Read about it in:

• The Economic Times
• The Times of India
• The AP

How much difference a comma makes:

“It is my duty to adopt a cautious, precautionary, principle-based approach.” <– Sounds like a reasonable person dealing with vocal discontent with the genetically engineered eggplants. Indian Environment Minister Jairam Ramesh quoted in Times of India

“It is my duty to adopt a cautious, precautionary principle-based approach.” <– Irrational standard* that can never be met. Indian Environment Minister Jairam Ramesh quoted in AP.

I don’t know what else to say about this story. Letting facts that should be settled by science becoming matters of opinion is one of the prices we pay for democracy, a form of government that’s still a head and shoulders above anything else yet discovered by modern man. Also, I totally called it:

This would seem to be the week for vegetables I hated as a kid. Yesterday was onion, today tomato, if there’s a story about brinjal/eggplant in the next few days we’ll have hit all the big ones.

*The precautionary principle as it has been quoted to me in the past: “Activities that present an uncertain potential for significant harm should be prohibited unless the proponent of the activity shows that it presents no appreciable risk of harm.” In other words, any and every action can be considered guilty until proven innocent of all accusations levels against it, and since people can come up with new accusations a lot faster than science can disprove them, it would seem that adhering to this version of the precautionary principle would mean not doing anything. Event

Author’s note: This would seem to be the week for vegetables I hated as a kid. Yesterday was onion, today tomato, if there’s a story about brinjal/eggplant in the next few days we’ll have hit all the big ones.

Ripening tomatoes. Photo: Photos_by_Lina, fickr (click to see photo in its original context)

I was recently pointed to an early publication paper that went up on the Proceedings of the National Academy of Sciences website on Monday, where a research group at India’s National Institute of Plant Genome Research describes two genes from tomato that, when knocked down by RNAi*, result in tomatoes that can remain ripe but not spoiled for up to three times as long as tomatoes where these two genes function normally.

Their approach targets specific genes involved in breaking down certain proteins found in the cell walls of tomatoes (in fact in the cell walls of all plants). Breaking down the cell wall is a key part of ripening in fruits (which the tomato is, botanically if not culinarily). Which makes sense if you’ll think about it for a moment. One of the traits we associate with ripening is getting softer, from bananas to peaches if it’s still crunchy when you bite into it, it wasn’t ripe. What makes plants stiff and crunchy? The strength of their cell walls. Since, unlike vegetables, fruits WANT to be eaten**, as they ripen they begin to break down their cell walls to make themselves more appealing to passing animals. Unfortunately, ripening and spoiling are, in a lot of ways, the same process. If fruits aren’t eaten when they become ripe, they continue to get softer, transitioning from delicious looking -> unappetizing -> inedible -> a puddle of mush on your kitchen counter.

Preventing ripening entirely is relatively easy, and there are plenty of known mutants in tomatoes and other species that never ripen (these naturally mutant tomatoes stay green and hard no matter how long you wait). But getting part of the way to ripeness but stopping before crossing the line into spoiled is a much less tractable problem.

A spoiled tomato. A rotting tomato is visible in the bottom left, but that's the result of the growth of microorganisms which is a more complex process. Cropped version of a photo from goldberg on flickr. Click to see the original photo on flickr.

To the non-cell wall biologist like me, one of the most attention grabbing parts of this paper was figure 3A, which simply shows photos of tomatoes that have been sitting at room temperature for 10, 20, and 45 days***. At ten days all the tomatoes look fine. By twenty days, the control (normal) tomatoes are shriveled. After 45 days sitting on the scientific equivalent of a kitchen counter the control tomatoes are basically brown balls of goo, while tomatoes with either of the two genes identified in this paper knocked down show no change in appearance over the same period of time. So what are these awesome genes?

Both genes studied in this paper are glycosyl hydrolases, a kind of enzyme that breaks the chemical bond holding a sugar to either another sugar or some other molecule, like a protein. Specifically the two genes, which are normally expressed in ripening tomatoes, each break specific kinds of sugar off of a specific kinds of protein found in the cell walls of plants. Plant cell walls are mostly made of hydrocarbon polymers like cellulose and lignin, but plants also use some structural proteins (usually less than 5% of the cell wall) and it is the sugars attached to these proteins that the glycosyl hydrolases studied here act upon.

This is where it gets scientifically cool. The prolonged ripe-but-not-spoiled state of the transgenic tomatoes they produced wasn’t simply a result of preventing the structural damage caused by the break down of the bonds between cell wall structural proteins and the sugars they’re connected to. Instead, when they looked at gene expression in plants where either of these two genes had been knocked out, they found that genes involved in breaking down cellulose, lignin and pectin (the main components of the cell wall) were also less expressed. The authors speculate that the kinds of sugars/carbohydrates these two genes break free from cell wall structural proteins actually serve as a signal to the plant to increase the production of all the other proteins needed to break down cell walls and in their transgenic plants, that signal never comes, letting the tomatoes stop ripening before the process leads to spoiling.

