James and the Giant Corn Genetics: Studying the Source Code of Nature

December 3, 2009

Make Sure Your Voice is Heard

Filed under: agriculture,Campus Life,Feeding the world,Politics — James @ 9:51 pm

Another positive side effect of extending my stay in Iowa for another week (besides having the chance to work from a room with a view), was getting the chance to see the Pamela Ronald and Raoul Adamchak give a presentation on the same themes are their book “Tomorrow’s Table” here on campus (I’ve reviewed the book itself).

Pamela Ronald is actually going to be talking in Berkeley late next month, but, in addition to a sneak peak of the presentation (which was really good) listening the the question session following their talk was a great chance to resample the perspective of the other major group involved in the debate on genetic engineering (besides anti-gmo activists, corporate public relations people, and plant scientists like me), farmers and agronomists.

What Pamela and Raoul advocate, distilled down to a single phrase, is agriculture utilizing “the best technology and the best practices.” The best technology is pretty clearly going to incorporate at least some genetically engineered traits, but the best farming practices will definitely incorporate approaches from organic agriculture. (more…)

November 30, 2009

State Dinners

Filed under: food,Politics — Tags: , , , , — James @ 8:55 am

Anastasia has started an interesting discussion over at Biofortified about the food served at the Obamas’ first state dinner, a reception for the visiting Prime Minister of India Manmohan Singh.*

The dinner was quite light on meat** and included both traditional American and Indian foods. As I said last night on the twitter feed: Anyone who serves naan and cornbread in the same meal has my approval.

*Prime Minster Singh comes from the Indian National Congress which formed a coalition government with several other Indian parties rule the country. Indian party politics are very complex, though in some ways it could be argued a complex multiparty system is more responsive to the wishes of voters than the two party system we have here in the US (I’m waiting for a program to run and have too much time to think).

**The reporter for the nytimes seems to have lumped prawns (a crustacean similar to shrimp, although I always associate them with the crayfish I had to dissect in intro bio) with the vegetarian parts of the menu…

November 19, 2009

This is Why It’s Important to Know What bt Stands For

Filed under: Feeding the world,Politics — Tags: , , , , , — James @ 7:23 am

We’ve been hearing more about India in the news lately. Along with the decision about whether or not to approve bt eggplants (brinjal), India is also debating a set of new biotechnology intellectual property laws. As I’ve said in the past India currently doesn’t recognize genetic patents, so anybody can breed transgenes into their own seeds and sell them. Of course the only legalized GE crop in India right now is cotton but as others are legalized, the same situation would apply.

I’ll admit I disagree with this quote:

Clinton said she favoured a strong intellectual property or patent regime (IPR) to safeguard the ownership of agricultural research, as that would be in ‘everyone’s interest’.

India is faced with the question of how best to balance protection for creators, to encourage biotech research, and the rights of farmers, to make sure they get the most possible benefit from that research. It is important to strike the right balance between the two, not just cater to the desires of one side of the other. It’s the same issue faced by every country when it comes to regulating everything from pharmaceutical research to the music industry.

And I have faith India will find the right balance. After all we’re talking about a country where cheap pirate copies of movies are available cheaply and easily on every street corner sometimes before movies even make it into theaters, yet Bollywood (the Indian film industry based in Mumbai) is quite profitable, turns out twice as many films as Hollywood, and is probably the only other national film industry, other than America’s, recognized around the world.*

So given all that could the people who write about the issue please PLEASE bother to look up what bt stands for? Case in point:

First, the Indian government has yet to greenlight the commercialisation of Bt brinjal — crucial for the future of these ‘Bt brand’ companies — even after a thumbs up from the Genetic Engineering Approval Committee (GEAC). … the MNCs who produce ‘Bt’ seeds, as genetically modified or GM crops have come to be popularly known (patents would ensure that no one else would be allowed to produce or sell these seeds).

*Off the top of my head I’d recommend Krrish and Salaam/Namaste as examples of entertaining movies Bollywood has put out recently, and Gol Maal as a hilarious one from several decades ago.

