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September, 2009:

SF Judge Comes Down on GM Sugar Beets

Today in San Francisco a judge worried about “the potential elimination of a farmer’s choice to grow non-genetically engineered crops, or a consumer’s choice to eat non-genetically engineered food.”, ruled that the USDA broke the law when it approved herbicide resistant sugar beets for sale.

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Sugar beet. Ironically an organic one Photo: medesrocha, Flickr.

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Very Irritated

I noticed a major drop off in traffic back in July (on the order of 50%). Since that coincided with a substantial drop off in my updates over the summer I didn’t think much of it. Recently I got suspicious and checked out the top keywords on my site using google webmaster tools. Corn doesn’t even show up until #13, all the spots above it were taken up with drug names and even less savory words.

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Updating the Blogroll

I’ve recently started following two more plant/ag blogs* that are both so interesting I want to share them with all of you:

First of all they have exciting perspectives and information. The author of Plants are the Strangest People has personal experience with literally hundreds of plant species.** While I can talk about the principles behind plant breeding and crop improvement***, writer of The Scientist Gardener works in the field and is a fountain of interesting posts.

That would be enough on its own, but to be honest I’ll also disclose that the authors are based in regions I’m unashamedly biased towards (central Iowa and central New York respectively) and were kind enough to link here (I discovered their blogs when their web addresses started popping up in the sources of my incoming traffic).

*The highly observant will have noticed links to these blogs were added to the blogroll (which I’ve moved farther up as it was previously getting lost in the clutter of the right-hand column) yesterday evening.
**Sadly the only species I’ve grown for my own research are Corn, Sorghum, and Arabidopsis. Beyond that I can draw on the knowledge I gained though social connections. For example: once dating a girl who worked on Soybeans, working next to a lab that studied Tomatoes, having a TA who worked in a Wheat genomics, or interviewing in a Carrot and Garlic breeding lab. A serious drawback of molecular biology (and even more so now that I’m moving into comparative genomics) is on a day to day basis we’re exposed to only a tiny fraction of the great diversity within the world of plants.
***I can’t be grateful enough that I was able to fit “Genetic Improvement of Crop Plants” a course in the plant breeding department into my schedule as an undergrad. That course, along with “Molecular Biology and Genetic Engineering of Plants” have proven incredibly useful when I get into the more applied side of plant biology. (On the more basic research side I’m  indebted to “Plant Development” and “Advanced Plant Genetics”)

Cool Jobs Graphic

Found this cool site that shows the breakdown of job titles over the past 150 years in the US. If you type in “farm” you can see that the percentage of the population employed as farmers and farm laborers has dropped from ~50% of the population when the Civil War was being fought to ~2% today although it looks like the decline has substantially slowed since the 1970s.

If you type in scientist you can see the post WWII explosion in the scientific professions to the point where today one in every three hundred (one third of one percent) working americans can claim that title. Which really is a major increase.

Matt pointed out in my post on Agricultural R&D that one of the reasons investment in research has dropped some much is that farming as an occupation has shrunk, giving farmers less electoral clout to advocate for publicly funded plant breeding, studies of plant pathogens and university outreach.

California’s Unemployment Rate Hit 12.2% in August

With all the usual caveats about unemployment stats undercounting the true number of jobless. Almost one out of every eight people. And it’s still going up.

GM traits in Mexican Landraces

Yesterday we had an ESPM (Environmental Science and Policy Management) guy crash PMB beer hour. It was an interesting experience, but one thing really worried me. In a discussion of “so what do you guys do in PMB?” the crasher mentioned “well I know about the people studying corn.” I’m sure you can just picture my face lighting up as I get ready to talk about the fascinating research of people like Sarah Hake and Damon Lisch, or worst case, to defend studying corn a person who might be radically anti-GMO. But of course I couldn’t be that lucky. When he said studying corn, he didn’t mean plant development, or transposons, or paramutation, or any of the other cool things corn can teach us. He meant the research of Ignacio Chapela.

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Investing in Agricultural R&D

I managed to miss it when it was initially published, but Science published an short article a couple of weeks ago titled Agricultural Research, Productivity and Food Prices in the Long Run that’s definitely worth reading.

