CNY Agritourism

Some friends came up from Brooklyn to visit me this weekend. We had a very-Upstate Saturday of apple picking and cider, and went to an alpaca farm festival on Sunday.



I picked a well-mixed quarter bushel of red and yellow, sweet and tart apples to make pies with. I'll let you know how it goes.


At first, I thought this machine might be a tree-shaking harvester, but it was a hydraulic cherry-picker with pole-mounted chainsaw and lopper for pruning. The extension to the upper right is a counter-balance for the platform that's lowered in the background.





The ground was littered with ripe and overripe apples, most of which showed symptoms of apple scab, the most economically devastating apple disease in Europe, Asia and the Americas. It's one of those classic diseases that causes largely aesthetic damage, but requires huge amounts of pesticide to maintain consumer acceptability. The low spray, IPM approach used in this orchard makes a lot of sense for a pick-yourself orchard, and the huge amount of uneaten fruit is a testament to the amazing yields capable in well-managed orchards. My friend pointed out scat that appeared to belong to (very happy) deer and bears.


Even at the end of September there were lots of wildflowers in the orchard, particularly yellow goldenrod and purple asters. I noticed that some of the goldenrod plants had highly-compressed shoot tips (see picture). These plants were most likely infected by phytoplasmas. Phytoplasmas are tiny, amorphous bacteria that lack cell walls and are known for two main symptoms: phyllody (the transformation of flowers into leaf-like structures) and virescence (the production of green flowers).


Commercial pointsettias are commonly infected with phytoplasmas intentionally in order to create more bushy, showy plants.

Amber Waves of Biofuel

The tide of support for field crop biofuels seems to be receding as quickly as it advanced. It's become routine to hear that the economics, environmental impact and fuel properties of turning grains into ethanol doesn't really add up, but I think there may still be some niche markets for it.

The Noble Foundation* and USDA are both doing some interesting work breeding forage crops that can be used both for cattle forage and biofuel. Switchgrass, made famous by President Bush's 2006 State of the Union Speech, is one of the favorites as it's native and vigorous (and has recently been shown to exhibit heterosis). However, I'm skeptical that this biofuel grass would be profitable enough to justify buying and establishing seed, let alone shipping and processing it - or that turning grass into biofuel would be more profitable than turning it into meat.

Ranching, like most agricultural businesses, has incredibly slim profit margins, so it's unlikely that straw could be shipped any farther than a few towns over to be processed. All the same, it may provide opportunities for agriculturalists to produce their own fuel, depending on oil prices. There are plenty of people heating their homes and communities by burning corn cobs and green waste from municipal parks, so I suppose there could be some market for planting these improved grasses. It's certainly aesthetically pleasing to picture widespread establishment of semi-wild, multi-use prairies, but we'll have to wait to see how the numbers work out.

Overall, I think the only way we'll see any mass produced biofuel is with engineered microbes that produce more practical fuels than ethanol, grown on some nutrient-dense, point-source, non-celluosic waste material (like sewage!). Of course this could all be moot if any of the wild prophecies of the chemists and physicists come true. Their futuristic claims of sky scrapers with painted-on solar panels and high-performance batteries are a lot more exciting than our promises of fermented corn stovers...


*This is the oil tycoon-financed research institute in Oklahoma (one of my favorite states). It's in Ardmore, one of a series of train-stop towns named after train-stop towns in Mainline Philadelphia (though many are pronounced differently!)

Do you Trust your Government?

The U.S. has done a pretty reliable job recognizing and regulating threats to our health. A system of 300 million people certainly doesn't move fast - and it's easy to point out scandals and tragedies that have occurred between recognition and regulation - but overall America's a pretty safe place to live.

Pesticide regulation is a good example of this familiar arc. Following some initial faltering in the mid-20th century, a comprehensive system of regulation was developed. This system is coordinated by the EPA, FDA and USDA, and independently regulates every combination of pesticide formulation and crop. Pesticide levels and application timing are set to assure that residue levels are many times lower than have been estimated to have any detectable biological effect on humans. The EPA has an outstanding website that puts their rationale where their registrations are. Here, for example, are the toxicology results for glyphosate (Roundup).

A healthy skepticism of any governmental, corporate or non-governmental organization plays a critical role in responsible citizenship, but it's important to keep things in perspective. It seems pretty irrational to me to trust vehicle safety standards, building codes, medical regulations and educational standards - but then spurn agricultural regulations. There are plenty of countries where you can't even mail a letter confidently - but the U.S. isn't one of them.

