Practical Agricultural Development

Among plant geneticists, breeders are always held up as the pragmatic experts who know what matters in the Real World. But not all fields perceive breeders this way...

Sustainable agriculture was a popular session topic at the tri-societies joint meeting in San Antonio. More specifically, many speakers took pleasure (rightly so) in pointing out the subtle complexities of local agricultural systems that many of us in breeding gloss over when trying to help.

Some highlights:

Genetic Engineering vs. Breeding

"Many administrators, private and public, have decided that the future of plant breeding lies in genomics, relying on claims that molecular genetics has revolutionized the time frame for product development. ‘Seldom has it been pointed out that it is going to take as long to breed a molecular engineering gene into a successful cultivar as it takes for a natural gene’" - Goodman 2002

openSNP and Personal Genomics

So if you haven't heard, Direct to Customer (DTC) genomics has hit the mainstream. Multiple companies (23andMe, deCODEme, etc.) will now genotype you, providing you with a detailed rundown of all your genetic traits and tendencies...
Well, not exactly.

California Almonds

I recently got a tour of some Cali Central Valley almond farms from the Almond Doctor.

The nuts were in the process of being harvested. The first step is to shake the nuts off the tree with a machine that grabs them around the trunk (here's a video*). One way you can tell almond and peach (both Prunus species) orchards apart is to look at how low the first branches are. Almond trees are trained to branch higher above the ground to give the machine room to grab them. Peach trees are trained to branch almost immediately above the ground to help most of the canopy stay low enough to be reached without ladders (due to the increased chance of injuries). Maximum canopy height is more rigorously limited in peaches for the same reason.

Blue Potato Chips

JetBlue airlines now gives out blue potato chips as their "official" snack.

I'm very impressed by the fact that these blue potato chips exist. It's no small feat to create a good-frying potato with excellent agronomic qualities in itself. I can't imagine crossing in blue coloring (anthocyanin expression) on top of this in a reasonable amount of time - especially since potatoes aren't true to seed. Non true to seed crops like potatoes have messy, highly heterozygous genomes that when crossed (or selfed) produce offspring that segregate for all the traits you care about. I've been told that potato breeders typically make a bunch of crosses in the first year of their program - and then spend the rest of their careers evaluating and propagating the resulting segregants asexually.

Though the chips really are purple, not blue...

Polycultures in Modern Ag?

The September issue of CSA news has a nice (open access) article entitled: "Do polycultures have a role in modern agriculture?"

Some key caveats:

• While diverse plant mixtures have been associated with many benefits, high biomass yield (i.e. what farmers get paid for) is usually not one of them.
• It's very difficult to maintain complex plant mixtures - usually a single species will come to dominate.
• Our crop monocultures represent those crops that are best adapted to a given region.
• Establishing, maintaing and harvesting polycultures will require significant effort, risk, investments and training for farmers.

They conclude that polycultures are intriguing but definitely require more (agronomically realistic) research. 

Thoughts?

Evolution of Fruit Shape in Tomato

Someday you'll be able to use CAD software to draw up what you want a plant to look like and the software (containing detailed growth models) will tell you what genetic constructs you need to bring it into the world...

But for now we barely understand how natural morphological variation is controlled. So I was excited to see this paper out of the van der Knaap and Francis labs. In it, they review some of the known levers by which tomato plants control fruit shape and investigate their historical appearance.

I have a yard!

I spent the day moving the first of my stuff into the new house I'm renting. I'm very excited to finally be somewhere besides a one bedroom apartment. The yard's pretty shady but presents some interesting gardening opportunities that I'm working over in my head.

Putting up Hay

It used to be a common sight for me this time of year (on the way to the maize experimental fields) to see straw and hay being raked into windrows by hay rakes (video 1 2). Though most of us tend to use these words interchangeably, hay is a crop grown specifically for animal feed and straw is the leftover stems and leaves of a harvested grain that may be used for animal feed, bedding or construction. Common annual and perennial hay crops include legumes (e.g. alfalfa and clover) and grasses (e.g. timothy, brome, orchard grass and tall fescue). Straw usually comes from whatever grain is being grown in your area (e.g. wheat or barley).

First! (to harvest garden sweet corn)

Well, it's not from the garden, per se. It's from the greenhouse.

When I got the keys to my greenhouse space, one of the first things I did was sow a bunch of field crop seeds. I didn't know if there would be a need for me to grow them in the greenhouse, but I did know that it can be a tricky proposition. Better to sketch out a quick SOP now than wait till I need one and then add a 6 month delay to the project as I figure it out on the fly...

