April 17, 2009

Mindless manipulation

This week I'll discuss a recent paper from our lab. But first, here are links to three other papers that look interesting:

Evidence from the domestication of apple for the maintenance of autumn colours by coevolution Some insect pests avoid trees whose leaves turn red in autumn and do poorly on those trees, but can trees "lie" or is there an unbreakable link between red color and poor quality as a host, perhaps because "aphids grow better on trees that drop their leaves later [because they have enough nitrogen they can risk losing high-N leaves in frost?], which are known to have fewer autumn colours [because, by the time they lose chlorophyll, UV levels are too low to require the protection provided by red anthocyanins?]."?

Functional morphology of the ankle and the likelihood of climbing in early hominins Modern chimps use their ankles, when climbing trees, in ways some early hominins (1-4 million years ago) probably couldn't, based on fossils.

Cooperation and virulence of clinical Pseudomonas aeruginosa populations
Patients with pneumonia are sicker when bacterial cells cooperate by producing individually costly virulence factors, but bacterial populations evolved "cheaters" that don't make these factors within 9 days.

In our paper, "Rhizobitoxine producers gain more poly-3-hydroxybutyrate in symbiosis than do competing rhizobia, but reduce plant growth", published online in The ISME Journal, my PhD student Will Ratcliff describes experiments showing how symbiotic nitrogen-fixing bacteria can manipulate their plant hosts.

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March 03, 2009

Mixed infections, for better or worse

If being infected is bad, is being infected by two different pathogens at once even worse? Not necessarily, as this week's paper shows. "Quorum sensing and the social evolution of bacterial virulence" was published in Current Biology by Kendra Rumbaugh and colleagues. Their results contradict an earlier prediction, although not the fundamental evolutionary principle behind that prediction.

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January 23, 2009

Staying ahead in the evolutionary arms race with viruses

This week's paper uses molecular methods to reveal new details of the evolutionary arms race between primates, including humans, and viruses. "Protein kinase R reveals an evolutionary model for defeating viral mimicry" was published in Nature by Nels Elde and colleagues in Seattle.

Protein kinase R (PKR) is an important defense against viruses in many species, from humans to yeast. When it detects a virus inside a cell, it activates eIF2-alpha, which shuts down protein production in that cell. With protein production blocked, the virus can't replicate and spread to other cells. Viruses, however, have evolved counter-measures. These include molecules that resemble eIF2-alpha. These molecular mimics interact with PKR and prevent its normal defensive activity.

Viral epidemics can be a major cause of death, so we expect populations to evolve PKR resistant to the eIF2-alpha-mimics produced by viruses. Can we find evidence of such evolution in primates?

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January 19, 2009

Safe-crackers have vaults in their cells

This is the most amazing thing I've seen in awhile. Vaults are abundant in our cells and bigger than ribosomes and apparently I'm not the only biologist who had never heard of them. They seem to be important in defense against bacteria, but nobody understands them in detail yet, apparently.

January 02, 2009

Ford Denison, amateur scientist

My NSF grant will run out soon, so I get to spend the year in which we celebrate the 200th anniversary of Darwin's birth and the 150th anniversary of The Origin of Species as an amateur scientist, like Darwin himself. I'm not as smart or as rich as he was, but I do have imaginative and hard-working students and much better equipment.

I'm working on two grant proposals and several papers while dreaming of getting back to writing my book, so no detailed paper analysis this week. But Nature is highlighting 15 major papers on evolution they have published in the last few years.

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.

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November 28, 2008

We cooperators need to stick together

Experiments on the evolution of cooperation can be simpler with microbes than with animals. Microbes do sometimes cooperate. For example, some amoebae get together and form a stalk (consisting of hundreds of individual cells) to elevate spores (many more individual cells) above the soil. Bacteria may collectively produce and release enough extracellular enzymes to make food available for all, when none of them could make enough enzyme alone. But why should an amoeba volunteer to be in the stalk (an evolutionary dead end) rather than becoming a spore? And why not save the cost of making expensive extracellular enzymes, by free-loading on enzyme production by others? Out of the goodness of their hearts? They don't have hearts.

Cooperation is easiest to understand among microbes that share the same allele (one of several alternative versions of a gene) for cooperation. Kin-selection theory says that an allele leading to some individually costly activity may spread if it preferentially benefits others with the same allele, relative to those with different alleles. Cooperation among relatives, who are more likely to share a given allele, is therefore easy to understand.

