Strange Maps

What a cool site!

h/t: Agricultural Biodiversity Weblog

Outlaw (DIY) Biology Symposium

The Outlaw Biology: Public Participation in the Age of Big Bio symposium is currently running at UCLA.

This whole genetic-engineering-in-your-garage movement scares me - particularly with all the anti-establishment language recorded by DIYbio's post. It's really easy to picture some malcontent reproducing some formerly-extinct human pathogen or changing the transmissibility of a living one. We're not there yet, but eventually we'll also be capable of creating organisms that affect ecosystems in really meaningful ways. It's easy to think of good and bad results of this (waves of new invasive organisms or acid-tolerant reef-building corals?) but I suppose it's all totally moot. It's going to happen in our lifetimes and no amount of regulation can stop it (not here, not in China...).

I guess the only solution if for professionals to get involved in the movement and encourage its development. Maybe if citizens get as involved in genetic engineering as they are with software and the Internet we can dilute out and keep an eye on the cranks.

Thoughts?

h/t: DIYbio

Advances in Genetic Engineering

Genetic engineering is slowly but steadily catching up to other forms of engineering in being more reproducible technical skill than trial and error art. Here are some cool new advances I heard about at PAG.*

Cis/intra-genics
Would you feel better about eating genetically engineered rice if you knew it only contained rice DNA and not DNA from mustard, bacteria or fish? Most people would. That's the idea behind cis-genic (a.k.a. intragenic) engineering (as opposed to transgenic, get it?). One speaker had a particularly fascinating presentation where he described how his group searched through the rice genome to find stretches of DNA sequence that were very similar to the flanking sequences that we already use to inject DNA into plant genomes (e.g. mimicking the TDNA left and right borders of the Agrobacterium plasmid).

This approach strikes me as somewhat cynical... I'd rather use the optimal sequence for any given engineering project than try to search for a native sequence that's close enough to work (while explaining to the public why genetic engineering isn't inherently scary in the first place). At any rate, I applaud them for the sophistication and precision of the tools they're developing. These types of advancements will really help us to engineer organisms rationally (as opposed to our current approach which generally involves making thousands and thousands of transgenic individuals and then exhaustively testing them all to see which one turned out right).

New Commercial Products
The big seed companies are getting close to releasing transgenic plants with traits that benefit consumers themselves and not just ag and food companies. I've predicted before that the public opposition to GMOs will largely evaporate as they see benefits of genetic engineering in their day to day lives - we'll see if I'm right.**

One company pointed out that 2/3 of fat in the American diet comes from soybeans - so changing the oil profile of soybean varieties can have a big impact on health. They're close to releasing new varieties that have no trans-fats and low saturated fats (through a combination of transgenic and natural*** mutants). These changes actually made the major oil profile of soybeans the same as olive oil! If olive oil really is as healthy as nutritionists seem to think, I'd bet a lot of money it's due to more than just the oil profile - but making 2/3 of the average American's fat intake better is definitely a step in the right direction.

They're also finishing up work on potato varieties that produce much less acrylamide when fried, and are less subject to browning, bruising and starch degradation (all important consumer traits). One speaker pointed out that many crops (like potato) are extremely difficult to improve by breeding and will greatly benefit from transgenic techniques. The same speaker pointed out that after a massive effort, a natural resistance gene for apple scab was once found, but by the time they were able to breed it into modern varieties the apple scab fungus had already evolved to overcome it! Similarly, the speaker invoked the story of Marge the cow, who has a natural mutation that makes her milk naturally skim. Butter made from this milk can apparently be spread even while frozen! Breeding a commercial herd from her would take a very long time, but genetic engineering could quickly make this trait available to everyone (no word on if anyone's been working on this).