What's Cooking, Uncle Sam?

I just went to the new "What's Cooking, Uncle Sam?" exhibit at the National Archives. It tells the history of the government's role in U.S. food and agriculture -  a story of market protectionism, social engineering and the regulated tension between the aspirations of business and the demands of the people...

Twitter Update

I love this stupid service. I can flag all the interesting papers and articles I find in a week (with room for a little commentary) but without needing to sit down and come up with a coherent 500 word essay!

I could automatically feed these tweets into the blog, but it would just clog my page up with text. If you're interested in tapping this new stream, just add my twitter account to your blog rss feed. I promise not to gum it up with updates on what I'm eating.

I'll probably continue to write actual blog posts at about the rate I've settled into.

Now on Twitter

Thought I'd give this stupid twitter thing a shot... 


Seems like a good way to share links and blog post updates for those times that I don't feel like putting hours into a full post. Follow me.

Commercial Perennial Crops?

The "perennial grain" story seems to pop up every few months. The basic idea is that perennial crops would have higher yields and lower environmental impacts than their annual kin.

The picture on the left explains pretty clearly why - large permanent root systems secure the topsoil, exhaustively scavenge water and nutrients and support more vigorous shoot growth over a longer season.

This week, it's perennial maize.

Weed Seedling ID

I've spent the past hour reacquainting myself with the likely weeds I'll find in my plot, which ones are useful and what they look like.

While pulling up some chenopods among other weed seedlings, it occurred to me that some of these "volunteers" would be worth sparing. I went through my "Wild Plants to Eat" book along with a mess of extremely helpful extension weed seedling ID websites and came to the conclusion that I'll spare the two little dicotyledonous pseudograin weeds: amaranth and quinoa. 

Opportunistic Gardening

It's amazing what you can accomplish with some reckless enthusiasm and an emergency shovel.

I've been out of grad school/postdoc for half a year now but have been slow to acclimate to my new budget. After spending 75 bucks to rent my garden plot, I couldn't help but balk at the idea of spending hundreds more on tools, containers, plants and fencing - so I started cutting corners.

Warning: irrational frugality will be a theme here...

Wednesday Links

1. Man, oh man. Possibly the coolest website ever and more chemical ecology than I know what to do with (and here's another).  h/t OrchidGrownMan from Biofortified
2. Open source Legos for grownups. Can I have a microtractor? or a microcombine? or a dimensional sawmill? Pleeeease?
3. More scientific sour grapes. Why won't grad students sacrifice their entire careers to do what we think is important?
4. And, as always, maps! This time, watch agriculture spread.  h/t Seed.Feed.Food

Ketchup and the Future of GM Food

It's 3 am local time and I'm wide awake, fixated on the challenge of brand differentiation in ketchup...

I recently spoke with one of the ketchup tomato breeders I know. Among other topics, he lamented the consumer's irrational fixation on price. He pointed out that most of us won't hesitate to grab a generic bottle of ketchup over a trusted brand for a difference of only 20 cents - which breaks down to no difference over the months it sits in your fridge: How do you sell a better product to a customer who's not willing to pay 1 cent more per week?

Craziest Landscape Tree Pruning Ever

It's how the Dutch do it.

A couple people told me it's common to see trees pruned like this out in rural areas - particularly willows. I assume the traditional purpose is to coppice for fuel and baskets - and here it's nostalgia for the countryside.

Heirlooms are Obsolete

"Heirlooms were varieties that were so unsuccessful that they wouldn't be sold today...

Every product declines until it's replaced by new heirlooms."

The backlash was inevitable.

Spring arrives in Metro DC

It showed up a couple weeks earlier in the heat island of the city proper.
The cherries bloomed first in DC, than along the highways and now in my apartment complex. I imagine my neighbors around the courtyard wished these Bradford pears smelled like cherry trees. I don't mind. The scent reminds me of my suburban street hockey days.

"car! ...         game on!"

Genomics in Business Meeting, Amsterdam

Anyone going to the Genomics in Business meeting in Amsterdam next week?

In hindsight, I should have asked earlier but it's been a crazy couple weeks...

Better Chemistry Through Breeding

I recently had the opportunity to visit the fabled heart of the USDA-ARS empire: Beltsville.

I heard all about the tornado that knocked down all the campus trees, smashed in the greenhouses and threw doors down hallways a few years ago, visited their food sensory lab (a controlled environment where fruit samples are passed through a wall to waiting taste testers), and saw greenhouses packed full of cacao (where research on one of my favorite fungi, Crinipellis perniciosa, is co-funded by M&M Mars Inc.).

