Friday, October 30, 2009

The Myth of Monocultures

Brendan sent me a link to the new PBS video special based on Pollan's The Botany of Desire. Ironically, I had been eyeballing the same book on my shelf the past few weeks wondering if it was due for a re-read.

The PBS special was very well done and I definitely recommend it.

The last 15 minutes though (an uninformed tirade against modern agriculture), were unwelcome and irritating. One telling moment was a local ag scientist lamenting the "tragic" public rejection of the environmentally-friendly Bt potato, followed by more fear-mongering by a partisan lobbyist.

Pollan should limit his lectures to topics he understands - which wears thin as he waxes on the horrors of monocultures. Plants (including crops) are in a continual arms race with pests and pathogens. The plants keep finding new ways to protect themselves while the parasites "keep trying to pick the lock." Picture a landscape filled with many different kinds of potatoes. According to the classic version of this story, a parasite that stumbles upon a new way to break into a certain potato variety may wipe out all individuals of this variety but it won't kill EVERY potato on the landscape.

The problem with this story is that plants varieties that look very different don't necessarily have different disease and pest resistance genes. Just like humans, which are known for tremendous phenotypic diversity, can be extremely susceptible to the same flu and HIV germs across all ethnicities, all the multicolored potatoes in the above picture may be similarity susceptible to diseases like late blight.

It's not so surprising that crops are notoriously vulnerable to parasites when you meet their wild relatives. The fruits and grain of the undomesticated relatives are usually barely edible - tiny, fibrous and full of poisons. It should be no surprise that the same qualities that humans love in their food (lots of easily-digested calories) are appreciated by many other creatures as well. Plant breeders have countered this inherent susceptibility by introgressing (moving) key resistance genes from wild relatives of crops into the crops themselves. This process has actually made modern industrial tomatoes more genetically diverse than either traditional Latin American or U.S./European heirloom varieties (although the traditional and heirloom varieties look more diverse).

Theoretically, it would be useful to maintain crop populations with diverse resistance genes. The industrial application of this (multilines) invovles breeding many different versions of a favorite crop variety that are identical except for their resistance genes. As appealing as this idea is, it hasn't really worked out in the real world. The alternate approach (pyramiding) seems to be more effective. Here, many different resistance genes are combined into a single crop variety. Pests and pathogens may be able to overcome a single gene at a time, but it's usually almost impossible to simultaneously overcome several.

PBS' The Botany of Desire also makes a lot of Bt resistance developing in insects exposed to genetically-engineered Bt crops, but this is nothing new. Insects and pathogens develop resistance to all kinds of pesticides - whether they're natural plant chemicals, artificial sprays, or genetically-engineered genes.

Evolution is a fact of life. The pests and pathogens will continue to adapt, and they will eat up our crops if we don't keep ahead of them. It's a problem you can never completely solve - which is good for me and my scientist colleagues!

Saturday, October 24, 2009

Division of Leaves

This picture shows some common tomato leaf shape mutants. Mutants (which generally are each broken at a single gene) are a really powerful tool for figuring out what individual genes actually do. In this case, they help us figure out how different plants are able to produce their extraordinary diversity of leaf shapes.

The top left image is a normal tomato leaf. Tomatoes have compound leaves with about 7 leaflets (which themselves can be further divided) with some little flat extensions of leaf tissue in between. Mutations in individual genes can force the leaf to bifurcate further or form one single, continuous blade.

Plant scientists have made some great progress figuring out how plants regulate leaf shape. Much of it is controlled by the plant hormone auxin. Scientists have found that if they add microscopic drops of pure auxin to baby leaves as they're developing, additionally leaflets will form at each drop. Additionally if they leave a long line of auxin, a flat leaf blade will emerge along the entire line. In normal plants, these spots form on their own as the leaf grows (and additional spots form in between as they're stretched apart). This way, tomatoes can form leaves with a consistent shape whether they're baby 3-leaflet leaves or large 9-leaflet ones.

