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March 31, 2011

This week's picks

Chimpanzees help conspecifics obtain food and non-food items "...given that the donor cannot get the food herself.... the key factor... is the recipients' attempts to either get the food or get the attention of the potential donor."

On the earliest evidence for habitual use of fire in Europe
"...spectacular cases of Neandertal pyrotechnological knowledge..."

Sizing up your enemy: individual predation vulnerability predicts migratory probability
"trade-off between seasonal fluctuations in predation risk and growth potential... Smaller, high-risk individuals migrate with a higher probability"

Plant-ants feed their host plant, but above all a fungal symbiont to recycle nitrogen
"In many ant-plant symbioses, a fungal patch grows within each domatium."

More closely related species are more ecologically similar in an experimental test
"Species also competed more with close relatives than with distant relatives in field soils; however, in potting soil this pattern reversed..."

Assassin bug uses aggressive mimicry to lure spider prey "vibrations from bugs had a temporal structure and amplitude... similar to vibrations generated by leg and body movements of prey and distinctly different... from courting males or leaves..."

Social and Ecological Synergy: Local Rulemaking, Forest Livelihoods, and Biodiversity Conservation "participation in forest governance institutions by local forest users is strongly associated with jointly positive outcomes"

Oxygen isotopes of East Asian dinosaurs reveal exceptionally cold Early Cretaceous climates "cold local climatic conditions linked to the paleolatitudinal position of northeastern China and global icehouse climates..."

Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia
"we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations."

March 29, 2011

International collaboration?

The Royal Society just came out with a report on the internationalization (if that's a word) of science. China now produces the second-highest number of papers, but rates last in percent of papers involving international collaboration. Why so little collaboration? Three hypotheses:
1) the rest of the world doesn't realize all the great science they're doing in China, so is missing out on opportunities to collaborate with excellent researchers,
2) Chinese scientists are doing great work, but are reluctant to collaborate with outsiders,
3) the average quality of science in China is less than you would expect from the number of papers.
These aren't mutually exclusive and there could be other possibilities. In any case, increased emphasis on science in China seems like a good thing, for various reasons, while I worry that budget constraints (and politics) may hurt science in the US.

The Royal Society report also shows that papers with authors from more countries get cited more. Three of the six papers I've published so far this year (and one we're submitting this week) have authors from 2 or more countries, but all three were review articles. So collaboration mainly involved emailing manuscripts back and forth. Collaborations involving experiments in two or more countries seem trickier.

Apart from airplanes, parcel express, and email, can any of you recommend tools useful for remote collaboration? Seems like being able to see the same data that's on collaborators' computer screens while talking over an audio connection would be useful. Are there better options for this than Skype's "share screen" mode (which seems to have some limitations)?

March 25, 2011

Inclusive fitness defended

Last year, I critiqued a paper arguing that inclusive fitness (reproduction by individuals who are more likely than the overall population to share alleles with a focal individual) isn't a useful concept. I disagreed, as did a lot of other blogging scientists.

This week, a significant fraction of the world's leading evolutionary biologists published letters in Nature in support of inclusive fitness, both as it applies to social insects and more generally. But the Templeton Foundation apparently liked the paper belittling the inclusive fitness concept and is giving the one of the authors millions of dollars to study "teleology and ultimate purpose in the context of evolutionary biology." More discussion at Why Evolution is True and The Loom.

The beaks of the finches

This week's paper is "Divergence with gene flow as facilitated by ecological differences: within-island variation in Darwin's finches", published in Philosophical Transactions of the Royal Society.

"If humans evolved from chimps", ask the creationists, "why are there still chimps?" Good question! Humans didn't evolve from modern chimps, any more than I am descended from my cousins. We just share ancestors.

But still... why are there now chimps and humans, rather than one species? More generally, how does one species split in two? If part of a species becomes isolated enough to be inaccessible for mating, or at least "geographically undesirable," then the two populations can diverge through natural selection or random genetic drift, eventually losing the ability to reproduce with each other.

