James and the Giant Corn Genetics: Studying the Source Code of Nature

October 31, 2009

Predictable Spinning of Squash

I dont have any picture of pumpkins handy, so this watermelon (and fellow cucurbit) will have to do.

I don't have any picture of pumpkins handy, so this watermelon (and fellow cucurbit) will have to do.

What could be a more fitting topic for a Halloween post than cucurbits, the family of plants that (in addition to crops like watermelon and cucumber) include squash and pumpkins? Yeah, I know it’s a stretch.

A week ago a paper came out in PNAS (the proceedings of the national academy of sciences. A very prestigious journal, one step down from Science or Nature), that showed when an artificially inserted gene in squashes that provided virus resistance was introgressed into a wild related species it actually made them less fit. Short version: the wild squash also suffer from the virus which attacked domesticated squash but are also attacked by beetles, and the beetles prefer to eat squash without the virus. Tomorrow’s Table has a much better and more complete explanation of the research.

In that post the very first commenter predicted the result, that in this particular case a transgene (like most genes involved in domestication) was beneficial for farmers but not for wild plants, would be spun into “another failure for GMOs” when the real message is “we were worried about pollen drift, but in this case it turns out we didn’t have to be.”

He was right. (more…)

October 30, 2009

Mt. Tamalpais, Invasive Species, and Herbicides

Filed under: agriculture,Plants — Tags: , , , — James @ 4:20 pm
On the side of Mt. Tamalpais in in the summer.

On the side of Mt. Tamalpais in in the summer.

Mt. Tamalpais sits across the San Francisco bay from me, on a clear day you can even see it from the hills behind the Berkeley campus. Apparently, the region around Tamalpais is also home to species, especially plant species, found no where else. These local species are threatened by other, invasive, species that have been brought to northern California from all over the world. Some accidentally, but many more imported as ornamental species for private gardens.

Invasive species aren’t something I worry a lot about, but we had a great presentation in one of my classes on Tuesday by a woman who’d spent several years fighting the good fight against them across the bay.

Take French Broom, a woody shrub from the Mediterranean. California’s native habitat is quite similar to the Mediterranean climate and the species is thriving, growing so densely that it chokes out tree seedling before they can grow big enough to escape the thicket. The plant is out-competing FORESTS! And it’s also taking a bite out of the ecological niche currently occupied by alpine grasslands like the one pictured.

I like grasslands. (more…)

October 29, 2009

Crops and Colbert

I love the Colbert Report, but could somebody who knows something about agriculture and plant genetics please sit down with Stephen Colbert until he knows what he’s talking about food wise? Every so often he’ll make these incredibly uneducated jokes about food production. It’s weird to be suddenly jerked out of enjoying the episode as I remember “These guys are comedians, not experts.”

Back in April he turned the debate about Michelle Obama’s organic garden into a crack at round-up ready soybeans. Yesterday*, in the middle of a funny bit about breeding people who might actually be able to get health insurance, we got the mocking:

After all, selective breeding and genetic modification have worked miracles for our fruits, vegetables and livestock.

Yes they really have. Let’s leave genetic engineering out of the mix (after all most people having eaten a genetically engineered fruit or vegetable in their lives, unless you’re a big fan of papayas, or certain kinds of squash, and genetic engineering of livestock is way behind where we are with plants). Selective breeding of plants over thousands of years is what feeds the wold today and has for millennia. Before the advent of agriculture, which was made possible by selective breeding to domesticate plants and animals, the world supported, what, 5-10 million hunter gatherers, spread across the entire face of the globe?

Without selective breeding of crops and livestock we wouldn’t have a civilization to begin with, let alone one advanced enough to have developed not only our complex (but good) system of medicine but also our complex (and not so good) medical insurance.

I’m serious, does anyone know if there’s a way to nominate people to be interviewed on the Colbert Report? I want to nominate Pamela Ronald and Roger Beachy.

*I have to catch the Daily Show and Colbert Report the day after  the fact on Hulu.

Try Ubuntu

Filed under: Computers and Coding — Tags: , , , — James @ 5:48 pm
Screen grab of Nymph my at-home Ubuntu Box. Click for fullsize.

Screen grab of Nymph my at-home Ubuntu Box. Click for fullsize.