November 6, 2009

More on why Science Isn’t a Perfect Fit with the Right or Left

Filed under: Politics — Tags: , , — James @ 2:40 am

In a follow up to my post yesterday afternoon.

The opponents of science are those who put ideology over empirical facts, putting how they want the world work over how data shows the world actual does. On one side the extreme left is fine with the observational side of science telling us everything that’s wrong with the world, but when scientists try to come up with ways we could try to solve those problems, we get shouted down. Since I’ve written plenty about genetic engineering, consider how Steve Levitt, the author of Freakonomics*, was received when he simply suggested we should evaluate geo-engineering techniques as one of the ways to mitigate climate change.

The Daily Show With Jon Stewart Mon – Thurs 11p / 10c
Steven Levitt
Daily Show
Full Episodes
Political Humor Health Care Crisis

Or watch the interview of Bill Frist (a former Republican Senator) with Bill Maher, and cringe at the discussion of vaccines.

On the other hand the extreme right is mostly ok of with all the goodies scientific reseach produces: modern “Western” medicine (including vaccines and antibiotics), genetically engineered crops, computers, and microwaves. But when it comes to believing anything science tells us from “hey, the planet is getting warmer” to evolution (without which, let me tell you, comparative genomics would be a very boring field of study, an I’m not bored, I’m fascinated!), to not so much.

I am exasperated with the world. Try back tomorrow.

*Freakonomics is a fascinating read. I haven’t had the chance to read Superfreakonomics, which is what apparently generated this controversy.

November 5, 2009

Bruce Sterling and Kim Stanley Robinson on Climate Change

Filed under: biology,Link Posts,Politics — Tags: , , — James @ 4:44 pm

This post was followed up by More on Why Science Isn’t a Perfect Fit with the Left or the Right

Bruce Sterling writes science fiction cyber-punk. Kim Stanley Robinson writes enormous science fiction trilogies. One on terraforming mars (Red Mars, Green Mars, and Blue Mars) that I read when I was younger and space mad. He’s also put out a more recent trilogy (40 Signs of Rain, 50 Degrees Below, and 60 Days and Counting) which I haven’t had a chance to read yet, but I’m told is quite good, and that at least the first book presents an accurate and depressing picture of the process for funding NSF grant proposals. Not something I want to think about I’m ~24 hours from submitting my own.

Kim Stanley Robinson recently did an interview for his new book Galileo’s Dream (you can find the whole text here). It’s a great read, although there’s plenty of stuff I disagree with.

One thing happening is that the Republican Party in the USA has decided to fight the idea of climate change (polls and studies show the shift over the first decade of this century, in terms of the leadership turning against it and the rank and file following), which is like the Catholic Church denying the Earth went around the sun in Galileo’s time; a big mistake they are going to crawl away from later and pretend never happened. And here the damage could be worse, because we need to act now.

What’s been set up and is playing out now is a huge world historical battle between science and capitalism. Science is insisting more emphatically every day that this is a real and present danger. Capitalism is saying it isn’t, because if it were true it would mean more government control of economies, more social justice (as a climate stabilization technique) and so on. These are the two big players in our civilization, so I say, be aware, watch the heavyweights go at it, and back science every chance you get. I speak to all fellow leftists around the world: science is now a leftism, and thank God; but capitalism is very, very strong. So it’s a dangerous moment. People who like their history dramatic and non-utopian should be pleased.

Reading the answer to this question made me feel a little weird about Mr. Robinson’s claiming of science for one side of the political debate (and also not a big fan science vs. capitalism, the climate change debate is more about the split between short and long term planning). Science isn’t a side in the political process, it’s a set of knowledge and tools that are openly available to all and political movements are free to either accept them, or, as sadly seems more common, toss them aside. Which is why Bruce Sterling’s response cracked me up: (more…)

October 23, 2009

Putting Prejudice over Science

Filed under: agriculture,Link Posts,Politics — Tags: , , , — James @ 3:56 pm

I read this when it came out, but it was before I’d restarted the site full time, and Pamela Ronald restarted the discussion over on scienceblogs today. Back in May the USDA posted a report on their website about how allowing genetically engineered crops to be certified as organic would have positive environmental effects.

