James and the Giant Corn

April 15, 2010

Don’t judge the genetic diversity of a species by its cover

Filed under: agriculture,Genetics,Plants — James @ 12:14 am

Photo: ekpatterson, flickr (click photo to see in original context)

There are more differences in the genomes of two unrelated corn plants than between the genomes of a human and a chimpanzee (two species separated by 3.5 million years of evolution).

On the other hand, two unrelated human beings, members of the same species, have more than four times as many genetic differences as two unrelated heirloom tomatoes.

Genetic Diversity:

Corn vs. Corn > Human vs. Chimpanzee >> Human vs. Human >> Heirloom Tomato vs. Heirloom Tomato

Now the fact that any two human beings are more closely related to each other than either is to a chimpanzee should be obvious to anyone who gives it a moments thought.

I plan to poll my sections tomorrow to see how many of them would put corn and heirloom tomatoes in the opposite positions, but many have figured out my feelings about corn, so they’ll probably guess it’s a trap.

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April 9, 2010

The Peach Genome Is Out

Filed under: biology,genomics — Tags: genome, peach — James @ 3:28 pm

1.1 pound peach from the Berkeley Farmer's market.

Here. I had no idea anyone was even considering sequencing the peach genome until I heard a single off-hand comment at the maize meeting last month, and all of the sudden here it is. And in better shape in its first release than some genomes are even after they’re published.

This is a pre-publication release, so the Fort Lauderdale Convention is still in effect,* but the peach genome looks really great from the quick and dirty analysis I have already run. They’ve already got the genome assembled into pseudomolecules (chromosomes), unlike some genomes I could mention that have already been published, and marked the locations and structures of genes in the geneome (there was a weird period last summer when there were pre-release versions of the maize genome organized into chromosomes, and pre-release versions with the genes marked, but none that had both.)

*In short, you or I can download the peach genome, play around and study it to our hearts content, but we can’t publish anything on it until the people who actually sequenced the peach genome publish a paper describing their work.

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April 6, 2010

NSF Fellowships and the Importance of Loving Your Work

Filed under: Uncategorized — James @ 3:08 pm

Late last night the National Science Foundation announced the graduate students who recieved the prestigious NSF-Fellowship. I was not among them, but I’m still pretty happy as my own average rating from reviewers climbed almost two points (consider Poors 1, Fairs 2, Goods 3, Very Goods 4, and Excellents 5). I certainly haven’t gotten any smarter or more diverse in the past year — which was why I didn’t have high expections for my application this year –, the main thing that changed was that I found (and was able to join) a lab where I could do science I was excited about, and I’m guessing that excitement came through in my research proposal and personal statement.

There’s a lesson here for anyone entering grad school in the near future or currently rotating through labs: being exciting about the research you’re doing is important. It can make the difference between grad school being the hardest most miserable years of your life, or some of the best.

It was certainly a successful year for my department (Plant and Microbial Biology), with four current graduate students and several new incoming students recieving the award! Congratulations to everyone who got great news last night (or woke up to the news this morning).

If you’d like to search the awardee and honorable mention lists, they can be found here.

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April 5, 2010

Why popcorn pops

Filed under: biofortified,food — Tags: corn, popcorn, sorghum — James @ 11:52 am

Popped corn Photo: D3 San Francisco, flickr (click to see photo in original context

Popping corn, or anything else, all comes down to pressure. Pop-corn has a particularly impermeable pericarp (the corn kernel’s shell), so as it is heated, the water inside the kernel vaporizes into steam and the starch turns into something close to a liquid. Eventually the heat creates enough pressure to split the pericarp and the starch of the corn kernel bursts out, resolidifying into the distinctive shape of popcorn. If there is even the smallest hole in the pericarp, the steam can escape from the kernel as it’s generated so the pressure never builds up enough to explode the pericarp — the reason some kernels will fail to pop in every batch. The explosive build up of steam is also the reason tea kettles need to be able to release steam while they’re used to boil water. The alternative would be exploding tea kettles which are a lot more dangerous (and a lot less tasty) than exploding corn kernels.