Free countries will always have a fringe who (legitimately or illegitimately) distrust the government, whether they're libertarians, militia survivalists or conspiracy theorists. Organic advocates are entitled to view the government (and farmers) as fundamentally untrustworthy, but they should acknowledge the radical nature of that decision.

If Rube Goldberg was a Maize Scientist...

Traditionally, a plant breeder created better crop varieties by crossing (with controlled pollination) two parents who each had good traits, and then selecting the individual offspring with the best combination of those traits.

Although this sounds straightforward, all organisms are highly affected both by their inherited genetic traits (i.e. "nature") and their environment (i.e. "nurture"). When a plant breeder walks into her field, she has no way of knowing if the "best" offspring (e.g. the ones with the highest yield, pest resistance or cold tolerance) really have the best combination of genetic traits (alleles), or whether they have inferior combinations of alleles but were lucky enough to be planted in a particularly nourishing part of the field (even the most flat and boring field has huge variations in water and nutrient availability).

When a breeder knows some of the gene alleles she's trying to keep in the offspring, marker-assisted selection (MAS) allows her to directly test which individuals have the alleles she wants. MAS is basically a genetic "fingerprint" test of each individual offspring. It's one of those (very common) situations where biotechnology is used to make non-GM crops (as the genomes are only manipulated by choosing which pairs of plants to cross). Potentially, you could test the genetic properties of the offspring before you even plant them!

A few months ago, I saw a presentation on how Pioneer Hi-Bred sorts through tons of corn, individually tests each kernel for its genetic properties and then plants only the individuals they want. A team of scientists and engineers invented this system, Laser-Assisted Seed Selection, which is one of the most brilliant and elegant inventions I've ever seen.

Step 1.
Each cob is mounted on a rotating peg and sprayed with magnetic paint.
















Step 2.
The kernels are knocked off the cob and all debris falls away except for the kernels themselves, which are caught by a magnetic holder (notice only the "outside" edge of the kernels have paint on them).




Step 3.
A laser is used to slice off a thin piece of each kernel.







The big piece contains the embryo and most of the endosperm. It is still viable to plant and is automatically sealed in barcoded-plates and stored until it's needed. The thin sliced piece is dropped into a corresponding barcoded-plate and sent to the molecular biologists to test for genetic traits. The breeders can then order whichever genotypes she wants to plant!

A New Low in our National Nutrition Obsession

This is the worst thing since whole wheat pasta.

People have been living healthy, fulfilling lives for hundreds of thousands of years without obsessively trying to optimize their health all the time. I'm sure I'll be just fine as I am, thanks.

Please don't medicalize my food.

Organic vs. Local Food

The current predicament of the U.K. meat industry says a lot about our food system.

Meat producers in the U.K. rely on soy grown across the Atlantic in the U.S., Argentina and Brazil, where, unfortunately, non-transgenic soy is quickly becoming obsolete. Losing this source of affordable feed will cause meat prices to skyrocket above levels that consumers are willing to pay. I don't know if there're any significant numbers of boutique/locally-fed cattle in the U.K., but I've been told that a U.K. cattle association recently forecasted an end to the British beef industry altogether if anti-GM regulations aren't loosened. Accordingly, the U.K. government will be lobbying the E.U. to streamline its approval process for transgenic crops.

If organic beef in the U.K. really does rely on feed shipped across the Atlantic, it would be an interesting wrinkle in the public understanding of "sustainable" agriculture. It's certainly not a model of sustainability to ship feed thousands of miles - especially if rainforests were burned to grow it. And as long as you're shipping it, it would use less energy to ship pounds of meat instead of the tons of grain that go into it...

I don't know what the best solution is - but arbitrary prejudice against transgenic crops isn't it. I hope the E.U. continues to warm to a more reasonable level of regulation.

My Allergy Test

I finally broke down and went to an allergist.

It was a pretty fascinating experience. The nurse first poked me with two plastic sticks that inoculated me with a positive and negative control (to confirm that taking OTC medicine a few days earlier wouldn't interfere with the test). After a few minutes, the 6-spotted poke-mark on the positive side rose up like a skeeter bite.

She then brought in two racks with dozens of little plastic pokers sitting in vials of colored extracts. Each extract contained a label such as "oak" or "alternaria." All together, there were dozens of individual preparations of different tree, wildflower and grass pollens, fungal spores and animal dander. She laid down three rows of pokes on my left arm of our most common local allergens and left me to react.

