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February 25, 2010

Evolution of symbiosis

This week's paper is "Experimental Evolution of a Plant Pathogen into a Legume Symbiont" published recently in PLoS Biology by Marta Marchetti and colleagues.

It's not hard to convert a highly beneficial rhizobium, which infects legume roots and provides them with nitrogen, into a slightly harmful one -- just knock out the nitrogen-fixation gene and you get a bacterium that has some cost to its host but provides no benefit in return. But how hard is it for a bacterium that causes disease to evolve into a beneficial bacterium?

One process that sometimes happens in nature is the wholesale "horizontal" transfer of a gene (or many linked genes) from one microbe to another. So the authors of this week's paper started by transferring the symbiotic plasmid (a loop of DNA with genes for infecting roots and then fixing nitrogen) into a plant pathogen.

The resulting microbe couldn't infect roots of the donor rhizobium's host plant. At least not at first. But bacteria mutate. Given enough mutants, there might be some that conferred the ability to infect host plants, forming root nodules. They applied lots of bacteria to 500 seedlings and got three nodules. What new genes had these mutants acquired?

It turned out that they had lost or modified some of the genes that made them pathogenic. In particular, these were genes for the type III secretion system, which harmful bacteria use to inject toxins into their hosts. (This "molecular syringe" is essentially the base of the bacterial flagellum, disproving the "intelligent design" claim that flagella couldn't have evolved in a series of steps, because they claimed that removing even one component of the flagellum makes it useless for anything.)

Modifying one pathogen gene got the bacteria into roots. A second modification got them inside plant cells, where rhizobia normally fix nitrogen. But, so far, the modified bacteria aren't fixing nitrogen, even though the plasmid they started with has most of the genes known to be essential for nitrogen fixation. Instead, they make lots of PHB, a storage molecule that benefits the rhizobia but has some cost to the plant.

I look forward to further research from this lab. Will they be able to activate nitrogen fixation in these bacteria? If so, will they do it by some process similar to natural selection, or by "intelligent design?"

February 19, 2010

Science fairs versus real scientific meetings

"But there's an invitation to read my paper before the Academy of Science." -- John Steinbeck, Sweet Thursday
This is part of a series on science fairs; click "science fairs" at right for more.

If you're a kid interested in science, people may encourage you to do a science project and enter it in a science fair. I agree with the "science project" part, but I'm not so sure about the "science fair" part. The thing I don't like about science fairs is the idea that someone wins and everyone else loses. That's very different from the way real science works.

We scientists do like to get together and tell other scientists about our projects. Some of us give talks, to audiences of a few other scientists or hundreds. Others put up "poster presentations", which are pretty similar to the displays at science fairs. The posters are typically up for at least a day, as part of a meeting lasting several days, but there are specific times scheduled when scientists will be at their poster to answer questions.

But, with a few exceptions, nobody is in charge of "judging" talks or posters. People ask questions and sometimes make positive or negative comments, but a student can criticize a Nobel-prize winner; there aren't any "judges."

When I was in high school in Oregon, the Oregon Junior Academy of Science put on real scientific meetings like this, where high-school students presented their work and discussed it with other young scientists. If there was any judging going on, it wasn't emphasized enough for me to remember it. It was an honor just to have your talk accepted for presentation, like it was for "Doc", the character (based on real-world scientist Ed Ricketts) speaking in the quote above. Most US states still have a Junior Academy of Science, but I get the impression that many are now infected by judging. Too bad. There's also a national American Junior Academy of Sciences, which meets alongside the grownup version, the American Association for the Advancement of Science or AAAS. Meetings of the AAAS always look interesting; I should go to one some year, but I usually end up spending my meeting-travel budget on more specialized meetings.

Although the Oregon Junior Academy of Science talks weren't judged, the rewards sometimes went beyond the satisfaction of interesting discussions. One year, six of us were offered an expense-paid trip to the national Junior Science and Humanities Symposium. There were only two catches. We had to give our talk at the state symposium, which was easy and fun. And... the state and local symposia are sponsored by the military.

This was the height of the Vietnam War, for which men about our age were being drafted to die propping up a South Vietnamese government that didn't seem to be any more democratic than the rebels -- I guess we would call them "terrorists" now -- trying to overthrow them. Lots of Vietnamese civilians were being killed, too, and the National Guard had just shot several students at Kent State. Nobody in the Oregon group was very enthusiastic about the military, but we agreed to go, anyway....

The national meeting was held at the University of Tennessee. I guess the organizers assumed there wouldn't be much opposition to the military in the South. But the evening we arrived, lots of students had organized a big rally against the war. I think Al Gore may have been one of the speakers. The organizers of our meeting were worried, and posted guards at the entrance to our dorm, to keep out trouble-makers. But one member of the Oregon delegation climbed out a window and got some antiwar flyers printed, addressed to the meeting participants. We all got up at 5 in the morning and slipped one under each door in the dorm. The next day, the meeting organizers were obviously upset, and moved the whole meeting off campus.

