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September, 2009:

Driving home how fortunate I am

According to this report (warning link is a PDF): 34% of workers under 35 still live with their parents. 52% of those under 35 and making less than $30,000 a year (me). Now from the way the statistic is phrased I assume that it includes teenagers with jobs, and excludes college kids without jobs. Even with those two caveats, it’s a frightening number.

Makes me grateful to be living in the apartment I share with only one roommate, noisy neighbors and all. It’s scary to realize how much of my generation is not so fortunate.

DNA Sequencing Technology

John Timmer has started a cool post on sequencing technology over at arstechnica. The writing seems like it would be quite accessible to someone without much biology or chemistry background. Sunday’s post is focused on Sanger sequencing which is the classical technique and still used by people working with one or a few genes at a time. There’s a whole new set of technologies that are now (or soon will be) used to tackle large scale projects like sequencing whole genomes and I assume that’s he will talk about in part 2.

The principles behind sanger sequencing are quite old but it’s a great example of the huge difference optimization and specialization can make. Back in the day, grad students and technicians poured their own gels, ran their own reactions with radioactive reagents and then ran the reactions out and interpreted a couple of hundred base pairs of dna sequence from the pattern of bands which appeared.

By the time I first needed to sequence something, I put my DNA in a little test tube (microfuge tube) with a little bit of the same DNA primer I’d used to amplify my sequence and walked it down two stories and across the hallway to drop it off in the sequencing lab. The technology had come so far that now a single technician loaded dozens of samples, dropped off from all over campus, into a giant machine, and a few hours later sequences data 4-5 times longer than back in the bad old days, was e-mailed back to all the researchers whose samples had been in that run. No radioactivity. No problems with gels and most importantly, so many fewer hours spent by researchers.

The ABI 3700 was a sequencing machine that represented the peak of those trends. It could sequence 96 samples at once and run up to eight times per day. Assuming 1 kb of sequence per sample, which is about the maximum of sanger sequencing, that means each machine could produce ~750 kilobases* of sequence data per day.

Two of the new sequencing technologies you may have heard about are 454 sequencing and solexa sequencing. A single machine using the 454 sequencing technique can generate as much sequence per day as 1,300 of the ABI 3700 machines. A Solexa sequencer can generate 4 times a much sequence as a 454 sequencer, four billion individual A’s T’s C’s or G’s. The only downsides are shorter read lengths (somewhat shorter for 454, and much shorter for solexa), and the fact sanger sequencing is the only technology that can start at specified point on the DNA molecule (specified by a primer.)

Very cool technologies and when Dr. Timmer posts part two which addresses these new techologies I’ll be sure to link to that one as well.

If you’re interested in how the new sequencing technologies stack up against each other PolITgenomics has a great reference chart.

*A kilobase is one thousand A’s T’s C’s or G’s of DNA

Making the Pie Bigger

When zero sum games are played for fun they can be very entertaining (see: poker). When they’re played for survival they’re miserable (see: who do we throw off the lifeboat, which person gets this kidney, and poker  when you can’t afford to lose). All too often keeping people alive (whether with regards about health care or food production) is seen as a zero sum game. But it’s not. My favorite example is the green revolution, but But that gets into a whole separate fight about the green revolution, and takes attention away from the real point about bigger pies being better than fighting over the pieces of a small one. So I have a new example. One almost no one can find fault with:

Cooking (more…)

That’s strange…

Words that have forewarned of many awesome discoveries in science, though they definitely are not doing so in this case.

In the past ten months I’ve dropped from 75% likely to be male to only 50% likely to be male 51% likely to be female according to a program that claims to be able to tell the gender of a blogs author from word choice and writing style. So I put it to you, my readership, have my entries started sounding more feminine?

I spoke too soon…

Just yesterday I said this about Roger Beachy getting appointed to head up the new National Institute of Food and Agriculture:

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?

But of course it couldn’t be that easy. It turns out people like Tom Philpott are quite capable of branding Beachy as a Monsanto insider regardless.

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Still Very Irritated

Turns out I declared mission accomplished too soon before. I’ve now done a clean install of wordpress itself, which unfortunately includes a new theme (plus side, rotating pictures in the header). Unless the corruption worked its way into the mySQL database itself*, this should have killed it.

