Plants « James and the Giant Corn

September 24, 2009

Herbicide Resistance

Filed under: agriculture,Plants — Tags: agriculture, genetic engineering, gmo myths, herbicide resistance — James @ 2:16 pm

Plant breeders can find natural resistance to pathogens. Some crops can be grown in regions where they have few or no natural insects attackers. But every crop with face the problem of weeds, other plants that threaten to steal light and nutrients. And the crops that sustain us will always suffer from an unfair handicap, as crop plants devote much of their energy to food production (whether that means fruits, roots, seeds, or even leaves) while weeds can devote all their energy to outcompeting their neighbors.

Since farmers as individuals and we as a species depend on growing fields of crops like like corn, eggplant or rhubarb and not weeds like kudzu, thistles or chickweed we need to protect our crops. A farmer can protect his crop physically, either sending people out with hoes to slay every plant but his own crops* or using a cultivator to turn over the soil between the rows, hopefully burying or slicing and dicing the majority of the weeds. The first costs money and is miserable for whoever does the work. The second burns extra fuel, bad from both global warming and cost perspectives, and increases soil erosion (top soil broken up by the plows of the cultivator can more easily be carried away by rainfall).

The alternative is for the farmer to defend his crop with herbicides (plant killing chemicals). The problem with this approach is to find chemicals that kill weeds but not the crop plants. Similar to the challenge of finding antibiotics which can kill the bacteria attacking a human body without killing the human her or himself, herbicide developers face the added difficulty that most weeds are much more closely related to the crops they’re competing with than bacteria and humans(which last shared a common ancestor more than a billion years ago). In many cases it is more comparable to finding a toxin that would kill mice, but not humans, at similar dose to body-weight ratios. And even when they find a suitable herbicide, it may have nasty effects on humans (and many herbicides do).

Herbicide resistant lines are can survive broad spectrum herbicides, herbicides that kill all plants, like glyphosate (Round-up when you the brand name version from Monsanto), glufosinate (Liberty) and Imidazolinone (Beyond). Without having to worry about finding chemicals naturally survivable by crop species, herbicides can be used that are far more effective at killing weeds, in addition to being less toxic to humans.** With more effective pesticides, farmers can stop using cultivation as an additional method of weed control, letting the soil remain unbroken, which reduces the loss of topsoil from erosion. The mistake I think a lot of people make is assuming all herbicides are equally bad. Given the choice I’d much rather get lost and wander into a field treated with glyphosate than a field treated with a quarter as much atrazine.

*The worst sunburn I ever got in my life came from a day spend hoeing a cornfield

**The MSDS for the active ingredient in round-up, glyphosate. Basically you shouldn’t rub it in your eyes or take a bath in it, but even then, the result would probably be irritation, not death. Extropolating from the LD50 in rats***(with apologies for nested footnotes), always a dangerous thing to do, a person of my weight would have to eat 500 grams of pure glyphosate to have an even chance of death. And that’s on top of it being classified as Group E (evidence that the chemical does NOT cause cancer)

***LD50 is a fancy way of saying how much of a toxin must be feed to a group of lab animals to kill half of them.

What herbicide resistance is, and why the trait is so valuable to farmers.

One of many enemies faced by crops, the spear thistle. Photo John Tann, Flickr

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September 23, 2009

More on Sugar Beets

Filed under: Plants — James @ 3:47 pm

Sugar beets in this country are produced by 10,000 farmers growing beets on an average of 110 acres each. These are the people who will be impacted by the ruling. NYtimes quoted the head of a sugar beet processing company saying they’ve been accepting the beets since they came on the market and it’s been “a big non-event” as far as consumer acceptance. Which makes sense considering that sugar is almost pure sucrose (which means there’s basically no protein, encoded by transgenes or otherwise in the product), and the sort of people who seem most upset about gmos arent going to be buying a lot of processed sugar (organic or otherwise).

