and that employment gains going forward could be a long time in coming.  Unsurprisingly, the Democratic politicians and operatives who turned up crowed about the effects of the stimulus, while the Republicans who spoke poo-pooed any potential bright spots in, well, just about everything.

At the other meeting I attended, last week in Charleston, SC, one panel of 10 people, composed Federal reserve and private bankers, traders, and journalists couldn't agree on anything.  The recovery would be V shaped.  No, no, W shaped.  No, no, no, reverse square root shaped (which was the consensus at The World in 2010 Festival).  No, no, no, no, L shaped.  But even those who agreed on the shape did not agree on anything else, such as the availability of credit, employment, etc.

Basically, as far as I can tell, nobody has the slightest idea what the future of the US economy looks like.  And I certainly don't have anything to add to that.  Except, of course, that the future is biology.

Here is John Oliver's opening monologue from the Festival.  He was absolutely hilarious.  Unfortunately you can't hear the audience cracking up continuously.  I nearly pissed myself.  Several times.  (Maybe the cocktails earlier in the evening contributed to both reactions.)



Back to Innovation in 2010.  Dean Kamen had this nice bit in response to a question about whether the imperative to invent and innovate has increased in recent years (see 36:20 in the C-Span video): "7 billion people can't be recipients, they have to be part of the solution.  And that is going to require advanced technologies to be properly developed and properly deployed more rapidly than ever before."

To this I can only add that we are now seeing more power to innovate put into the hands of individuals than has ever occurred in the history of humanity.  Let's hope we don't screw up.

While in London last month I sat down for tea and an interview with Geoff Carr at The Economist (permalink).  We covered a lot of ground, though as befitting a brief chat over tea we didn't get too deep in to the weeds.  Alas, they cut out the bit where the good Dr. Carr tried to put milk in my peppermint tea.  A topic for discussion in itself.

I just received the schedule for my plenary talk at the 2009 Bio Pacific Rim Summit in November; 07:15 AM Hawiian Time, on Wednesday the 11th.  That's Pacific Time minus two hours.  The coffee better be damn strong.

News today that a federal judge has rejected the approval of GM sugar beets by the USDA.  The ruling stated that the government should have done an environmental impact statement, and is similar to a ruling two years ago that led to halting the planting of GM alfalfa.  As in that case, according to the New York Times, "the plaintiffs in the [sugar beet] lawsuit said they would press to ban planting of the biotech beets, arguing that Judge White's decision effectively revoked their approval and made them illegal to grow outside of field trials."  The concern voiced by the plaintiffs, and recognized by the judge, is that pollen from the GM beets might spread transgenes that contaminate GM-free beets.

A few other tidbits from the article: sugar beets now supply about half the US sugar demand, and it seems that GM sugar beets account for about 95% of the US crop (I cannot find any data on the USDA site to support the latter claim).  A spokesman for the nation's largest sugar beet processor claims that food companies, and consumers, have completely accepted sugar from the modified beets -- as they should, because it's the same old sugar molecule. 

I got lured into spending most of my day on this because I noticed that the Sierra Club was one of the plaintiffs.  This surprised me, because the Sierra Club is less of a noisemaker on biotech crops than some of the co-plaintiffs, and usually focuses more on climate issues.  Though there is as yet no press release, digging around the Sierra Club site suggests that the organization wants all GM crops to be tested and evaluated with an impact statement before approval.  But my surprise also comes in part because the best review I can find of GM crops suggests that their growing use is coincident with a substantial reduction in soil loss, carbon emissions, energy use, water use, and overall climate impact -- precisely the sort of technological improvement you might expect the Sierra Club to support.  The reductions in environmental impact -- which range from 20% to 70%, depending on the crop -- come from "From Field to Market" (PDF) published earlier this year by the Keystone Alliance, a diverse collection of environmental groups and companies.  Recall that according to USDA data GM crops now account for about 90% of cotton, soy, and corn.  While the Keystone report does not directly attribute the reduction in climate impacts to genetic modification, a VP at Monsanto recently made the connection explicit (PDF of Kevin Eblen's slides at the 2009 International Farm Management Congress).  Here is some additional reporting/commentary.

So I find myself being pulled into exploring the cost/benefit analysis of biotech crops sooner than I had wanted.  I dealt with this issue in Biology is Technology by punting in the afterword:
 

The broader message in this book is that biological technologies are beginning to change both our economy and our interaction with nature in new ways.  The global acreage of genetically modified (GM) crops continues to grow at a very steady rate, and those crops are put to new uses in the economy every day.  One critical question I avoided in the discussion of these crops is the extent to which GM provides an advantage over unmodified plants.  With more than ten years of field and market experience with these crops in Asia and North and South America, the answer would appear to be yes.  Farmers who have the choice to plant GM crops often do so, and presumably they make that choice because it provides them a benefit.  But public debate remains highly polarized.  The Union of Concerned Scientists recently released a review of published studies of GM crop yields in which the author claimed to "debunk" the idea that genetic modification will "play a significant role in increasing food production"  The Biotechnology Industry Organization responded with a press release claiming to "debunk" the original debunking.  The debate continues.

