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.

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).

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.

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...

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).

Waldsterben all over again?

Michelle tipped me off to yet another "all the bees are dying" article.

The new wrinkle in the story is a leaked EPA memo that suggests that Bayer CropScience's seed treatment, chlothianidin, was registered without sufficient proof that it didn't hurt bees. Aside from the fact that this registration was completed in 2004 and (according to the same article) this whole bee business started in the mid-1990s, I'm skeptical that any new pesticide is causing all this. We were SO much more indiscriminate and profligate with our agricultural sprays and industrial dumping in past decades (and with much more dangerous chemicals) than we are now - it seems a funny time for a problem to pop up. I haven't paid a lot of attention to the CCD story, but the persistent failure to identify a cause makes me wonder if the cause really is as simple as an anthropogenic chemical or exotic pathogen.

Now I've Seen Everything

I was watching cable just now and came across Glenn Beck accusing Monsanto of being part of some kind of paranoid socialist conspiracy. This company, apparently, has teamed up with the tyrannical FDA to help Obama gain control of and destroy the American food system. 

for some reason... 

ooooooh!   [read in spooky ghost voice]

I bet Monsanto's PR dept misses when they just sold flooring.

Stem Sells

The supermarket's now selling brussel sprouts still-on-the-stem. It's a pretty clever marketing tactic - makes people think they're fresh off the farm.* 

You know how they've started selling tomatoes on the truss? It used to be a standard breeding trait to make sure the tomatoes came off the truss cleanly (stems can pierce stacked tomatoes). And now some varieties are bred to keep them on...

*Plus it's fun, which I won't argue with!

Holland Infographics

I just got back from Wageningen, NV.* The Netherlands is a very wet country, but we had excellent weather and I had a lot of fun meeting everyone at the headquarters. And such a cool town! Same population size as Ithaca or Davis, but with a denser downtown, older buildings and a much more bike-friendly infrastructure...

On the Road (again)

It feels weird to be packing up my bindle-Civic again.

Toothpaste for Dinner on Mass Spec

h/t: Mass Spectrometry Blog

Recycling means it never happened - a rant

The NY Times has a great article about environmentalism in the Fashion & Style section: "Buying into the Green Movement"

Basically it describes a trend I've gotten very tired of - people using "eco-conscious" choices to justify indulgent consumption.

• It's not good for the environment to throw out perfectly-good item A so that you can replace it with more efficient and eco-friendly item B.
• Composting food does not mean you didn't waste your leftovers.
• Buying "biodegradable" stuff is worse than meaningless.
• Recycling doesn't magically mean that you never consumed that item in the first place... *cough* reduce, reuse *cough*
• Using cloth grocery bags is pointless if you're just going to buy plastic bags to throw your garbage and recycling in anyway
• Bottled water is stupid unless your town has a specific problem with contamination. You weren't too good to drink out of the hose as a kid, why are you too good for a faucet now?
• You can't justify burning jetfuel on overseas vacations because it "helps people from different cultures understand each other."
  

The best I've heard recently? A new "biodegradable" kitty litter made from a wheat product. Awesome. So now we're also turning something inherently valuable (food) into something for cats to pee on. Thank god our subsidies make food so affordable!

Tobacco!

Humans sure love tobacco. It's the world's most widely-grown non-food crop (117 countries) and exists as 1500 varieties in the USDA database alone.

It's also one of the most-studied and best understood of all plants. 3,000 chemicals have been identified in the plant itself and 4,000 have been identified in its smoke!

Nicotiana tabacum is the main commercially-grown species and is thought to be descended from some combination of wild species such as N. sylvestris (the gardener's woodland/night-scented tobacco). Many of these wild Nicotiana species, which are found around the world, are also able to accumulate nicotine and related alkaloids just like N. tabacum.

Vanishing Veterinarians

I shouldn't have been so surprised to learn that the same trends I've seen in plant ag research are going on over in the veterinary buildings.

I hear that the famous vet schools are all replacing their large animal vets with medical mouse scientists as rapidly as they can get the old dudes to retire. We still have a big chicken research center here in Upstate NY, thanks to the influence of the professor who invented the nugget, but apparently the only other remaining U.S. poultry programs are in Arkansas and Delaware. I guess all the ag schools are fighting to climb aboard the NIH's cancer train. And I suppose no sensible student is willing to spend one or two hundred thousand dollars to learn how to birth calves in the middle of the night...

a Call for Translational Genetic Engineering

Anti-GM activists love to point out how the much-hyped promises of genetic engineering never really came to pass, and they're absolutely correct - we've had this technology for 25 years and have almost nothing to show for it. The thing is, many of these game-changing, high-tech crops have been created, they just haven't been released.

