Science online, urban evolution edition

Freddie Fungus and Alice Algae have no likin’ for prions. Photo by 0olong.
  • Genetically determined, except when it isn’t. The evolutionary context of misogyny.
  • Queering evolution? The new frontier for evolutionary biology may be tracking adaptation to human-built environments.
  • Mad lichen disease? Some lichens can apparently break down prions.
  • Really, where would it have gone? That big underwater plume of oil spilled into the Gulf of Mexico is still there.
  • No surprise to field scientists, I suspect. Commercial GPS systems have some downright dangerous issues with their databases for rural and wilderness areas.
  • “This was the original peer review: immediate and open” The increasing use of online platforms for post-publication peer review may be taking scientific discourse back to its Enlightenment-era roots.
  • Guess I’d better get some more gel packs. Carbohydrate supplements during exercise do, in fact, help you work longer
  • I’m sure that if/ I took even one sniff/ It would bore me terrifically, too … Pair-bonding with a mate seems to make voles less prone to amphetamine addiction.
  • Time to revise the bat “pollination syndrome.” A bat-pollinated tropical vine has leaves that collect and reflect its pollinators’ echolocation signals.
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Of mice and men, making a living in rarefied air

(A)

High-elevation populations of deer mice have evolved “stickier” hemoglobin to cope with the thin atmosphere. (Animal Diversity Web)

ResearchBlogging.orgIt’s easy to walk through the woods and fields of North America and never spot Peromyscus maniculatus, the deer mouse, but you’ve probably heard them scampering off through the leaf litter or under cover of tall grass. They’re exceptionally widespread little rodents, found in forest undergrowth and fields from central Mexico all the way north to the Arctic treeline. In all this range, they look about the same: small and brown, with white underparts and big, sensitive ears.

That apparent sameness is deceptive, however.

A big, varied range presents lots of different environmental conditions to which a widespread species must adapt. And when that big, varied range includes the Rocky Mountains, one of those environmental conditions is as basic as the air itself. At high altitudes, atmospheric pressure is lower, which means lower partial pressure of oxygen, the gas that makes life as we know it work.

The fundamental problem at high altitude is to pull more oxygen from thinner air. Natural selection is good at solving problems, and it has multiple options for adapting a mammal to thinner air at high altitudes, to the extent that these traits are heritable. Selection could favor individuals who more readily respond to thin air by breathing faster and deeper, pulling in more air to make up for its lower oxygen content. Or selection could favor individuals who produce more red blood cells, so that a given volume of blood pumped through their lungs picks up more oxygen. Or, at the most basic level, selection could favor individuals whose individual red blood cells are better at picking up oxygen, via a new form of hemoglobin, the oxygen-binding molecule that packs every red blood cell.

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Concerning pseudonyms

A pseudonym is an identity.

It may not be the identity with which the pseudonymous person was born, but it’s an identity nevertheless. Far more excellent writers than I write online under pseudonyms, building up reputations around those not-given-at-birth names that are every bit as valid as whatever praise or contempt I’ve earned under my given-at-birth one.

Furthermore, there are some excellent reasons (see under “Bosses, not with it” and “Stalkers, online and otherwise” and “Crackpots, fielding endless e-mails from”) that given-at-birth identities can be risky online, and potentially disproportionately risky for women. Which is to say, disproportionately risky for, um, half of everyone everywhere.

Which is why it’s frankly rather silly and shortsighted of Google+, the hot new social network of the moment, to be closing accounts registered under pseudonyms. I mean, I understand that the big G would consider identities associated with, e.g., actual credit card accounts and consumer behaviors, to be strongly preferable. But if I were building a social network, I think I’d probably want Scicurious in it, because even if I can’t get useful consumer behavior data out of her pseudonymous profile, I’ll bet there are people who would join a not-quite-baked social network if it meant yet another opportunity to watch the fun when Sci puts on her ranty pants.

Which is to say, if you’re trying to get people to join a club, you really don’t want to kick out all the cool kids.

So, hey, there’s a petition you could sign, if you think maybe Google should know they’re being a mite dense about this whole thing. It is, as they say, the least you can do.

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Science online, certified organic breakfast edition

This organic breakfast may not be “chemical free,” but it could change your brain. Photo by lauren glanzer.