Un-popped popcorn photo: MissTessmacher, flickr (click to see photo in its original context)

It was this reason (along with my discovery of the website on April 1st) that I was so suspicious of the idea of popped sorghum a few days ago. Thanks to Party Cactus and Jeremy, I now know that sorghum does indeed pop like corn (there’s even a variety called “Tarahumara Popping”) and, in fact, thanks to the link Jeremy provided, I’ve discovered that most grains and even some other things (including cowpeas!) can be popped using the proper equipment. (more…)

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April 1, 2010

This one has me stumped

Filed under: Uncategorized — James @ 9:07 am

Was pointed at a website for popped sorghum marketed under the name popghum. The greater supposed advantages over normal popcorn are:

It’s got fewer calories and less fat than popcorn, and best of all, it has no hulls to get stuck in your teeth!

Website is very slick with lots of text recycled from page to page and without many confirmable details and you can’t actually place an order but the story stops just short of the being outrageous enough to be an obvious april fools prank.

I’d like this to be true (even though they use organic sorghum) because I’m almost as pro-sorghum as I am pro-corn, but I don’t even know if sorghum can be reliably popped. If you were ever been bored enough as a kid to try popping sweet or field corn, you too know what an unrewarding experience it is.

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Best of April Fools So Far

Filed under: Link Posts — James @ 8:04 am

Plant Gene Ring Tones: “My species ring tone sounds a lot like Arabidopsis thaliana. How can I find a better one?”

Science and Nature become one: “readers will have the option of Skyping authors directly to share their thoughts and feelings about a paper simply by clicking that author’s name” Cover of the first issue of Natural Science.

Undergrads sequence sea lion genome: “uses next-generation sequencing technology as one of the tools to investigate the interactions between the large and small organisms within an ecosystem.”

Early review of the iPad: “Anyone who asks this has obviously never sauntered up to a highly fortified UPS depot and emerged with one of the hottest new tech gadgets before anyone else.”

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March 31, 2010

BBC on drought tolerant maize/corn

Filed under: agriculture,Feeding the world,Link Posts — Tags: africa, bbc, corn, maize, monsanto — James @ 8:31 am

There’s a new episode of BBC’s Discovery: Feeling the World out this morning. It’s only 26 minutes long, and the full piece is definitely worth a listen, but if you don’t have 26 minutes, the meat of the post can be summarized in 8 minutes:

3:20-7:54: Introducing the subject, developing drought tolerant varieties of maize in Africa, and the fact that the researchers working on it as using conventional breeding, marker assisted breeding and a genetically engineered trait Monsanto. When battling starvation, you use any tool that comes to hand.

18:40-21:20: This part is almost hard to listen to. You can hear the raw emotion in the researcher’s voice as the reporter keeps trying to make genetic engineering sound, at best, like a last resort. Couldn’t they just try irrigating more crop land she suggests?

25:10-end. Conclusion. I also thought this part was very powerful.

A few complaints: (more…)

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March 30, 2010

What is the Joint Genome Institute?

Filed under: Uncategorized — James @ 8:49 am

They’ve produced an incredibly slick video to answer that question for the general public.

Of course now I want a video like this to introduce my own research…

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March 26, 2010

The two genomes of maize

Filed under: genomics — Tags: maize, sorghum, synmap — James @ 12:24 pm

I recently go back from the maize meeting. I mentioned before that big part of the reason to do poster presentations is to get comfortable discussing ones research with people who haven’t specialized in the exact same subject. In my case, my poster got a fair bit of interest which was great. (Although I was surprised which parts people were most interested in.) But there were also a couple of concepts I had a lot of trouble getting across.

It’s too late to do me any good at the maize meeting, but I have created the figure I think I needed to explain those ideas. Too late for the maize meeting, but maybe I can squeeze it into my qualifying exam proposal. Or maybe the next time I get a chance to give a talk on campus. Let’s just not get into how much of my morning I spent putting this together, and pretend it was a good investment of my time ok? (more…)

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Marriage vs The PhD

Filed under: Uncategorized — James @ 9:45 am

If you have been associated with academia for any length of time you probably already read PhD comics, but anyone who doesn’t read it already should definitely check out today’s comic “Marriage v The PhD”