With the latest release of Ubuntu (a flavor of Linux) open source operating systems have never been more user friendly. It’s still not for everyone, but how are you going to know whether it is for you or not if you don’t try? And trying Linux is so easy these days. After burning a CD or DVUD with the disk image downloaded from the Ubuntu website, simple restart your computer and you should be given the option to either install the OS to boot direct into Ubuntu’s version of the Linux desktop. Trying out the desktop without installing it doesn’t affect anything installed on your hard drive, your computer has just booted up from the CD. (The downsides are that reading data from external media can be slower than from the hard drive, and since the CD is read only, nothing you do in this test mode will be remembered after a restart.) But starting up your computer this way isn’t a long term solution, it’s just a way to find out whether Linux is something you’d be interested in installing and learning to use. If you do, the CD will walk you through installing Linux next to your existing OS so you’ll have the option to start your computer into either one.

Why should you try Ubuntu? There are all sorts of philosophical big picture arguments people make about open source software (software than can be freely redistributed or modified by anyone), and another set of pragmatic ones about never having to pay for another version of Windows or Mac OS X, let alone Microsoft Office, and Ubuntu’s safty from viruses and spyware. There’s even a third set based on personal hatred of Microsoft and everything it represents. I can get behind all of those, but for me, there’s a single compelling reason to spend at least part of every day using Ubuntu or another version of Linux.

On a window’s computer the gap between being a computer user and a computer programmer is a vast and gapping chasm. Trying to jump from a person who uses computer programs to someone who writes them takes a lot of knowledge, and it takes a long time before what you learn about programming actually helps you accomplish useful tasks. On Macs the gap is narrower, and that’s where I first started writing code. In Linux the gap is the smallest of all. People can even drift across it accidentially. And the code you start writing is immediately useful for things like data analysis.

Linux breeds superusers. People who don’t just use programs others have written, but when confronted with a question no one else has ever asked, or a problem no one else has ever addressed, can still get their computers to do what they want. Two guys who came in the same year as me started using linux this past summer for the first time for a two week python course (only one week of which was useful, I was there). Now one of them is writing C++ code for his phylogenetics project, and the other programs his lab’s liquid handling robot. Both are getting things down in weeks or months that without the ability to write their own code would take a big part of their entire doctoral research (or just wouldn’t even have been considered feasible in the first place.) As in any field, once you know enough to get results, learning begins to snowball and before you know it you’re doing things you never thought you’d be able. (more…)

October 28, 2009

I’m disappointed in the Des Moines Register

Filed under: agriculture — Tags: , , , — James @ 10:45 pm

Normally the Des Moines Register is pretty good about getting their facts straight when it comes to crop breeding and genetic engineering. After all of the major newspapers left in this country, their readership is probably the most likely to catch any slip ups.

So I was surprised when reading a story about a small breeder who’d developed soybeans resistant to nematodes to find this:

The seed industry has battled the parasite in the usual way, with genetically modified seeds designed to resist the parasites. As has happened in the age of genetic engineering, the nematodes* gradually evolve to overcome the biotech resistances.

I have no idea where Dan Piller, the author of this piece, got this information. Unlike new media outlets like blogs, newspapers don’t ever have to cite sources, the assumption being that they’re reliable enough to be taken at their word. But I defy the Register in general, Dan Piller in particular, or any of the people already linking to this piece to name a seed company currently selling seed genetically engineered to resist nematodes. It would be a very beneficial trait. When I worked at the Danforth Center, Chris Taylor was studying how nematodes interact with their prey. I’m also told Monsanto recently announced that they have been working on nematode resistance using RNAi (though I couldn’t find any internet sources to back that up). Even so that’s a trait still in development, and this article gives the impression transgenic nematode resistance has already been commercially sold and failed.

That said, nematode resistant soybeans would be a Very Good Thing™ regardless of whether the resistance is the result of transgenes or conventional breeding. Nematodes are a big problem for yield. However, whether the trait is transgenic or non-transgenic, any single resistance trait will eventually be overcome by the continued evolution of whatever organism it is protecting against.  One of my plant breeding instructors in undergrad said that a good resistance allele (talking about conventional breeding, not genetic engineering) is one that protects a crop from a disease or pest for a decade after the trait becomes widely available.