Special congratulations this week to Ed Yong, who is officially a full-time freelance writer as of Wednesday. I can only imagine what he’ll achieve now that this science writing thing isn’t restricted to his spare time.

  • Please note that “direct” experiments ≠ clearer results. Groundbreaking experiments that would be ethically impossible to conduct.
  • Pre-emptive incest? Hermaphroditic scale insects impregnate their offspring just after conceiving them.
  • In other words, bugger off, Senator McCain. Why would you want to sample bears’ DNA? Because bears are actually pretty important, for starters.
  • No word on whether they also dance quadrilles. Teeny-tiny lobsters buzz to scare off predators.
  • The first one alone may cause a spit-take. Four myths about organic agriculture may surprise you quite a bit.
  • Or, less likely to draw, anyway. You’re more likely to win at “rock-paper-scissors” if you play blindfolded.
  • “Ooooh, changes in grey matter.” Scicurious soft-boils a study purporting to show that eating breakfast changes your brain.
  • Population control. When doing observational research on humans, the way you group people into populations may make a big difference.
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This is my Senator

It’s nice to be living in a blue state. I just wish that it wasn’t necessary to move halfway across the country to finally acquire a Congressional delegation that actually reflects my values.

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Post arising: Anole vs. anole vs. predators

A brown anole, with dewlap extended. Photo by jerryoldnettel.

ResearchBlogging.orgLast June, I discussed a study with big ambitions: to experimentally compare the effects that competition and predators have on island populations of brown anoles, Anolis sagrei. Now the current issue of the journal that carried that study, Nature has a brief communication from the godfather of anole evolutionary ecology himself, Jonathan Losos. Losos and his coauthor Robert Pringle raise some serious questions [$a] about the results of that experiment.

The authors of the original study [$a], Ryan Calsbeek and Robert Cox, concluded that competition was more important than predation because natural selection acting on anoles was stronger on experimental islands with higher anole population density, while the presence or absence of predators on those islands made no difference in the strength of selection. Losos and Pringle object that anole population density is entangled with other factors that may make Calsbeek and Cox’s results uninterpretable.

This experimental design is confounded in three fundamental ways. First, density is confounded with island area. All analyses treat lizard density as a surrogate for intraspecific competition. However, an inverse correlation with island area explains 95% of the variation in density, such that it is impossible to disentangle the two factors statistically. This is a crucial problem, because multiple factors related to both predation and competition are known to vary with island area. For example, as island area increases, so too do the number of bird species (which increases the number of potential predators) and mean vegetation height (which might increase lizards’ susceptibility to avian predation). Likewise, because larger islands have lower perimeter/area ratios, they receive relatively lower input of marine-resource subsidies and have lower arthropod densities; a study of A. sagrei in this system showed that lizard densities vary significantly with the amount of seaweed deposition, and that experimental seaweed deposition increased lizard densities by more than 60%. [In-text citations removed for clarity.]

That point alone is a pretty big problem with Calsbeek and Cox’s result. Then Losos and Pringle re-analyze the data presented in the original study, and discover the very odd result that anoles in the experimental populations had higher rates of survivorship on the high-density islands—which is exactly the opposite of what you’d expect if competition for important resources were more intense in high-density populations. At the very least, this indicates that there could be more going on than Calsbeek and Cox originally supposed, in which case their data don’t support their conclusions.

Losos and Pringle raise other objections, including the issue of small sample size I noted in my original post. You should read the whole thing [$a] for the details, as well as the response [$a] from Calsbeek and Cox.

References

Calsbeek, R., & Cox, R. (2010). Experimentally assessing the relative importance of predation and competition as agents of selection. Nature, 465 (7298), 613-616 DOI: 10.1038/nature09020

Calsbeek, R., & Cox, R. (2011). Calsbeek & Cox reply. Nature, 475 (7355) DOI: 10.1038/nature10141

Losos, J., & Pringle, R. (2011). Competition, predation and natural selection in island lizards. Nature, 475 (7355) DOI: 10.1038/nature10140

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Pacifism as the conservative position

Via The Dish, which I haven’t read in ages: Bryan Caplan distills pacifism into a comparison of E[benefits of war] and E[costs of war]. That is, we know wars are expensive and awful, but we have much less assurance that they’re going to be worth it:

Of course, “Fight when it’s a good idea, make peace when it’s a good idea” counts as a philosophy. And you might think that this case-by-case approach has to yield better results than pacifism. But that’s only true with perfect foresight. In the real world of uncertainty, case-by-case optimization is often inferior to simple rules.