Obviously we will all be talking about biotech crops for years to come.  I don't see how we are going to address the combination of 1) the need for more biomass for fuel and materials, 2) the mandatory increase in crop yields necessary to feed human populations, and 3) the need to reduce our climatic impacts, without deploying biotech crops at even larger scales than we have so far.  But I am also very aware that nobody, but nobody, truly understands how a GM organism will behave when released into the wild.

We do live in interesting times.

The Times is running a nice profile piece on Eric Schadt and his work at Rosetta and now Sage Bionetworks.

Biodesic evaluated systems biology investments for a large organization about 18 months ago, and Schadt's approach makes more sense to me -- by far -- than anything else we looked at.  I sat in on the pitch that Schadt and Stephen Friend made to that same organization, and it was crystal clear to me that Sage -- now residing at the Hutch here in Seattle -- should be on the receiving end of piles of money.  The stacks of Nature Group publications Schadt is accumulating suggest he is on to something, and it appears that his methods can be used to make predictions about the behaviors of complex networks.  Time and experimentation will tell, of course.  The open source aspect is a huge bonus.

Schadt's move to Pacific Biosciences is interesting because during his talk he suggested that genome sequencing provides enough information about variation to fuel his statistical methods for predicting interactions not just between genes but between tissues -- he is working at the level of describing the behavior of networks of networks.  It seems he will now have access to plenty of data.

Various hard drive crashes have several times wiped out my records for the longest published synthetic DNA (sDNA).  I find that I once again need the list of references to finish off the edits for the book.  I will post them in the open here so that I, and everyone else, will always have access to them.

Year	Length	Refs
1979	207	Khorana (1979)
1990	2100	Mandecki (1990)
1995	2700	Stemmer (1995)
2002	7500	Cello (2002)
2004.4	14600	Tian (2004)
2004.7	32000	Kodumal (2004)
2008	583000	Gibson (2008)

1979
Total synthesis of a gene
HG Khorana
Science 16 February 1979:
Vol. 203. no. 4381, pp. 614 - 625
http://www.sciencemag.org/cgi/content/abstract/203/4381/614

1990
A totally synthetic plasmid for general cloning, gene expression and mutagenesis in Escherichia coli
Wlodek Mandecki, Mark A. Hayden, Mary Ann Shallcross and Elizabeth Stotland
Gene Volume 94, Issue 1, 28 September 1990, Pages 103-107
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-47GH99S-1J&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=84ca7779ff1489d5e18082b9ecb80683

1995
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides
Willem P. C. Stemmer, Andreas Crameria, Kim D. Hab, Thomas M. Brennanb and Herbert L. Heynekerb
Gene Volume 164, Issue 1, 16 October 1995, Pages 49-53
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-3Y6HK7G-66&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=83620e335899881aac712a720396b8f2

2002
Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template
Jeronimo Cello, Aniko V. Paul, Eckard Wimmer
Science 9 August 2002: Vol. 297. no. 5583, pp. 1016 - 1018
http://www.sciencemag.org/cgi/content/abstract/1072266

2004
Accurate multiplex gene synthesis from programmable DNA microchips
Jingdong Tian, Hui Gong, Nijing Sheng, Xiaochuan Zhou, Erdogan Gulari, Xiaolian Gao & George Church
Nature 432, 1050-1054 (23 December 2004)
http://www.nature.com/nature/journal/v432/n7020/full/nature03151.html

Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster
Sarah J. Kodumal, Kedar G. Patel, Ralph Reid, Hugo G. Menzella, Mark Welch, and Daniel V. Santi
PNAS November 2, 2004 vol. 101 no. 44 15573-15578
http://www.pnas.org/content/101/44/15573.abstract

2008
Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome
Daniel G. Gibson, Gwynedd A. Benders, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B. Stockwell, Anushka Brownley, David W. Thomas, Mikkel A. Algire, Chuck Merryman, Lei Young, Vladimir N. Noskov, John I. Glass, J. Craig Venter, Clyde A. Hutchison, III, Hamilton O. Smith
Science 29 February 2008: Vol. 319. no. 5867, pp. 1215 - 1220
http://www.sciencemag.org/cgi/content/abstract/1151721

We are all familiar with the aromas used by stores in the hopes of motivating consumer frenzy.  Walk into some establishments and you may feel as if you have been smacked with a fragrant bunch of flowers.  Or possibly a fragrant leather shoe.  Maybe this actually encourages people to spend money.  It usually just makes me sneeze.

But what if the general strategy of behavior modification via perfumes of one kind or another really does work?  At the 2008 World Economic Forum in Davos, there was an explicit attempt to influence discussions through the use of custom scents designed for the occassion.

Here is a short excerpt from "Davos Aromas Deodorize Subprime Stench, Charm Dimon, Kissinger", by A. Craig Copetas (Bloomberg News):

"I know a lot of people think this is foolish,'' says Toshiko Mori, chairwoman of Harvard University's architecture department and one of the WEF delegates who initiated the perfume project. ``But the global economy is in dire straits and we must improve the quality of human spirits. Perfuming is a powerful tool in a much broader discourse. The fragrances will help us reach economic and political solutions at Davos.''