But can microbes recognize kin, i.e., whether another microbe has the same alleles? Sometimes, apparently. In this week's paper, Elizabeth Ostrowski and colleagues report in PLoS Biology that Kin discrimination increases with genetic distance in a social amoeba.

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November 07, 2008

Can an NPR gene explain gregarious and solitary behavior?

This week's issue of Science has a special section on the genetics of behavior. In humans, at least, conflicting results seem to be common. According to the overview paper, one study found that people who were abused as children have a two-thirds chance of depression as adults, if and only if they also have a particular version of a serotonin transporter gene; an analysis of several studies on this gene rejected this conclusion, however. Other combinations of genes affecting testosterone and the rate at which certain brain chemicals break down may increase criminal activity, but maybe not. One company is already offering genetic testing of potential mates for a gene possibly linked to divorce. How soon will we see "in-vitro tourism", to countries that offer genetic modification of behavior-linked genes in human germ-line cells? Clinics that currently offer untested or dangerous "cancer cures" might not wait for answers to the many scientific, technical, and ethical questions that such services would raise. But genetic effects on behavior are complex and hard to predict, even in the simplest cases, as seen in this week's paper.

"npr-1 regulates foraging and dispersal strategies in Caenorhabditis elegans" was just published in Current Biology by Andrea Gloria-Soria and Ricardo Azevedo.
C. elegans is a tiny worm, barely visible without magnification. Two alleles of the npr gene produce two different versions of the NPR signal-receptor protein, differing in a single amino acid. (Despite the connection to signals, the NPR gene actually has as much to do with National Public Radio as the famous "sonic hedgehog" gene has to do with hedgehogs.)

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October 10, 2008

Experimental evolution of predation and sexual attractiveness

Fossils and DNA-sequence comparisons among species are like fingerprints and other clues found at crime scenes. We can often draw reliable conclusions about past events (evolutionary or criminal) from such physical evidence, but some people prefer eyewitness accounts. So evolutionary biologists are increasingly doing experiments that let us see evolution in action. Evolution is a change over generations, so the short generation times of microbes make them especially useful for experimental evolution.

Two recent examples, both published in Proceedings of the Royal Society, are "Experimental evolution of a microbial predator's ability to find prey", by Kristina Hillesland, Greg Velicer, and Richard Lenski, and "Experimental evolution of a sexually selected display in yeast", by David Rogers and Duncan Grieg.

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July 26, 2008

Would the host want anyone to starve?

This week’s paper (Ratcliff, et al., in press) is from my lab.

The relationship between a legume plant and the rhizobium bacteria living in its root nodules is usually beneficial to both. Rhizobia convert nitrogen from the atmosphere into a form their plant host can use to make proteins. Rhizobia benefit from infecting plants because they reproduce more inside nodules than they would in the soil. They can also acquire certain resources in nodules. In particular, they can accumulate large amounts of energy-rich PHB – up to 50% of their own weight!

But there can also be conflicts of interest between rhizobia and their host plants. Resources used to make PHB could have been used, instead, to acquire more nitrogen for the plant. Therefore, mutant rhizobia that don’t make PHB provide their hosts with more nitrogen (Cevallos, et al., 1996). So why do most rhizobia make PHB? Our hypothesis has been that the rhizobia themselves benefit from having more PHB. This contrasts with an earlier hypothesis that rhizobia store PHB so that they can use the energy for the benefit of the plant. Consistent with our hypothesis, mutants defective in PHB metabolism reproduce less (Cai, et al., 2000). However, mutations can have complex interacting effects, making it hard to be sure that differences in PHB were the only cause of differences in reproduction. So Will Ratcliff decided to compare rhizobia that were genetically identical but had different amounts of PHB per cell.

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June 29, 2008

Evolution 2008: sexy plants, battling bacteria, durable cooperation

About 1500 scientists attended Evolution 2008 here last week. The four-day meeting was filled with 15-minute talks (usually ten at once, in different rooms), plus two evening poster sessions (like a science fair, for grownups, with discussions rather than judging), scenically located on a pedestrian bridge over the Mississippi. Reports that “scientists are abandoning evolution�? appear to be exaggerated.

Here are summaries of some of the talks I enjoyed.

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June 11, 2008

Explaining the evolutionary persistence of persisters

This week’s paper is “Nongenetic individuality in the host-phage interaction�, published in PLoS Biology by Silvan Pearl and others. This is one of many recent papers on bacterial “persisters,� a topic we are also starting to explore in my own lab.