Soon after, I became aware of a building itching sensation over one of the central pokes, eventually accompanied by lesser itches by my wrist and elbow. When the doctor returned, two large puffy bumps had swelled in the middle of my forearm, with lesser bumps around it. The two most prominent bumps were due to two kinds of dust mites, and the smaller ones, cat dander and the pollen of timothy (a common pasture grass)!

I left with a prescription and a better sense of how to lessen my exposure to dust mites.

Know your Crickets (and Katydids)!

NPR had a cool story yesterday on a project to document the insects of New York City. Much of the story focused on identifying night-singing crickets and katydids by their songs (7 examples here). Very cool stuff, though I'd love to hear a companion story on frogs and whatever else is out there. I spent many summer nights falling asleep to that wooded cacophony - it'd be pretty cool to recognize some of the participants!

The Life of Norman Borlaug

I just read that Nobel laureate, Norman Borlaug has passed away. He was the architect of the Green Revolution and, without a doubt, has done more good for humanity than any single person who has ever lived.

Monsanto's blog has a nice remembrance of him.

Harvest in Central New York

I spent a cool, early fall morning hustling to harvest our research fruit before the inevitable first frost. It was a great day for some outdoor manual labor among the wooded hills of rural New York. The farm was littered with the pickups of scientists and the sky overhead was repeatedly pierced by small flocks of southbound geese, happily gorging themselves on our freshly-mowed grain fields. The field corn of the neighboring dairymen will stay green for another few weeks while the ears dry, but everything else needs to come out of the ground as soon as possible.

There are plenty of extra fruit at the moment. The tomatoes and tomatillos in this picture will be salsa before the weekend's over. The bowl contains Ailsa Craig, a go-to lab rat originally bred in Scotland (and still a favorite heriloom variety in the U.K.). The rest, from left to right, are Banana Legs, Hank, tomatillos, husk cherries and Black Plum. Each of these heirloom tomatoes is excellent, but if I had to pick one, I'd probably pick Hank, which produces heavy yields of little, pink, lobey fruit. If I'm feeling ambitious this weekend, I also might try making jam from our sunberries or garden huckleberries. A number of our more tropical varieties (notably peppers and eggplants) have failed to produce ripe fruit during our short, cool summer and will be transplanted to the greenhouse as a last-ditch effort.

All of our fruit are in family Solanaceae, which includes potatoes, peppers, eggplant and numerous nightshades. The tomatillos and husk cherries are covered by a papery calyx, resembling their close relative, the Chinese Lantern.

Some of our fruit are still dusty with recent pesticide sprays (as our farm managers have been waging a valiant battle against late blight). Today was well after the 12-hour [safe field] re-entry period and luckily New York's pesticide regulations don't require a longer wait period before sale than they do before re-entry - so the fruit are safe to eat today, though I'll definitely wash them extra-well!

Mutant Two-Headed Corn!

The chemist across the hall was eating sweet corn with his family last night when he saw that one cob had a tiny little 2-inch ear growing out of one of the spots where a kernel should have been!



Our resident maize geneticist had seen this before. Apparently, part of the molecular blueprint that a corn plant uses when making ears is to continuously suppress the ear tissue from producing branches. Most of us have 10 fingers and 10 toes, but as robust as the molecular blueprint is, sometimes it goofs up. In this case, the ear messed up and allowed a second little ear to start growing out of the middle of it!

Biotechnology FROM the Developing World

A few months ago I "attended" the UN Food and Agriculture Organization's email conference "Learning from the Past: Successes and failures with agricultural biotechnologies in developing countries over the last 20 years." I really enjoyed hearing the opinions of dozens of working scientists and regulators from the developing world (and a few based in the developed world) regarding the best uses of biotechnology in their countries.

They haven't posted their promised summary yet, but I seem to recall three major themes:

1) Many plant pathogens (particularly viruses) are unable to infect plant seeds, allowing plants to produce healthy offspring even when they are sick. Unfortunately, many important tropical crops (e.g. plantain, potato and cassava) can only be reproduced by cuttings (not by seed) - leading to chronic crop infections in many developing countries. A distributed network of small laboratories could play an essential role providing clean, disease-free cuttings at low cost or free to smallholder farmers and could also supply locally-appropriate agronomic advice and a link to national/regional universities and the greater scientific world beyond.