So the people who are impacted are people living in sugar beet producing states (especially Michigan, Minnesota, North Dakota, and Idaho) who are facing the risk of exposure to more toxic herbicides from switching sugar beets back to conventional agriculture, and the ten-thousand sugar beet farmers who today don’t know if they’ll be able to purchase the herbicide resistant seed next year, and may still not be allowed to sell the crop they currently have growing, depending on what remidies Judge White decides to impose.

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September 22, 2009

SF Judge Comes Down on GM Sugar Beets

Filed under: Plants — James @ 10:09 pm

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.

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

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September 13, 2009

Norman Borlaug

Filed under: Plants — James @ 12:24 pm

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.

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September 11, 2009

The Family of Wheat

Filed under: Plants — James @ 3:03 pm

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.*

*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.

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June 17, 2009

Phylogeny of Pineapple, an further explanation of awesomeness

Filed under: Plants — James @ 9:34 pm

If you had to guess, how would you rank these species in order of how closely they’re related to to pineapple:

Orange, Papaya, Corn, Avacado, Juniper, Banana

Answer after the jump.

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June 15, 2009

Why Pineapples are awesome

Filed under: Plants — James @ 11:42 pm

Inspired by an exchange on facebook with a friend from high school who wanted to know why I was obsessed with pineapples (when obviously I’m in fact obsessed with corn), I’ve developed a list of why pineapples are awesome even though they’re no Zea mays.

Firstly and most importantly: As much as I love corn, corn is not tasty. Pineapples are tasty.
Among fruits, I’d say pineapples give me the justification for using the biggest knife.
In xkcd pineapples proudly stand in the upper left quadrant, indicating both their tastiness and difficulty of preparation making the preparation and consumption of Pineapple a worthy occupation of manly men see previous comment regarding knives.
You can’t make jello with fresh pineapple because it’s so corrosive it breaks down the gelatin and other proteins. Hence, more dangerous, and therefore more manly.
According to wikipedia the fruit of the pineapple plant is formed by the fusion of two helixes of flowers (like the double helix of DNA!).
Pineapples appear is some form in almost every episode of Psych
The phylogeny of the pineapple. This will be explained in a more detailed phylogeny post tomorrow evening.

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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.

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March 13, 2009

Maize Meeting 2009 part 1

Filed under: Plants,research stories — James @ 1:10 pm

In a lot of ways its like a reunion. Of the five people I did science for as an undergrad (this is what happens when you work in a new lab every summer) four of them are here. No to mention the grad students and post docs I’ve worked with, or took classes with, or who TAed classes I took. One of the reasons I like working in maize so much is the how connected the community is.

The rest of this entry will be a random collection of cool things I took note of on my iPhone:

*Arabidopsis genome cost 70 million dollars and took approx. 500 people seven years to complete. Today re-sequencing that genome costs 7000 dollars and takes two postdocs a week. (Note that this is re-sequencing a known genome. Having to assemble a new genome from scratch costs more because you need longer reads and takes a LOT longer.)

*The talk on developing exemplars of transposons was very cool. All sorts of complicated statistics related to defining families by relatedness, and then using that to pick the “most normal” copy for that family in the genome

*A guy presented a tool that, given a single gene, will find all the related genes in a genome. Define their gene structure, and then build a phyogenetic tree of the genes. Basically everything I had to do to make the tree in this entry, only instead of taking one grad student 2-8 hours, it takes a computer program 1-3 minutes.

*Talked to a woman who has a poster here looking at FT-like genes in maize. (That giant phylogenetic tree I made was looking at FT genes in grass species.) Great to meet a total stranger with a common research interest.

More to come later. I’m considering posting my raw notes as a text file at the end of the meeting. Between the random things I think are worth copying down and the iPhone exaserbated spelling errors, I at least, find them hillarious. I’ve beat a strategic retreat from the poster session for little while to post this update and should probably return now.

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