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

Seems to be becoming a habit:

Olivia Judson, one of the best people are making biology exciting for the general public (I can’t recommend her book enough) has a new article up on nytimes on genomes and asking the question, what genome  would you choose to sequence if you could. Probably won’t tell you much you didn’t already know, but it’s a warm fuzzy feeling none the less.

From the title “The Fantasy Genome Project” I was all ready to advocate for the dragon genome! After all it’s a hexapod vertebrate , which is awesome even without considering that dragons are cool!

Hybrids are good. Excellent even. If anyone tells you otherwise, you send them to me.

Alright I’ll take a couple of steps back. Hybrids are always hard to explain, I’ve tied myself in nots a couple of times tying to, but maybe this time is the charm. At it’s most fundamental levels, a hybrid is nothing more than the offspring of two dissimilar parents. When Gregor Mendel discovered the fundamental principle of genetics* he wasn’t setting out to study genetics, or the basic principles of life, but instead the traits of the offspring of dissimilar pea plants. And he published his findings under the title Experiments on Plant Hybridization.

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An article yesterday on the science website yesterday discusses the loss of groundwater in northern India. The technical details of how this are measured* are interesting in their own right. But just keep in mind what the final outcome will be if nothing changes from the way it is today.

The region of northern India supports 600 million people many of them in abject poverty and is drawing 54 cubic kilometers of water a year more than is replaced by rainfall. The end result will be human suffering on a scale even greater than currently found around the world.

What can avert this disaster? Three things:

• Substantial increases in rainfall throughout the year in northern india (beyond human control)
• Major breakthroughs in desalinization and pumping (desalinization isn’t my field, so I don’t know how likely that one is, however humanity has been studying the field of moving water from one place to another for thousands of years so the odds of a new pumping breakthrough are slim to none)
• “Drip” irrigation systems. Most irrigation wastes a lot of water. Drip irrigation reduces waste by irrigating each plant individually (no point in getting the ground between plants wet) and doing so slowly so the water soaks entirely into the ground eliminating run off which both saves water and addresses a major source of agricultural pollution and topsoil loss. The downside is drip irrigation is, comparatively, expensive. Which means someone other than the subsistence farmers who need it would have to pay for it.
• Water-use efficient and salt tolerant crops. Plants that need less water means less irrigation obviously. The benefit of salt tolerance is in the ability to reclaim land where the earth has become too salty for crops to grow well** as a result of irrigating with salty water, and using that same salty water to irrigate, reducing the demand for fresh water.

I’ve listed these option in what I’d guess is increasing return in investment. Throwing 10 billion dollars are changing the earth’s weather patterns won’t make any difference at all. Throwing the same money at desalinization would have real benefits. Investing ten billion in subsidizing drip irrigation systems for subsistence farms would have a huge impact. It probably wouldn’t cost ten billion dollars to get draught and salt tolerant crops into the hands of the farmers who need them. The benefit of stress tolerant crops is that after they’ve been breed, the cost of actually getting them to those who need them is quite low.*** After all plants, like people, are self replicating. Now if someone would just invent a drip-irrigation system that could build additional copies of itself we’d be set.

*Two satellites orbit the globe and can measure water loss based on changes in their orbit which are caused by variation in the strength of earth’s gravitational field.

**Salt is very bad for plants that can’t handle it. Plowing salt into their farmland is an effective if time consuming method to deal with people you don’t like.

***Especially in countries like India where there is a substantial grey market for things like bt cotton seed.

Dan Barber had a column in the new york times on Saturday addressing the major attack of tomato blight in the northeast this summer. Late Blight is a fungal disease that attacks tomatoes and potatoes (edit: Maybe also eggplants? They’re all pretty closely related). When potato harvests fail, people starve (see: Irish Potato famine). With tomato harvests fail… the price of tomatoes goes up and people eat less tomatoes. But I have a serious point to make so please keep reading.

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Pineapple phylogeny has been delayed as a result of a publication in the household requiring celebration. Hopefully tomorrow.

When I was a kid I had a children’s illustrated bible (and a children’s illustrated book of greek myths, the juxtaposition which did a fair bit to inform my young worldview). But in that book, the story of Cain and Abel is presented as being about the evils of jealousy… sort of a prelude to the tenth commandment. That’s generally the moral people think of whenever the story is mentioned.