But genetic divergence doesn't always require geographical isolation. For example, if birds with medium-size beaks get less food than those with large or small beaks (on an island with many large and small seeds but few medium seeds), will the resulting "disruptive selection" tend to split the population into two subpopulations, with genes for small and large beaks? Maybe, but not if small- and large-beaked birds interbreed, combining genes for large and small beaks. And why wouldn't they?


The Galapagos Islands host several finch species, which vary greatly in beak size and shape. But what about differences in beak size within a species? Usually, that shows some form of normal ("bell-curve") distribution. Peter and Rosemary Grant have studied these finches for decades, showing how wet and dry years favor one end or the other of this distribution.

This week's paper discusses Geospiza fortis finches from one location on Santa Cruz Island. This population is unusual because it has a bimodal (two-peak) distribution in beak size. Genetic differences between smaller- and larger-beaked finches were statistically significant and greater than genetic differences among locations on the same island. Based on these data, they calculated gene flow (essentially, interbreeding) and concluded that smaller- and larger-beaked birds mated less with each other, especially at the site with bimodal beak size, than they did with finches with similar beak size from other parts of the island.

Why wouldn't a smaller-beaked bird mate with a larger-beaked one, or vice versa? Sure, they eat different sizes of seeds, but so what? Female finches prefer to mate with males whose songs are like the ones their fathers used to sing. And previous work by the authors shows that beak size has a major effect on songs. So females tend to mate with males with similar beak size, limiting the gene flow or interbreeding that would prevent divergence in bill size.

But a low rate of interbreeding wouldn't cause divergence in bill size. That would probably require disruptive selection, in which finches with intermediate bill sizes have lower survival or reproduction. Previous work by the authors did seem to show lower survival for birds with intermediate-size beaks. Finches with intermediate bill size were more likely to disappear from one year to the next. But did they die? Or did they fly to the other end of the island, where potential mates weren't quite so fussy?

Either way, this paper and others by the authors are an impressive demonstration of how much we still can learn, even from such highly-studied species as Darwin's finches.

March 22, 2011

Self-sabotage?

Suppose one country wanted to slow the growth of an economic and political rival?

The costs and risks of a direct military attack would greatly exceed any possible benefits. Secretly introducing crop or livestock pests might be significantly less risky, but any nation caught doing that could expect various nasty consequences, especially if the disease spread beyond the borders of the target country.

Small-scale sabotage of the target country's communications, though, might trigger only small-scale retaliation,even if discovered. And it could certainly suppress economic growth. Of course, I would never advocate such a thing.

But what if a fast-growing country sabotaged its own communications? Would any government be stupid enough to do that? Apparently so. Mention certain words, in any context, and your cell phone call drops or your email doesn't go through.

When mentioning "freedom" is banned, can "free radical", "ribonuclease-free", and "free-machining" be far behind? If "protest" is banned, will "in favor of testing" be next? Can I discuss statistical tests, develop a new cancer test, study for the GRE? If I can't announce a political "demonstration", how do I invite people to a demonstration of a new invention?

If you love free-machining aluminum, let's meet at KFC for a t-test !

This could be just the opportunity the US needs to catch up. Of course, we're busy sabotaging ourselves, undermining the basic-research foundation of technological progress, replacing science education with religious indoctrination, and pursuing wars that create new enemies faster than we can kill them....

Let's see, what should we call "evolution" after the creationists take over? "Environmentally acquired inheritance", maybe?

March 18, 2011

The problem of pronatalist professors

"I never trust anyone who's more excited about success than about doing the thing they want to be successful at." -XKCD

Suppose there were some cultural group that made more than their share of positive contributions to society. Suppose members of this group overwhelmingly believed in evolution, liberal democracy, and [insert your favorite meme here]. Suppose, for the sake of argument, that they bicycle to work, insulate their homes, etc., making their per-capita consumption of nonrenewable resources less than average for their society. The only thing is, their numbers increase twofold with each generation, so the total consumption of resources by this group increases, despite their low per-capita consumption. Is this group a problem?

The group, of course, is people with PhDs in science. The PhD population will increase until, as Malthus wrote:

"the actual population [is] kept equal to the means of subsistence, by misery" [or, perhaps, by some form of birth control?]