Tomatoes at a farmers market in NYC. photo: SeenyaRita, flickr (click to see photo in its original context)

The authors themselves point out the huge potential upside to reducing spoilage in the developing world. As much as 50% of produce is lost to spoilage between harvest and diner plate in the developing world. Reducing spoilage is one of those rare almost-a-free-lunch opportunities to increase the food supply without bring more land under the plow, or increasing the inputs (in the forms of fertilizer, pesticide, and all to often back-breaking manual labor).

At this point you may be thinking, haven’t we heard this story before? There are lots of differences between these tomatoes and the Flavr Savr tomato produced by Calgene in the 90s. Scientifically they come at the problem from very different angles, but rather than get into that let me point out two crucial practical differences:

1. The authors present data that the tomatoes with knocked down expression of either of these two genes are twice as firm as normal tomatoes of comparable ripeness. An important trait for transporting ripe tomatoes over any significant distance as illustrated in this segment of First Fruit talking about the Flavr Savr tomatoes of the 1990s:

The shipping test out of Mexico, however, proved to be yet another disaster. It was designed to test, not only whether the Flavr Savr gene would enable vine-ripened fruit to survive 2000 miles in a truck … The test results were clear before the vehicle came to a complete stop. Tomato puree seeped from the truck’s back end.

2. If these research leads to a commercializable fruit, it will likely be grown first in India, where, as described above, spoilage of produce is a major issue. In the United States, the Flavr Savr tomato had to go up against an existing system built on tomatoes that, without any genetic engineering, never ripen on their own, described in this way by MAT_kinase of TheScientistGardener:

Fresh market tomatoes, in nor cal, are all picked green and gassed with ethylene to force ripening (imperfectly). In the midatlantic, virtually all tomatoes have a natural gene mutation that prevents them from ever ripening completely in the first place. Either way, you end up with an inexpensive, pretty, red tomato that’s often hard and white on the inside. Heirloom varieties taste great, but are very susceptible to pests, have to be hand picked and turn to goo shortly after ripening.

When Pamela Ronald of Tomorrow’s Table talks about the development of transgenic crops, she points out that by 2015, it is projected that more than half of transgenic crop varieties will be produced by the national research labs of developing countries like India, China, and Brazil for they own farmers. If this paper is a sample of the sort of research such labs produce, 2015 should be a truly fascinating year for agriculture.

I shouldn’t have to say this, but there are currently no genetically engineered tomatoes on the market. For a short time in the 1990s Calgene sold the Flavr Savr tomato in California grocery stores, but they weren’t able make a profit doing so, so they stopped. The poor taste of most tomatoes for sale in the grocery store today is purely the result of conventional breeding (my post on the subject and Mat_kinase’s)

Meli, V., Ghosh, S., Prabha, T., Chakraborty, N., Chakraborty, S., & Datta, A. (2010). Enhancement of fruit shelf life by suppressing N-glycan processing enzymes Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0909329107

-The gene knocked down in the Flavr Savr tomato was Polygalacturonase.

-The two glycosyl hydrolase genes studied in this paper are alpha-mannosidase and beta-D-N-acetylhexosaminidase.

*Using RNAi means inserting a backwards version of part of a gene into a plant under a strong promoter (so the plant makes lots of RNA copies of the backwards bit.) Those backwards copies will bind to the RNA transcript of the actual gene, creating double stranded RNA. One of the main times a plant cell normally sees double stranded RNA is when it is being attacked by viruses (the genome is made of double stranded DNA and the RNA messages transcribed from the genome are single stranded), so making a double stranded copy of the a particular gene causes the plant to treat that gene itself like an invading virus and keep the protein that gene encodes for from being produced. (<– this is the simplified version of the story, this work actually uses synthetic microRNAs which are a much more refined version of the technique.)

**When a plant produces a sweet and tasty fruit in the wild, its goal is to attract some animal that will eat the fruit and carry the plants seeds to someplace new where the seeds can grow into new plants. Domestication has changed the rules of that bargain somewhat, as we artificially selected for bigger and tastier fruits, but fruiting plants still trade animals (us humans) food in exchange for having the seeds of their species distributed across whole fields by farmers, and have their growth protected and nurtured by human hands and human ingenuity.

***There’s also numerical data which is probably better science (the images only track two fruits of each type which I’m sure isn’t statistically significant), but the best scientific papers will include hooks like that image of unrooting tomatoes to draw the reader in long enough to read the exciting data itself.

From the article:

China produces 31 percent of the world’s rice and 20 percent of its corn, U.S. Department of Agriculture data show. …[China] uses 7 percent of the world’s arable land to feed a quarter of its population.

China has only 7% of the world’s farmland yet feeds more than 1.3 billion people (and still growing). No wonder they’re investing so heavily in crop/plant science.

Another one I recently read (if it was you, sorry for not attributing it properly, the comparison just stuck in my head) was that India and Argentina are about the same size (India is about a quarter bigger) yet India must feed 30 times as many people!*

*Of course this isn’t quite a fair comparison since Argentina exports so much food to Western Europe, since those countries can afford to buy food abroad instead of focusing on increasing local production, and China and India must

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…

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.

