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March, 2009:

Isaiah 40: All Flesh Is Grass*

After a little experimentation to compensate for the fact that it didn’t seem worth it to go out and buy a cast iron pot, I’ve gotten the No-Knead bread recipe that was all the rage on food blogs two years ago to work for me. It’s a very simple recipe calling for only two ingredients flour and salt (four if you count water and the tiniest amount of store bought yeast for the first batch), and it makes a tasty and attractive bread:

No Knees bread

It’s a starkly simple food. The sort of staple our ancestors depended on to stave off hunger and give them strength thousands of years ago. And it really is bread (well wheat really) along with a couple of other grasses that gave the human race the surplus food to build civilizations. Everything that has come since rests on the backs of wheat (and rice and corn).

A single pound of corn contains 2400 calories -presumably the figure for wheat or rice is comparable, but corn in what I know- and an acre of corn can easily produce 9000 pounds (4.5 tons!) of corn, enough to meet the caloric needs of 29 and a half people. Now those people still need a patch of vegetables as the big three staple grains aren’t great sources of micronutrients and some essential amino acids (although the latter can be partially addressed by treating the corn with alkali compounds, a trick used by the Mayans), but the energy needs an individual person can be met in a field of grain smaller than the average size of a newly built american house. (less than 1500 square feet vs 2,349

Today grains are under attack as “empty calories” in some parts of society, and considered good for nothing but animal feed in others, take a moment to consider all the aspects of civilization you’re grateful for, and how they can all trace their roots back to the surpluses of food and labor created by three grasses: wheat, rice, and maize.**

*Of course you have to use the King James version. The New International makes the phrase “all men are like grass” which ruins my attempt to tie it in with this entry.

**With apologies to the potato. I’ll write you your own post one of these days.

False Alarm

I was worried for a moment that the first plants grown on the surface of the moon were going to be arabidopsis. After all they were described only as “Seeds for a rapid-cycle type of Brassica plant – basically, mustard seeds”, but further digging turned up that these are just a breed of Brassica rapa marketed as “fast plants.” Kind of cool actually. A generation time of only fourteen days.

Real Blogging Plant Geneticists

So it’s a day late and a dollar short but I wanted to mention to two bloggers I had the chance to meet at the Maize Meeting a couple of weeks ago. Anastasia Bodnar writes Genetic Maize, and Karl Mogel Karl Haro von Mogel writes Inoculated Mind, (and also makes his own corn pattern shirts!) and the two of them are both contributors to Biofortified along with Pamela Ronald, the author of Tomorrow’s Table, a book on the shared goals of genetic engineering and organic agriculture that I can’t recommend enough. 

It was a real pleasure to meet a couple of people who are really dedicated to communicating what we do as scientists to the general public. It was something I’d intended to do part time with this blog, but writing articles that actually inform takes a lot of work. From the search terms that bring in traffic to this blog, I can tell some of my traffic really is coming here looking for information of research. So I’m going to be making a minor layout change to this blog and add a list of blogs by those who really are blogging about plant genetics. These will be the first blogs I enter on that list.

End of Battlestar Galactica (Or Why Technology is a Good Thing)

By this time I’m going to hope that anyone following the show has watching the series finale. If you do follow the show but haven’t watched the end yet, stop now.

If you have no intention of watching the show, here’s briefly what happened: In the final half hour of the show the survivors of an apocalyptic war arrive at Earth 150,000 years in the past, inhabited only by pre-lingual humans living in hunter gatherer tribes. They land and make plans for beginning to rebuild their civilization. But no, one guy has a great idea, why don’t they give up all their technology and go back to the land. And so that’s what they do. Burn their ships, throw away their computers, give up “their little luxuries” as one character describes their technology.

It’s easy to see human progress as nothing more than a desire for luxuries and a more comfortable life. To do so overlooks the far more fundamental motivator of technology and progress; battling starvation disease and death. The writers of Battlestar Galactica leave us with the implication that it’s simple enough to walk into a pristine wilderness with nothing but the clothes on our backs and, as long as we’re willing to give up the little luxuries, live a long and enjoyable life. And it frightens me to imagine how many people actually believe that. Because in the show people don’t make the decision individually. One group (a majority?) makes the decision for everyone in the fleet and all the unborn generations to come.

