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December 30, 2008

This year in "intelligent design"

This year, I haven't found a single paper in a scientific journal presenting new data and claiming to show a role for a supernatural "designer" in the origin or subsequent evolution of life. Readers are invited to call my attention to papers I missed. Any paper published in a journal with a citation impact of at least 1.0 and containing actual data will do. In your comment, please quote the text that invokes intelligent design. Comments not meeting these three basic requirements may be ridiculed or deleted.

If scientists ever find any actual evidence for intelligent design, it will modify our understanding of evolution rather than completely replacing what we already know. In biology, "evolution" refers to genetic changes in populations over generations, by any mechanism. The mechanisms for which there is evidence are mutation (direct changes to DNA by various means), selection (including sexual selection, kin selection, deliberate selection by humans, etc. ), gene flow (e.g., migration or blowing pollen), and the random genetic drift of small populations. If there were any evidence for supernatural intervention, we would add that to the list, but there isn't, so far. Whining doesn't constitute evidence.

"Intelligent design" never got off the ground as a scientific field and now it seems to be dead even as a religious movement.

This year in evolution, in Nature

The leading general-science journal, Nature, published many papers on evolution this year, two of which made it into their annual list of the editors' "favourites." One paper described laboratory experiments using the power of "directed evolution" to improve enzymes. The other explains the rapid evolution of new fish species in the wild. The editors also highlight two papers giving ice-core records of atmospheric carbon dioxide and methane over the last 800,000 years. These greenhouse gases both affect and are affected by life on earth, so they provide valuable context for recent evolutionary trends.

In a paper titled "Kemp elimination catalysts by computational enzyme design", Daniela Rothlisberger and colleagues started by designing enzymes using computer software. I don't know how the "RosettaMatch hashing algorithm" works, but the process seems to have a lot in common with natural selection's approach, selecting the best from "more than 100,000 possible realizations" rather than going directly from first principles to the ideal design. Furthermore, they noted that "our in silico design process seems to be drawn towards the same structural features as naturally occurring enzyme evolution."

Their next step was even closer to natural evolution. They started with their best design and generated lots of random mutants, testing each for activity. After seven rounds of this directed evolution, they got a 200-fold increase in enzyme activity. They noted that "in vitro evolution... is currently the most widely used and successful approach for refining biocatalysts."

Once again, nonrandom selection among random variants solves problems beyond the reach of (present) human ingenuity. How many more examples do we need before people stop saying "it's sophisticated, must have been designed" and instead say "it's sophisticated, must have evolved"?

In the second paper, Ole Seehausen and colleagues describe "Speciation through sensory drive in chichlid fish." For a species to split in two, interbreeding between two groups has to be low enough that they can evolve differences. This is easy if they are geographically separated, as on different islands or on continents drifting apart. But what if they're all fish in the same lake?

Even within a lake, there can be major differences in light conditions. Females often prefer brightly colored males, but the definition of "brightly colored" depends on lighting and on how sensitive female eyes are to different colors. They compared two related species, one with red males and one with blue males. These color differences in the males corresponded with differences in color perception by the females. The red fish were found at greater depth, where more red light penetrates.

Speciation depended on how rapidly light conditions changed with distance. If it didn't change at all, selection operated similarly across the range, giving no differences in light sensitivity. But apparently the same was true if light conditions changed too rapidly. In that case, fish had to cover a range of light conditions, so didn't evolve the specialization that would lead some females to prefer blue males and others to prefer red males.

December 24, 2008

Celebrating Science Seasonally

Olivia Judson's column today is great, as usual. But I have some reservations about her proposal to celebrate Dec. 25 to January 4 as the Festival of Newton.

Dec. 25 is already taken. It is, of course, Family Day, although the name is used mainly in Uruguay. The date also has religious significance to many. And the connection between Newton's birth anniversary and Dec. 25 is a mere fluke of human attempts to impose a calendar on a year with an uneven number of days.

