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

January 29, 2010

New SOLiD Sequencers, and the ever dropping cost of sequencing

Filed under: Uncategorized — Tags: , , — James @ 8:20 pm

David Dooling, writing at PolITgenomics, brings word of the announcement of a new generation of SOLiD sequencing machines. The statistics aren’t quite as impressive as the Illumina HiSeq 2000 announced a couple of weeks ago, but it will be cheaper per gigabase of sequence.

As long as SOLiD sequencing can keep giving Illumina a run for its money, the price of sequencing is going to keep dropping, and the R&D departments of both companies will be working round the clock to keep the improvements coming (SOLiD is already promising upgrades that will triple the amount of sequence generated per run, while cutting the cost of each run by half (6x reduction in cost/GB of sequence)… by the end of this year.) (more…)

January 28, 2010

Grad School Admissions Essays

Filed under: Campus Life — James @ 4:19 pm

This is the second year I’ve had the privilege of reading the personal statements of the prospective new grad students being interviewed by our department. It’s interesting to see the strategies people take in trying to sell themselves. Broadly applicants can be grouped into three categories (at least successful ones, the department doesn’t let us see the essays of the people it rejects so I can’t comment on those):

  • #1 Ever since an early age I’ve been fascinated with plants…
  • #2 The research I already do on plants is so exciting let me tell you about it…
  • #3 There are a lot of problems with the world, in plants/agriculture/biology I see the potential for solutions, which is something I want to devote my life to because …

Of course, as with any gross over-generalization, this skips over a lot of complexity and individual variation* but these do seem to be the predominant, successful, strategies. I really wish I could take a peak at the reject pile though, to see if there are only so many ways to writing a personal statement for a plant biology program, or if it simply that these approaches appeal more to admissions boards than the alternatives.

Thinking back to my personal statement, I definitely fell into category #2 “I don’t have much interesting to say about me, but let me tell you about the awesome plant science I’ve worked on so far!”

*One repeated trait that showed up in some essays belonging groups 2 and 3 was “[I was going to be/my parents want me to be] a doctor, but…” I’m not sure whether I would recommend this to people writing their admissions essays or not. It seems to me that this can even come off as flattering (this person could have been making a six figure salary and do a job depicted on countless TV dramas, but they liked our field so much they chose it instead!) or annoying (so they didn’t make the cut/were afraid to apply to med school and though plant biology would be an easy fallback did they? I’ll show them!).

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 27, 2010

A new plant (in the apartment, not the world)

Filed under: Photo Posts,Plants — James @ 7:53 pm

A christmas gift from my folks that only just arrived:

I don’t believe people can identify this plant from this picture, but just in case someone wants to take a shot at it, I won’t reveal the answer until below the fold. (more…)

First Day Teaching (epilogue)

Filed under: biology,teaching — Tags: — James @ 2:37 pm

Belated I know. The first section I ever taught could have gone better. Twenty-nine people showed up for a section with an enrolment cap of 25 in a classroom with only 17 desks and no eraser for the chalk board. So that was fun. Still, I made it through a review the parts of a plant (roots, shoots, and leaves), the parts of a flower (sepals, petals, stamens and carpels), and a diagram of why a plant needs both mitochondria and chloroplasts (chloroplasts harvest and store light energy, mitochondria turn stored energy into the form used by the cell, ATP). And the second section I taught, later that same afternoon, went a lot better (In addition to being more sure of the material, I had time to steal back enough desks to bring the room to its rated capacity of 25, hunt down an elusive chalk board eraser, and draw the first set of figures on the board before the students showed up.)

A recreated example (should be familiar to anyone who, like me, took the first two weeks of intro botany):

The basic diagram of four parts of a (eudicot) flower. From the outside in. A: Sepals, small, generally boring green bits that look a fair bit like tiny petals. B. Petals. C. Anthers. The male part of the flower, responsible for producing pollen. D. Carpal(s) The female part of the flower. Pollen lands on the top surface, then grows a tube down into the flower to fertilize the eggs and central cells.

