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

April 1, 2010

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.”

March 31, 2010

BBC on drought tolerant maize/corn

Filed under: agriculture,Feeding the world,Link Posts — Tags: , , , , — 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…)

March 23, 2010

Paintings of the last supper reflect growing abundance of food.

Filed under: Link Posts — James @ 8:35 am

“The last thousand years have witnessed dramatic increases in the production, availability, safety, abundance and affordability of food…. We think that as art imitates life, these changes have been reflected in paintings of history’s most famous dinner.” – Brian Wansink (Cornell University)

Read more at Discoblog. Note that these results are normalized to head size, so I suppose the alternative explanation is painters have started giving their subjects smaller heads over the past 1000 years.

March 11, 2010

Chromosomes and Ploidy at PATSP

Filed under: Link Posts — James @ 10:09 am

Mr Subjunctive who writes a really fun site for plant lovers and amateur to professional horticulturalists (who I’m pretty sure are also plant lovers or they would have gone into another field), set out to write a post on Phalaenopsis (a kind of orchid*).

I started this off with really good intentions, but quickly wound up on weird tangents, and then some of the tangents had tangents, and then at some point I looked up and saw that I’d written 2000 words without ever getting to how you’re supposed to take care of them. So if you’re here to find out how to actually grow Phalaenopsis, you’ll want to skip on ahead to Part II (which will post next Wednesday). Otherwise, read on.

Briefly, he covers chromosomes, the sex chromosomes of humans, weird changes in chromosomes numbers from changes in ploidy (have one or more extra copies of each chromosome) and aneuploidy (having more or less copies of individual chromosomes than normal) and some of the advantages and disadvantages of working with such plants. All while staying easily readable (something I can never seem to do once I get into talking about science).

Anyway, the point of this entry can be summed up in two words:

Go. Read.

And if you like it, check out his List: House Plants You’ll Be Growing During the Zombie Apocalypse of 2014

*Orchids are monocots (the group of species that grasses also belong to, along with pineapples, bananas and all sorts of other cool plants), so I start out biased in their favor.

March 10, 2010

Food Nostalgia

Filed under: Link Posts — James @ 1:20 am

James McWilliams, writing at the nytimes, makes the point that the idealizing the diets of generations past has been going on for at least 150 years. Michael Pollan’s rule: “Don’t eat anything your great-grandmother wouldn’t recognize as food” loses some of its effectiveness when you picture all four* of your great grandmothers (who were probably alive in the era of the world wars) idealizing the diets of diet of civil war era american, and so on.

h/t to Greed, Green, and Grains.

GG&G is well worth checking out in its own right. On this particular subject Michael Roberts, the blog’s author, makes the point that just because nostalgia for the foods of the past isn’t a new development, doesn’t mean there aren’t real problems with the food we eat today.

There are real problems with the ways we produce and consume food in this country. (And a whole separate set of problems in other parts of the world.) But by over-idealizing the food our great grandparents ate we’re looking for the answers to today’s problems in the past, when the real answers to the problems we face can be found (you guessed it) in the future.

Which is not to say we can’t learn from the mistakes and successes of the past. I just don’t think it’d be a good trade to exchange my diet for that of my great grandmother (any of the four).

*Four great-grandmothers (eight great-grandparents!), but consider that if we go back ten generations (perhaps an average of 250 years) we’re each descended from over 1000 people. (1024 assuming your family tree was completely free of inter-marriage).

February 19, 2010

The Dragon Genome

Filed under: Link Posts,Photo Posts — James @ 10:07 am

Since starting grad school, I’ve had a running joke with a couple of other guys about the importance of sequencing the dragon genome. There is even a sign.

Why sequence the dragon genome? Because dragons are an example of vertebrate hexapods (most descriptions of dragons found in our, non-exhaustive, literature search include four limbs plus two wings*). Because we could start our paper off with “To the best of our knowledge, the work reported here represents the first complete genome sequence of a mythological creature to be published.” But mostly, we should sequence the dragon genome because, like Mt. Everest, the dragon genome is there.**

Wait what? Dragons! Little tiny ones. I do hope this isn’t some elaborate hoax. Story from sciencepunk, h/t to denim and tweed for pointing me to it.

Note the four limbs as well as two independent wings. (In all honestly this isn't really a hexapod. The wings clearly didn't evolve from a set of limbs, the origin bird wings, bat wings and pterodactyl wings.)

Now somebody bring me its DNA! (Ideally in pre-sequenced form so I can get straight to the fun parts.)

*The same is true of descriptions of angels, but who wants to walk around campus with a sign saying “sequence the angel genome”? Although I feel like there’s a sleazy genomicist pick-up line in there somewhere if I think about it hard enough.

**George Mallory is famously quoted as having replied to the question “Why do you want to climb Mount Everest?” with the retort: “Because it’s there.” <– quoted from wikipedia give it as much or as little credence as you like.

February 13, 2010

Plant Links of the Day: Diverse Citrus, Extinct Cucurbits, and more

Filed under: Link Posts,Plants — Tags: , — James @ 9:27 am

When I woke up (which yes, was only a couple hours ago, but remember I’m on pacific time) I found a whole bunch of interesting plant links waiting in my RSS reader, and I thought I’d pass along a few to you guys.

Keith Robinson writing over at Omics! Omics! posted Celebrating Citrus where he catelogs some of the diversity available to him from local grocery stores before pointing out a citrus review article that suggests all that diversity can be traced back to only three wild species and wraps it up by pointing out the project to sequence the sweet orange genome.

Imagine if you could have a whole series of clementine-like fruits, with the size & easy peeling characteristics but with the whole range of other citrus flavors and colors genetically grafted in — cara cara clementines and blood clementines and ruby red clementines and perhaps even sweet lemontines and key clemenlimes.

