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

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? 😉

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!

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?

“We know it will hasten the demise–it will hasten the demise of organic farming, a rapidly developing business in this country.” – Lawrence Robbins (one of the lawyers arguing before the supreme court in the herbicide resistant alfalfa case)

As quoted here

Is there any real risk of the organic food business will be disappearing any time soon? Not so far as I can see. It really is a rapidly growing sector of agriculture,* and pollen contamination is an issue farmers have had plenty of experience dealing with long before genetic engineering ever entered the scene. If you’ve ever tasted an ear of sweetcorn that was pollinated by field corn, you know what I’m talking about.**

So here’s my question. Using only current trends (ie it’s fair to assume more genetically engineered crops are introduced in the future, but not that congress will pass a law requiring all farmers to plant them), can you make an argument for how the organic industry could be wiped out in the US, by genetic engineering or anything else?

*Whether that’s a good or a bad thing depends on whether you think the environmental benefits of organic farming outweigh the long-term downsides of defining good farming not with science, but with what feels natural.

**The majority of the corn kernels we eat are made up of the endosperm and embryo. Both of these get DNA from the mother plant (the one the ear grows on) and the father plant (the one whose tassel shed the pollen grain that fertilized the single corn silk attached to where that kernel of corn would later develop). A kernels of an ear of sweetcorn can each have different fathers, but if enough of those fathers were field corn, you’ll know it, because the father’s DNA will provide a working copy of the gene that lets corn kernels turn all that sugar that makes sweet corn sweet into starch, so your sweetcorn would’t taste sweet at all. The vast majority of the corn grown in the US is fieldcorn, yet I don’t think anyone would argue the sweetcorn industry is being hastened towards towards its immident demise. For more about the genetics of what makes sweetcorn sweet, read this discussion of the shrunken2 gene.

I’m out in the hallway while the first of my two sections fills out their reviews of me as a GSI (graduate student instructor).

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.

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.

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…

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”