That misery has arrived. NSF receives ten times as many grant proposals -- at least five times as many good grant proposals, in my experience -- as they can fund. An assistant professor who can't get a grant may not get tenure, even if his or her teaching and research potential are excellent. One professor's failure to get tenure may create a new opening, but each opening attracts many qualified applicants, eager to trade postdoctoral misery for a chance at a tenured faculty position.

Can we end this misery?

The most commonly proposed "solutions" require allocating more money to science. If only there were more grant money, every high-quality proposal would be funded, right? On the jobs front, one frustrated postdoc suggested that postdocs should be given "permanent research staff positions." These would presumably be paid more than postdocs and their greater job security might make them less motivated, but she argues that their greater experience would make them worth their higher cost. Maybe. But would creating such positions solve the problem of too many postdocs and not enough jobs?

Only temporarily. There have been more PhDs than faculty jobs for decades, but students keep signing up for PhD programs. Improving career options for science PhDs would tend to attract even more students, worsening the PhD surplus a few years from now. Similarly, increasing funding available for grants leads (immediately) to more grant applications and (in a few years) to more faculty competing for grants.

The latter point is interesting. How does grant availability lead to increased faculty numbers? Aren't faculty hiring decisions based on teaching needs? Not at major research universities. Research grants typically include "indirect costs" or "overhead", which can exceed 50% of the actual or "direct" costs of the research. Indirect costs include heating buildings, clerical staff, journal subscriptions for research libraries, etc. But the university would have to pay most of those costs, at least in the short term, with or without any particular grant. In other words, current overhead rates exceed the short-term marginal costs of grants to the university. (In the long term, getting lots of grants may require new buildings, etc., but university administrators mostly think short term. Hiring more grant-getting faculty than would be needed for teaching gives them money to support new initiatives that strengthen their next job application.)

So cutting overhead rates on grants -- but not so low that universities start rejecting grants -- would be the simplest way to limit the professorial population explosion. Assuming constant total funding, cutting overhead would also let them fund more grants -- maybe even most of the best ones? -- so professors could spend more time doing research and less time writing grants. If our only goal were to reduce the increase in faculty numbers, we could do that by cutting total grant funding, but do we really want professors to waste their time writing 20 proposals for each one that's funded?

Note that I'm not arguing against an increase in research funding. Basic and applied research can lead, directly and indirectly, to more-sustainable agriculture, better ways to protect environmental quality, more-efficient industrial processes, and improved medical care, with a much better benefit:cost ratio than such alternative societal investments as propping up corrupt dictatorships. But allocation of funds for research should be based mainly on the potential direct and indirect benefits of that research, not on how easy it makes life for professors. The only exception to this principle is that we want to keep research careers appealing enough to attract creative and energetic people. (While we're at it, any ideas for how to attract top, rather than bottom, students to precollege teaching? Sabbaticals, maybe?)

Elsewhere in this blog (or am I thinking of my forthcoming book?), I've also argued that granting agencies should give preference to labs that don't already have a grant. This is because a professor who already has a grant can usually put together a more impressive grant application, with lots of preliminary data, even if his or her ideas are somewhat less creative than someone who doesn't have a grant yet. (Now that I'm on three grants, I'm reconsidering this idea!)

Even if we slow the growth in number of professors, each professor is likely to have more than one PhD student over a career. I got criticized, at Davis, for not taking a PhD student until I had an applicant I thought would eventually be successful even in a tight job market. (She was!) So the PhD surplus isn't going to go away. If you're an individual considering grad school in science, already in grad school, or starting a postdoc, how should the scientist surplus affect your individual decision-making?

First, don't enroll in (or stay in) grad school unless grad school itself appeals to you. That way, even if grad school doesn't lead to the career you wanted, you won't consider those years wasted. Also, if you enjoy grad school, that means you enjoy working long hours in the lab and reading and writing scientific -- exactly what you need to do to have a shot at a research career. See this earlier post.

If you're already a postdoc, I've noticed a very strong correlation that may interest you. Postdocs that aren't in the lab on weekends don't get research jobs. Those I always see in the lab on weekends have gotten jobs as professors or research scientists. This may not be true always or everywhere, but it makes me question the statement (from the postdoc mentioned above) that "a lab-head position requires a strong publication record, which can be as much about luck as skill and hard work." Maybe, though, the postdocs that are working weekends are doing so because they're getting exciting results, rather than getting exciting results because they work harder.

