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

December 19, 2009

Lack of Daily Updates

Filed under: Site Business — James @ 1:48 am

Just a quick update. I’ve been trying to keep a couple too many balls in the air, with the result that I have, unambigiously, ended my stretch of daily updates (and basically dropped off the face of the internet).

Anyway, to any loyal readers, I intend to return to daily updates either after Christmas or at the start of the new year. I’ve proven I can do it. It’s just a matter of making the time.

December 14, 2009

You Think I’m Evil… What Next?

Filed under: Link Posts — Tags: , , , — James @ 11:18 am

I’m a public sector plant biologist. Your tax dollars at work for better or worse. But even I have had similar encounters to the one Janice so accurately describes in this post I was pointed to on twitter*:

I asked what she does and she says mostly volunteer work now.  She asks me and I reply that I work in the cotton business for a company that improves seeds… its Monsanto & the seeds are called Deltapine.

There was an audible gasp, and her eyes opened so much it startled me. She said “Monsanto is evil.” This is where the stress came in. I have read this before, but the fact that I was hearing it today since I’d been making a lot of effort to stay positive seemed like a test. Really. And to have the person, who I’ve pleasantly visited with for five minutes, looking right at me like I’m evil,having just said that heard I am part of Monsanto. It was certainly a test…a test of the Janice-response system.

Seriously, how often do you call someone evil & mean it? She was dead serious.

But the moral of this post isn’t that it sucks to be a plant biologist, it’s that, as painful as it is to have someone look to in the face, and call you evil, there’s still the chance for engagement. At this point I probably would have either changed the subject or put in my iPhone earbuds and hoped the flight would be over soon, but Janice didn’t get mad, didn’t drop the subject, and it sounds like she actually managed to get the other woman to reconsider her categorical opposition to biotechnology. I highly recommend reading her whole post.

*Thanks @MikeHowie and @cornguy

December 13, 2009

Panda Genome

Filed under: biology,Genetics — Tags: , , , , — James @ 5:11 pm
Can you imagine how much easier it would be to get funding if you too worked on panda biology?

Can you imagine how much easier it would be to get funding if you too worked on panda biology?

Nature just released a pre-publication copy of a paper detailing the sequencing of the panda genome. The genome was sequenced and assembled using entirely 2nd generation sequencing technologies (specifically the Illumina sequencer) which produced reads that averaged only 53 basepairs long.*

The panda they chose was a three year old female, and they got such resolution (the average individual base pair was sequenced 73 times!) they were even able to identify individual changes in sequence between her two copies of each chromosome.** From this they were able to estimate a difference in the DNA sequence (called a SNP***) occur once every 740 bases which is almost twice the rate of humans. (more…)

December 12, 2009

The Water Chestnut

Filed under: Crop Profiles,food,Plants — Tags: — James @ 7:45 pm
Botanical illustration of Eleocharis dulcis, the Water Chestnut

Botanical illustration of Eleocharis dulcis, the Water Chestnut

The water chestnut is one of those foods I’ve eaten my whole life without knowing anything more about it than flavor and appearance (and that only because it so often shows up in frozen vegetable mixes).

The scientific name for the Water Chestnut is Eleocharis dulcis, and it’s often classified as a sedge.* It’s also a quite awesome plant. Consider:

  • The visible parts of a water chestnut plant are leafless stems that perform photosynthesis. (The water chestnut has almost completely abandoned leaves!)
  • The edible part of the plant is a botanical structure called a corm** which is a modified underground stem used by a plant to store energy (water chestnut plants are very much about stems). Not to be confused with bulbs like those of onions and garlic, which can look similar, but are instead made up mostly of leaves
  • The reason water chestnuts remain so crunchy after cooking is that their cell walls are reinforced by special phenolic compounds, the same class of molecules as capsaicin, the molecule that makes chilli peppers spicy.

The genus Eleocharis also contains species like Eleocharis vivapara which switch between C3 and C4 forms of photosynthesis depending on whether they’re grown on dry land or in swamps. The relative advantages and costs of these two different forms of photosynthesis are worth a post on their own, but I’d always assumed it was an either/or choice and didn’t realize ANY plant species could pick to use whichever system was best suited to the local environment.[citation]

Domestication: (more…)

December 11, 2009


Filed under: evolution,Genetics,Link Posts — James @ 7:48 pm

It was a very long day at work and I have nothing interesting to tell you.

Go check out MAT Kinase and John Hawks‘s posts on how human evolution has been driven by the dietary changes of our relatively recent ancestors, farmers and herders rather than hunter-gatherers. (At least in many cases, it’s quite possible someone reading this blog can trace their ancestry back to human populations that remained hunter-gatherers into the 20th century.)

December 10, 2009

More on the Good Guys (CGIAR)

Tracked down a paper published just under a year ago in Food Policy (a peer reviewed journal). “The impact of agricultural research on productivity and poverty in sub-Saharan Africa” by Arega Alene and Ousmane Coulibaly.* 

CGIAR spending on research targeted at agriculture in Sub-Saharan Africa (178 million dollars a year in 2003) provides 1.3 million people with an escape from extreme poverty (living one dollar a day or less) every year. Simple division would indicate the agricultural research of the CGIAR centers is saving human beings from the trap of extreme poverty at a cost of just under 137 dollars per person. Of course it isn’t that simple, there are both economies of scale** and, eventually, diminishing margins of return*** to consider, but it seems the work of the CGIAR centers in Africa are big enough to have achieved those economies of scale, and, given their calculations on the elasticity on poverty to investment in agriculture, Africa is a LONG way from having to worry about diminishing marginal returns on agricultural investment.

