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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 29, 2007

Selfish sperm cells

Usually, those alleles (versions of a gene) that become more common over generations are those that are most beneficial to the organisms in whose cells they live. But not always.

The latest issue of PLoS Biology has an open-access article on a particularly selfish gene responsible for Apert syndrome in humans.

The allele that causes this disease is much more common than expected, based on the assumption that it arises by mutation at the average rate for most DNA. Some regions in a DNA molecule have higher mutation rates, but could there be another explanation?

To find out, the authors of "The molecular anatomy of spontaneous germline mutations in human testes" cut human testes (from dead donors) into hundreds of pieces and analyzed the frequency of the mutant Apert allele in each piece, using quantitative PCR.

The mutant allele was up to 10,000 times more common in some pieces than in others, suggesting that cells with the mutant allele were reproducing rather than just replacing themselves, as spermatogonial cells normally do.

The bad news is that an allele whose affects favor its own reproduction will tend to spread, even if its effects on our bodies or our children are negative. Similar effects have been seen in plants, where genes transmitted only in the seeds block pollen production, freeing resources for seed production. Fortunately, natural selection will also favor any other genes, anywhere in the genome, that suppress recklessly selfish genes.

August 23, 2007

Scientist glut as a tragedy of the commons

Lots of discussion on Pharyngula today on a Nature story on the PhD glut. 7000 new biomedical PhDs per year and only 20,000 tenured positions. I remember looking at all the grad students and postdocs at the Ecology meetings and thinking "there aren't nearly enough job openings for this many ecologists", at least not at major research universities. Comstock commented

I see the universities as eager players, ready to get their share of the grant money, and not worrying that much of it relies on the labor of a servant class who will never be made master of the house.
I tend to see tragedies of the commons everywhere, but is this one?

In a tragedy of the commons, individuals rationally pursuing self-interest have a collective impact (e.g., overgrazing) that harms them all. Professors making decisions that harm students may be evil, but it isn't necessarily a tragedy of the commons. Professors and students are two different groups, so we need to consider them separately.

The more students do PhDs, the tougher competition will be for PhD jobs. This hurts PhD recipients, so "too many students pursuing PhDs" could be considered a tragedy of the commons, if getting a PhD is rational for individuals -- this isn't clear -- but collectively harmful.

From the standpoint of professors, the more students that earn PhDs in our labs, the tougher competition will be for PhD jobs. Does this hurt professors? As word gets out about the PhD glut, it gets harder for us to recruit new students. Plus, many of us like our students and want them to have satisfying careers. So we face a tragedy of the commons also.

Personally, I will not accept a student for a PhD unless I am reasonably confident that he or she has the potential (with enough hard work) to be competitive for the type of job sought, even if this means fewer papers coming out of my lab. But I'm motivated by concern for the welfare of individual students, and the hassles of working with less-qualified ones, not my own small contribution to the PhD glut. Some professors seem to take all the students they can get, while investing less in each one.

NSF could reduce the PhD glut. They could insist on funding technicians and MS students rather than PhD students (with some exceptions, such as their highly competitive PhD fellowships), thereby providing jobs for some PhDs and encouraging other students to do an MS instead.

But NSF's mission is to promote the national interest, not the interests of PhD students or professors. Is a PhD glut, perhaps, in the national interest? Universities and research labs get to choose from a large pool of highly qualified applicants (like the farmers in Grapes of Wrath), and those not finding jobs in research will mostly make other important contributions to society. There could be an opportunity cost to society as highly intelligent people delay their entry into the workforce, but that neglects the substantial contribution of grad students to research and teaching.

If you are a potential or actual PhD student and more interested in your own self-interest -- who should be, if you're not? -- than in the national interest, see my earlier posts.

August 22, 2007

Evolution of cooperation reviewed

The theme of the latest issue of Current Biology is "Biology of Societies." There are reviews on the social life of spiders, crows, hyenas, amoebae, and insects, plus the role of cognition in social interactions among humans. If you are interested in the evolution of cooperation, it might be worth a trip to your nearest university library (if you don't have access via the web) to browse this issue.

