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

May 31, 2010

Welcome to transposon week here at James and the Giant Corn!

Filed under: biology,Genetics,genomics — Tags: , — James @ 2:23 pm

I’m just about wrapped up with the big project I’ve been working on recently. Hope to be able to say more about it in the not-too-distant future. Having to be secretive in science sucks.

But there’s a lot of be happy about! I’m done teaching for a long time. As much as I enjoyed working with the kids in my class, the other responsibilities of teaching (grading, sitting through lectures without the chance to break in for the discussions and arguments that make academia so fun, grading, designing assignments, grading) were really starting to wear me down.

And I’m only three weeks (June 22nd) from either passing my qualifying exam or becoming a beaten and broken shell of a man. For three hours four professors will question me on everything I’ve learned (or should have learned but didn’t) in my education up to this point, and everything I propose to spend the next few years of my life doing. This may not sound like a good thing, but it is. Because my qualifying exam has been hanging over my head all semester,

The lab has a new paper in press, having run the sequential gauntlets of Peer Review, Editorial Evaluation, and finally (and perhaps most dreaded) Your-Figures-Aren’t-High-Resolution-Enough e-mails from the journal’s publication department. But more on the details of that whenever the paper actually shows up.

But what was the point of this entry again? Oh yeah. Transposons. I have a soft spot from transposons (I’m guessing most people who work with maize genetics do). Today we may know that transposons are found in practically every genome under the sun, but they were discovered first in maize using old school genetics (breeding plants together and counting traits in the offspring), before DNA sequencing was a gleam in its inventor’s eye.

And on top of that, some delightfully high-copy number transposons are in the middle of proving a major scientific point for me, so I figured the least I could do was devote a week to them here on the site.

If you’re not a geneticist, should you still care about transposons? Absolutely! Transposons are one of the best arguments, not for why genetic engineering is safe, but for why, if anyone worried about hypothetical unintended consequences of genetic engineering should be worried about any food with DNA in it (and as far as I know, that’s all food.) To paraphrase a seinfield character: “No food for you!”

The week’s schedule: (more…)

May 25, 2010

Selaginella moellendorffii genome

Filed under: Uncategorized — Tags: — James @ 12:26 pm

Public domain image of selaginella from wikimedia commons.

Added another genome to our sequenced plant genomes wiki, Selaginella moellendorffii, better known as as a spikemoss. Selaginella is a vascular non-seed plant which split from the lineage that gave rise to most of the plants you seed around you every day hundreds of millions of years ago. At 110 megabases, Selaginella is currently the smallest sequenced plant genome (smaller than Arabidopsis!).

Un-related to genomics, did you know plants recognizably belonging to the Selaginella genus can be found in fossils 335-350 million years old? This is a plant that has remained mostly unchanged since BEFORE dinosaurs walked the earth! This was just one of the many interesting facts I learned from reading Jo Ann Bank’s review: Selaginella 400 Million Years of Separation.

As far as I could tell the Selaginella genome paper has not yet been published (I couldn’t find it anyway). The good news is that according the the Selaginella wiki (Yes, Selaginella gets its own wiki … I kind of wish maize had a wiki… ), the paper was submitted back in August of 2009, so it’s possible that any day now this genome will move from the fun-to-play-with category into the awesome-to-publish on one.

May 15, 2010

The Problem With Metaphors

Filed under: Uncategorized — James @ 12:44 pm

Sometimes they sound so cool it takes a while to realize you’ve got no idea what it actually means:

Just as a bookcase can fit more paperbacks than hardbound books, ARMAN’s fit more scaled-down genes into the same space

From an article describing a new tiny microbe (a member of the archaea) found in abandoned acid mines. The name comes from “archaea Richmond Mine acidophilic nanoorganisms”. And I have no idea what the actual meaning is behind that metaphor.

The cells really are tiny ~1/50th the width and ~1/2500 ~1/125,000 the size of a human cell.* To put that in context, if you’ve ever seen one of those to-scale comparisons of Earth and Jupiter,  this is a substantially bigger difference.** Of course we already knew microbes had smaller cells than human cells, so the real claim to fame of this article is that these microbes are “1/3 smaller than E. coli” E. coli being a pretty average bacteria.