Dennis Gonsalves, famous for the transgenic fruit that saved the Hawaiian papaya industry,* spoke recently on campus. The approach he used to create transgenic virus resistance has been proven for years and yet virtually no resistant crop varieties have been released - which is especially tragic given the many crippling viral diseases of the developing world.

Dennis' experiences illuminate some reasons behind this.

Don't wait for your variety to be perfect
The photo above is from his first greenhouse trial after transforming the papaya on the left with novel virus resistance. Conventional wisdom dictates that the next step would have been years of tests and breeding to produce the best possible version - but by then (with additional years required for regulation) the papaya industry would have been wiped out and there'd be no farmers left to adopt the resistant varieties.

Don't overthink it
Learning to navigate regulation was much more complex and difficult than Dennis could have imagined. He repeatedly asserted that it was best to be a little naive and overly optimistic and just jump in with both feet. There are always people who "know" that you won't be able to get your variety through regulation or that the public won't accept it, but the truth is you never really know until you try.

Don't miss cultural opportunities
He also emphasized opportunities that arise from cultural issues. Hawaiian papaya farmers were desperate for a cure for papaya ringspot disease and were eager to try the transgenic variety. Furthermore, this population (many of who were of Asian and Japanese birth) had a sophisticated understanding of the Japanese consumer and fruit market. Their industry organization was therefore able to make great inroads into the Japanese papaya market.

Although regulation of transgenic crops is extremely rigorous in Japan, it's also apolitical. When transgenic papayas were found in loads of putatively non-transgenic Hawaiian papayas twice, Japanese regulators worked with the Hawaiian industry to establish proper identity preservation systems. If the same had happened in Europe, it surely would have led to a scandal and a ban on all Hawaiian papayas. As it stands now, Japanese approval of the transgenic variety is expected this year, 12 years after the process was initiated.

Dennis also described his disappointing failure to get virus-resistant papaya approved in Thailand, where this fruit is a core part of the traditional diet. Despite promising field trials, interested farmers and a rapidly growing virus epidemic, the Thai government has vacillated with moratoriums on transgenic field tests (largely thanks to Greenpeace protesters who broke into one of his test plots). It's unclear whether the government will lift the current research ban.

Overall he emphasized the importance for scientists to take this process into their own hands and really be tenacious.* It's not easy to usher a variety through the regulatory process, but it's profoundly important. Paraphrasing Dennis, 12 years from now, no one will read your articles, but your crop may help feed a nation.


*I should emphasize that the Hawaiian papaya "industry" consists of indigenous and immigrant family farms, hand-tended on small plots of land.
**As opposed to giving away control to a company or, more commonly, never doing anything with it at all.
Interestingly, an audience members asked what difficulties he had with corporate patents (as they key technologies required for genetic engineering are all patented by companies such as Monsanto). He said that on the contrary, companies provided absolutely no obstacles to his work. This sector was trivial to the big seed companies anyway and, more importantly, they've learned over the past two decades that their profits depend on good communication with the public, especially with altruistic projects like transgenic papaya.

Cultural Consquences of Corn Color

Corn meal in Africa is white.

Although the carotenoids that color yellow corn are great for human nutrition, they make make corn meal more susceptible to going rancid. On a hot continent with limited refrigeration, this is a real drawback. The same story has played out with rice - although many modern people enjoy the more complex taste* and greater nutrition of whole grain "brown" rice, "white" rice (free from the oily bran and germ) can be stored much more easily (especially in tropical climates). In both these cases, practical food choices have become entangled with deep cultural meaning over time. Although rice seems like a homogeneous commodity to most Westerners, many Asian cultures take great nationalistic and ethnic pride in "their" variety of white rice.

Corn meal in the United States is yellow because virtually all our corn varieties are yellow (whether for corn flakes or cows).** In many parts of Africa, however, yellow corn is exclusively used for animal feed. This pattern was likely established for practical storage reasons, but now many (especially more wealthy) Africans have a strong cultural preference for white corn. This apparently has caused some tense diplomatic moments as the U.S. offered donations of what was seen locally as animal feed...

My boss read that the same thing happened when the U.S. helped to rebuild Germany after WWII. Our corn-loving forefathers sent huge shipments of their favorite grain to a country that considered only wheat and barley to be fit for human consumption, apparently producing some very insulted and hurt East Germans who felt patronized by an arrogant U.S. that expected them to eat "animal feed."


*not me, yuck!
**it's easy to find white fresh sweet corn here, but the field corn (that's dried and processed into meal) is almost exclusively yellow