Given the elasticity of poverty reduction to agricultural research spending they calculate (-.22) the marginal cost* of reducing poverty by another person in Sub-Saharan Africa through investments in agricultural research is only $71. (i.e. spending one billion dollars more on agricultural research would save an additional 14 million people from poverty.) This doesn’t consider the additional postive effects of improving local agriculture (for example reducing the incidence of famine).

Finally consider this quote from the paper for a sense of the work the CGIAR centers are funding and try not to feel as impressed as I do: (more…)

December 9, 2009

Funding the Good Guys

Filed under: agriculture,Feeding the world,Politics — Tags: , — James @ 5:47 pm

Some changes are happening for CGAIR (the Consultative Group on International Agricultural Research). If you don’t know about CGAIR, they’re definitely the good guys. But don’t take my word for it. How would you classify a non-profit organization that’s been working for close to 40 years to fight hunger and poverty by improving the agricultural productivity of poor and subsistence farmers around the world. Also consider on other key fact: while plenty of people and organizations fight hungry and poverty, the effort of the CGIAR centers works.

But, like any non-profit, the work of the CGIAR centers depends on the funding they can secure. The news today is about a structural reorganization of CGIAR which, at least in theory, will make research more efficient. Previously donors who wanted a say in how their money was spent would give grants to individual researchers. Which had two undesirable consequences: (more…)

December 8, 2009

My Zygocactus is Getting Ready to Bloom

Filed under: Photo Posts,Plants — Tags: , , — James @ 11:51 am

Some background: as an exciting and awesome plant scientist as myself might be expected to maintain a wide range of plants around the house. Instead I have exactly one*, a Christmas Cactus that’s been clonally** in my family for four generations (human generations, my Christmas Cactus is only a third generation plant).

My Christmas Cactus is not happy. At my old apartment I had it on the kitchen table, where…someone… had an accident involving it and a pressure cooker. Right after we moved I left it on a windowsill with the window open and the blinds (blowing in the wind) cut into it even more. On top of all that, the new place offers only north facing windows***.

So needless to say I wasn’t expecting so much as a single flower given everything it’s been through. Which is why I was so surprised when I went to water it and discovered…

Christmas Cactus blooming... also a sample of the less than thrilling view out my bedroom window.

Christmas Cactus blooming... also a sample of the less than thrilling view out my bedroom window.

Before I rotated the plant, those two branch tips were pressed right against the window, which makes me think something like a vernalization response (temperature dependent) is involved in signaling to a Christmas Cactus that it’s time to flower. There are buds on many of the rest of the branches, but they’re still tiny.

Thanks to Mr. Subjunctive for introducing me to the name Zygocactus, even if it was in a post about how he was giving up on the (awesome sounding) name in favor of Schlumbergera.

I also want to name-drop Liza of Good to Grow. My plan is to continue following her site and use it as inspiration to increase my plant collection so by next year my Christmas Cactus won’t be so alone.

*This is what happens when you’ve moved into a new place six times times in the past six years, plus two moves of ~1000 and ~3000 miles respectively.

**The easiest way to make new Christmas cactuses is to break off several of the segments that make up one of it’s branches, put them in water to root and then plant the new plant in soil. Since the new plant is genetically identical to the old (after all it grew from a PIECE of the old plant), in other words it’s a clone. Cloning plants is much easier than cloning animals…

***When it warms up I’m planning a commando raid to sneak the poor plant onto my roommate’s balcony for a bit more sun.

BBC Frontiers on Genetically Engineered Crops

Filed under: Feeding the world,Link Posts,Politics — James @ 1:28 am

Without realizing it I’d begun to fall into the trap of thinking of European positions on genetically engineered plants mostly as they impact countries in the developing world (European donors funding Greenpeace activity in Thailand, or the threat of losing access to European markets being used to discourage the use of genetically engineered crops in Africa), so it was great to stumble across this segment on BBC Frontiers and be forcefully reminded that the position of the EU (and of it’s member nations) is not set in stone and continues to be the subject of strong debate.

The segment is available streaming from the BBC’s website and it’s a fascinating listen. (Budget ~25 minutes, the stream is a little longer, but the end is just bookkeeping and transitioning to the next show.)

If you don’t have the time to listen to the whole thing (and you really should), here are a couple of key quotes: (more…)

December 7, 2009

To Accomplish the Impossible

Filed under: Plants,Politics — James @ 8:52 am

Here’s an inspirational quote about science:

“It was believed impossible to create a blue rose, since roses lack the gene to produce the color blue. However, a Japanese company spent 14 years in research and finally succeeded in developing the world’s first blue rose. I explained to President Obama how this blue rose, which holds the meaning ‘to accomplish the impossible,’ was created and said, ‘Let us work together to accomplish the impossible.’”

-Japanese Prime Minister Yukio Hatoyama as quoted here (and boy will I feel silly if the whole story is a hoax)

“To accomplish the impossible”. When it comes to assigning meanings to flowers (as well as picking life goals), I’d call that a pretty good one.

The blue rose was actually developed by an Australian company called Florigene which has been acquired by a Japanese company called Suntory. I went into more detail about Florigene’s products here.

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