Imagine the man who depends for survival on a medicine that is synthesized in the medical department of one of the ships send callously into the sun. Or a newlywed woman from a family prone to difficult births. Or the parents of a handicapped child, who would be unable to hunt or grow food in a pre-technology society. But the society you belong to has not just renounced their “sinful” technology, but destroyed it root and branch to prevent any hint of dissent, and who cares if a few are sacrificed, willingly or otherwise, on the path to rightiousness.

But that’s just a few people, right? Most of them should be fine in this new life as farmer/hunter/gatherers, no? Except leaving aside the risk of dying from conditions that are completely treatable in modern society (bust appendixes, cuts that get infected, serious allergic reactions), what are they going to eat?

Farming is hard work. It requires specialized knowledge (that most of the members of a technological civilization don’t possess), doing it well requires proper tools (I was waiting for the scene where someone goes “d’oh! Why didn’t we make some practically indestructable plow blades and hoe heads out of modern alloys before we sent all our metal and tools to melt in the center of the sun!”), and most importantly it requires that one actually have crops to grow. 

No matter how hard you look, you won’t find corn growing in the wild. Or wheat. Or potatoes. The domestication of staple crops like these is one of the real gifts we receive from our ancestors*, a gift that was thousands of years in the making. Without domesticated crops, it doesn’t matter how good the tools you have are, it doesn’t matter how much you know about farming. Without those crops, there is no way to survive other than boom and bust life of a migratory hunter/gatherer, a niche the native humans already occupy.

In the end it’s just a TV show, but I fear that the ideals and ignorance put forward in that last half hour reflect the worldview of far too many of my peers who don’t that technology is the frail barrier between all of us and miserable deaths from disease, starvation, and injury, and idealize the idea of a more natural existence.

*Phrasing stolen shamelessly from an interview on Modern Marvels.

Pamela Ronald Talks About The Limits of Organic

If you have a couple of free minutes, check out Pamela Ronald’s new post on Michelle Obama’s organic garden and the limits of organic agriculture as it is currently defined. If you do, be sure to scroll down to the bottom to see the comparison between organically grown sweet corn and sweet corn engineered to resist pests. Sweet corn is one of the crops where a significant fraction of consumers actually prefer to purchase GM over organic, because GM sweet corn will have substantially less worm damage than corn produced using organic or conventional techniques.

Still, I love the symbolism of it, and though it will be costly (vegetables harvested from showcase gardens such as the Obamas’ are much more expensive than produce from an organic commercial farm), it will provide a great education tool for the fifth graders that will help tend the farm and for White House visitors.

I hope one of her assistants plants some corn and teaches them about insects and disease. She can show them how to feel the tip of a mature ear to see if it is filled out. As we described in “Tomorrow’s Table”, they may discover some ears with hollow spots created where a corn earworm has been feeding. 

The corn earworm is not a picky eater and will eat almost any crop that we rotate in such as tomatoes, beans, or lettuce, and the adult moth is a good flyer. Even conventional breeding has failed to solve this problem because scientists have not yet been able to find a corn gene that gives protection from earworm. So organic controls dont work very well for the corn earworm making it difficult to control this pest on organic farms. Most organic farmers and consumers accept this problem in exchange for the benefits of not spraying insecticides. 

Nerds And Middle/High School

A friend of mine from back during my own years of torment recently sent an essay on why nerds (almost almost everyone else) are miserable in middle and high school.

I really recommend it to anyone who remembers there own unpleasant experiences from back then, or who remembers having to deal with their own offspring wasting their precious non-school hours explained repeatedly, and at long length just how terrible the whole process was.

And that, I think, is the root of the problem. Nerds serve two masters. They want to be popular, certainly, but they want even more to be smart. And popularity is not something you can do in your spare time, not in the fiercely competitive environment of an American secondary school.

Adults can’t avoid seeing that teenage kids are tormented. So why don’t they do something about it? Because they blame it on puberty. … There’s nothing wrong with the system; it’s just inevitable that kids will be miserable at that age.

I’m suspicious of this theory that thirteen-year-old kids are intrinsically messed up. If it’s physiological, it should be universal. Are Mongol nomads all nihilists at thirteen? I’ve read a lot of history, and I have not seen a single reference to this supposedly universal fact before the twentieth century.

Maize Meeting 2009 part 1

In a lot of ways its like a reunion. Of the five people I did science for as an undergrad (this is what happens when you work in a new lab every summer) four of them are here. No to mention the grad students and post docs I’ve worked with, or took classes with, or who TAed classes I took. One of the reasons I like working in maize so much is the how connected the community is.

