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

October 14, 2009

Potato Breeding

Unfortunately the purple potatoes aren't a Cornell Breed

Unfortunately these purple potatoes aren't one of the Cornell breeds

A lot of people may not share my enthusiasm for the potato genome, hopefully you all enjoy eating potatoes. The stereotype of potatoes is lots of boring sameness one identical to the next.* Reality, as usual, is much more complicated. Tens of thousands of cultivars can still be found in the South American regions where potatoes were first domesticated. In America, breeders are constantly working to bring in desirable traits from those (often really cool looking) breeds and even wild relatives of the potato. They face both genetic barriers (species barriers are bad enough normally, but trying to introgress genes across a tetraploidy can be a mess) and consumer acceptance ones.

This was driven home in a story at the NYtimes about Cornell potato breeders who have developed breeds which grow much better in upstate New York, but run into problems because the potatoes look and taste different than the couple of varieties of potatoes consumers and restaurants are used to (most notably Idaho grown Russet Burbanks**). Cornell Extension has been working on overcoming that barrier providing the potatoes to restaurants and, in what I think is a genius move, culinary schools throughout the region.

If you happen to visit New York farmers markets take a moment to ask sellers about the breeds of potatoes they have for sale.*** The potatoes covered in the story are Salem, Eva (both white potatoes), Lehigh, Keuka Gold (yellow breeds), Adirondack Blue and Adirondack Red (both of which are just the color you’d expect from the name.) Purple potatoes in particular just look really cool, see image above.

*There was a saying about accepting differences that I vaguely remember from a childhood TV show, something along the lines of “People aren’t the same like potatoes, and that’s a good thing because potatoes are boring.”

**The Russett Burbank was developed by a truck gardener outside of New York City called Luther Burbank in the 1800s who was initially inspired to become involved in plant breeding by Charles Darwin’s 1868 The Variation of Animals and Plants Under Domestication. He later moved to California where he became famous plant breeder and, among other things championed the practice of grafting (connecting a cutting from one plant (usually a tree) to the stem of another, which, if done properly grows the two together and the cutting will grow flower and produce fruit like it would normally) a practice at the time condemned as unnatural. <– This info from Mendel in the Kitchen by Nina Fedoroff and Nancy Brown a great resource

***In fact, whenever you’re buying directly from a farmer, if you get a chance, ask about the breed of whatever you’re buying. More often than you’d expect there’s an interesting story about why he or she is growing that particular breed and where it came from.

October 9, 2009

How viable is local food?

Filed under: agriculture,Fun With Numbers — James @ 7:21 pm

Before I begin, let me say there’s absolutely nothing wrong with supporting your local farmers through CSAs, farmers markets, or direct purchases. I’ve done similar things before and it makes sense in the same way I’d prefer to support local businesses over national chains It keeps money in the local economy and even if it didn’t, it is always more fun cheering for the home team.*

That said how viable is solely local food (usually with an arbitrary cut off of 30 or 50, or even 100 miles from its point of origin) for providing all the food for all the residents a major city? (more…)

October 8, 2009

Superweeds

Filed under: agriculture,biology — James @ 5:46 pm

I’m sure everyone reading this has heard the term ‘superweed.’ These are the terrible new creations that will, or in some cases have, been created by herbicide resistant crops. What makes them so super and terrible? They’re resistant to the same herbicide as the herbicide resistant crop they grow among. Treating crops with herbicides selects for herbicide resistance crops in the same way treating infections with antibiotics selects for antibiotic resistant bacteria. Taking antibiotic drugs kills all the bacteria susceptible to the antibiotic. That means any individual bacterium which can survive the treatment is much more likely to reproduce and thrive now that all its competitors were killed by the drug. In the same way, spraying fields with an herbicide, while good at killing off weeds, also gives a big selective advantage to any weeds that carry traits which allow them to survive the spray. Thusly are the superweeds born. Why isn’t that the end of the world? Read on the find out.

(more…)

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…)

October 2, 2009

The Real GM Tomato

Filed under: agriculture,Plants — Tags: , , — James @ 11:10 am

In my previous post I mentioned that the only people who actually knew what GM tomatoes tasted like where a few who’d lived in California in the mid-90s. That was when Calgene, a biotech start-up founded in the university town of UC-Davis, introduced a tomato that would last longer without tasting like cardboard. And the trait wasn’t the result of a gene from fish or deadly nightshade* but simply a copy of a gene already in tomatoes, reversed so it would reduce the effect of the existing copies. But how did it taste? Click read more to find out: (more…)

September 28, 2009

Making the Pie Bigger

Filed under: agriculture,food — James @ 7:38 pm

When zero sum games are played for fun they can be very entertaining (see: poker). When they’re played for survival they’re miserable (see: who do we throw off the lifeboat, which person gets this kidney, and poker  when you can’t afford to lose). All too often keeping people alive (whether with regards about health care or food production) is seen as a zero sum game. But it’s not. My favorite example is the green revolution, but But that gets into a whole separate fight about the green revolution, and takes attention away from the real point about bigger pies being better than fighting over the pieces of a small one. So I have a new example. One almost no one can find fault with:

Cooking (more…)

September 26, 2009

I spoke too soon…

Filed under: agriculture — James @ 9:45 pm

Just yesterday I said this about Roger Beachy getting appointed to head up the new National Institute of Food and Agriculture:

He’s spent his entire life working 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 ever worked in industry to head up the NIFA?

But of course it couldn’t be that easy. It turns out people like Tom Philpott are quite capable of branding Beachy as a Monsanto insider regardless.

(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…)

September 24, 2009

Herbicide Resistance

Filed under: agriculture,Plants — Tags: , , , — 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.

Spear Thisle

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

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.

(more…)

Red Skies in Sydney

Filed under: agriculture,Photo Posts — James @ 1:40 am

Australia is in the middle of one of their worst drought of recorded time. Bone dry topsoil is vulnerable to be swept away by the wind, the same thing that happened in America during the dust bowl. The windborne soil is creating enormous dust storms like this one which hit Sydney yesterday. The pictures are both gorgeous and disturbing. To me they look like something out of science fiction. Can you imagine going about your business on what you think is just a foggy morning until the sun comes over the horizon and everything turns red?

All the dust used to be topsoil. The fertility of central Australia is literally blowing away in the breeze, and for me that tips the balance solidly from gorgeous to disturbing.

« Newer Posts

Powered by WordPress