Needless to say the organic movement was not pleased, and the report has since been pulled from the website. Now I previously celebrated the idea that the Obama administration was going to let organic and biotech go head to head and take the best parts of both. I’m confident in the benefits of genetic engineering when people judge the technology based on the data instead of preconceived opinions.

Making reports disappear because they step on the toes of well connected interest groups is not letting the data speak for itself.

h/t’s to Tomorrows Table and Biofortified.

And hey, if you’re willing to spend 10 minutes you can register and vote for Biofortified in the Ashoka Changemakers Contest. There’s a good chance you’ll help win $1500 to support a website fighting the good fight to correct the misinformation about genetic engineering, but even more importantly from my perspective, winning this contest means the guy on the left (yes he’s wearing a corn cob patterned t-shirt) will get a chance to meet with Michael Pollen. There’s also a stuffed corn cob with glasses in the picture.

October 7, 2009

Vilsack in the News Again

Filed under: agriculture,Politics — James @ 10:02 pm

This time for being the force behind a program to provide the equipment for farmers markets to accept food stamps, something that everyone should agree is a good thing. People have access to cheaper*, healthier food, farmers take home more money themselves. This comes on top of the increases in the money provided for the food stamps program (which was both long overdue and, along with increasing unemployment benefits, has been shown as one of the most efficient ways to stimulate the economy) as well as experiments at some farmers markets to redeem food stamps at twice face value. Keeping in mind actual stamps were replaced by EBT cards years ago.

Up until now the problem has been that the “food stamps” program switched to an electronic swipe card system some years ago which require a swipe reader. No problem at a grocery store where a single checkout lane can easily do five-figures of sales in a single day, but purchasing the readers (which also require internet access to function) is a major finacial burden for individual farmers, who, if they’re doing well, are making one or two thousand dollars one day each week at farmers markets. (more…)

September 25, 2009

What is the NIFA?

Filed under: agriculture,Politics — James @ 5:14 pm
More than a year ago, in May of 2008, Congress passed the Food, Conservation and Energy act of 2008. It was weird going back to read up on the coverage of the bill and reading how President Bush objected to X or proposed Y. His presidency already seems so distant. One of the things this farm bill did was create the National Institute for Food and Agriculture by reshuffling some departments withing the USDA (United States department of Agriculture which manages everything from the National Forest Service to subsidized school lunches) and providing more money for the newly created institute to disburse in the form of competitive research grants. The USDA supports a lot of cool research internally through the Agricultural Research Service* but they’ve historically had much less money to fund grants to outside researchers than the National Science Foundation or the National Institutes of Health. (Anyone know how Department of Energy funding stacks up?)
It’s not yet clear how much money the NIFA will have to fund competitive grants (the horse trading in congress hasn’t finished yet), but we can hopefully expect the new institute to recieve at least $250 million a year for the purpose, a substantial increase from pre-NIFA funding of $120-$180 million. Although to put it in perspective, $250 million is still only one-hundred of the funding NIH awards through competitive grant processes. In addition to this general grant money that can be spent on plant breeding, biotechnology and everything in between, there will be a second pot of money devoted to sustainable ag and specialty crops (fruits and vegetables) but, as with the general fund, the exact number seems to still be in flux.
As I was just talking about here, we definitely need to be investing more in agriculture and the NIFA is a step in the right direction. If it were up to me I’d have thrown a couple of billion at the problem. I think there are a lot of low hanging fruit in the public agricultural sector after decades of underfunding. Regardless the NIFA is a good thing.™ And I’m even more confident of that fact now that I found out President Obama has picked Roger Beachy to be the first head of the new agency.
Roger Beachy has had a broad ranging career working in plant pathology (during which he was involved in developing the technology that would be used to create the ring spot virus resistant papayas that prevented the collapse of papaya farming in Hawaii). His CV is 18 pages long in 10 pt font. He has the, unfortunately rare, combination of scientific talent, administrative skills, and the personal gravitas to interact with politicians and super rich donors. And on top of that, he’s spent his entire life working the in the public and non-profit sectors (places like Cornell, Wash U, the Scripps Institute, and most recently president of the Danforth Plant Science Center). Can you imagine the screaming if Obama had picked someone who’d worked in industry to head up the NIFA? The fact that after picking my former governor to run the whole USDA, President Obama picked a guy I’ve actually shaken hands with the run NIFA is just a bonus**
*Including people like Ed Buckler who created the maize nested association mapping populations, which are just plain awesome (and deserve their own entry), Doreen Ware, a top notch computational biologist who’s been very involved in the maize genome project, all the people at that Plant Gene Expression Center we’re lucky enough to have quite close to Berkeley. Also the author of Geneticmaize.
**If this paragraph goes on a little too long, it’s only because Roger Beachy represents the sort of person I want to be when I grow up…nevermind that being twenty-four probably already puts me solidly in the grown-up category myself.