I particularly liked "Evolutionary Explanations for Cooperation" by Stuart West, Ashleigh Griffin, and Andy Gardner. Their review reprints figures from several recent papers, so you can see some of the data upon which their generalizations are based. I won't try to summarize the whole thing, just some points that may have been neglected in other reviews of this topic.

They begin with a definition: "A behaviour is cooperative if it provides a benefit to another individual and if it has evolved at least partially because of this benefit." Plants benefit when soil bacteria breaking down organic matter release nitrogen in the process, but do the bacteria release some of the nitrogen in the organic matter (rather than using it themselves) because it benefits plants? Plant growth benefits bacteria near their roots, but do plants selectively benefit those bacteria that release the most nitrogen, relative to other bacteria nearby? If not, then bacteria that let others shoulder the cost of supporting plant growth (by giving up some nitrogen) would out-compete any bacterial "altruists." (If bacteria don't have any use for additional nitrogen, then leaving it in the soil has no cost, but neither would it qualify as cooperation.) Similar Tragedies of the Commons have the potential to undermine cooperation at all levels, from cooperation among cells in a multicellular organism to cooperation in human societies.

Kin selection can favor altruism ("behaviour that is costly to the actor and beneficial to the recipient") towards close relatives. W.D. Hamilton predicted that a gene that leads to altruistic activity will spread when the cost (decrease in reproduction of the actor) is less than the benefit (increased reproduction) to the recipient times their relatedness.

West and coathors point out that research to test Hamilton's Rule has emphasized relatedness, but benefit and cost are also important. For example, species in which help raising young is most important to the survival of those young are more likely to help closer relatives (kin discrimination) as previously shown by Griffin and West (Science 302:634).
Indiscriminate helping may not be the result of kin selection, but rather some individual benefit to the helper, such as being allowed to remain in another's territory.

The authors reiterate an important point they have made previously, related to the effects of migration on kin selection. Animals that don't move around much may end up surrounded by relatives. This may be even more true of plants. This increased relatedness favors altruism, except that it may also increase the cost of altruism or reduce the benefits. If a bunch of relatives are all competing for the same resources, help that lets one sister reproduce more may come at the expense of the altruist's own reproduction (increasing cost) or that of another sister (reducing total benefits).

Cooperation between unrelated individuals, often of different species, can also be favored by enforcement mechanisms that tie individual benefit to cooperative behavior. For example, cleaner fish that bite their hosts get chased and other potential hosts avoid them. Humans (at least Swiss college students) tend to punish noncooperation in "experimental economics" games, even at some expense to themselves.

Enforcement mechanisms need not require conscious intelligence, however. The review mentions research by Toby Kiers in my lab showing that soybean plants punish rhizobium bacteria that fail to provide them with nitrogen. We assume that the soybean plants, in contrast to Swiss college students, obtain some individual benefit, such as saving scarce photosynthate, from doing so. Further work in this area was discussed last week.

The review points out that the mechanisms that prevent "cheaters" from undermining cooperation may be different from the mechanisms by which cooperation arose in the first place.

They make the important point that

we do not need to keep reinventing the wheel with more theoretical models that incorrectly claim to provide a new mechanism for the evolution of cooperation [12,97,98]. This has especially been a problem with models that examine limited dispersal or group structures [99–103] and which are, therefore, just reinventing kin selection.
Second, we do not need redefinitions of terms that already have specific and useful meanings.

Instead, they say "we need greater integration between theoretical and empirical work." They suggest that there has been too much emphasis on "birdwatching or the glamour of working with fluffy mammals" while neglecting bacteria and "interplay between mechanistic (proximate) and evolutionary (ultimate or selective value) approaches." I can only hope that scientists reviewing my latest NSF proposal will agree.