The rest of this entry will be a random collection of cool things I took note of on my iPhone:

*Arabidopsis genome cost 70 million dollars and took approx. 500 people seven years to complete. Today re-sequencing that genome costs 7000 dollars and takes two postdocs a week. (Note that this is re-sequencing a known genome. Having to assemble a new genome from scratch costs more because you need longer reads and takes a LOT longer.)

*The talk on developing exemplars of transposons was very cool. All sorts of complicated statistics related to defining families by relatedness, and then using that to pick the “most normal” copy for that family in the genome

*A guy presented a tool that, given a single gene, will find all the related genes in a genome. Define their gene structure, and then build a phyogenetic tree of the genes. Basically everything I had to do to make the tree in this entry, only instead of taking one grad student 2-8 hours, it takes a computer program 1-3 minutes.

*Talked to a woman who has a poster here looking at FT-like genes in maize. (That giant phylogenetic tree I made was looking at FT genes in grass species.) Great to meet a total stranger with a common research interest. 

More to come later. I’m considering posting my raw notes as a text file at the end of the meeting. Between the random things I think are worth copying down and the iPhone exaserbated spelling errors, I at least, find them hillarious. I’ve beat a strategic retreat from the poster session for little while to post this update and should probably return now.

It’s good to have your own Linux Box

It’s good to be such a tech geek sometimes. On Friday the lab’s servers came under a DDOS attack from east asia. The professional computer guys are still formulating a response, but until then I can’t access the servers. And since right now my project requires hours and hours of computing time to narrow down the the tens of thousands of genes found in a plant genome to a handful of good candidates for genes that are bound by an important transcription factor, it was looking like I might have to take the whole weekend off from work, falling days behind schedule.

What the DDOS types didn’t count on was the strength of my personal computational resources. (Actually I’m pretty sure they don’t even know what we do in the lab, random attacks are just part of the risk of being on the public internet.) Two 2.5 Ghz cores and 2 gigs of ram might not look like much compared to four servers containing eight cores and 16 gigs of ram each, but I can tie my own linux box up indefinitely without stepping on the toes of other people’s research. My roommate and I have had to make due without anywhere in the apartment streaming high quality video for a weekend, but I’m already running my second set of comparisons between the gene sets of rice and sorghum (each one should be a little faster as I narrow down the characteristics of real binding sites) and generating my own ad-hoc list of rice-sorghum-brachy gene pairs.

And on top of that I’ve got a great (if completely inaccurate) hacker vibe going, spending all day today and most of last night splitting my attention between two computers (three counting the linux box in the other room being controlled by command-line and VNC connections), rocking out to trance, and troubleshooting perl scripts at my L-desk with dirty plates and glasses accumulating around me as cryptic updates scroll by in terminal windows.

Weather Still Great

The weather out here continues to be amazing.

However I’ve recieved word of over 70 degree weather back home in the midwest, so I don’t get to gloat about this nearly as much as I did in January.

Long Overdue

Since my last real post, I’ve started a new rotation and the rainy season has started out here in the bay area.

This new rotation as been … a lot of work. I went from a first rotation in a traditional genetics lab, to a second rotation doing molecular biology with a little gene annotation thrown in on the side, and now I find myself working on a purely computational project, and I spend half my time teaching myself all the thing I would have learned about Perl if I’d ever had the time to take a formal class in it or reinventing the well because I haven’t realized someone already found a solution to the problem. I feel like I’m learning quickly, but since I was starting essentially from zero, I’m making a lot of newbie mistakes and then have to work twice as hard to catch up.

I’m four weeks in to my current rotation and have yet to so much as pick up a pipetter or run a PCR reaction. In fact the only laboratory chemical I’ve had any interaction with is Isopropanol and that was just because I was helping one of the techs in the lab upgrade the processors in one of our servers and isopropanol works great at cleaning the thermal paste off of processors.

Getting the chance to assist with the upgrade process was fascinating in its own right, the labs servers are co-located in the primary hosting facility for UC-Berkeley. To get access we had to call up and have them send an elevator down and show ID once we got up to the central command chamber for the facility. Walking through the rows of actual server racks, one is buffeted by alternating blasts of hot and cold air (heat exhaust from the servers and the outlet vents of the enormous air conditioning system respectively), and the process of actually pulling, upgrading and reassembling of the server was coordinated by pantomime and shouts half hear over the roar of the assembled equipment and the mandatory earplugs.