Now I’m sure there are actually many fascinating things about ARMAN, and fortunately I have other options to learn about those things other than the popular press. I can read the PNAS paper itself because I’m fortunate enough to be employed by an institution that pays for me to get access to the paper, and I’ve spent the last six years of my life learning the art of extracting meaning from scientific papers.

I could also just e-mail the guy in my program who works on the same acid mineshaft were these microbes were identified.

But until then… I have no idea what the difference between a softcover gene and a hardcover one is.

If your curiosity has been sparked, check out the actual paper, which looks to be an interesting read.

*Assuming both cells are spheres for ease of calculation.

**Thanks to Jeff for catching that I mixed up circles and spheres, making my original estimate of the differences in cell volume a DRASTIC underestimate. Maybe I need to institute a peer review approval policy for this site? 😉

May 11, 2010

Where the superpowers of superweeds come from

Filed under: agriculture,biofortified,Genetics,Plants — Tags: , , — James @ 11:53 am

Superman had the yellow sun of earth, spiderman had a radioactive spider-bite, but what about superweeds, where does their super power (surviving application of Round-up/glyphosate) come from?

To understand how superweeds survive, we first have to understand why normal weeds (the Jimmy Olsens and Lois Lanes of the plant world) die. <– last superhero reference of this post I promise. (more…)

May 5, 2010


Filed under: Uncategorized — James @ 4:44 pm

Long time readers will know I have serious problems with using the term superweeds to describe weeds that have resistant to a herbicide. Yes, herbicide resistant weeds are a serious issue (just like antibiotic resistant diseases), but they are ONLY a problem for people who use the herbicide in the first place. A nytimes article from a few days ago on herbicide resistant weeds, while earning a little of my ire for still calling them superweeds, makes this point amazingly concisely:

The National Research Council, which advises the federal government on scientific matters, sounded its own warning last month, saying that the emergence of resistant weeds jeopardized the substantial benefits that genetically engineered crops were providing to farmers and the environment.

The danger, if we don’t do a better job of managing resistant weeds (through strategies ranging from crop rotation to developing crops resistant to different herbicides to allow farmers to rotate between different herbicides) is that we will lose some of the environmental benefits genetic engineering is ALREADY providing. Farmers who don’t use crops genetically engineered to resist herbicides, whether they grow their crops conventionally (using other herbicides, plowing, or hand weeding to control crops) can deal just as well — or as poorly — with giant pigweeds* that are “superweeds”, as those which are not.

*Which the nytimes informs us can grow 3 inches a day under ideal conditions. In other news, that’s pretty awesome! Corn might be able to beat it unless the pigweed got a head start**, but weeds are a much more serious issue for crops like cotton and soybeans which don’t ever get as far up off the ground.

**This is entirely my own amature speculation, I’ve never had to grow corn in a production environment and the last time I was responsible for a real field of research corn, we controlled weeds the old fashioned way (long days in the sun with a hoe***) until the corn plants got big enough to hold their own.

***Everyone should really spend at least one day hoeing corn (or some other crop, I’m not particular). For a little while it’s fun and exhilarating, and by the end of the day you have a much better understanding of why very few people would ever CHOOSE a life of manual agricultural labor, whether as subsistence farmers or migrant laborers.****

****Sorry for going so crazy with nested foot-notes. Clearly I’ve been missing this style of writing more than I realized!

May 4, 2010

CoGe in the News

Filed under: Uncategorized — James @ 8:33 am

Happy Star Wars Day everyone!

I just wanted to draw your attention to a guest post by Eric Lyons over at OpenHelix. Eric is the man behind CoGe, the tool I use for most of the genomics eye candy I put up on this site, and which also makes most of my research possible.

Among other things, he’s putting out a call for more biologists to try using CoGe and provide suggestions for either new useful features or ways to make the features CoGe already has more intuitive.

Changes between version 1 and version 2 of the grape genome. Cool, no?

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