August 17, 2007

Almost a no-brainer

How sophisticated behavior would you expect from an animal with a brain as small as a wasp's? Few, if any, female wasps have read David Lack's classic paper on the optimum number of eggs to lay, or even John Dennehy's clear summary of it. This week's paper asks whether they, nonetheless, adjust egg numbers optimally in response to competition from other wasps and resource availability.

"Encountering competitors reduces clutch size and increases offspring size in a parasitoid with female–female fighting" was written by Marlene Goubault, Alexandra Mack, and Ian Hardy, of the University of Nottingham, and published in Proceedings of the Royal Society.

I discussed trade-offs between the size and number of eggs (or seeds, for plants) in one of my first posts. A plant or animal with a given amount of carbon and nitrogen can make a few large eggs or seeds or many small ones. But how does competition change things?

Parasitoid wasps lay eggs in butterfly or moth larvae. The resulting wasp larvae devour the caterpillar and may also fight among themselves, as Carl Zimmer explains in this week's edition of The Loom and the New York Times.

Female wasps may also fight other females for the right to lay eggs in a given caterpillar. The winner kills any existing eggs and replaces them with her own. Bigger females tend to win these battles.

So theorists have previously suggested that, when competition with other females is likely -- in the next generation -- wasps should lay larger eggs, which will develop into larger adults, even though there will be fewer of them. It's better to have a few daughters whose eggs survive than many daughters with no surviving eggs. As the authors put it, "anticipation of the competitive environment of offspring should affect maternal clutch size decisions."

But how can an insect with such a small brain anticipate anything? An evolutionary response to the average level of competition would not require any information-processing ability at all. Egg number could be under genetic control. Those with genes for the optimum egg number in a given environment would out-compete those with lower or higher egg numbers.

But the environment, specifically the availability of caterpillars, is not constant. Can individual wasps adjust egg numbers appropriately? They can't know how much competition their daughters will face, but can they at least adjust egg number based on how much competition they face?

To find out, the authors used wasps guarding a caterpillar which they had paralyzed but into which they had not yet laid their eggs. They made each wasp fight from zero to four other wasps. Then they counted how many eggs were laid and how big the eventual daughters were.

With big caterpillars, competition had no effect on number of eggs laid. This is consistent with wasps being ignorant of trade-offs. However, there was also no effect of egg number on the final weight of daughters, in this case, presumably because they had enough to eat that initial egg size didn't matter. If there's plenty of food, maybe laying as many eggs as possible is the smart thing to do, even if the eggs will initially be smaller than if there were fewer of them.

When they used smaller caterpillars, the number of eggs laid did depend on competition, but also on the size of the wasp and the caterpillar. As expected, daughters emerging from small caterpillars were smaller when there were more of them. There were fewer of them, but they were a little bigger (1.10 versus 0.97 milligrams) if their mother had faced competition, as predicted. (Is this enough size difference to affect competition?)

These results are consistent with the hypothesis that wasps lay fewer and therefore larger eggs when two conditions are met: 1) they faced competition, so their daughters might also, and 2) the available caterpillar is small enough that small eggs may result in small, less competitive, daughters.

Do other animals produce fewer but larger offspring when competition is more severe? Does this pattern disappear when resources are abundant enough that the size of an egg or baby has little relation to adult size? Does brain size have any effect on the ability to make such decisions?

August 15, 2007

Defining "transformative research" for NSF

According to a National Science Foundation survey, 30% of grant panel members say that they often recommended "transformative research" projects for funding, but only 10% of other panel members (who also, presumably, answered the same question) did. This seems like a mathematical impossibility, like men having had more girlfriends, on average, than women have had boyfriends. But, just as the definition of "girlfriend" (or "sex", for that matter) may vary, so may the definition of "transformative research."

Can we do better than "the projects I like are transformative; those you like aren't"?