This suggests that compound leaf development requires isolated spots of auxin. Accordingly, genes have been discovered that are either required to initiate these spots or to inhibit auxin in between the spots. Using genetic engineering techniques to increase or decrease the expression of these genes has predictable results and can produce non-compound leaves that are completely surrounded by a continuous blade, or that lack blades completely (and look like cactus spines!).

Both tomato and its sister species, eggplant, have relatives with leaves that have different levels of complexity. Different versions (alleles) of these genes have been found in these species. Ultimately these genes are translated into proteins, which react with other proteins and DNA to control leaf morphology. Some of these proteins have been found to vary in their binding affinity among species - e.g. a protein that positively regulates large numbers of leaflets is "stickier" in a complex-leafed species, interacting more with its partners and making a stronger "make leaflets!" signal.

So why do plants go through so much trouble to create such a variety of leaf shapes? This is still an open question, but leaves of different dimensions, with different degrees of division, lobey-ness and serration likely differ in temperature conduction, gas exchange, water relations, herbivory, disease susceptibility and light interception.

I love this black and white picture,* which illustrates how leaves vary with the environment. The big leaf on the left is a red maple grown in Vermont. The tiny leaf on the right is the same species, but grown in Florida! The color picture is my conception of what a "red maple" looks like - and reflects that my youth was spent in between these two latitudes!

















*Royer at al. 2008. New Phytologist. 179: p.808-817.

Thursday, October 22, 2009

Flowering Bulbs and the Atom Bomb

Our local colchicums bloomed recently (at least before it started snowing)...

Colchicum is a genus of flowering bulbs that's native to the Mediterranean coast. This picture shows Colchicum autumnale, aka the "autumn crocus," which, predictably, blooms in the fall and looks like a crocus.

This genus is also known for producing the poisonous alkaloid, colchicine. Used in various traditional remedies, this chemical has anti-inflammatory properties and prevents cell division by (for those of you who remember your basic biology) binding to tubulin and therefore preventing the assembly of the microtubule scaffolding required for mitosis.

The ability of this chemical to prevent cell division (but not DNA replication) can also be used to double the number of chromosomes within a plant cell, which has various applications in plant breeding. Although we can now use genetic engineering to add, remove or change genes in pretty much any way we want, traditionally, the only way to find new versions of genes (and therefore new phenotypic traits) was to wait for one to mutate naturally or use chemical tricks to induce mutations.

Many of our most important grain varieties were intentionally mutated with chemicals and ionizing radiation half a century ago. Because the mutations are random, they sickened or killed almost all of the exposed seedlings, but, just like occurs with natural selection, a few happened to change in beneficial ways. One such induced mutation is dwarfism, which produces short, strong plants that can carry heavy seed heads without falling over. In addition to mutating plants within controlled laboratory experiments, one of my professors told me that they actually left bags of wheat and corn seed on the decks of test ships (like those in this picture) when the U.S. government tested the atom bomb on Bikini Atoll!













Some activists have begun to refer to these mutated plants as "hidden GMOs." However, unlike true genetic engineering, "mutation breeding" breaks DNA in exactly the same types of ways that produce natural mutations - it's just much faster.

Over 2,500 of our crop varieties have been improved with this "mutation breeding." Currently many companies are using this technique to generate novel genetic diversity while avoiding the stigma and regulatory obstacles associated with genetic engineering - especially for crops like sunflower, which are often planted within pollination range of their wild relatives.

Monday, October 19, 2009

Science Reporting Ethics

Do you have any thoughts on the ethics of blogging about scientific presentations?

The issue (for you non-scientists out there) is that scientists generally give presentations (whether to departments or international meetings) with the assumption that what they display, say or imply probably won't travel very far outside the room.

So, how do you report something that isn't meant as public knowledge?

For me, it's not so much an issue of presenting "scoopable" data out to the wider world because I generally blog from ideas (usually anecdotal) given in presenters' introductions - which I try to tie into other ideas I've been exposed to. What I don't want to do is imply that the author has opinions they didn't state (or don't want to announce publicly), not give credit where it's due, have to approach every person and ask them if it's ok or never talk about stuff presenters say in the first place.