More than a year ago, in May of 2008, Congress passed the Food, Conservation and Energy act of 2008. It was weird going back to read up on the coverage of the bill and reading how President Bush objected to X or proposed Y. His presidency already seems so distant. One of the things this farm bill did was create the National Institute for Food and Agriculture by reshuffling some departments withing the USDA (United States department of Agriculture which manages everything from the National Forest Service to subsidized school lunches) and providing more money for the newly created institute to disburse in the form of competitive research grants. (more…)

April 29, 2009

Was the Green Revolution Helpful?

Filed under: Plants,Politics — James @ 9:40 pm

This will be a post on policy. Ideally I should maintain separate blogs for policy/science and personal posts, but I have enough trouble finding the time to maintain one blog, let alone two.

Via LaVidaLocavore

“Prior to the Green Revolution, Indians were poor and starving but their agriculture was sustainable. And the U.S. gave them help – money and technical support – but it was very short-term help. The help we gave, along with the low cost chemicals and seeds their own government gave them, prevented starvation from the 1960’s to the 1990’s only to cause an epidemic of suicides later. And – knowing that – it seems to me that what we gave them in the 1960’s and 1970’s wasn’t actually help.”

I’m speechless. Fortunately typing doesn’t require the use of the voice. In 1968 the population of Indian was 523 million. In 2008 it was 1.15 billion. In the 1960s India was confronted with a stagnant food supply and a growing population. The improved crop varieties of the Green Revolution, along with investments in technology like irrigation and fertilizer staved off the specter of famine from the subcontinent for the past four decades. If Indian farmers had been no option but to continue with their “sustainable” methods of farming prior to the green revolution, India might have continued to “sustainably” produce enough food to feed half a billion people. Which means the other 600 million people living in India are alive today because of the green revolution. Only the most literal and dispassionate definition of sustainability can disregard the lives of more half a billion people. The aid the world provided to India in the 1960s and 1970s really WAS help for those six hundred million lives. Help that bought four decades for technology to advance and global population growth to slow.

I’m not saying the Green Revolution has not produced some negative side effects. The author mentions issues with salinization of farm land, and increased debt for small farmers, leading some to the tragedy of suicide. These are real concerns, and there is a lot more we could be doing to address these issues, particularly the higher stakes input intensive agriculture place on small farmers who don’t have the resources to rebound from even a single bad harvest. But to argue the Green Revolution was no help at all is comparable to arguing we should stop treating cancer patients, and that further research is harmful, because many of the therapies meant to kill the cancer cells cause negative side effects for the patient as well. 