I think most scientists woud agree that transformative research is that which overturns existing ideas or opens up a new area. Predicting, in advance, which projects will do that may be difficult, but can we at least come up with an objective measure of "transformativeness", after the work has been published long enough to see its impact?

A variation on citation analysis might work. The total number of times a paper is cited (in effect, linked to by other researchers in their publications) is a widely-used measure of impact. OK, but many of the papers cited confirm earlier results, perhaps more thoroughly, rather than challenging old ideas or opening up new areas. I suggest that a paper should get one "transformation point" every time it is the oldest paper in a cluster of citations. So

Mitochondria are descended from bacteria (Margulis 1975; Smith 1985; Jones 1995).
would earn one transformation point for Margulis but none for Smith or Jones. On the other hand
Margulis (1975) proposed that mitochondria were descended from bacteria, which has subsequently been confirmed empirically (Smith 1985, Jones 1995)
would earn transformation points for both Margulis and Smith.

Maybe citations during the first year or two after publication should be excluded. Many early citations could be either unfairly negative (from those whose ideas are being challenged) or uncritical acceptance of an interesting idea prior to confirmation. If a paper is still being cited years later, however, and it's the earliest of the citations on some question, doesn't that meet an objective definition of "transformative?"

If NSF rewarded reviewers who correctly predict which projects will be most transformative, perhaps with small travel grants, that would probably lead to the right balance between openness to new ideas and skepticism of unsupported assertions.

August 14, 2007

Cooperation gets complex

This week, instead of discussing a paper, I will summarize some presentations from the Ecological Society of America meetings last week in San Jose, California (a much more interesting place than I expected, including hands-on transformation of bacteria at the Tech Museum).

I ran into two people who admitted to reading this webblog: Madhu Katti and Don Strong, but didn't get to talk to either of them for long. There were usually several interesting sessions going on at once, from 8 AM to late evening, plus lots of informal discussions, but I will limit my summary to a few of the presentations on the evolution of cooperation, my own area of research.

Rhizobium bacteria and mycorrhizal fungi both infect plants. Both are often beneficial, providing host plants with nitrogen or phosphorus, respectively, "in exchange for" carbon. But is this really an exchange, in the sense that there is some mechanism to ensure that a rhizobium cell gets a certain amount of C from the plant if and only if it provides a certain amount of nitrogen to the plant? This seemed to be an implicit assumption in the "market model" of Claire de Manzancourt and Mark Schwartz, presented at the meeting, but this hasn't yet been demonstrated even in rhizobia, much less in other species.

Providing the plant with nitrogen increases plant growth, which may automatically increase carbon supply to the rhizobia, collectively. But if these benefits were shared indiscriminately with every rhizobium strain infecting a given legume plant -- strains which will soon be competing for the next host plant! -- then modeling by Stuart West on a visit to my lab showed that natural selection would favor little or no investment by rhizobia in nitrogen fixation.

Our model assumed that carbon that is not respired by a rhizobium cell to power nitrogen fixation can instead be used to support the rhizobium's current or future reproduction. My students and I addressed various aspects of this assumption at the meeting.
Other researchers (Cevallos et al. 1996 and Hahn and Studer 1986) have shown that there is a trade-off for rhizobia between fixing nitrogen and accumulating the energy-rich molecule, polyhydroxybutyrate (PHB). But does PHB help rhizobia reproduce? In his talk, Will Ratcliff showed that it does. He used a centrifuge to separate genetically identical rhizobia into low- and high-PHB fractions. Under starvation conditions, the high-PHB rhizobia reproduced two-fold, using up their PHB in the process, before starting to die off. The low-PHB rhizobia started dying immediately. So rhizobia that accumulate more PHB might be expected to out-compete those that fix more nitrogen. But read on!
Ryoko Oono's poster presentation discussed some legume plant species that prevent nitrogen-fixing rhizobium cells from reproducing inside their root nodules. Like worker bees, these rhizobia will have no direct descendants, so hoarding PHB would be pointless -- so they don't. But why do rhizobia give up the ability to reproduce? Once inside a root nodule, the plant may be in charge, but then they why do rhizobia infect plants in the first place? Because not all of the rhizobia inside the root nodule change into the nitrogen-fixing, nonreproductive form. Apparently, enough reproductive clone-mates eventually escape the nodule into the soil that a rhizobium cell founding a nodule will still have more descendants than if it stayed in the soil.