Which is why I tend to think of pacifism as a small-c conservative position: simple risk-benefit analysis, and a little honest evaluation of history.

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Science online, indirect costs of royal jelly edition

A queen bee, indicated with a red dot of paint. Photo by reway2007.
  • Not so much explanation as warning, really. The intricacies of indirect costs in grant funding, explained.
  • Motivation is key. Anoles demonstrate learning ability in an experiment that has them playing find-the-worm.
  • Paging Doctor Pangloss? Bats might be most active at night because flying is hot work.
  • Long live the queen! The specific protein in honeybee “royal jelly” that makes bee larvae develop into queens has been identified [$a], in part by giving the protein to fruitflies to make “queen” flies.
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So what does it take to strike Stephen Colbert speechless?

I’m super late to this one, but … holy blithering wow, man.

Dan Savage—nationally syndicated advice columnist, It Gets Better co-founder, serial contributor to This American Life, and all around alpha-gay—was on the Colbert Report to discuss the recent New York Times profile about his views on monogamy, which views may be briefly summed up as why ruin a perfectly good marriage by insisting on complete sexual fidelity? And about midway through said interview, Savage drops a line which, while requiring no censorious bleeping whatsoever, stops Colbert dead in his metaphorical and satirical tracks and had me just about on the floor in laughter and/or amazement. I’m frankly still a mite breathless, and in full-on Wallace-esque run-on mode as a result.

And, well, you probably don’t want to see it if you’re not particularly cool with Savage’s aforementioned feelings about monogamy, but if you are in fact generally on board or at least don’t get the howling fantods after reading my summary or obliquely contemplating what I shall delicately call the mechanics of love, and if you are even later to this than I am* you really ought to right now.

The Colbert Report Mon – Thurs 11:30pm / 10:30c
Dan Savage
www.colbertnation.com
Colbert Report Full Episodes Political Humor & Satire Blog Video Archive

All of which is a rather long way to go to say, gods (or whoever) bless Dan Savage and Stephen Colbert.

————–
*Which probably means you didn’t have an internet connection till this evening, in which case let me take this footnote to say, welcome to the World Wide Web!

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Choosing your partner is only as helpful as the partners you have to choose from

Picking teammates. Original photo by humbert15.

ResearchBlogging.orgWhen you need partners for some sort of cooperative activity—say, teammates for a game of kickball—you’d probably like to have a choice among several candidates. That lets you weigh considerations about kicking strength and running speed—and who promised to give you his dessert at lunch period—to build a winning team. However, if the other team captain snaps up the good players first, the fact that you have a choice among the others might not make much difference.

Plants and animals looking for mutualists face a similar situation. Being able to choose among possible partners should allow the chooser to work with helpful partners and avoid unhelpful ones, but a new study suggests that in one widespread mutualism the process of choosing between partners can leave the chooser worse off than if it had no choice at all [$a].

Coauthors Erol Akçay and Ellen Simms focus on the effects of partner choice in the mutualism between plants and nitrogen-fixing bacteria—the interaction I’m studying in my current postdoc position, as it happens. All living things need nitrogen, but only some strains of bacteria are able to collect nitrogen from the atmosphere and “fix” it into a form that other organisms can use. Many plants, particularly members of the big and diverse bean family, have evolved to allow nitrogen-fixing bacteria to infect their roots—the plants form a nodule of root tissue around the infection and supply the tissue with sugar for the bacteria to feed on as they fix nitrogen. Eventually the nodule dries up and dies off, and the bacteria are freed into the soil, having multiplied many times over thanks to the food supply from the host plant.

A plant’s root nodules, some cut open to show the interior. Photo by pennstatelive.

To see how this choice might work in practice, Akçay and Simms construct a mathematical model of a plant with two nodules. Each nodule produces some level of nitrogen, and recieves some level of sugar from the plant. The plant negotiates with the two nodules in what’s called a “war of attrition” game: whichever partner wants a better deal cuts off the exchange of services, and holds out until the cost of losing the service it recieves is greater than the benefit it hopes to gain in the war of attrition.