That window can be stretched with proper care. Bt crops that resist against specific insect pests have been on the market for ~15 years and the development of resistant insects has been slowed planting refuges of non-resistant crops.

*Nematodes are microscopic worms that live in the soil. They latch onto the roots of crops (and other plants) and suck out nutrients. They’re the plant equivalent of tapeworms. With all that energy going to feed parasites, plants have less energy left to … well produce food for us humans.

October 27, 2009

Banana Biology

When I was giving my lecture to on phylogeny and tetraploidies, I found out not everyone knows why bananas don’t have seeds.

The reason the bananas we eat don’t have seeds is that they are all sterile. A long time ago the Cavendish bananas first came into being when a tetraploid banana (that is a plant that has four copies of every chromosome instead of the normal two) mated with a normal diploid banana. The result, a banana with three copies of every chromosome couldn’t mate or produce seeds. One of the steps in making reproductive cells (the analog of human sperm and egg cells) is the even dividing of a plant’s chromosomes into two reproductive cells.* Normal diploid cells can easily divide into two cells (one copy of each chromosome in each cell), tetraploid plants can divide the same way (two copies of each chromosome in each cell). Hexaploid, three copies in each and so on. Odd numbers of chromosomes don’t work. The plants can’t successfully make the cells it needs to reproduce, if it can’t reproduce it can’t make seeds, and that is why bananas (or seedless watermelons) don’t have seeds. (more…)

October 26, 2009

Time to Eat The Dog

Filed under: Feeding the world,Fun With Numbers — James @ 11:37 am

With a title like Time to Eat the Dog? A real guide to sustainable living you can sure a book will sell a lot of copies, and earn the authors a fair bit of hatemail at the same time. The book itself by Robert and Brenda Vale received mixed reviews on amazon.uk. But what about the premise of the book? (Which isn’t actually that dogs make great food sources, but rather that keeping carnivores as pets is a major resource burden.)

In an article on new scientist, the authors calculate that it takes .84 hectares (that’s over 2 acres!) of farmland to support a medium sized dog. Larger dogs like German Shepherds have a footprint of 1.1 hectares (2.7 acres)  Through some calculations they then start comparing the impact of a dog to various cars, but that hinges on assigning energy production values to farmland, which in my opinion is the weak link in their calculation.

So why not look at how dog ownership compares to the land required to feed a human being? (more…)

October 25, 2009

Bananas: The Original Not-From-Here Fruit

Filed under: agriculture,Crop Profiles,food,Plants — Tags: , , — James @ 6:03 pm
A banana storage room in Salt Lake City in 1913.

A banana storage room in Salt Lake City in 1913.

As early as 1905 the United States was importing 33 million bunches of bananas a year. Bunches averaged more than 100 individual bananas. Billions of bananas were being consumed in America before the Ford Model-T car was first produced. (more…)

October 24, 2009

Microbial Art

Filed under: biology,Link Posts — James @ 5:45 pm

Check out some of the gorgeous art people can make in petri dishes.

Clearly the people who create these have far steadier hands than I do when it comes to smearing out colonies.

by Niall Hamilton

by Niall Hamilton

Relaunched Tomorrow’s Table

Filed under: Link Posts — James @ 4:58 pm

Yesterday I linked to Pamela Ronald’s relaunched blog at Scienceblogs. There are over one hundred million blogs on the web (and that’s already an outdated number). Many are abandoned, as for all intents and purposed jamesandthegiantcorn was this summer, but even so, simply getting heard over the background noise is a struggle.

Becoming part of a popular and well known community greatly increases those odds of having the voice to each a substantial audience. It’s been a real treat to follow the discussions the posts of the new Tomorrow’s Table have already launched. I highly recommend checking them out.

I can also speak from personal experience in saying that increased traffic and comments definitely make updating a blog more exciting, which in turn leads to more interesting, and just plain more, updates. And so-on in one of those wonderful positive feedback cycles. Given that I expect we’ll be hearing a lot more from Tomorrow’s Table in the future.

I also hope it is ok that I am a litte envious. Will just have to use it as a motivation to work even harder both here and on my actual research.

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