I’ve seen variants of this figure in 3 courses I took as an undergraduate, and now I’m using it myself. I’d be interested to hear if anyone has seen (or can think up) variants that might be easier for people with no background studying plants to grasp. (more…)

January 26, 2010

“New” Cruciferous Vegetables

Filed under: food,Genetics,Plant breeding,Plants — Tags: , , , , — James @ 7:02 pm

A stalk of brussels sprouts photo credit: cbmd, flickr (click for photo in original context)

Last week Greg over at Pie-ence was talking about the amazing variety of vegetable crops breed out of a handful of species within the genus Brassica, specifically Brassica rapa and Brassica oleracea.* I’m referring to these as cruciferous vegetables, which is actually a wider category including all the vegetables within the mustard family of plants (scientifically this is called the Brassicaceae). But one of the cool things about having so many kinds of vegetables within the same couple of species is that, because they’re the same species, they can still be interbreed with each other to create “new”** vegetables. (more…)

January 21, 2010

My First Day Teaching (prologue)

Filed under: Campus Life — Tags: — James @ 11:57 am

Random photo of the blooming zebra plant (of the Aphelandra sqarrosa variety) in my office. Because I've been writing too many picture-less posts lately,

I don’t actually start for another two and a half hours. But at 2 pm pacific time I’m going to assume the role of a graduate student instructor (Berkeley’s fancy name for a TA) in the first of the two discussion sections I’ll be teaching every week.

As first classes to TA go, this one feels like a good fit for me. It is an introductory course in plant biology aimed at non-science majors. A couple of the people in my year did this for the first time last semester with courses on plant biochemistry or computational biology and spent the whole time trying to keep one week ahead of their students in learning the material. In a course on introductory plant biology and agricultural/biotech issues we’re going to be discussing stuff I know and am excited about!

The professor who gives the lectures seems pretty awesome too. In a semester she’s planning to cover everything from basic biology cell cycle and DNA->RNA->protein to plant specific biology like floral development and plant pathogens, and at the same time get the students thinking and writing about their views on biotechnology, agriculture, and biofuels.

It should make for an exciting semester.

Also, lectures are in an auditorium with over 100 seats and at the first one, on Tuesday, every single one was taken and there were people sitting in the aisles. At Cornell the only plant biology class I ever took that even approached that kind of enrollment was the two weeks I took of Intro Botany. Great to see so many people excited about plants and their molecular biology (or at least willing to sit through a semester of lectures and discussion sections on the subject to fulfil some distribution requirement)!

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)?

How to Give an Interesting Research Talk?

Filed under: Campus Life,research stories — Tags: , , — James @ 2:07 pm

Corngrass1 a dominant mutant that keeps maize from making the transition to adult growth. The stalk of a normal maize plant is shown to the left for comparison. According to George Chuck, in some genetic backgrounds where they never flower, corngrass plants are potentially immortal, as cuttings of the stalk can be transplanted to new soil and simply continue to grow. (Normally corn plants are annuals, they stop growing once the end of their stalk turns into a tassel and eventually die off even if they're grown in temp. controlled greenhouses.) Photo courtesy of MaizeGDB.org

Just got back from a great talk given by George Chuck, who works on microRNAs that control the transitions between the juvinile and adult phases of plant development in maize at the USDA’s Plant Gene Expression Center. In trying to figure out why it was such a great talks (besides the obvious, that he had exciting data to present).

The obvious ones I could spot where: (more…)

January 19, 2010

Genome Sequencing vs Genetic Mapping

There was a recent paper in Science about the mapping of the Artemisia annua genome. I’ve seen several people interpret this as another genome sequence. It’s hard to blame anyone for this confusion given headlines like “Scientists map the maize genome!” to describe the sequencing of the maize genome. So what’s the difference between a sequenced genome and a mapped genome? I’m glad you asked! (more…)

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