Rather like ant-defended plants, plants that host nitrogen-fixing bacteria don’t seem to screen potential mutualistic bacteria before allowing them to infect their roots. However, after root nodules are established, the success of the mutualism from the perspective of both partners depends on the genetics of each [PDF], and when host plants receive supplemental nitrogen, they put fewer resources into growing nodules [PDF]. Host plants have been observed with different strains of bacteria in different nodules, and some nodules could contain diligent nitrogen fixers while others are full of freeloaders. This may be the point at which the plant has a choice of partners—it can potentially direct sugar to helpful nodules, and cut off unhelpful ones.

Because the plant has two nodules to choose from, it can potentially outlast an uncooperative nodule by relying on the other one. This works if the plant can shunt more resources to the cooperative nodule and recieve more nitrogen from it in return. However, the success of this strategy depends on two traits of the bacteria inhabiting the nodules—how readily they ramp up nitrogen production in response to more sugar, and how stubborn they are in the war of attrition game.

If both nodules are stubborn but responsive to extra sugar, the plant can negotiate with one nodule by giving the other more sugar and receiving extra nitrogen. This lets the plant hold out longer in the war of attrition. On the other hand, nodules that are not responsive to extra sugar but also not very stubborn yield quickly in the war of attrition even though they don’t help much in negotiations. In either of these two cases, the negotiations find an equilibrium in which the plant receives a benefit about intermediate between what it would recieve if both nodules were infected by the same strain of bacteria.

However, if the plant hosts a stubborn-responsive bacterial strain in one nodule and a yielding-unresponsive strain in the other, it finds itself in a trap: the yielding-unresponsive strain is no help in negotiation against the stubborn-responsive strain, and the help provided by the stubborn-responsive strain isn’t an advantage in negotiating with the yielding-unresponsive strain. Over successive negotiations, the stubborn-responsive strain can ratchet up the sugar it extracts from the plant, and the plant ends up worse off than it would be if the two nodules were identical.

Just like humans haggling in a marketplace, the outcome of the interaction depends strongly on whether the other party plays along as expected.

Akçay and Simms find a way out of this trap by adding another wrinkle to the model. Much like the contract-theory models of mutualism I’ve discussed before, they modify the model to allow cooperative nodules to benefit from being cooperative. This makes a good deal of intuitive sense—if a nodule provides a better deal to the plant, the plant can potentially grow more leaves to produce more sugar, which would allow it to offer a better deal to the bacteria it hosts. Akçay and Simms call this “partner fidelity feedback,” and they find that, if it is sufficiently strong, it can allow the plant to out-negotiate a stubborn strain of bacteria.

Although it has a good deal of intuitive appeal, the model presented by Akçay and Simms does a fair bit of speculating in the absence of data. This is also a problem for the contract-theory model, and really all models of this widespread and important interaction. We know a great deal about the chemical details of plants’ interaction with nitrogen fixing bacteria. However, we don’t have a good sense of whether and how plants can redirect resources among nodules to haggle with the bacteria they host, and we don’t know whether and how bacteria could adjust their behavior to haggle with the plant. Akçay and Simms devote a big section of their online appendix [$a] to discussing just this point.

To figure out what’s going on inside those nodules, we need to determine how different models of interaction between plants and their bacterial mutualists may shape patterns in things that are easier to observe—both in the compatibility between plant genotypes and bacterial strains in greenhouse tests, and in the broader population genetics of both partners.

References

Akçay, E., & Simms, E. (2011). Negotiation, sanctions, and context dependency in the legume-rhizobium mutualism. The American Naturalist, 178 (1), 1-14 DOI: 10.1086/659997

Heath, K. (2010). Intergenomic epistasis and coevolutionary constraint in plants and rhizobia. Evolution DOI: 10.1111/j.1558-5646.2009.00913.x

Heath, K.D., Stock, A.J., & Stinchcombe, J.R. (2010). Mutualism variation in the nodulation response to nitrate Journal of Evolutionary Biology, 23 (11), 2494-2500 DOI: 10.1111/j.1420-9101.2010.02092.x

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