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Norman Borlaug

Norman Borlaug passed away yesterday. I was never lucky enough to meet him, but I know my father had the chance a few times at the World Food Prize which is given away in Des Moines every year. Never the less, he’s the reason I am who I am today. Because his story, even more than the stories of people like Alexander Flemming (the man who discovered penicillin), shows the good science does in the world. The internet is, I hope, full of better tributes to the man than I can to write, but if you’ve never heard of the man, or know the name but can’t place why you do, I thought I’d give the very appreviated version of the life of the only man in the world to earn the Nobel Peace Prize through agricultural achievemnet.
Norman Borlaug was born in smalltown Iowa in 1914. He went to a one room school. He learned to be a scientist at the University of Minnesota. After working for the Forest Service and DuPont, he accepted a job working in Mexico on improving wheats productivity there. Over the next two decades he developed lines of wheat that were both more disease resistant, and shorter. Shorter in this case meant less trouble with being blown over by wind, more branching (good since each branch ended in a head of wheat), and a greater precentage of the total energy of the plant going into seed production. Although it’s not as pronounced as in wheat, you can see the same trend in corn breeding. Look at a picture of a cornfield fron the 1920, and you can see it’s much taller (and less densely planted) than corn grown today.
Wheat yields per acre in Mexico came close to doubling between 1960 and 1965. Which is all the more impressive when you remember I was just talking a couple of days ago about how much harder it has been to increase wheats productivity than that of maize. In 1963 Mexico, a country that had been importing 60% of its wheat less than two decades before, became a net exporter of wheat.
http://www.dallasobserver.com/2002-12-05/news/green-giant/4
Bringing those same benefits to Indian and Pakistan, while the two countries were at war over Kashmir no less, is a story in its own right. Read from the second page of this article if you don’t believe me. But in five years from 1965-1970** wheat production in both countries almost doubled, not from chopping down forests or displacing other crops, but by producing more on the same acres.
It was this work, feeding the hungry not for a day, but by giving them the tools to feeds themselves for a lifetime, for which Norman Borlaug recieved the Nobel peace prize in 1970. Today the population of India is more than twice what it was in the early 1960s. Through the work of Norman Borlaug, the scientists around the world who came after him and continue to breed crops from rice to wheat to cassava, and the backbraking work of uncounted farmers, India feeds those hundreds of millions of people.
There are hundreds of millions of people alive today because of Norman Borlaug personally, and billions alive because of the work inspired by the proof he showed up all that fighting starvation was not a battle we were predestined to lose. He was a great man and he will be terribly missed.

Norman Borlaug passed away yesterday. I was never lucky enough to meet him, but I know my father had the chance a few times at the World Food Prize which is given away in Des Moines every year. Never the less, he’s the reason I am who I am today. Because his story, even more than the stories of people like Alexander Flemming (the man who discovered penicillin), shows the good science does in the world. The internet is, I hope, full of better tributes to the man than I can to write, but if you’ve never heard of the man, or know the name but can’t place why you do, I thought I’d give the very appreviated version of the life of the only man in the world to earn the Nobel Peace Prize through agricultural achievement.

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The Family of Wheat

The latter is a result of wheat’s amazing family tree. The wheat that produced the bread for that sandwich you had for lunch can trace its ancestry back to two grasses growing in the middle east thousands of years ago and a third growing somewhere along the shores of the mediterranean. The wheat first domesticated in the middle east was already a combination of two native grasses, containing the complete genomes of both. While humans have 23 chromosomes and two copies of each, this wheat had only seven chromosomes and four copies of each (two from each of the grasses that had given rise to it).  This wheat was already a good crop, its seed was spread from tribe to tribe and village to village. And it was somewhere along that journey that wheat encountered the third grass, and one of the offspring generated when pollen from that wild grass landed on wheat growing in some farmers field, instead of being a sterile hybrid as usually happens when dissimilar species mate, was able to reproduce and had a better gluten, the combination of proteins that gives wheat the elasticity to hold together as dough, which lead to better bread and soon bread wheats swept across the continents in many places replacing the older wheats that had been grown before.*****
The problem from a genomicist is that each bread wheat cell how contains 42 chromosomes. Remember each of the grass species that gave rise to wheats had seven chromosomes, each with two copies for 14 chromosomes per cell. Seven chromosomes each from of its parents (for 21) and two copies of each brings us to 42. Which is still four less than human cells, so where’s the problem? The different from the human genome is that each of set of seven chromosomes makes up a closely related yet distinct genome. So as bits of DNA are sequenced it is hard to know whether the pieces their overlap are really from the same part of the genome, or instead related sequences from one of wheats other parents (and located on an entirely separate chromosome). Imagine a giant heap of puzzle pieces from three puzzles each made with identically shaped pieces and make very similar pictures although you don’t know what any of the pictures will look like. That’s what trying to sequence the wheat genome will be like

As promised the second part of my giant entry on wheat. Yesterday I talked about yield and breeding techniques. Today I’m going to talk about where wheat can from, and why, if you ever happen to meet a wheat genomicist, you know you’re in the presence of someone incredibly hard core.