Thumbnail image for EffectiveAlfalfaNodules.jpg
Photo by Alex May.

Plants that limit rhizobium reproduction typically have nodules with indeterminate growth, leading to an elongated shape. By reducing the incentive for rhizobia to accumulate PHB, at the expense of nitrogen fixation, suppression of rhizobium reproduction should benefit plants. But the ancestor of all nodulated legumes is thought to have had indeterminate nodules. If indeterminate nodules are so great, why would beans, birdsfoot trefoil, etc., switch to roughly spherical, determinate nodules, in which rhizobia retain the ability to reproduce? Ryoko looked at rhizobia in indeterminate nodules of species thought to resemble ancestral legumes and found no evidence that rhizobium reproduction is suppressed in these species. Apparently only a subset of legumes with indeterminate nodules suppresses rhizobium reproduction. Maybe in a few million years this plant trait will be more widespread, although a few rhizobia have apparently evolved a new trick to beat this system: rhizobia that are able to fix nitrogen transfer some carbon to their reproductive sisters instead.

What keeps this trick (or PHB hoarding, by reproductive rhizobia) from spreading? Toby Kiers, previously in my lab at UC Davis, showed that rhizobia that fail to fix any nitrogen are subject to host plant sanctions that greatly reduce their reproduction, but moderate cheating by rhizobia may be punished much less severely (Kiers et al. 2007).

Katie Heath (working with Peter Tiffin here in Minnesota) found no evidence of sanctions against any of three rhizobium strains from a plant with indeterminate nodules. The three strains differed in the benefits provided to a given host plant genotype, but some of that difference could have been due to limited ability to nodulate, which would not be expected to trigger sanctions, rather than differences in nitrogen fixation rate per nodule. Maren Friesen (UC Davis) commented that severe cheating (fixing no nitrogen) is punished in this species, as indicated by much smaller nodules containing few rhizobia.

Do sanctions also ensure fair trade between plants and mycorrhizal fungi? In his talk, Jim Bever (Indiana University) showed that a plant with each half its roots infected by a different fungus sends more carbon to the side with the fungus most beneficial to the plant. But when two fungal species are thoroughly mixed in the soil, the strain that is worse for the plant sometimes wins. He concluded that spatial structure is important to maintaining more beneficial mycorrhizal fungal species. The question is whether the degree of spatial structure in natural soils is more similar to the half-root experiment or the mixed-soil experiment. What about agricultural soils?

Speaking of agriculture, my favorite talk was by Cameron Currie (University of Wisconsin) on fungus-growing ants. I have discussed this system previously, most recently in a draft chapter for a proposed book on Darwinian Agriculture. (Discussions at the meeting with a publisher were encouraging, but I need to prepare a more-detailed proposal.) The ants use antibiotics, produced by specific bacteria, to control parasitic fungi that threaten the fungi they grow for food. I have always wondered why mutant bacteria that don't produce these costly antibiotics don't take over. There's a long-term collective benefit to bacteria from living in a healthy ant colony, but natural selection is notoriously blind to the long term and to collective benefits.

So I was very interested in Cameron's report that Ainslie Little has found a yeast fungus that attacks the bacteria. I suggested that defense against yeast might provide an individual benefit to the bacteria from producing antibiotics, with defense against other fungi as a side effect, but Cameron says the yeasts have typically evolved resistance to the antibiotics produced by the bacteria in a given ant nest. It would be interesting to track antibiotic production and resistance over time, to see if there could be an arms race in progress. He says transfer of bacteria from ant to ant seems to be carefully controlled. Can the ants tell which bacteria are most effective at producing antibiotics?