Any thoughts?

Sunday, October 18, 2009

Paw Paws!

Whenever I wandered through the hills and swampy bottomlands during my youth, I always kept an eye out for pawpaws. I never found one of these fascinating North American "bananas" until today - at our University orchard store.

Asimina triloba is a small understorey tree graced with large, dark green leaves that allude to the primarily tropical home of its family. The pawpaw received its name from an early Spanish explorer who confused this plant with the tropical papaya.

In spring, pawpaws produce small, maroon flowers. Although these flowers contain both male and female parts, they are self-incompatible. Some botanists estimate that fewer than 1% of flowers ever produce fruit! Inefficient pollination (plus poor storage properties) limit commercial production of this fruit.
(although Kentucky State is working hard to change this)

Poor pollination efficiency may also arise from the evolutionary strategy that the pawpaw takes. Some flowers in the pawpaw family (e.g. white-flowered Asimina species) pursue an "honest, rewards-based" strategy, exuding sweet-smelling, fruity scents that attract and feed beetles. Maroon-flowered species (like the pawpaw itself), instead exude fermented/decaying scents, mimicking rotting meat in an effort to trick flies into pollination. Some farmers have attempted to attract more flies by hanging rotting meat from their trees! (but hand pollination is recommended).

I left the green fruits in a paper bag to ripen until they were mostly black and smelled faintly of pineapple and licorice. Like thin-skinned avocados, the inside of the fruit contained a few large seeds and a custard-like fruit that tasted kinda like mango.


I put the seeds in the fridge to see if I can break dormancy and germinate them.





Charles Fergus. Trees of Pennsylvania and the Northeast. 2002.

Saturday, October 17, 2009

Cooking With Tomato Leaves

Here's a neat story from the New York Times about the presence of the poisonous alkaloid tomatine in tomato plants and the use of the possibly-toxic leaves in food.

Thursday, October 15, 2009

An Unwelcome Visitor

I walked into by basement bedroom, brushing my teeth, when I spotted a shape on the floor. Some deep module in my brain instantly recognized the familiar image of a plastic dinosaur toy - as a voice slowly volunteered that, unlike my childhood home, this apartment contained no dinosaur toys...

It was a big 6" spotted salamander staring at me from my bedside!

This happened a few months ago. My herpetologist sister pointed out that they go a little crazy in the spring breeding season and that it probably wandered its way in through some crack in the foundation or extra space along some pipes. It sat calmly while I scooped it up and set it outside. The maintenance guy sealed up some holes the next day and I thankfully haven't had any uninvited boarders since.

Bluestem-Fed Beef

Life on a Cattle Ranch has a great post describing how cattle are raised sustainably on native North American prairies in the Flint Hills of Kansas. A strategy of prescribed burns and field rotation allows the ranchers to turn grass into meat year after year without chemical inputs.

The reason this system works out so well is that this ecosystem is already adapted to the pressures of regular wildfires and heavy grazing - by bison! The bison are pretty much all gone, but the cattle are a pretty good functional ecological replacement.

There aren't many situations where resources can be extracted from the land this intensively with this little impact, but it's great when it works.

The picture, by the way, is of some bison on the Konza Prairie, a famous nature preserve/experimental research station in the Flint Hills. It's part of an ambitious ecology research system known as the LTER (Long Term Ecological Research Network) that endeavors to discover fundamental ecology operating at large spatiotemporal scales.

Wednesday, October 14, 2009

Firewood Kills Trees

I was reading a cool article on some new Cornell-bred potato varieties that Marcie sent me when I noticed a stark black and white ad in the margin (that had mug shots of insects):

Be a Beetlebuster. Don't Move Firewood.

The link takes you to a site featuring a big flash-animated Asian longhorn beetle, a devastating invasive pest that's marching its way through the Northeast. These beetles lay their eggs on trees, where they eventually develop into big grubs that feed on the tree's tissues and exit through perfectly round holes as adults - killing native trees in the process. Federal and local governments are doing everything they can to keep this critter from getting established in the States.