*Is that even possible? Databases are right after objects on my list of coding relating things I should learn about since I know practically nothing about.

What is the NIFA?

More than a year ago, in May of 2008, Congress passed the Food, Conservation and Energy act of 2008. It was weird going back to read up on the coverage of the bill and reading how President Bush objected to X or proposed Y. His presidency already seems so distant. One of the things this farm bill did was create the National Institute for Food and Agriculture by reshuffling some departments withing the USDA (United States department of Agriculture which manages everything from the National Forest Service to subsidized school lunches) and providing more money for the newly created institute to disburse in the form of competitive research grants. The USDA supports a lot of cool research internally through the Agricultural Research Service* but they’ve historically had much less money to fund grants to outside researchers than the National Science Foundation or the National Institutes of Health. (Anyone know how Department of Energy funding stacks up?)
It’s not yet clear how much money the NIFA will have to fund competitive grants (the horse trading in congress hasn’t finished yet), but we can hopefully expect the new institute to recieve at least $250 million a year for the purpose, a substantial increase from pre-NIFA funding of $120-$180 million. Although to put it in perspective, $250 million is still only one-hundred of the funding NIH awards through competitive grant processes. In addition to this general grant money that can be spent on plant breeding, biotechnology and everything in between, there will be a second pot of money devoted to sustainable ag and specialty crops (fruits and vegetables) but, as with the general fund, the exact number seems to still be in flux.
As I was just talking about here, we definitely need to be investing more in agriculture and the NIFA is a step in the right direction. If it were up to me I’d have thrown a couple of billion at the problem. I think there are a lot of low hanging fruit in the public agricultural sector after decades of underfunding. Regardless the NIFA is a good thing.™ And I’m even more confident of that fact now that I found out President Obama has picked Roger Beachy to be the first head of the new agency.
Roger Beachy has had a broad ranging career working in plant pathology (during which he was involved in developing the technology that would be used to create the ring spot virus resistant papayas that prevented the collapse of papaya farming in Hawaii). His CV is 18 pages long in 10 pt font. He has the, unfortunately rare, combination of scientific talent, administrative skills, and the personal gravitas to interact with politicians and super rich donors. And on top of that, he’s spent his entire life working the 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 worked in industry to head up the NIFA? The fact that after picking my former governor to run the whole USDA, President Obama picked a guy I’ve actually shaken hands with the run NIFA is just a bonus**
*Including people like Ed Buckler who created the maize nested association mapping populations, which are just plain awesome (and deserve their own entry), Doreen Ware, a top notch computational biologist who’s been very involved in the maize genome project, all the people at that Plant Gene Expression Center we’re lucky enough to have quite close to Berkeley. Also the author of Geneticmaize.
**If this paragraph goes on a little too long, it’s only because Roger Beachy represents the sort of person I want to be when I grow up…nevermind that being twenty-four probably already puts me solidly in the grown-up category myself.

More than a year ago, in May of 2008, Congress passed the Food, Conservation and Energy act of 2008. It was weird going back to read up on the coverage of the bill and reading how President Bush objected to X or proposed Y. His presidency already seems so distant. One of the things this farm bill did was create the National Institute for Food and Agriculture by reshuffling some departments withing the USDA (United States department of Agriculture which manages everything from the National Forest Service to subsidized school lunches) and providing more money for the newly created institute to disburse in the form of competitive research grants. (more…)