After the meeting, my wife joined me for a weekend at Point Lobos, where we saw lots of lichens (another classic example of cooperation between species) and begging in cormorants and gulls, and the Monterey Bay Aquarium. We had dinner twice at Sea Harvest in Moss Landing, a good place for fresh local (and nonlocal) fish and great views of sea otters from their deck.

August 8, 2007

Ecology meetings

I'm at the Ecological Society of America meetings in San Jose, as are at least two readers. The talks I've seen so far haven't had too much evolutionary content, but that may change this afternoon. I will try to post something while here, but there's always a line for the computers, so I don't want to tie them up for too long!

August 3, 2007

Catfish beats Columbus to America

So did the ancestors of American Indians, of course, but a catfish seems to have beat them by about 50 million years. "Discovery of African roots for the Mesoamerican Chiapas catfish, Lacantunia enigmatica, requires an ancient intercontinental passage" by John Lundberg, John Sullivan, Rocio Rodiles-Hernandez, and Dean Hendrickson, was published in Proceedings of the Academy of Natural Sciences of Philadelphia.

This aptly-named catfish species, recently discovered in Mexico, appears to be most related to catfish in Africa. A family tree based on DNA and calibrated using fossils suggests that the last common ancestor of the Mexican and African species lived 75 to 94 million years ago. This was after continental drift separated Africa from South America.

How did the fish get to Mexico? It swam, presumably. The problem is that catfish are freshwater fish. The authors suggest that partial melting of polar ice during the Eocene may have made the Arctic Ocean warm enough and fresh enough for the ancestors of the Mexican catfish to survive a long ocean swim.

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?

About 1% of cells in the slug were found to accumulate various fluorescent dyes at up to 10 times the rate of other cells. The authors suggest that these "S cells" may accumulate a variety of toxins, thereby protecting other cells from poisoning. No calculations were presented to show that the rates of toxin accumulation are high enough to provide useful protection, however.

In any case, accumulation of fluorescent molecules makes it easy to identify S cells, and even to separate them from other Dictyostelium cells. The cells can be sorted using a flow cytometer, in which thousands of tiny droplets per second, some containing cells, pass individually through a laser beam. Droplets can be deflected into different tubes, depending on their fluorescence.

Apparently the cells left behind by the slug are mostly these S cells. Ideally, the fluorescent microscopy photo showing fluorescent cells left behind would also include some way of detecting non-S cells, such as a dye taken up by all cell types.

When slugs were injected with bacteria, at least half of the cells that took them up were S cells, even though S cells were only 1% of the total. The other bacteria-ingesting cells may have been S cells that could not be identified as such. The slugs eventually ejected almost all of the bacteria, apparently by leaving them behind inside S cells. If so, the S cells apparently died in the process, as the ejected bacteria "appeared to be surrounded by cell debris."

A gene similar to an immune defense gene in animals, tirA, was found to be expressed at eight times the rate in S cells. So was a plant-related defense gene. When the animal-like gene was knocked out, the S cells were killed by bacteria to which they are normally resistant.

So Dictyostelium S cells act like our phagocytes and use a similar gene. Could our immune system really have an evolutionary origin that predates the evolution of true multicellularity?

Humans did not evolve from modern Dictyostelium , but the common ancestor of humans and Dictyostelium was probably more like them than like us. The authors note that, because amoebae live in the soil and interact with bacteria all the time, "they might have retained key characteristics of plant and animal innate immunity if those functions existed in their common ancestor."

If so, then S cells might be similar to phagocytes in other ways. For example, do human phagocytes have the same enhanced uptake of fluorescent dyes as S cells?

If the S cells are genetically identical to the other cells in the slug, sacrificing themselves to protect their clone-mates from bacteria is not much more surprising than similar self-sacrifice by our phagocytes. But it would still be interesting to know how the "volunteers" are chosen.