The site asks citizens to report sightings of this beetle (or signs, such as the holes it bores in tree trunks. Take a minute to flip through their pictures so you'll know it when you see it - or at least check out the animated beetle!

Not moving firewood is one of the key ways of slowing down treekillers like the ALB because you never know if there are some baby bugs hiding out inside it. The USDA parking lot near my work is full of pickup trucks and station wagons plastered with red "Don't Move Firewood. It BUGS Me!" bumper stickers. I couldn't find a picture, but I think the bumper sticker came from the campaign against the emerald ash borer (another invasive that's decimating ash trees out from the Midwest, which a bunch of the local scientists work on).

Tuesday, October 13, 2009

From Farm to Food Bank

I was standing in a lettuce field with some fellow grad students while on a tour a few years ago. The crop wasn't in great shape, but we anticipated a decent harvest. We were shocked to learn that the field had already been harvested! Hundreds of perfectly edible heads lay all around us, left unpicked because they didn't meet stringent appearance standards for consumer acceptance.

California's Food Banks Go Locavore
, in Sunday's New York Times describes a solution to this waste that's long overdue. California food banks have been working hard to take advantage of the huge amount of good (but not pretty) food that gets thrown out every year. Sweet potatoes are a good example - it's currently trendy to buy white sweet potatoes in specialty grocery stores, but undersized, lumpy and scarred white sweet potatoes have no use in the food industry because downmarket uses (like potato chips and pie filling) only use the traditional orange-colored sweet potatoes. The small and ugly white sweet potatoes are simply left in the field to rot! Thanks to the people in this article, these rejected sweet potatoes are now collected for local food banks.

One of the neatest things about this story is that a huge role has been played by a bunch of retired executives from major ag businesses like ADM. These guys know the farmers, the processors, and how low peach prices have to fall before (tons of) peaches are unsalable and have to be thrown out. They've coordinated food banks to buy up the perfectly edible "waste" for pennies a pound.

Some food banks have gone so far as to contract with farmers to produce extra food for them. It's incredible how cheap (even produce) can be when artificial appearance standards aren't imposed.

Saturday, October 10, 2009

Another Kink in Eating Local

Somehow I missed this article from last year. In it, two professors from Carnegie Mellon describe how despite the enormous distances that modern foods are shipped, transportation as a whole accounts for only 11% of the total greenhouse gas emissions produced by agriculture. Delivery of finished food products to retail stores accounts for only 4% of the total emissions. They conclude that "buying local" is less effective in lowering our carbon footprint than shifting from red meat and dairy to less carbon-intensive poultry, fish and veggies.

The greater efficiency of concentrating agriculture in the best locations is reflected in Jeremy's post at Ag Biodiversity. Check out his stunning maps that illustrate the global distribution of farming in 1995 versus the concentration of agriculture in only the best locations (it's not clear if this is hypothetical or actual). Like any other industry, agriculture is most efficient when located where the competitive advantages lie (e.g. good soil, weather and cheap and available labor). Unlike other industries though, I think agriculture may be an industry that we should sacrifice some efficiency in order to maintain the robustness of a distributed network. No one will starve, overthrow their government or start a war if political or natural obstacles suddenly cut them off from iPod factories on the other side of the world...

I don't have the time (or probably the qualifications!) to dig into the authors' methods to see exactly how they calculated all this, but it's a good reminder of how unintuitive complex systems can be. It's easy to suggest aesthetically-pleasing ideas such as buying local, but the devil is in the details. As James points out, there's not even close to enough land surrounding major population centers like NYC or Philly to feed all the inhabitants within a "local" number of food miles - let alone the fact that very few crops are grown in many of these regions to begin with (e.g. pretty much just dairy in upstate NY). It's often more efficient to grow crops year-round in sunny Arizona or California, or in the deep soils of the Midwest (and ship them thousands of miles) than grow them locally in cool, short summers on rocky soil.