When a large population of bacteria (in an infected person, for example) is exposed to antibiotics, a few of the bacteria may survive. One explanation, which is often true, is that these survivors have genes that make them resistant to the antibiotic. For the purposes of this discussion, it doesn’t matter whether they have mutated versions of genes also found in the susceptible bacteria, or an extra gene acquired by horizontal gene transfer from another bacterial cell. Either way, those without the gene (or with the nonmutated version) mostly get killed by the antibiotic. Therefore, subsequent bacterial generations are founded mainly by these surviving resistant mutants. Therefore, the frequency of the resistance gene increases over generations: a classic example of evolution.

Sometimes, however, testing the “evolved� population for antibiotic resistance shows the same results as in the previous unevolved generation: most of the bacteria die, but a few survive. If there’s no change in gene frequency over generations, then the population hasn’t evolved. But then why did any of the bacteria survive?

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May 25, 2008

Pest control for ants


(Top) A small leafcutter worker atop a leaf guards her sister against attacks by parasitic flies. Ants carrying leaves cannot use their mandibles for defense, so they carry hitchhikers to ward off the parasites. (Bottom) The fungus garden in a nest of Atta leaf-cutter ants. Notice the diversity of ant sizes within a colony, from the large red soldier ants to the minute orange ants tending to the garden. Atta ants have some of the most sophisticated caste systems among the social insects. -- photos and captions from Alex Wild (

This week’s paper, “Black yeast symbionts compromise the efficiency of antibiotic defenses in fungus-growing ants" by Ainslie Little and Cameron Currie, was just published in Ecology. Elsa Youngsteadt interviewed me, among others, for a story in Science about this research.

I’ve never done research on the fungal “farms" of ants and termites, but I’ve been interested in them every since a camera company bought a close-up photo (not Photoshopped like this one) of an ant carrying a leaf along a barbed wire “bridge" on its way back to its nest, from my mycologist father, William Denison. Dad was best known for pioneering research in the tops of tall trees, but never had to fight a shaman, as far as I know.

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May 03, 2008

Sharing diseases with relatives and neighbors

Not enough people voted on the Reader’s Choice, so this week’s paper is “Phylogeny and geography predict pathogen community similarity in wild primates and humans� by Jonathan Davies and Amy Pedersen, published in Proceedings of the Royal Society.

Many humans diseases, from flu to AIDS, come from other species. Similarly, diseases from dogs are an increasing threat to lions, while cat diseases kill sea otters. Are there general rules that predict how likely two species are to share diseases?

To find out, the authors analyzed several large data sets on diseases of humans and 117 other species of primate (apes, monkeys, etc.). They hypothesized that species are more likely to share diseases if they live near each other and/or if they are more closely related, that is if they share a more recent common ancestor. This is similar to how we define relatedness in humans: brothers and sisters have more recent common ancestors (parents) than cousins do (grandparents). Fortunately, the family tree for primates is relatively uncontroversial, at least among scientists.

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April 09, 2008

Welcome, fellow Dr. Tatiana fans!

Olivia Judson's latest column includes a good summary of work in my lab on cooperation between soybean plants and the rhizobium bacteria that (typically) provide them with nitrogen. As she points out, "cheating" is less likely to evolve in symbiont populations if they are transmitted in eggs or seeds, relative to symbionts that are acquired from the environment. In the former, if the host dies before reproducing, the symbiont dies, too. Symbionts without brains (bacteria, say) can't anticipate the effects of their actions; it's just that those whose genetically programmed behavior increases host survival become more common over generations.

Similarly, low symbiont diversity within an individual host may favor symbiont investment in costly activities that benefit the host. If each host has many different symbionts, on the other hand, then helping the host indirectly benefits competing symbionts sharing that host.

Rhizobium bacteria reach new host plants through soil, not via seeds, and they can do so even if the host dies without reproducing. Furthermore, each individual plant has multiple strains of rhizobia, which should undermine cooperation. Why then, do most rhizobia use their limited energy supply to fix nitrogen, giving most of it to the host plant? Why not use that energy for their own reproduction, instead?
Although there are several rhizobium strains per plant, they are typically segregated into individual root nodules. So, Toby Kiers and I reasoned, if plants monitor individual nodules and do something nasty to those that provide less nitrogen, that would act as a form of natural selection against cheating rhizobia. A computer model by Stuart West came to similar conclusions. To test this hypothesis, we forced some nodules to cheat, by surrounding them with an argon-oxygen atmosphere lacking nitrogen gas. Control nodules on the same plant got normal air, which is 80% nitrogen. Would rhizobia freed from the burden of fixing nitrogen redirect resources into their own reproduction? Would the plant impose sanctions on nonfixing nodules? If the answers to these questions are yes and yes, what would be the overall effect of cheating on rhizobium reproductive success?