But I was there mostly to visit the pepper breeding program.

Plastic-Wrapped Bananas Not So Crazy?

The Daily Show ran a very funny bit on Del Monte's new single serving, plastic wrapped bananas the other night. Though they might not be as crazy as they sound...

h/t: Daily Mail:

These bananas, intended to be sold at convenience stores and gas stations, are wrapped in bags containing "Controlled Ripening Technology" (some sort of ethylene inhibitor?) that is said to extend shelf life up to 6 days. The bananas are placed in their bags while green and ripen more slowly than those piled on the shelf. They're being marketed as 'Natural Energy Snack on the Go,' for a U.S. cost of $1 each. 7-Eleven enthusiastically adopted these single serving bananas in thousands of stores last year due to customer disdain for brown bananas and the fewer (carbon/cost-intensive) deliveries that are required to stock produce with an extended shelf life.

It's also been pointed out that getting fresh, (culturally?)-appealing produce into quickie marts and bodegas in inner cities and isolated small towns might do more good alleviating food deserts than it does harm in generating extra trash.

Transgenic Papayas, Take 2

I must have been busy last year when Genomic Gastronomy tried to engage my post on transgenic papaya because I didn't really give much of an answer...


So with apologies, here's more!

Monsanto on the Metro

Farmboys, Allergies and Microbial Diversity

It's apparently been noticed for some time that children who grow up on farms are less likely to have asthma than other rural (and urban) dwellers.

This ties into the "hygiene hypothesis," the idea that a lack of exposure to microbes and parasitic worms somehow primes the body for auto-immune disorders like asthma and allergies. A new study suggests that this may be due to the diversity (or composition) of microbial communities that farmboys (and girls) are exposed to, rather than the quantity. (Unfortunately, I don't have access to the original NEJM article.)

As a former environmental microbiologist, I love the idea that culturing robust and complex microbial communities on our bodies is somehow optimal for our health - though I think the jury's still out as to what extent this is actually true. Ever since grad school, I've been waiting to hear someone take the next logical leap and claim that toothbrushes destroy our co-evolved dental flora, leading to cavities.*

I'll be interested to see if anyone tries to take this idea that far...

h/t: as described by The Great Beyond


*I've long been baffled by the rate that many of us rack up cavities despite intensive dental care. Our ancestors must have been toothless by 40.

Taro: Past and Future

I just discovered the local international supermarket (which is awesome by the way). It's filled with exotic fruits and vegetables, assorted sea creatures in boxes of ice and freezers full of animal pieces usually reserved for industrial uses.

I didn't find any dragonfruit (which I've been wanting to try), but they had cherimoyas, jackfruit, different cacti pieces, sugarcane, cassava, weird bananas, all kinds of odd leafy vegetables and squash-like things that were a couple feet across! Faced with a produce section full of things I barely recognized, I thought I should do some homework...

GM Vegetable Oil

Hooray for Seed Today helping me to clear another story out of my "drafts" folder!

How GM Overcame Soy's Fatal Flaw

It's an exciting time in genetic engineering! I've long been bored by the simplicity of our contemporary transgenic crops and the single-minded focus on agronomic traits. Dropping in an herbicide or pest resistance gene is good for the environment and the farmer, but it doesn't visibly benefit the consumer very much and just doesn't impress me technically. Now, Monsanto and Pioneer's new soybean varieties are heralding a new era of more sophisticated metabolic engineering of traits that will directly benefit the public.

New to Agriculture?

The Cornell Hort Blog just linked to the new Northeast Beginner Farmers Project website: 

"Do you wonder how other farmers breed pigs, process chickens and transplant seedlings? The new site features a growing selection of videos capturing experienced farmers and their successful production techniques in action. You’ll also find our popular library of video interviews with farmers sharing advice on profitability, choosing an enterprise, evaluating land, and much more."

Looks interesting! I'll definitely check it out more when I have extra time.

In the meantime, back to trying to find a CSA and community garden plots in the MD DC area... Any suggestions?

Data Visualization a Gateway to Statistics?

Yes! Personally, I'm a big fan of data visualization as a way of mining complex information. Pictures of data tend to contain more information than text summaries and also make associations much easier to recognize. Humans may be much less unbiased and logical than we like to think, but we're awesome pattern-detecting machines (whether there's something there or not).

Is Science Getting Harder (or just more social)?