Here is CNN's take: "Smelly Davos unveils new world odor."  Ha.

The reader might imagine a room full of national security professionals debating the merits and ethics of this "technology".  We see two camps emerge.  The first group is shocked -- shocked! -- that biochemical warfare is being brought indoors to induce in captains of industry and policy makers a mood of compromise.  The second group notes that all it took to hack the mood of Boris Yeltsin was an open bottle of vodka.  The latter strategy has, of course, been used for millennia.

Hacking a the mood of an entire room full of people at once is an interesting twist, though.  What happens when someone modifies airborne rhinoviruses to express neuroactive peptides?  (See my post on iGEM 2008: "Surprise -- the Future is Here Already".)  Science fiction gave us the answer long ago.  Isaac Asimov had his characters wearing anti-viral filters in their nostrils even in his early stories.  Seems like filters with sufficiently small pores might make it hard to breathe.  And what happens if you sneeze?  "Ouch!" or "Ewww", I imagine.

Anyway, how would we even know that mood hacking was occurring?  Aside from simply noting changes in behavior, or getting, um, wind of the threat via human intelligence, we would have to measure any chemical or biological weapon directly.  But before pulling out the Tricorder and identifying a threat, we would first have to be constantly monitoring our environment in order to get a baseline of environmental signals.  So, we have already struck out.  No such monitoring is really happening.  We are just cherry picking a few things that are easy to see.  Oh, and still no Tricorder.

If the mood altering mechanism was delivered via a virus, we would have to not just monitor the number of viruses of any given species in the air, but also be sequencing all of them, all the time.  Again, we are striking out.

I have a hard time imagining that viral mood hacking threats are going to show up any time soon, but then we have no means of knowing either way.  Perhaps such things are already about.  How can you be sure you aren't part of "The Giving Plague"?

I have a short essay in a special edition of the McKinsey Quarterly, What Matters.  My piece is waaaay back at the end of the printed volume, and all the preceding articles are well worth a look.  Other essayists include Steven Chu, Hal Varian, Nicholas Stern, Kim Stanley Robinson, Yochai Benkler, Vinod Khosla, Arianna Huffington, Joseph Nye, and many more.  Good company.

Here is the link: "The New Biofactories", Robert Carlson, What Matters, McKinsey & Company, 2009.

I'm giving a short talk to the University of Washington iGEM interest group tonight based on my experience watching the competition from the beginning and as a judge for the last couple of years.

The judges are given a long list of criteria for the various medals and awards.  The list has grown longer and more involved -- if the trend holds next year I expect it to be even more complicated.  There are many more teams than judges, so each of us sees only a small fraction of the teams in person on the first day of the Jamboree.  The only way we can keep things fair (and keep the teams straight in our heads) is to follow the judging criteria very closely.  We have a checklist.

It is important to remember in what follows that my academic training is in experimental physics, and I spend most of my time today trying to build stuff out of DNA.  I don't have anything against elegant and cool models; I simply groove more on elegant and cool atoms.  I speak only for myself and not for any other of the judges or organizers.

Here is what I plan to say this evening:

1. You need to make easy for the judges to understand your objective and your design.
2. Web pages can be too cool.  A rough rule of thumb: the cooler the web page is, the harder it is to understand.  A cool web page may be full of information, but as a judge it is the baud rate I care about.
3. Fun is good.  Demonstrating actual learning is better.  Data trumps everything.
4. In my experience, the more equations in your model, the less likely you will produce experimental data.  I find complexity as distracting in my own work as I do when I have something like 15 minutes to figure out the theoretical details of an iGEM project.  Keep it simple!
5. Find a mentor to help tailor your story to your customers, namely the judges.  This past year the judges were a mixture of academics and industry types -- biologists, engineers, computer scientists, physicists; theorists, experimentalists, hackers.  All probably have PhDs in something or other, which means we are used to rapidly parsing stories that are packaged more like papers in Science and Nature than like facespace/mybook/twitterwikirama/whatever.  Those things may be the future of science for all I know, but your customers (the judges) don't play that game -- we are fogeys as far as you are concerned.  You have to market to us.
6. Follow the directions!  Follow the checklist.  Make sure your DNA is to spec (e.g. meets the Biobrick(TM) standards).  Make sure it is in the Registry.  Get everything in on time.  Sometimes the organizers and judges screw up this part -- the way to resolve complaints is with reason and your own checklist.  No whinging.
7. Here is a suggestion I made to the organizers after the last competition.  Even if they don't implement it, you should.  Everyone in the competition has completed some sort of laboratory course requiring basic experimental write-ups.  Make sure your web page has a basic lab write-up, no clicking or hunting required. You will do better if the judges don't have to spend even thirty seconds trying to figure out if you have actual data and where it might be hiding on your wiki, especially if other pages are better designed and easier to read.  If I recall from my student days, those write-ups go something like this, mostly in this order: "1. Here is what we wanted to do and why.  2. Here is what we did.  3. Model.  4. Data.  5. Conclusion."  Bonus: if it didn't work, why not?  iGEM and the Biobricks Foudation both need a failure archive.
   

Good luck next year!