One of the Monsanto talks showed an impressive graph charting the increases in yield (and decreases in water and chemical input per bushel) that have occurred in the past several decades. Pesticide and water use in particular seemed to rise from the '70s to the early '90s, when it began to crash accompanied by increased regulation and introduction of transgenic resistances. The speaker talked about the wide differences in corn yield in different parts of the world (from an average of 150 bushels/acre in the Midwest to only 20 in Sub-Saharan Africa). Their stated goal is to double corn yields and cut chemical inputs by 2/3 by 2030. Some corn breeders I've met thought this absurdly optimistic, but we didn't land on the moon by shooting for Antarctica...

Finally, there was another plug that both Monsanto's famous first generation glyphosate herbicide and Bt pesticide traits will be entering the public domain very soon. The speaker, of course, emphasized how much better their patented, second generation versions of these traits were. I know there's been a lot of concern about whether Monsanto would require farmers to destroy all seed with the original trait (they won't), but you all should know that the DNA sequence of these traits are freely available and I (and thousands of my colleagues) could walk into my lab any day of the week, build these DNA sequences, and stick them into any plant I wanted to easier than I can change the oil in my car.**** I'm sure there are some little seed companies doing this right now.


Also - Howard Jacobs, one of the plenary speakers, told a series of amazing, rambling stories on the frontiers of medical science - one of which seemed to involve forcing human somatic cells to become stem cells and then injecting them next to the liver of a mouse - which then (based on the types of cellular signals are present in that part of the body) induced the human stem cells to form a tiny, anatomically correct liver next to the mouse's liver... Our communications technology seems to have surpassed the original Star Trek and now, I guess, our medicine is getting close!

* As a total aside, our complementary notebooks contained high-quality paper that was marked "100% recycled." Since when can we make any paper 100% recycled?
** Roger Beachy once gave the example of a lab that tried to commercialize a strawberry that was resistant to Botrytis gray mold (i.e. why almost all supermarket strawberries are gross and go bad in a few days)
*** Companies are putting huge amounts of effort into finding new traits in natural germplasm - it's easier than reinventing the wheel and presents less of a regulatory/PR hurdle.
**** The oil plug bolt's all rounded off and the idiot mechanics at walmart always put it on with air

Organic Crop Rotations

Crop Rotation on Organic Farms: A Planning Manual (Mohler and Johnson, free download here) is the result of an organized effort to capture local knowledge of popularly-nominated expert organic vegetable growers in the Northeast.

It was interesting to listen to the seminar speaker describe the impetus and main findings of this study. Textbook descriptions of crop rotation apparently tend to be rigid and idealistic - so the authors made an attempt to describe them in a more intuitive fashion that will facilitate on-the-fly rotations that allow for unpredictable weather and markets.

Crop rotations are key to preventing the buildup of host-specific pests and pathogens, while evening out soil nutrition when chemical applications aren't an option. Completely stripped down, they basically recommend that you keep a given plant family (e.g. tomatoes-potatoes-peppers-eggplants, legumes or melons-squash-cucumbers) in a given plot for only 1 in every 4 years. Grasses can be cycled more quickly since our local pests and pathogens here tend to be specific at the Genus instead of Family level. They also give common sense advice on how to prioritize which crops should go in the best fields.

I was shocked to hear that these farmers have virtually NO weeds in their fields. Apparently they pull this off with zero-tolerance for weed seed contamination in crop seed or compost and summer fallows (e.g. no bare dirt), finished off with hand pulling. On most farms, weeds are the No. 1 problem - so this is pretty impressive management!

I was also impressed by the extensive use of intercropping.

During the Q&A, we learned that overcomposting is a major problem (that doesn't help keep weeds down and is at times absurdly unsustainable). I guess being surrounded by horse farms looking to get rid of tons of manure is tempting towards overuse...

These farmers don't rotate animals onto their fields since they don't want the soil (that they work so hard to fluff up) to get compacted. They may occasionally bring in chickens or ducks (to eat slugs), but having to deal with fences to keep the animals in and predators out is rarely worth the effort.

One audience member asked if today's expert organic farmers are any better than their counterparts in the Middle Ages. The speaker mused that since all of this knowledge simply arose from lifetimes of local observation, that they probably aren't.

(Outside of new technologies of course!)