The wheat that produced the bread for that sandwich you had for lunch can trace its ancestry back to two grasses growing in the middle east thousands of years ago and a third growing somewhere along the shores of the mediterranean. The wheat first domesticated in the middle east was already the offspring of two native grasses, containing the complete genomes of both. While humans have 23 chromosomes and two copies of each, this wheat had only seven chromosomes and four copies of each (two from each of the grasses that had given rise to it).  This wheat was already a good crop, its seed was spread from tribe to tribe and village to village. And it was somewhere along that journey that wheat encountered the third grass, and one of the offspring generated when pollen from that wild grass landed on wheat growing in some farmers field, instead of being a sterile hybrid as usually happens when dissimilar species mate, was able to reproduce and had a better gluten, the combination of proteins that gives wheat the elasticity to hold together as dough, which lead to better bread and soon bread wheats swept across the continents in many places replacing the older wheats that had been grown before.*

The problem from a genomicist is that each bread wheat cell how contains 42 chromosomes. Remember each of the grass species that gave rise to wheats had seven chromosomes, each with two copies for 14 chromosomes per cell. Seven chromosomes each from of its parents (for 21) and two copies of each brings us to 42. Which is still four less than human cells, so where’s the problem? The different from the human genome is that each of set of seven chromosomes makes up a closely related yet distinct genome. So as bits of DNA are sequenced it is hard to know whether the pieces their overlap are really from the same part of the genome, or instead related sequences from one of wheats other parents (and located on an entirely separate chromosome). Imagine a giant heap of puzzle pieces from three puzzles each made with identically shaped pieces and make very similar pictures although you don’t know what any of the pictures will look like. That’s what trying to sequence the wheat genome will be like.

*Durum wheat, which is still grown for pasta, is still a tetraploid wheat without the additional chromosomes from the third parent of bread wheats. I guess the gluten of bread wheat doesn’t hold up as well in pasta, the same trait that makes it excellent for breads.