I hope that almost everyone would agree treating cancer is preferable to allowing the disease to run its course, and is there anyone at all who would argue against further research to increase cancer survival rates while decreasing the negative side effects of treatment? Similarly the proper response to flaws of the Green Revolution should not be to dismantle the progress that has been made, but to continue the search for more effective, less costly, and yes, more sustainable technologies, crop varieties, and agricultural techniques. Always keeping in mind that we have an obligation to keep from starvation all of the many and varied people of the earth today, not simply that number of people we might consider ideal for the Earth to support.

December 10, 2008

Bad Teachers

Filed under: Electronics,Free Stuff,Politics — James @ 12:04 pm

Edit: Upon reflection it is quite possible this woman is excellent at teaching whatever it is she teaches. The more important lesson of this incident should perhaps be the importance of learning to distinguish between where one is actually an expert and one is not. This mistake can be made by anyone, including myself, when we think our knowledge in a particular field translates into knowledge of ALL fields. Just yesterday I was taken to task for my assumption that there are no fundamental differences in complexity between prairie ecosystems and woodland ones. (I’ve never had an ecology class in my life.)

Just today I wrote about building a computer to run BLAST for my whole lab essentially for free (once the lab orders a new graphics card, and I can put mine back in my computer at home, it will have cost a total of $40). There was no piracy involved, all the software running on that computer, specifically the operating system, the web server, and wwwblast, has been made available free of charge. When you can build a computer for $150, buying even the home version of windows adds 60% ($90) to the cost of your computer.

The desktop version of Ubuntu, a kind of linux, provides almost all the, non-gaming, functionality anyone expects from their home windows computer (going up against apple is another matter), doesn’t get viruses, runs fast on cheap or old hardware, and almost never crashes. For free.

I tell you this, not to evangelize about the wonders of Free and Open Source Software in general, or Linux in particular, but so you will understand the outrageousness of what follows:

“…observed one of my students with a group of other children gathered around his laptop. Upon looking at his computer, I saw he was giving a demonstration of some sort. The student was showing the ability of the laptop and handing out Linux disks. After confiscating the disks I called a confrence with the student and that is how I came to discover you and your organization. Mr. Starks, I am sure you strongly believe in what you are doing but I cannot either support your efforts or allow them to happen in my classroom. At this point, I am not sure what you are doing is legal. No software is free and spreading that misconception is harmful. These children look up to adults for guidance and discipline. I will research this as time allows and I want to assure you, if you are doing anything illegal, I will pursue charges as the law allows. Mr. Starks, I along with many others tried Linux during college and I assure you, the claims you make are grossly over-stated and hinge on falsehoods. I admire your attempts in getting computers in the hands of disadvantaged people but putting linux on these machines is holding our kids back.

This is a world where Windows runs on virtually every computer and putting on a carnival show for an operating system is not helping these children at all. I am sure if you contacted Microsoft, they would be more than happy to supply you with copies of an older verison of Windows and that way, your computers would actually be of service to those receiving them…”

Karen xxxxxxxxx
xxxxxxxxx Middle School

The recipient of this e-mail makes a remarkably calm and rational rebuttal here. I’d add only that the argument she makes about all computers running windows would apply equally to giving children apple computers as to giving them linux ones.

We have here a teacher who knows little or nothing about technology, who sees students gathered around a computer excited, not about a game or a video, but an operating system, and her first response to this display of curiosity and excitement is to chew everyone out and “confiscate the disks.”

Speaking from personal experience, running Linux for any length of time is going to spark the development of high level computer skills. Unlike the strong line between a computer programmer and a computer user in windows, Linux has a gradual transition where each new piece of knowledge proves immediately useful to user. If even one of those kids could have grown up to be a programmer or a computational biologist or an IT guy and instead ends up flipping burgers for a living, that child’s suffering is on her head.

We need more teachers in this country, but new teachers cost more money and the quality of education in this country would also be improved by getting rid of the substantial fraction of teachers who do more harm than good. I know I would have happily traded sitting in a classroom of 60 students instead of 25-30 to learn from a competent teacher, or at the least a kind-hearted one…

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