As a big fan of New Urbanism, I'd be happy to vote for legislation that encourages dense, mixed zoning with lots of subsidized parks (including garden plots and farms) in and around cities, but that's more a statement of aesthetic preference than of effective conservation. I think we would benefit from a more clear understanding of not only the facts involving the environmental and social impacts of modern agriculture, but also our personal motivations for our beliefs.

If some sort of concentrated feed lot system turns out to be the most environmentally-friendly form of beef production, would you advocate it?

Wednesday, October 7, 2009

Too Much of a Good Thing

I saw this link on David Tribe's blog.

Free radicals (e.g. reactive oxygen species) are highly reactive chemicals that play various biological roles, including acting as signaling molecules. They're most famous though for reacting with (and breaking) cellular machinery (due to their highly-reactive unpaired electron) and contributing to cellular stress and disease. Antioxidants deactivate radicals, and therefore protect native proteins, lipids, DNA, etc.

The article cited above describes a new study that found that reactive oxygen species appear to play a protective role against Type II Diabetes. The implication is that consuming too many antioxidants (e.g. loading up on vitamins) may backfire.

This just goes to show how much we don't know about how our foods affect our health (and why I don't believe in vitamins). I'm just going to keep eating a reasonably diverse diet and not worry about the consequences.

Tuesday, October 6, 2009

Glow-in-the-dark Mushrooms

Brendan tipped me off to the discovery of 4 new glowing mushroom species (and 3 old species that no one knew glowed). These tiny mushrooms (with caps less than 1 cm in width) continuously emit a bright yellow-green light and belong to the genus Mycena, which also contains most other known luminescent mushroom species.

The genus Mycena contains innumerable tiny, dull-colored species that are much more common than anyone would normally notice. Their tiny caps can be found sprouting from decaying vegetable matter wherever it's found. Mycena species (and those of a few other genera) are often referred to as "little brown mushrooms" or "little brown jobs," reflecting their nondescript ubiquity and the near-impossibility of actually identifying them. Back when I worked in redwood forests, I often saw putative Mycenas popping out of fallen Doug-fir cones.

Dennis Desjardin, author of the above discovery, points out that luminescence appears in 16 separate lineages of Mycena species - suggesting that the ancestor of all Mycena species was capable of glowing, but that some species and lineages have since lost this ability. Desjardin came to this conclusion because one of the key tactics in science is to assume that the simplest explanation is most likely to be correct - and should be assumed to be correct until proven otherwise. Because it is more difficult/unlikely for an organism to acquire the ability to glow than to lose the ability, it is more likely that many Mycena species lost the ability (and a few retained it) than that many Mycena species acquired it independently. When shared traits are used to place evolutionary links between related species on a phylogenetic tree, this is known as "parsimony."

Desjardin suggests that the glow of these tiny mushrooms may attract nocturnal animals, which disperse their spores.

So the next time you kick open a rotten log and find the inside glowing, think of Mycena!

Sunday, October 4, 2009

Invasion of the Stink Bugs

Dusk fell in as I neared the end of my drive into West Virginia. Large industrial harvesters crawled over the soybean-covered hills, piercing the dark with their headlights and trailing wide clouds of brown dust that settled in the hollows.

Here, I met a new exotic agricultural pest, the brown marmorated stink bug. This insect likely hitched a ride to the U.S. from China or Japan, where it feeds on numerous fruits and legumes (e.g. soybeans!). This new stink bug has established itself throughout the Mid-Atlantic and Pacific Northwest, where it's introduced itself to the locals by forcing its way into their homes as the weather cools (like its obnoxious brother, the box elder bug). When alarmed (or smashed), these creatures release a scent that's been compared to rancid almonds.

Apparently, smashing one may be enough to make a room temporarily uninhabitable AND attracts more stink bugs (which are simply trying to aggregate in a good hibernating spot in the first place).

"Marmorated," by the way, supposedly means "Having a marbled or streaked appearance."

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