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March 09, 2008

Tricky parasites winning the evolutionary arms race

Two papers this week describe recently discovered sophisticated adapatations of two different parasites: Gall insects can avoid and alter indirect plant defenses, published in New Phytologist by John Tooker and colleagues, and Parasite-induced fruit mimicry in a tropical canopy ant, published in American Naturalist by Steve Yanoviak and colleagues (if you're in a hurry, skip to the end for amazing photos).

Various plants recruit "bodyguards" when attacked by insects. For example, when caterpillars start munching on corn (maize) plants, the plants (including uninjured leaves) release gaseous chemicals called terpenoids. These terpenoids attract parasitic wasps, which lay their eggs into the caterpillars. This eventually kills the caterpillars, which presumably benefits the plant. But what if the caterpillars could prevent the plant from signaling to the wasps? As far as I know, caterpillars haven’t evolved this trick (yet), but there are apparently some insects – the Hessian fly, Mayetiola destructor (say) – that do not trigger signaling when they feed on wheat plants. There are at least two possible explanations…

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March 01, 2008

Knowing when not to cheat

This week’s paper is Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae published in Nature by Lorenzo Santorelli and colleagues at Rice University and Baylor College of Medicine, both in Texas.

The evolution of cooperation is a central problem in the history of life. Darwin explained how sophisticated adaptations -- “the structure of the beetle which dives through the water… the plumed seed which is wafted by the gentlest breeze� -- can evolve in a series of small improvements over generations. But some of the major transitions in evolution are harder to explain, because It seems that they should have been opposed, rather than supported, by natural selection. The origin of multicellular life is a good example. It’s not that hard to imagine independent cells working together in loose groups for mutual benefit – huddling together for defense, say – but why would a cell give up the ability to reproduce, as most of the cells in our bodies have done?

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December 07, 2007

The ghost of infections past, present, and future

Summary: A 39-year record of host-parasite interaction, recovered from sediment layers in a pond, is consistent with rapid coevolution.
Link: Host-parasite /`Red Queen/' dynamics archived in pond sediment

As I've discussed previously, archival samples often prove useful for answering questions that weren't being asked when the samples were collected. But what if nobody collected and preserved the samples you need for your research? Maybe you can find a "natural archive" that has what you need.

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November 16, 2007

Communication doesn't automatically prevent cheating

There are enough examples of ‘‘cheating’’ in bacteria ... that mindless obedience to such [quorum-sensing] chemical signals cannot be assumed. Mindlessness can be assumed, but not obedience. -- Denison et al. (2003) Ecology 84:838-845
Millions of cooperating cells can do things far beyond the ability of an individual cell. This is most obvious in multicellular organisms, whose cells cooperate because they are all genetically identical, or nearly so. Genetically diverse populations of cells could often benefit from cooperating, but do they? For example, the mixed bacteria populations associated with plant roots might benefit from keeping the plant healthy, so that it can continue to feed them with its root exudates. But for this to happen, they need some method of coordinating their plant-benefiting activities. Furthermore, cells whose genes lead to this form of cooperation must, on average, survive and reproduce more than "cheaters" who don't invest in cooperative activities. Otherwise, cooperative traits will disappear.

Quorum sensing, an exchange of chemical signals among bacteria, can solve the coordination problem. But this week's paper Cooperation and conflict in quorum-sensing bacterial populations shows that quorum sensing doesn't automatically solve the problem of cheaters. The paper is by Stephen Diggle, Ashleigh Griffin, Genevieve Campbell, and Stuart West and published in Nature.

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September 27, 2007

Cooperation and cheating in microbes: quorum sensing and persisters

Two papers on cooperation this week. If you were trying to help someone, but end up causing problems for them, were you being cooperative? I have no idea, so I like to study cooperation in microbes. Microbes don't have brains, so "intent" isn't a factor. And the only definition of "benefit" that makes sense is an increase in Darwinian fitness or reproductive success, which is often easy to measure in microbes; just count them.
I like these definitions:

Cooperation: a behaviour which provides a benefit to another individual (recipient), and which is selected for because of its beneficial effect on the recipient. [Exhaling CO2 isn't cooperation; it evolved as a side-effect of breathing oxygen, not to benefit plants.]
Cheaters: individuals who do not cooperate (or cooperate less than their fair share), but are potentially able to gain the benefit of others cooperating. ["Equal share" might be less ambiguous.]

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August 31, 2007

Whose genes are these, anyway?