Highly recommended.

The Biogeography of Darwin’s Gourd is a post I discovered through research blogging (speaking of which I should really write another entry that meets their standards some day). The gourd of the title is Sicyos villosus, a cucurbit (the group of plants that includes squashes, melons, and pumpkins) collected by Darwin from one of the islands in the Galapagos the better part of two centuries ago … and never again recorded by science. At this point the dried sample collected by Darwin may be the only existence the species ever lived:

The analysis of the cucurbit’s DNA, extracted from the seed samples taken by Darwin, revealed that S. villosus is closest in relation to cucurbits in North America and Mexico. The species probably diverged roughly 4 mya, when the Galapagos were still geologically young. Dispersal was not human in origin, meaning long distance from the mainland, potentially from its spiny fruits stuck to birds, the authors suggest.

How cool is it that we can learn so much from a single sample of a species that has otherwise vanished from the earth?

Finally, by way of DailyKos, comes a pointer to this valentine’s day themed article, clearly written for the non-scientist, where a summary written by me seems superfluous given the title: Sex, Drugs, and Paleo-botany! And yes, the exclamation point is in the original title as well.

February 7, 2010

Ford Denison on Why Creating Drought Resistant Crops Is Complicated

Filed under: Link Posts — James @ 2:54 pm

From the post in question:

… natural selection is unlikely to have missed simple, tradeoff-free improvements. So I’m always skeptical when someone speculates that we could double crop yield just by increasing the expression of some newly discovered “drought-resistance gene.” My rationale is that mutants with greater expression of any given gene are simple enough to have arisen repeatedly over the course of evolution.

Sounds grim doesn’t it, and I completely agree with his logic. Fortunately the author goes on to explain all sorts of loopholes where it should be possible to improve water use efficiency by looking at more complex traits or exploiting the differences in how natural selection (evolution) and artificial selection (farming and plant breeding) judge success.

One example being that in a whole field being grown for harvest we don’t care about the relative success of one plant compared to its neighbors (how natural selection normally works) but the success, or lack thereof of the whole field. So selecting against various traits that help in plant-plant competition, but reduce the efficiency of water use overall is probably a path worth being pursued if it isn’t already. This parallels the early work done in corn breeding that, sometimes unconsciously, selected for plants that didn’t compete with each other as much for light, as all the energy corn plants spent trying to outgrow their neighbors was wasted, from the point of view of the farmers. If you look at really old pictures of cornfields, you’ll notice the plants were much taller then than they are today. Modern cornfields are also planted much more densely, which would have provoked even more wasteful struggles for sunlight in old breeds of corn, but today ensures that even more of the sunlight that hits and acres of corn will fall upon the leaves of SOME corn plant.

The whole post is a great read, I highly recommend it and now Denison’s forthcoming book is on the long list of things I really want to find the time to read.

h/t to Agricultural Biodiversity Weblog

January 28, 2010

An Interview with Roger Beachy

Filed under: agriculture,Feeding the world,Link Posts — James @ 8:47 am

Pam Ronald, writing at Tomorrow’s Table points out an interesting interview with Roger Beachy the new head of the National Institute of Food and Agriculture (itself a newly created government organization) in Nature Biotechnology. He talks about everything from restoring support for the, very successful, programs that used to fund the training of plant breeders and plant biologists from around the world* to increasing the number of research grants that have specific money set aside for education and outreach. I’m guessing this is the comment that will get the most play if the interview gets noticed by the popular press:

In the early days of agbiotech, regulations were fairly minimal, which kept development costs low. The safety of a product was judged on the product itself and not the method used to develop it. Regulatory agencies have lost some of that focus in the past ten years. … I am very interested in having a regulatory structure that is science based and gets back to what we originally had.

I continue to be impressed with President Obama’s choice to head up the new agency, as I have been since the appointment of Roger Beachy was first announced. Though I will say I got this part wrong in my original post about Beachy’s appointment:

And on top of that, he’s spent his entire life working in the public and non-profit sectors (places like Cornell, Wash U, the Scripps Institute, and most recently president of the Danforth Plant Science Center). Can you imagine the screaming if Obama had picked someone who’d ever worked in industry to head up the NIFA?

As we’ve seen from the reaction to Roger Beachy’s appointment, finding a respected scientist who has done both basic and applied research, with proven skills as an administrator (plenty of great researchers make horrible administrators) and who’d spent his entire like working in the public and non-profit sectors instead provoked so much screams one might have thought President Obama had appointed Hugh Grant (the CEO of Monsanto, not the actor) to head the NIFA instead of Roger Beachy.

*Such funding contributed to the training of, among others, Gebisa Ejeta, who won the World Food Prize in 2009 for his work developing striga resistant sorghum, and who, from his testimony to the senate foreign relations committee, sounds like he would agree with this goal.

January 20, 2010

More Bill Gates

Filed under: Link Posts — James @ 8:38 pm

Bill Gates has an interesting new post up on the risks of of buying into the false choice between sustainability and productivity:

The global movement to help small farmers is increasingly divided into two camps. On one side is a technological approach focused on improving productivity. On the other side is an environmental approach that promotes sustainability. Productivity or sustainability – they say you have to choose.

As I said during my speech at the World Food Prize in October, this is a false choice that is dangerous for the field of agricultural development.

At a time of rising population and climate change, we need both organic solutions that promote sustainability and the technological approaches that increase productivity – and there is no reason we can’t have them both.

Whatever you think of the man’s operating system, he clearly possesses a different perspective* on the solutions to a whole host of global problems, and the willingness to put his money where his mouth is.

*How could he not, as, perhaps, the most prominent member of that tribe: Geeks Who’ve Changed the World (and found fame and fortune in the processes)?

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