A recent blog post over at the WSG asks if it's getting harder to discover new things:

"If you look back on history, you get the sense that scientific discovery used to be easy. Galileo rolled objects down slopes. Robert Hooke played with a spring to learn about elasticity; Isaac Newton poked around his own eye with a darning needle to understand color perception. It took creativity and knowledge to ask the right questions, but the experiments themselves could be almost trivial. Today, if you want to make a discovery in physics, it helps to be part of a 10,000 member team that runs a multibillion dollar atom smasher. It takes ever more money, more effort, and more people to find out new things."

Weekend Short Stories

Some pretty cool links for your weekend:

Jurassic Park beer:

Fossil Fuels Brewing Co. makes beer with an Eocene-era yeast, formerly encased in a 45 million year old chunk of amber! Incredible, but apparently true. Viable Bacillus spores were discovered first in 25-40 million year old amber by Raul Cano (these spores are so tough you can't kill them with an autoclave). He then founded a startup (Ambergene) with the hopes of discovering ancient antibiotics (this was back during the natural products craze - when pharma companies sent explorers to coral reefs, rainforests and geothermal hot pools to find new biologically-active chemicals. Now, most just do combinatorial synthetic chemistry). The company failed, but when you can't make money, make beer!    h/t: AncientFoods

Living off the land:

The Resilient Gardener teaches us how to be subsistence farmers in a temperate climate: corn, potatoes, beans, squash and eggs.   h/t: Living the Frugal Life

A reason to like kale:

Organisms can optimize their fitness by reproducing early when times are good and holding back and focusing on survival when times are bad (if your population is about to experience an involuntary bottleneck, offspring born afterwards will contribute proportionally more genes to the population). This Week in Evolution discusses the reproductive advantages that an organism would accrue if it could delay reproduction specifically in times of environmental stress.* In PLoS one, Will Ratcliff cites examples of creatures from yeast to rats showing increased longevity (and delayed reproduction) when exposed to minor environmental stresses (calorie restriction, temperature stresses, low dose toxins).** They hypothesize that the consumption of "famine foods" (e.g. low calorie and nutrition and moderate toxicity) would be an effective cue for an organism to switch to survival mode.

"Plants high in insect-repelling toxins might be an example of such "famine foods", even if some modern humans have developed a taste for kale, coffee, or hot peppers. These plant toxins might have small negative effects on our health. But, if our bodies respond to the information carried by those toxins -- famine! population decline likely! delay reproduction! -- then those negative effects may be outweighed by the health benefits of setting our hormone levels etc. to values optimized for longevity rather than reproduction."

and Maps!

The U.S. by last names, but why no Italians?***
An incredible morphing cartogram displays everything
The world according to Americans
Intriguing, yet almost impenetrable

* Not to be confused with my long-favorite, TWIS.

** Whom I played in a band with out of the very-Davis J St Coop

*** I assume this map is more biased by the redundancy by which different cultures reuse the same names than the spatial scale at which the immigrant populations currently dominate. 


Ratcliff, W., Hawthorne, P., Travisano, M., & Denison, R. (2009). When Stress Predicts a Shrinking Gene Pool, Trading Early Reproduction for Longevity Can Increase Fitness, Even with Lower Fecundity PLoS ONE, 4 (6) DOI: 10.1371/journal.pone.0006055
Cano, R., & Borucki, M. (1995). Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber Science, 268 (5213), 1060-1064 DOI: 10.1126/science.7538699

Investing in Innovation

James (of the giant corn) recently posted on George Will's column on why we should be maintaining (or increasing) basic science research funding despite the economic downturn.*


Some people have the annoying habit of repeatedly dismissing the economic and public benefit of federal research funding. As an industry scientist, I thought I'd give my two cents.

US [transgene?] Testing Network

"With over 80% of the corn grown in the US genetically modified, and biotechnology companies phasing out non-GMO corn seed varieties, American farmers have fewer choices for finding non-GMO seeds to grow. 

As a result of this narrowing of farmer choice, a new initiative was launched in 2009 by Practical Farmers of Iowa (PFI) to address the problem. The US Testing Network (USTN) aims to develop and introduce new non-GMO corn hybrids in the market, while improving the quality and quantity of non-GMO corn hybrids available."

I haven't heard of any of these organizations before (and would be interested if you know something about them), but it sounds like an interesting project. I couldn't care less about avoiding transgenes, but I love the idea of small companies, public sector scientists and enthusiastic individuals working together to improve germplasm for niche markets too small for the big seed companies to serve. 

Do you have any experience with these organizations?

h/t: Seed Today