2) Simple, locally-appropriate technologies (such as fermentation of certain crops) can improve the nutritional quality and shelf life of available resources. There are lots of great scientists documenting (and improving) these techniques but implementation has been limited by a lack of extension workers.

3) Genetic engineering holds great promise to add valuable traits to locally-adapted crops (e.g. eggplant) - but has been stymied by very well-funded environmental special interest groups from the United States and Europe. This is all the more ironic/tragic as many of these new crops are being developed by public sector scientists for their smallholder countrymen. No less ironic is the role these "liberal" special interest groups are playing denying self-determination to their former colonies.

War of the GMOs

Nature has an important News Feature this week. It describes how the aggressively uncivil debate over genetic engineering has permeated the scientific community. Several examples are given where scientists publish (poorly-executed or overstated) evidence against the safety of transgenic crops and are viciously, and personally attacked by their colleagues.

I empathize with the frustration of the scientific community here. The huge potential of biotechnological applications to feed millions of starving people and lessen our environmental impact has been absolutely suffocated by over-regulation and the outcries of special interest groups. It has also led to repeated vandalism of the experimental fields of public sector scientists - with devastating personal consequences for the scientists. Overall, we are basically 30-years behind we're we could be, with the only transgenic plants in widespread use being endowed with unprepossessing agronomic traits, sold only by massive seed companies. This isn't the Second Green Revolution we've been waiting for.

Every highly-visible scientific paper that suggests the fears of environmentalists are justified is quickly snapped up by these special interest groups and has huge, long-term impacts on politics and regulation. This is how science and democracy are supposed to function - except that the public doesn't have the time or training to identify which papers are excellent and which are completely worthless (a fact that the public seems to be catching on to when every few months we hear completely contradictory medical and nutritional advice from newly published papers).

This is how science works: Every individual scientist puts in their two-cents, and over time, enough evidence accumulates to make it obvious what the true answer is. This process is short-circuited when special interest groups use papers (ANY paper that supports their viewpoint) simply as ammunition. Each of the "anti-GMO" papers mentioned in the Nature article was fundamentally flawed, or at least overstated the extent to which their results could be generalized from small lab experiments to regional ecosystems.

Ultimately it's the importance of debates such as the use of transgenic crops that make the discussion so contentious. It's therefore critical that scientists step into the public spot light and make their opinions known when bad (or at least over-extended) science is poised to influence society.

Nevertheless, this Nature paper is an important reminder for scientists (as well as all other citizens) not to allow their personal emotions and frustrations to overcome their professionalism. This discussion doesn't need to be cloyingly friendly, but it does need to be civil.

More Carrot Mixups

I was stopping to smell the flowers on my deck the other day when I noticed that my "carrot" flowers smelled like... some kind of spice.. maybe licorice. If this is normal for carrots, I've never noticed it before.

I pulled a few leaves and crushed them between my fingers. Some shared this scent while others smelled just like carrot roots. I then noticed that some of the leaves were more finely-divided than others. I think the plant on the left (with flowers) is actually anise.

Chances are, the (cheap!) seeds I bought were contaminated by anise seeds. Sometimes you get your money's worth with seed. Cheap, poorly-produced seeds are often contaminated with weed seeds, pests and pathogens.

Another good reason to know your plants!

In grad school, we were repeatedly encouraged to recommend "certified seed" to farmers. It costs a little more, but this certification is a guarantee of minimal seed quality. The AOSCA helps to coordinate this with crop-specific requirements that generally fall into 4 classes:

Breeder Seed - is the original, genetically pure seed carefully produced and stored by individual plant breeders
Foundation Seed - is the offspring of Breeder seed, is often contractually produced by local Foundation Seed organizations and is labeled with a white tag.
Registered Seed - is the offspring of above, is sometimes skipped for some crops in some states and is labeled with a purple tag.
Certified Seed - is seed bought by farmers growing food, is produced by a smaller group of farmers (who sell high quality seed instead of food) and is labeled with a blue tag. Farmers who grow crops in order to sell certified seed often locate their farms far away from the places where these crops are normally grown in order to avoid pests and pathogens.

Overall, this certification scheme (which is increasingly stringent as you move up the list), guarantees that a given crop has passed field and laboratory tests for:

Kind/variety - e.g. that the seed are from the correct crop and variety
Purity/Inert matter - e.g. that the seed has minimal non-seed debris
Germination percentage - e.g. that the most of the seed is viable
Other crop seed/Weed seeds - e.g. anise seeds in my carrot seed!