Why Wheat Is Losing Out in the Era of Modern Crop Breeding

Wheat occupies a special place in the mind of anyone who grew up surrounded by western cuisine. Wheat is the source of bread, and bread is intrinsic to our concept of food. In the same way rice, in all it’s many gorgeous and delicious incarnations, is central the the idea of food in south indian and east asian cultures. Or corn tortillas in mexico. Human civilization was built upon of the unrivaled productivity of these three grains. And when modern medicine increased the rate of population growth, it was primarily these three grains (and wheat first of all) that we turned to in the green revolution to fill the gap between what current farming methods could produce and what was needed to save our fellow human beings from starvation.
In the US the technologies that made the green revolution possible, were available earlier. Around the end of world war two, most of the infrastructure that had been built up to fight the war could be turned over to peaceful uses, one of which was man-made nitrogen fertilizer. Nitrogen, for centuries on of the major limits of yield was now available in quantities that couldn’t have even been dreamt about at the turn of the century. At the same time, hybrid corn seed* began to be available in substantial quantities from, among other sources, Pioneer Hi-bred.
Wheat received the benefits of increased fertilizer, but the architecture of wheat flowers, with male and female parts combined in a single flower makes creating hybrids difficult** and as far as I know even today not cost effective. So wheat yields increased but through no fault of its own as a food crop, not to the same extent as corn. Rice was in a similar predicament, reaping the benefits of increased fertilizer and greater attention to breeding, but not the huge benefits of hybrid vigor.***
And how it looks like wheat may once again miss out on new advances in the form of genetic engineering. GM maize was one of the first crops brought to market and as been an agricultural (if not public relations) success. I’m not sure if GM rice is on the market or not, but I do know many lines are in development from golden rice that addresses the vitamin A deficiencies found in people dependent on rice for almost all their calories****, to rice that can be irrigated with brackish (salty) water where fresh water is scarce, to flood resistant rice that can thrive what fresh water is TOO abundant.
I know of no one planning to release GM wheat and even wheat genomics is far behind the rice and maize communities.
The latter is a result of wheats amazing family tree. The wheat that produced the breed for that sandwich you had for lunch, can trace it’s ancestry back to two grasses growing in the mediterranean thousands of years ago and a third growing somewhere along the shores of the mediterranean. The wheat first domesticated in the middle east was already a combination of two native grasses, containing the complete genomes of both. While humans has 23 chromosomes and two copies of each, this wheat had only seven chromosomes and four copies of each (two from each of the grasses that had given rise to it).  This wheat was already a good crop it’s seed was spread from tribe to tribe and village to village. And it was somewhere along that journey that wheat encountered the third grass, and one of the offspring generated when pollen from that wild grass landed on wheat growing in some farmers field, instead of being a sterile hybrid as usually happens when dissimilar species mate, was able to reproduce and had a better gluten, the combination of proteins that gives wheat the elasticity to hold together as dough, which lead to better bread and soon bread wheats swept across the continents in many places replacing the older wheats that had been grown before.*****
The problem from a genomicist is that each bread wheat cell how contains 42 chromosomes. Remember each of the grass species that gave rise to wheats had seven chromosomes, each with two copies for 14 chromosomes per cell. Seven chromosomes each from of its parents (for 21) and two copies of each brings us to 42. Which is still four less than human cells, so where’s the problem? The different from the human genome is that each of set of seven chromosomes makes up a closely related yet distinct genome. So as bits of DNA are sequenced it is hard to know whether the pieces their overlap are really from the same part of the genome, or instead related sequences from one of wheats other parents (and located on an entirely separate chromosome). Imagine a giant heap of puzzle pieces from three puzzles each made with identically shaped pieces and make very similar pictures although you don’t know what any of the pictures will look like. That’s what trying to sequence the wheat genome would be like.
But a complicated (and awesome) genome isn’t the only thing holding back wheat research. After all GM maize has been on the market for more than a decade and the genome hasn’t been available until recently and still hasn’t been officially published. The other major barrier is a side effect of wheat’s success and cultural status.
Corn is essential to feeding Americans (and Europeans) every day, but we don’t see it as most of it is camouflaged in cornfed beef and pork, and hidden in the ingredient lists of processed foods. Rice feeds people directly, but far to many of the people who depend on it are more worried about whether they’ll have enough to feed themselves and their children than the techniques used the harvests don’t fail, and yields increase. Wheat on the other hand mostly eaten in recognizable forms like bread and pasta and much of it is consumed by people who are a generation or more removed from the sort of food insecurity that still plagues hundreds of millions around the globe. These are people, like myself, who can say, “this new technology feels wrong” because the difference for them is a few more quarters for a loaf of bread, not whether they have to spend the money that could have gone to sending one of their children to school on food, or whether they can feed all their children at all.
And that’s the reason no one is investing in biotech wheat. Saving a little money on production, or even reducing the use of the most toxic pesticides and/or reducing topsoil loss by being able to switch to no-till farming, hasn’t been worth the risk to farmers that their harvest will become worthless if consumers refuse to purchase GM bread. Without the demand from farmers, seed companies won’t invest the resources, and even with the demand, they’d weigh the profit of selling the seed against the risk of stirring up more opposition among consumers. Monsanto really doesn’t need any more negative publicity.
*For a summary of what hybrid seed is and its benefits check here
**To make a hybrid you have to mate two dissimilar parents. To do that with plants, you often have to prevent the plants from mating with themselves. This is a simple process for corn since the female flowers (the ears) are physically separate from the male flowers (the tassel). All thats required to to bus a bunch of high school kids willing to work for minimum wage out to a cornfield, and have them walk down the rows pulling the tops off of the “female” parent. After the females are pollinated by the “male” parent, the male plants (which still have both male and female flowers) are chopped down to allow more light to reach the female plants and at harvest, and the seeds are hybrid since their female parent must be the plant they’re growing on, and their male parent can only be corn plants that kept their tops (and tassels). Now imagine how much work it would be to go through a field of, say tomatoes, with a magnifying glass and a pair of tweezers removing only the male parts of each flower and leaving it otherwise intact.
***I’ve heard there’s actually been some success recently with producing hybrid rice using CMS. Cytoplasmic male sterility is a mutation carried in one of the organelle genomes (the small genomes of the chloroplast and mitocondria) which keeps plants from producing pollen (plant sperm). Because the cytoplasm of an embryo (whether cucumber or human) comes from only the mother, CMS traits are passed from a mother to all offspring. So you have a female inbred that’s male sterile and when you grow it with a normal you know all the seeds on the female plants must be hybrid since the only pollen avaliable to fertilize them was from the other inbred line. It’s even more complicated than my confused explanantion makes it sound, but it’s a lot better than hiring people to go out their with magnifying glasses and tweezers.
****We don’t have to worry about that particular problem with corn since the vast majority of corn grown in the US carries a gene which produced carrotinoids (vitamin A precoursors) in the kernals. Before plant breeders started selecting for that trait, most corn we grew was white. Of course if you go even further back, corn looked all sorts of different ways.
*****Durum wheat which is still used for making pasta and for some traditional breads in the middleeast survived competition from bread wheats and is one of the few remaining agriculturally significant tetraploid wheats.

Wheat occupies a special place in the mind of anyone who grew up surrounded by western cuisine. Wheat is the source of bread, and bread is intrinsic to our concept of food. In the same way rice, in all it’s many gorgeous and delicious incarnations, is central the the idea of food in south indian and east asian cultures. Or corn tortillas in mexico. Human civilization was built upon of the unrivaled productivity of these three grains. And when modern medicine increased the rate of population growth, it was primarily these three grains (and wheat first of all) that we turned to in the green revolution to fill the gap between what current farming methods could produce and what was needed to save our fellow human beings from starvation. Yet wheat is falling behind the other members of the big three grains.

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