But why is Cain jealous of Abel? It’s not because Abel has a better car, a nicer house, a more desirable wife. The bible explains that it’s because god likes meat more than plants. Abel grows up and decided to be a keeper of sheep, while Cain becomes a tiller of the ground. A farmer. Since Abel can sacrifice sheep to god while Cain can only offer  the grains and vegetables, god likes Abel more, and doesn’t particularly care for Cain. Cain becomes violently jealous and the story goes from there.

Now the obvious reasoning here is that meat tastes better than vegetables. A statement I definitely don’t disagree with, especially in mesopotamia thousands of years ago when the old testament was being written. Keep in mind that among the uncountable number of benefits civilization brings to us today is easy access to an array of flavoring agents from around the world. With enough of the right herbs and spices even eggplant, a vegetable I particularly dislike, can be made delicious. But in that era even something as simple as salt would be scarce and valuable. Given the  choice between a hunk of lamb and, say, a bowl of unseasoned chick peas, I know which on I’d prefer.

All that said, presumably god isn’t presumed to actually be sitting down to dinner with the sacrifices. So is the message here actually something about the relative importance of shepherds and farmers? I mean the shepherds in the bible include big names like Abraham, Moses and David. Shepherds get to be present at the birth of Jesus. Farmers? Hopefully someone more familiar with the concept will correct me if I’m missing something obvious, but when farming is mentioned in more than passing it’s to give instructions on how to grow crops, or how to sacrifice them (because by the time we get to Leviticus god has decided he’s ok with accepting plant sacrifices after all).

Jealousy and murder are bad things. But is that moral the whole message of the story of Cain and Abel?

My uncle is in wired for building his own CPU!

It took giving up delivery food completely for a month, and slashing the beer budget, slashing it to the bone in fact, but I’ve increased my central server’s storage capacity to 7.5 terabytes: 5.5 in internal storage and another two in a myBook external. (Doubling internal storage and increasing total storage by 50%).

It’s really a ridiculous amount of storage for one man. But when you can catch 1.5 TB drives open box drives for $95 (6.3 cents per gig!), ridiculous things become a lot more practical.

Additionally this gave me a chance to use one of the new drives to replace my old 500 gig system drive. I’m seeing much faster and more consistant transfer speeds than I had with the old drive, which apparently was reaching the end of its useful lifespan. I’d already had to replace a drive of similar make and purchase date that gave up the ghost. So, faster speeds, greater reliably, and of course the upgrade from ubuntu hardy heron to the newest version jaunty jackalope.

There’s a new study out from some fellow California scientists that have calculated that it’s much more productive and better for the planet to use energy crops to produce electricity to run electric cars vs converting it to ethanol for fuel. If this finding becomes policy, a lot of the work devoted to fine tuning plants to be more efficiently digested into ethanol is going to be bypassed. (Optimizing cell wall structure and make up (cellulose is good, lignin is bad), engineering plants to produce the very enzymes needed to digest them into ethanol.) Now it isn’t certain that such a change will take place, but this report, like many others before it, reminds us that there is a significant argument for why a change in priorities could happen.

Changes in the methods pursued to create biofuels are likely to change a number of times as our nation attempts to scale back its dependence on fossil fuels. And it can really suck both emotionally and career wise to be invested in a branch of research that ends up appearing superfluous. So all things being equal, when deciding on an area of research to write a grant for, or what lab to join, or what projects to fund, remember TAMBITAM (Twice as much biomass is twice as much!). Meaning whatever method is deployed to convert plants into energy, the more biomass we can produce on the a given amount of land, with the same inputs, the more energy we’ll produce. If tomorrow I discover a mutation that makes switchgrass grow twice as big*, that’s a great discovery that doesn’t hinge on its applications to a single technological process.

*Realistically these are more likely to be genes that increase water or nitrogen use efficiency or that change the partitioning of resources between vegetative and reproductive growth. (Something we can already do with flowering time mutants or growing tropical lines at higher latitudes where the day length doesn’t trigger flowering until much later in the year.)

Updated with photos from my parent’s visit to the Bay Area last weekend. Mostly from the hills above Muir Woods and more pictures from Berkeley Botanical Gardens. <– the “Crops of the World” exhibit was very disappointing, but the rest of the garden is still cool.

This update returns visually attractive photos to the badge on the left, instead of the black on white graphs from discussion section that were previously occupying that screen real estate.