Newton was born on the perihelion, the day when the earth is closest to the sun, and that is when we should celebrate him. This is approximately January 4, depending on the year. Taking that day as given, I see two logical time-spans for a winter festival celebrating science.

1) Winter solstice to perihelion. If astronomy were the whole of science, this would be a great choice, but it's not. This period is already enriched with family get-togethers and religious celebrations with generally positive themes and there's more to life than science. Furthermore, US scientists are frantically revising grant proposals to NSF, due the beginning of January.

2) Newton's birthday (and perihelion) to Darwin's birthday (Feb. 12). Most scientists would agree that these two changed our understanding of the universe and ourselves as much as anyone before or since. We could use the time between their birthdays to celebrate past scientific advances, but also today's most exciting frontiers, across all of science.

I'll spare you the words to We All Evolved from One, sung to the tune of All Creatures Great and Small.

December 21, 2008

Spatial structure and the evolution of cooperation between microbes and plants

Evolutionary theory suggests that cooperation should often be unstable, even when it benefits all concerned. Toby Kiers and I discussed this problem and some possible solutions in a recent review article in Annual Review of Ecology and Evolution. Meanwhile, Jim Bever and colleagues have published some important experimental data in Ecology Letters, helping to explain cooperation between plants and fungi, a little too late to include in our review. Their paper is titled: "Preferential allocation to beneficial symbiont with spatial structure maintains mycorrhizal mutualism."

Many bacteria and fungi associated with plant roots benefit more from healthy plants than from dead or dying ones. If each individual plant were colonized by only one strain of bacteria or fungus, then strains that helped their host plants (by providing them with nitrogen or phosphorus, for example) would indirectly help themselves, gaining an evolutionary edge over their competitors of the same species. These beneficial strains would become more common in each generation. In other words, cooperation would evolve.

The problem is that each plant is typically associated with several strains of each species of bacteria or fungus. Strains that invest less in helping the plant have more resources to spend on their own reproduction. If less-generous strains benefit equally from the contributions of more-generous strains on the same plant, then less-generous strains will become more common over generations. In other words, “cheating� will evolve.

As a Ph.D. student in my lab, Toby showed how legume plants that depend on root-nodule bacteria for nitrogen solve this problem. They monitor individual nodules and cut off oxygen supply (and perhaps other resources) to nodules that provide them with less nitrogen. This reduces the reproduction of rhizobium bacteria in nodules that provide no nitrogen to less than half that of those that provide lots of nitrogen. So cheaters don’t prosper.

Our review suggested that something similar could explain cooperation between plants and the mycorrhizal fungi that provide them with phosphorus and other benefits. The mathematical models that Stuart West developed in our lab to explain cooperation between plants and rhizobia could probably be extended to apply to these fungi as well. But what about actual data?

Previously, Bever showed that, when fungal strains were thoroughly mixed together, less-beneficial strains became more common. (This is the same result we would expect with rhizobia, if individual root nodules each contained many different strains: the plant wouldn’t be able to help the good strains without also helping the bad ones.) But what if different fungal strains are found in different patches of soil around a plant? Do plants send more resources to fungi that supply them with more phosphorus? If so, does that let these more-beneficial fungi reproduce more?

To answer this question, they used wild onion plants with their roots growing into two separate containers of soil. (One of Toby’s experiments also used this split-root approach.) The two containers were inoculated with either the same or different fungal strains, using strains expected to differ in benefits to the plant. The main resource plants provide to their fungal partners is carbon compounds. Plants were exposed to radioactive carbon dioxide, so that carbon compounds produced by photosynthesis, including those the plant provided to the fungi, would be radioactive.