In some ways India mirrors the world as a whole, with growing urban populations and high tech industries co-existing with poor farmers working small parcels of land. In other was it doesn’t. In the United States, a tiny fraction of our population feeds every one of us*. I assume most of them enjoy their work, since many will even take second jobs so they can afford to keep their farms going.

In India:

But this is not easy in a country where inflation is always an election issue and a state government was voted out because onion prices soared.

From before the election.

In the US food prices used to be a political issue. That’s where the idea that a politician should know the price of milk came from. Being able to pay for food used to be something a lot more Americans worried about. Our current agricultural policies in part are the result of the decision to eliminate food prices as a political issue (and in the process remove the specter of famine from millions of American homes.) Admittedly both systems have their disadvantages.

Anyway, my point is, can we at least all agree that 1. people shouldn’t have to worry about the price their food spiking, or whether they’ll be able to afford to feed their families. 2. It’s preferable for a few million people who love farming to produce food than for hundreds of millions who’d rather be doing something else, but can’t 2. farming should be productive enough that those who love farming can feed everyone (thanks greg)?

Field of Cotton in South Carolina. Photo: hdport, flickr

Scientific Name: Gossypium itscomplicated*

Genetically Engineered Traits: Insect Resistance (bt), Herbicide Resistance

Details of Genetic Engineering:

Cotton has been genetically engineered to resist both glyphosate (by Monsanto) and glufinsate (by Bayer CropScience) under the names Roundup Ready and LibertyLink respectively. As I’ve discussed in previous posts, there are both economic and scientific advantages to having more than one herbicide/herbicide resistance system as it tends to keep prices down, and slows the development of resistant weeds when any resistance they evolve to one herbicide will be useless if the farmer switches to the other for the next growing season.

But the big deal when it comes to genetically engineered cotton is bt cotton that substantially reduces insect damage (and insecticide applications). In the US both Monsanto and Dow AgroSciences sell their own versions of bt cotton using different bt proteins with different specificities. The Chinese government has also developed and deployed their own bt cotton varieties. Bt cotton is the most widely grown** type of genetically engineered plant in the world today, grown in countries like China, India***, and Australia, where other genetically modified crops are not yet approved, for the obvious reason that it’s harder to get people upset about wearing “unnatural” things than eating them.****

Cotton plant in Turkmenistan. Photo: flydime, flickr

About Cotton:

Cotton was first domesticated in Mexico eight thousand years ago, and a separate species was domesticated in present day Indian and Pakistan approximated a thousand years later. It was the second cotton that first found its way to Europe, along with the spice trade, where it was used by people who had never seen the plants themselves, and were all amazed that it came from a plant, unlike their primary source of clothes at the time, wool.

Much of the cotton grown today, even in India, can trace more of its heritage to the cotton domesticated in the Americas than to the original cotton of Eurasia. It’s not 100% though, as cotton breeders (like so many others), has been pulling useful genes across the species barrier long before genetic engineering entered the picture.

*Several different species produce the fibers we refer to as “cotton”. The four most signficiant are Gossypium arboreum, Gossypium barbadense, Gossypium herbaceum, and Gossypium hirsutum, with the last one, hirsutum, being the primary producer of cotton in the world today.

**In terms of countries were farmers grow it, I haven’t checked about total acreage.

***In India, there are no patents on genes, so in addition to seed sold by local partners of Monsanto (I don’t know anything about Dow’s present in India), Indian farmers can buy cotton seeds containing the bt transgene Monsanto developed or at least one of the ones developed by the Chinese government from small local seed producers that have legally “pirated” the genes. The genes are introgressed into all sorts of local cotton varieties. Make no mistake, being a small farmer in India is neither a happy nor secure length. When the rains don’t come, or any of a dozen other agricultural disasters occur, the farmers have no reserves to allow them to survive until the next harvest, in fact many of them go heavily into debt to finance every seed the goes into the ground, and every drop of fertilizer and pesticide they must spray upon it. Bt cotton can reduce the need to spray pesticides by two thirds, which, in a country where the cost of pesticides can easily make up 40% of the cost of growing cotton, is a big deal. More importantly, the health impacts for the people who are living on ~dollar per day, and were working in pesticide fields with little or no protective gear are huge. Bt cotton is not a cure for the plight of debt ridden farmers with no safety net (that’s one issue that needs societial action, not a scientific fix), but it’s still a Good Thing™, especially in a country where anyone who wants can start breeding and selling bt cotton.

****Especially when you consider the genome of a genetically engineered cotton plant is 99.99% identical to its untransformed parent, a claim I couldn’t make for everything from polyester (originally designed to be a synthetic substitute for cotton), nylon (originally designed to be a synthetic silk, where it replaced actual silk, and make paratroopers a lot more feasible during and after World War II when the US was cut off from sources of real silk) and pleather (not touching this one with a stick).