"And we was fined $50 and had to pick up the garbage in the snow, but that's not what I came to tell you about." -- Arlo Guthrie

I was telling you about scientific meetings for junior and senior scientists. Once you're in college, even as an undergraduate, you can probably do more sophisticated science projects, typically with some advice from a professor and/or a graduate student. If you get some interesting results, you should consider presenting them at a regular scientific meeting. I remember giving talks on my undergraduate research at a regional Academy of Science meeting (or something similar) and at the International Symposium on Acid Rain (or similar). My college paid my travel costs.

There are also meetings just for undergraduate researchers, such as the National Conference on Undergraduate Research. The University of Minnesota is paying costs for several students, including Carolyn Anderson, who did her research in our lab, to participate in this meeting.

If you go to graduate school in science, you should definitely plan on giving talks and poster presentations at one or more of the meetings for scientists in your field. You can hear about research that isn't published yet, get useful feedback on your own research, and find collaborators or a job.

These meetings can be expensive. Your major professor may be able to pay some of your expenses to talk about work done in her lab. Or your department may have travel grants. But keeping costs down is the key. Staying in hotels is expensive, but meetings held at or near a university often offer inexpensive dorm housing. Dorm housing can be a really good deal. By staying in the dorm at one meeting, I had access to the campus Olympic pool, whereas hotel pools are usually too small (and too warm) to swim laps. At the Applied Evolution Summit, last month, most people stayed at the resort, but a few of us stayed in dorms at the research station. Unlike the resort, the research station had internet access. Actually, I was planning to write about the Applied Evolution Summit today, but this post is long enough.

February 12, 2010

Happy Darwin Day!

"You don't use science to show that you're right, you use science to become right."
-- from the web comic XKCD.

Also this week:

Darwinian Evolution of Prions in Cell Culture
Any set of replicators with heritable differences affecting survival and reproduction can evolve.

Reconstructing the ups and downs of primate brain evolution: implications for adaptive hypotheses and Homo floresiensis
Mapping trends in brain size on the primate family tree shows more increases are more common than decreases, but both have occurred. "Hobbits" could be an example of a decrease.

Evolution of a unique predatory feeding apparatus: functional anatomy, development and a genetic locus for jaw laterality in Lake Tanganyika scale-eating cichlids
Fish that eat scales from the left or right side of other fish have asymmetric jaws; they've found the gene responsible for this "handedness."

Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits
They're really old, they're really big (probably visible without magnification, but apparently some bacteria get that big), and maybe they were once alive.

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection
Various methods can show that some large DNA sequence has increased under natural selection, but can't usually narrow it down to a particular gene. Combining methods can help.

A bony connection signals laryngeal echolocation in bats
Some bats (including the big ones we saw recently in Brisbane) don't use sonar. But what about bat species known only from fossils? Different species "ping" in different ways, but a connection between two bones appears to have a consistent link to echolocation.

February 5, 2010

Tradeoff-free drought resistance?

I'm working on the last chapter of my book, Darwinian Agriculture: where does Nature's wisdom lie?, and will be sending it to Princeton University Press soon for their review process. So I'm alert for any information that might make me change my main conclusions.

One theme of the book, and also of my recent talk at the Applied Evolution Summit, is that past natural selection is unlikely to have missed simple, tradeoff-free improvements. So I'm always skeptical when someone speculates that we could double crop yield just by increasing the expression of some newly discovered "drought-resistance gene." My rationale is that mutants with greater expression of any given gene are simple enough to have arisen repeatedly over the course of evolution. (This contrasts with more-complex adaptations, like the ability to form a symbiotic relationship with nitrogen-fixing bacteria, which natural selection may have had fewer opportunities to test.) If past natural selection has repeatedly rejected these "drought-resistant" mutations, then they must have been some negative effects on fitness, at least in past environments.

But could some mutations repeatedly rejected by past natural selection still be beneficial in agriculture? Maybe. Tradeoffs that constrained past natural selection need not always constrain us, as discussed below. But, I suggested at the meeting, we can't just ignore them.

However, someone called my attention to Drysdale wheat, developed in Australia, and reported to have higher yield under drought than older varieties, without any apparent yield penalty under wetter conditions. Is this an example of a tradeoff-free improvement missed by past natural selection?

The answer can be found in a very interesting paper, Breeding for high water use efficiency, published in Journal of Experimental Botany in 2004 by A.G. Condon, R.A. Richards, G.J. Rebetzke and G.D. Farquhar. If you are at all interested in this topic, the entire paper is well worth reading. But here are some key points....

Yield of Drysdale wheat, relative to a previously recommended "check" variety, as a function of increasing water availability (as indicated by yield of the check variety). Condon et al. 2004 J.Exp.Bot.55:2447.

As shown above, Drysdale outyields a good older variety by up to 40% under the driest conditions (when the older variety yields only about 1000 kg/ha or about 1000 pounds/acre), while having similar yield to the older variety under wetter conditions, when the old variety yields about 5000 kg/ha. This is clearly a major practical advance. But does it contradict my hypothesis, that natural selection is unlikely to have missed simple, tradeoff-free improvements?