When both sides of a plant’s root system were inoculated with the same fungal strain, one strain provided essentially no benefit: plant growth was the same as an uninoculated control. The other strain helped the plant a lot, leading to almost twice as much growth as the control. Surprisingly, perhaps, plants inoculated with both strains, on different sides, grew about as well as plants inoculated with only the good strain. (Similarly, Toby found that three old soybean varieties did as well with a mix of good and bad rhizobia as with good rhizobia alone, although this was not true of three modern varieties.) One way that a plant could do well with a mixture of good and bad symbionts is to preferentially allocate resources to the good ones and that is what Jim Bever’s plants did: the good strain got more than an equal share of the carbon compounds from the plant’s photosynthesis.

But did the good strain actually benefit from getting more carbon? “Benefit� to an evolutionary biologist, means reproducing more. As Darwin wrote:

“I use the term Struggle for Existence in a large and metaphorical sense, including dependence of one being on another, and including (which is more important) not only the life of the individual, but success in leaving progeny.�

The relative success of the two strains depended on spatial structure. When the two strains were mixed together on both sides of the root system, the less-beneficial strain produced more spores. This suggests that this strain was not simply defective, but rather a “cheater�, benefiting by investing less in helping the host and more in its own reproduction. When the two strains were separated, however, the host’s preferential allocation of carbon compounds resulted in higher spore production by the better symbiont.

A key question, identified by Bever et al., is whether spatial structure in the field is more similar to inoculating two sides of the root system with different fungal strains, or mixing the two strains together on each side. They cite previous studies showing that field soils have patchy distribution of different fungal strains, perhaps sufficient to let plants favor better fungal strains. Plowing, however, would result in more uniform mixing of fungal strains. This could give cheating strains an evolutionary edge.

As we noted in an earlier paper, however, soil mixing from plowing could also have the opposite effect. If soils are mixed up regularly, the descendants of symbionts that share an individual host plant this year are unlikely to encounter each other in the future. One strain on a plant doesn’t benefit from helping the others, by providing their shared host with phosphorus, but the only cost is the direct cost of providing the phosphorus. In unmixed soils, however, this year’s neighbor is next year’s competitor: the descendants of fungi that share a plant this year are likely to compete in the future. In unmixed soils, therefore, benefiting other strains on the same plant is negative -- given the option, killing them might be better -- rather than neutral. Figuring out the balance between positive and negative effects of plowing on the evolution of mutualism could be quite a challenge.

December 11, 2008

Intelligent design falls into chaos?

The advocates of "intelligent design" claim there is enough scientific evidence for their theory that it should be taught in science classes. In support of this claim, they list a grand total of nine articles published in peer-reviewed journals over the entire history of intelligent design. This is fewer papers than evolutionary biologists publish every week, but every new field needs to start somewhere, I guess. The most-recent paper was published in 2006, however, which makes intelligent design look a bit moribund. Now it turns out that peer-review is suspect at the journal that published the last ID paper (ever?), Chaos, Solitons, and Fractals.

Furthermore, Nature reports that the editor, who apparently uses the journal mainly to publish his own papers and those that cite him,

"is not, as he claims on his website, a distinguished fellow of the Institute of Physics at the Johann Wolfgang Goethe University in Frankfurt, Germany, says Walter Greiner, a former director of the institute. Greiner also says El Naschie has ignored his requests to remove his name from the list of members of the journal's honorary editorial board."
OK, maybe this is guilt by association, but I did wonder whether the editorial boards of that journal or the International Journal of Fuzzy Systems had the expertise to review biology papers.

December 5, 2008

December 5

Until I finish my book, Darwinian Agriculture, I am cutting back detailed posts to once or twice a month, but here are some links to some papers that looked interesting this week.
Pollinator experience, neophobia and the evolution of flowering time


Diversification trajectories and evolutionary life-history traits in early sharks and batoids


Centromere-Associated Female Meiotic Drive Entails Male Fitness Costs in Monkeyflowers


Honest sexual signalling mediated by parasite and testosterone effects on oxidative balance


Oscillations in continuous culture populations of Streptococcus pneumoniae: population dynamics and the evolution of clonal suicide


A female songbird out-sings male conspecifics during simulated territorial intrusions


The Long-Run Benefits of Punishment