March 16, 2011

Tsunamis, earthquakes, disaster relief... Just Give?

Three Japanese scientists have done lab or field research with me over the years. All survived the earthquake and tsunami, although they may have lost friends or relatives. I don't know anyone in Haiti, but they may need help even more than Japan does. We can't prevent earthquakes or other natural disasters -- reducing production of greenhouse gases, not building on floodplains, and protecting mangroves might reduce hurricane and flooding risks somewhat -- but investing more in disaster recovery could reduce death and disruption. The US military has made some positive contributions in this area and we might find that having them do more disaster relief would reduce the number of people who want to attack us more efficiently than trying to kill them all has.

Meanwhile, we can support Red Cross/Crescent, Doctors Without Borders, etc. Recently, I've been donating through JustGive.org. They will pass your donation to the groups you select, minus a small fee, and can withhold your address or other contact information. That way, I can support the groups I like, without getting monthly letters asking for more money, from every group they to which sell my address.

March 11, 2011

Aging primates, agricultural ants, efficent cooperation, etc.

Lots of interesting papers this week, but I only have time for some brief comments.

I can't believe Obama's response to the earthquake in Japan was to go ahead with a speech on gasoline prices. (BBC cut him off!) Higher prices for nonrenewable resources are an efficient way (relative to rationing, say, or complicated mandates) to encourage us to use them more slowly, so they'll last longer. And although adding more carbon dioxide to the atmosphere may increase photosynthetic efficiency and make our winters here in Minnesota a little less cold, I'm not willing to bet that those benefits will outweigh risks such as rising sea level from melting glaciers. If civilization must be at war with nature, I'm on the side of civilization, but let's not shoot ourselves in the foot. For example, we can stay warm inside insulated houses, while agricultural pests perish in the cold, reducing the need for pesticides later. Cold winters are good! Hmmm... maybe I should turn comments back on; but I'm still deleting all commercial links.

Aging in the Natural World: Comparative Data Reveal Similar Mortality Patterns Across Primates "in neither females nor males did we find evidence of a negative correlation between IMR [initiral mortality risk, at onset of adulthood] and RoA [rate of aging, increase in mortality with age],which would be indicative of a trade-off..."
[I wouldn't have expected a trade-off between those parameters, but what about a tradeoff with reproduction (mentioned only in the definition of adulthood)?]

How within-group behavioural variation and task efficiency enhance fitness in a social group "females of both phenotypes [aggressive versus docile] experience increased fitness when occupying colonies containing unlike individuals"

Experimental peripheral administration of oxytocin elevates a suite of cooperative behaviours in a wild social mammal

Co-Residence Patterns in Hunter-Gatherer Societies Show Unique Human Social Structure

The influence of maternal effects on indirect benefits associated with polyandry

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

Evolution of cold-tolerant fungal symbionts permits winter fungiculture by leafcutter ants at the northern frontier of a tropical ant-fungus symbiosis

Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog

Global CO2 rise leads to reduced maximum stomatal conductance in Florida vegetation

March 9, 2011

No comment

I am disabling comments, at least temporarily. The vast majority of "comments" lately have been thinly veiled attempts to generate links to commercial sites. I have to finish revising my book and don't have time for that nonsense. If you have a genuine comment, send me an email.

March 4, 2011

Sex, sexiness, viruses, nematodes, and horses

Haploinsufficiency and the sex chromosomes from yeasts to humans
"orthologues of S. cerevisiae HI genes (those for which a reduction in copy number in a diploid from two to one results in significantly reduced fitness) are significantly under-represented on the X chromosomes of mammals... accumulation of HI genes on the sex chromosomes would compromise fitness in both sexes, given X chromosome inactivation in females"

Natural selection stops the evolution of male attractiveness
"lack of genetic variation that would allow an increase in sexual fitness while simultaneously maintaining nonsexual fitness"

A Virophage at the Origin of Large DNA Transposons

Computational and phylogenetic validation of nematode horizontal gene transfer

Dietary Change and Evolution of Horses in North America