No. There are many different kinds of tradeoffs. Actually, the paper discusses several of these tradeoffs in lucid detail, as summarized below. But some tradeoffs that were key to past natural selection are relatively unimportant to us today. For example, how well would Drysdale do under wetter conditions, beyond the range shown in the graph above? Such conditions might be very rare on Australian wheat farms. From a practical standpoint, it wouldn't matter if Drysdale has slightly lower yield under conditions that hardly ever occur. But the wild ancestors of wheat must occasionally have experienced wet years, so that even slight tradeoffs could have affected past evolution.

What about other tradeoffs? Any plant that survives drought may be considered "drought-tolerant." But Drysdale was selected for water-use efficiency (WUE), the ability to actually grow and produce grain with a limited water supply. Water-use efficiency at the leaf level is the ratio of photosynthetic uptake of carbon dioxide, divided by transpirational water loss from leaves. Carbon dioxide diffuses into leaves through the same stomata that water vapor diffuses out, so

WUE = photosynthesis/transpiration = (Ca-Ci)/(Wi-Wa)

where Ca and Ci are CO2 concentrations in the atmosphere and the leaf interior, while Wa and Wi are corresponding water vapor concentrations. (I have left out a constant that doesn't affect any of my conclusions.)

So, one way to increase WUE is to increase Wa, the CO2 concentration in the atmosphere. You can help by burning more coal. Unfortunately, this approach can have various negative side-effects, including increased temperatures, which can raise Wi and thereby lower WUE.

A more-practical approach is to decrease Ci. Drysdale may do this by closing its stomata more than other varieties. With partial stomatal closure, CO2 can't diffuse into the leaf interior quite as fast, so photosynthetic uptake pulls leaf-interior CO2 concentration (Ci) lower, increasing WUE.

So here's our first tradeoff: lower CO2 diffusion into the leaf can mean higher WUE, but a lower photosynthesis rate. Wouldn't a lower photosynthesis rate result in lower yield? Not necessarily. Lower total seasonal photosynthesis would probably mean lower yield. But, by using water more efficiently, Drysdale may photosynthesize for more weeks before running out of water. Slightly lower photosynthesis per day, times more days, could give greater total seasonal photosynthesis.

How would past natural selection have responded to a tradeoff between photosynthesis rate and water-use efficiency? A key point is that an individual plant gets to keep the carbon it takes up via photosynthesis, but the soil water it conserves by using it more slowly may be used by a profligate competitor nearby. Given this tradeoff between individual-plant fitness and the collective efficiency of the plant community, it's not surprising that past natural selection has left some opportunities to improve whole-crop performance.

Here are some other tradeoffs discussed in the paper. Another way to decrease Ci and increase WUE is to crank up photosynthesis, pulling more CO2 through given stomata. The key photosynthetic enzyme, like other proteins, contains nitrogen, so one way to increase WUE is to be sure our crops have enough nitrogen. The paper notes that a crop with limited access to nitrogen could decrease Ci by making a few high-nitrogen leaves rather than many low-nitrogen leaves. At the individual-leaf level, this would increase WUE. But a crop with fewer leaves won't capture as much sunlight for photosynthesis -- another tradeoff.

And it gets worse. Sunlight not intercepted by smaller, high-N leaves will instead hit the soil, increases evaporation of water from the soil surface. The water-use efficiency of water evaporating from the soil is a big, fat zero. So making lots of leaves fast may increase season-long WUE, even if individual-leaf WUE is lower. Dr. Roberts, the plant breeder who developed Drysdale, is working to increase "early vigor", to completely shade the soil surface as soon as possible.

A related tradeoff is apparently a side-effect of the Green Revolution. Shorter wheat plants tend to have higher yield, because they waste fewer resources on stem growth, but they are also less competitive. (This is another example of the tradeoff between individual competitiveness and the collective performance of plant communities.) A side-effect of shorter height at maturity was reduced ability of a young seedling to reach the soil surface when seeds are planted deep. But deep planting can be very useful, particularly when the surface is dry, but there is moisture for growth deeper in the soil. Dr. Richards has found a way to get the best of both worlds: good emergence from deep-planted seeds, yet short stems in mature wheat. So this particular tradeoff wasn't as intractable as those discussed above.

Finally, if you want really big increases in water-use efficiency, the paper suggests a very different approach, namely, increasing Wa, or humidity. This isn't always possible, unfortunately. But they mention one example of farmers in Syria doubling the yield of chickpea by growing it in winter, rather than in spring. This became possible, however, only after plant breeders developed varieties resistant to diseases that previously destroyed winter-grown crops. This is a long way from the naive, tradeoff-ignoring approach of looking for "drought-resistance" genes and increasing their expression!

February 4, 2010

Carnival of evolution

A roundup of recent blog posts on evolution at Skeptic Wonder.