Most of the genome of Wolbachia, a bacterial parasite of fruit flies, has been incorporated into the genome of the fruit-fly itself. Discussion at Not Exactly Rocket Science. Bacteria tend to pass genes around, or (more accurately, perhaps) bacterial genes tend to move themselves around (usually to other bacteria), but this is amazing.

August 03, 2007

Left behind: social amoebae

This week's paper, published in Science (317:679) is "Immune-like phagocyte activity in the social amoeba" by Guokai Chen, Olga Zhuchenko, and Adam Kuspa of the Baylor College of Medicine.

Cells of the social amoeba, Dictyostyleium discoideum forage individually, but eventually group together into a "slug", which crawls through the soil for days before eventually forming a spore-tipped stalk. Previous work with this species has looked at conflicts of interest over which cells have to sacrifice future reproduction (as spores) and become part of the stalk. This week's paper uncovers another example of apparent altruism in Dictyostelium, which may shed light on the evolution of a key part of our immune system.

As a Dictyostelium slug crawls through the soil, some cells are left behind. Are these just random sluggards? Or do they function like human phagocytes, the immune system cells that gobble up bacteria?

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July 12, 2007

Rhizobia, pesticides, and peer review

I have some comments on a recent paper that's only tangentially related to evolution. Actually, it's more relevant to science fair projects, the topic of my last post.

One type of science fair project my fellow judges and I are really sick of is "The effect of X on plants", where X is mouthwash, vinegar, cola, etc. The obvious question, which we always ask, is "how often are plants in the field exposed to high concentrations of mouthwash?" Unfortunately, whoever reviewed this paper in Proceedings of the National Academy of Science, claiming that "Pesticides reduce symbiotic efficiency of nitrogen-fixing rhizobia and host plants" apparently failed to ask this question.

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June 27, 2007

Individual and kin selection in legume-rhizobium mutualism

OK, I've been critiquing other people's work for a while. Your mission, should you choose to accept it, is to critique something I've written. It's the summary for a grant proposal I'm about to submit. It will be reviewed by ecologists and/or evolutionary biologists, but they're not likely to be specialists in legume-rhizobium symbiosis. So if something isn't clear to an intelligent but nonspecialist audience, you'll let me know, right? If you're not all too busy reading the many interesting evolution articles in today's New York Times, that is. By the way, the great Myxococcus xanthus photo in Carl Zimmer's article is from Supriya Kadam, who did her PhD with Greg Velicer and just finished a year as a postdoc in my lab.

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May 20, 2007

Rapid evolution of beneficial infections

Given my location halfway between the Twin Cities of Minneapolis and St. Paul, and my childish love of clever acronyms, I sometimes wish I'd named this blog This Week In Natural Selection. But then I suppose I'd have to review a pair of closely related papers each week. I'm going to do that this week, anyway.

This week's twins were both published in PLoS Biology, so both are freely available on-line. Both have new data on bacteria that infect insects. Both help us understand the conditions under which infecting bacteria evolve to be beneficial, rather than harmful. Finally, both disprove, again, the popular idea that any evolutionary change big enough to matter (except antibiotic resistance, which a creationist commenter once claimed always involves "horizontal transfer" of genes among bacteria, even though resistance often evolves in bacteria in a closed container all descended from a single cell) always involves lots of genes and takes millions of years. Evolution is our present and future, not just our past.

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May 18, 2007

Helpful cheaters?

Paul Rainey has a very interesting essay in the April 5 issue of Nature. Much of what we know about "cheating" in bacteria that form floating mats comes from his research, including collaboration with Michael Travisano, recently hired here at University of Minnesota. See my earlier post, "how disturbed are cheaters", for background on this system. Although cheaters that don't invest in the goop that holds floating mats together can result in mats breaking up and sinking, Rainey's new essay suggests that a similar form of cheating may have contributed to the evolution of multicellular life.

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May 06, 2007

How disturbed are most cheaters, really?

Yesterday, my wife asked, "why are there so many theoretical papers in evolutionary biology?" I suggested one reason may be that evolutionary theory is better developed, in the sense of making accurate predictions, than theory in much of biology. This week's paper, comparing results from an evolution experiment to predictions of a mathematical model, is a good example.

The paper is about the evolution of cooperation. This is a hot topic and also my own area of research. Humans enforce cooperation, to varying extents. For example, we often punish cheaters, those who try to benefit from cooperative activities of others without contributing anything themselves. Human cheaters are mostly pretty stupid -- don't even think about plagiarizing this blog for a term paper! -- but what about cheaters with no brains at all?

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