Herbicide Resistance

Plant breeders can find natural resistance to pathogens. Some crops can be grown in regions where they have few or no natural insects attackers. But every crop with face the problem of weeds, other plants that threaten to steal light and nutrients. And the crops that sustain us will always suffer from an unfair handicap, as crop plants devote much of their energy to food production (whether that means fruits, roots, seeds, or even leaves) while weeds can devote all their energy to outcompeting their neighbors.
Since farmers as individuals and we as a species depend on growing fields of crops like like corn, eggplant or rhubarb and not weeds like kudzu, thistles or chickweed we need to protect our crops. A farmer can protect his crop physically, either sending people out with hoes to slay every plant but his own crops* or using a cultivator to turn over the soil between the rows, hopefully burying or slicing and dicing the majority of the weeds. The first costs money and is miserable for whoever does the work. The second burns extra fuel, bad from both global warming and cost perspectives, and increases soil erosion (top soil broken up by the plows of the cultivator can more easily be carried away by rainfall).
The alternative is for the farmer to defend his crop with herbicides (plant killing chemicals). The problem with this approach is to find chemicals that kill weeds but not the crop plants. Similar to the challenge of finding antibiotics which can kill the bacteria attacking a human body without killing the human her or himself, herbicide developers face the added difficulty that most weeds are much more closely related to the crops they’re competing with than bacteria and humans(which last shared a common ancestor more than a billion years ago). In many cases it is more comparable to finding a toxin that would kill mice, but not humans, at similar dose to body-weight ratios. And even when they find a suitable herbicide, it may have nasty effects on humans (and many herbicides do).
Herbicide resistant lines are can survive broad spectrum herbicides, herbicides that kill all plants, like glyphosate (Round-up when you the brand name version from Monsanto), glufosinate (Liberty) and Imidazolinone (Beyond). Without having to worry about finding chemicals naturally survivable by crop species, herbicides can be used that are far more effective at killing weeds, in addition to being less toxic to humans.** With more effective pesticides, farmers can stop using cultivation as an additional method of weed control, letting the soil remain unbroken, which reduces the loss of topsoil from erosion. The mistake I think a lot of people make is assuming all herbicides are equally bad. Given the choice I’d much rather get lost and wander into a field treated with glyphosate than a field treated with a quarter as much atrazine.
*The worst sunburn I ever got in my life came from a day spend hoeing a cornfield
**The MSDS for the active ingredient in round-up, glyphosate. Basically you shouldn’t rub it in your eyes or take a bath in it, but even then, the result would probably be irritation, not death. Extropolating from the LD50 in rats***(with apologies for nested footnotes), always a dangerous thing to do, a person of my weight would have to eat 500 grams of pure glyphosate to have an even chance of death. And that’s on top of it being classified as Group E (evidence that the chemical does NOT cause cancer)
***LD50 is a fancy way of saying how much of a toxin must be feed to a group of lab animals to kill half of them.

What herbicide resistance is, and why the trait is so valuable to farmers.

Spear Thisle

One of many enemies faced by crops, the spear thistle. Photo John Tann, Flickr

Plant breeders can find natural resistance to pathogens. Some crops can be grown in regions where they have few or no natural insects attackers. But every crop with face the problem of weeds, other plants that threaten to steal light and nutrients. And the crops that sustain us will always suffer from an unfair handicap, as crop plants devote much of their energy to food production (whether that means fruits, roots, seeds, or even leaves) while weeds can devote all their energy to outcompeting their neighbors.

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Red Skies in Sydney

Australia is in the middle of one of their worst drought of recorded time. Bone dry topsoil is vulnerable to be swept away by the wind, the same thing that happened in America during the dust bowl. The windborne soil is creating enormous dust storms like this one which hit Sydney yesterday. The pictures are both gorgeous and disturbing. To me they look like something out of science fiction. Can you imagine going about your business on what you think is just a foggy morning until the sun comes over the horizon and everything turns red?

All the dust used to be topsoil. The fertility of central Australia is literally blowing away in the breeze, and for me that tips the balance solidly from gorgeous to disturbing.

More on Sugar Beets

Sugar beets in this country are produced by 10,000 farmers growing beets on an average of 110 acres each. These are the people who will be impacted by the ruling. NYtimes quoted the head of a sugar beet processing company saying they’ve been accepting the beets since they came on the market and it’s been “a big non-event” as far as consumer acceptance. Which makes sense considering that sugar is almost pure sucrose (which means there’s basically no protein, encoded by transgenes or otherwise in the product), and the sort of people who seem most upset about gmos arent going to be buying a lot of processed sugar (organic or otherwise).

So the people who are impacted are people living in sugar beet producing states (especially Michigan, Minnesota, North Dakota, and Idaho) who are facing the risk of exposure to more toxic herbicides from switching sugar beets back to conventional agriculture, and the ten-thousand sugar beet farmers who today don’t know if they’ll be able to purchase the herbicide resistant seed next year, and may still not be allowed to sell the crop they currently have growing, depending on what remidies Judge White decides to impose.