Muck and Mystery
   Loitering With Intent
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March 31, 2009
Sex & Seed

Tyler read a book: Deconstructing Darwinian Selfishness.

The book rejects the "Red Queen" hypothesis for why there is sex (e.g., outracing parasites by frequently rolling the genetic dice) and presents a "portfolio diversification" view:
The explanation for why asexual species keep popping up and quickly dying compared with sexual species would seem to be completely explained by thinking of asexual species as genetic versions of get-rich-schemes and of sexual populations as genetic versions of long-term mutual funds, without any need to invoke cost-of-meiosis considerations.
In other words, sex brings a genetic diversity which protects against rapidly changing environmental conditions and thus favors parental genes.
I haven't read it, and haven't seen an informed review, but the first thing that comes to mind is epigenetics: the ability to variably express a genome and rapidly respond to rapid changes such as changing environmental conditions. This is useful, perhaps necessary, since natural environmental variability such as periodic drought and temperature swings are common. This is useful for the never ending battle with disease and parasites too, since they are just as able to quickly change tactics. The argument that rapid environmental change, as opposed to rapid predator change, somehow favors sexual reproduction doesn't seem compelling. Both drivers have rapid as well as longer term variability.

Though the idea doesn't seem compelling it does provide an opportunity to recycle more old posts about subjects having to do with agriculture and old Richard Manning articles and books. It's been 5 years and more since I did that so it may be almost fresh again. The Wheel, linked in the previous post, pointed to Seed Without Sex, which discussed apomixis.

A farmer wishing to grow hybrids would need four fields and expend great effort to make sure that each was pollinated correctly. This can sometimes be done by having isolated fields far from possible contaminating influences but this doesn't work for controlled crosses since many crops self pollinate. Often hand pollination is required to produce target crosses. This is far too much trouble and far too difficult for most farmers. . .

Not only must great effort be spent to create useful cultivars, great effort must be spent to forever maintain the race, to make sure that each cultivar is bred to the proper other. It would be so much simpler if sex wasn't necessary, if desirable cultivars could just be cloned repeatedly. This is possible for some plants. Some can be grown from cuttings, a common practice for many orchard plants. Some reproduce by budding off daughter plants by a variety of methods. A very few plants produce asexual seeds. These aren't self pollinated seeds, they are not pollinated at all, instead using a class of methods collectively called apomixis (as opposed to amphimixis) whereby viable seed is produced internally. . .

Apomictic cultivars would be a very great benefit to farmers in developing countries. It would allow them to have the benefits of improved cultivars without the prior development of a seed industry since they could set aside a portion of each year's crop for use as next year's seed. They would only have to acquire improved seed once, not every year. The cost of such seeds would be lower since no special efforts would be needed to isolate fields or hand pollinate. Several organizations, notably the International Maize and Wheat Improvement Center ( CIMMYT) have research projects to develop apomictic cultivars for use in food insecure developing countries. . .

The fact that apomictic plants don't out cross with native land races would help preserve existing diversity, avoid contaminating that gene pool, but would also slow evolution and perhaps have a future consequence when predators and diseases adapt to them and overcome their natural defenses. Sexual reproduction allows plants to evolve new defenses. See Bananas, Sex and the Red Queen for more on this issue.

There seems to be a bifurcation, two wildly divergent issues. On one hand we have emo activists who want to stop the wheel, stop progress and regress a little bit to the way the world was about a century ago, but with iPods and birth control pills. They express this longing in advocacy for "sustainability" or "diversity" or precaution and the like. OTOH we have sooners who want to speed the wheel up, accelerate progress and have some sort of singularity which results in a world that by definition is beyond our ken but that they imagine will be superior. On the gripping hand we have those who want it all.
Smart breeding holds the promise of remaking agriculture through methods that are largely uncontroversial and unpatentable. Think about the crossbreeding and hybridization that farmers have been doing for hundreds of years, relying on instinct, trial and error, and luck to bring us things like tangelos, giant pumpkins, and burpless cucumbers. Now replace those fuzzy factors with precise information about the role each gene plays in a plant's makeup. Today, scientists can tease out desired traits on the fly - something that used to take a decade or more to accomplish.

Even better, they can develop plants that were never thought possible without the help of transgenics. Look closely at the edge of food science and you'll see the beginnings of fruits and vegetables that are both natural and supernatural. Call them Superorganics - nutritious, delicious, safe, abundant crops that require less pesticide, fertilizer, and irrigation - a new generation of food that will please the consumer, the producer, the activist, and the FDA.

Nearly every crop in the world has a corresponding gene bank consisting of the seeds of thousands of wild and domesticated relatives. Until recently, gene banks were like libraries with millions of dusty books but no card catalogs. Advances in genomics and information technology - from processing power to databases and storage - have given crop scientists the ability to not only create card catalogs detailing the myriad traits expressed in individual varieties, but the techniques to turn them on universally. . .

Generations of unscientific plant breeding have inadvertently eliminated countless valuable genes and weakened the natural defenses of our crops. . .

The science behind some of these techniques makes transgenics look unsophisticated. But the sell is simple: Smart breeding is the best of transgenics crossed with the best of organics. It can feed the world, heal the earth, and put an end to the Big Ag monopoly.

Transgenic researchers treat the genome like software, as if it contained binary code. If they want an organism to express a trait, they insert a gene. But the genome is more complicated than software. While software code has two possible values in each position (1 and 0), DNA has four (A,C,T, and G). What's more, a genome is constantly interacting with itself in ways that suggest what complexity theorists call emergent behavior. An organism's traits are often less a reaction to one gene and more a result of the relationship between many. This makes the expression of DNA fairly mysterious.

It sounds like Wired style breathless hype, and it is so far, but the general idea of leveraging advances in genomics, to undo some of the harms that have been done to food crops with eons of dumb breeding that has lost many useful characteristics in the pursuit of others, is good. The complexity of genomic expression makes it difficult to do cut and paste style synthetic biology so "smart breeding" looks like a good approach for now.

But it won't satisfy the emo activists longing for a mythical past (with iPods), and it won't satisfy the singulatarians longing for rapture. There is only a very small constituency for these efforts even though they make the most sense. And so I suspect that it will be the large ag businesses that will make the best use of genomics. They are less affected by populist monkey-wrenching and budget weapons, less subject to political disruptions, and may quietly make progress until we wake up one day to find that farmers are growing better crops that flew under the radar of anti-GMO activists, while singulatarians still wait for nano-assemblers that can give us Star Trek type replicators for synthesizing food on demand, or mind uploads to a non-carbon platform that doesn't need food, just energy.

Posted by back40 at 10:33 AM | Ag-tech

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