Tuesday, April 21, 2009

The Free Encyclopedia and 'Hairless' Apes

Without having done extensive checking, I would guess that Wikipedia is the only encyclopedia in the world in which the section on primate taxonomy includes nude photos of male and female humans with all their body-hair removed.

I suppose one could argue that body hair would obscure some portion of our typically primate anatomy, or make the photos appear less clinical. That said, none of the other primates pictured are shaven, so why the humans? And honestly, human's body hair doesn't hide that much anyway. As humans are naturally the least hairy of any primate, the clean shaven models seem to me to unduly exaggerate our distinctness from other primates. I don't approve.

On further consideration of the nature of Wikipedia, the inclusion of these photos could be intended purely to annoy social conservatives who object on religious grounds to the placement of humans among the primates. In that case the hairlessness would presumably be intended to emphasize the nudity of the models.

Monday, April 20, 2009

Wherefore art thou, niche conseratism?

"Niche conservatism is the tendency of species to retain ancestral ecological characteristics." (PDF)

But why do species have this tendency, or more particularly, why do ecological traits not change more rapidly than they do as a lineage evolves? Wiens and Graham state that, "We refer to niche conservatism as a process, although it may be caused by more than one factor at the population level," but don't say what those factors may be, or provide a reference to someone who does.

So what causes niche conservatism:

Two basic mechanisms occur to me. The first is that new traits simply don't arise, and therefore can't be selected for or against. Why don't we have rats that can eat iron? There is lots of elemental iron around these days, and it is very high in energy. Surely a rat that could eat iron and extract all that energy would do very well, and make lots more iron-eating rats. But that trait has not occurred (and is not likely to do so) and as such there is no way for natural selection to favor the iron-eating rats. But for traits like sexual mass dimorphism, this type of constraint seems unlikely. We know that closely related species sometimes have very different mass dimorphisms (compare gorillas to humans). But closely related species usually don't have wildly different mass dimorphisms, so there is conservatism in the trait even though it is pliable.

The second possibility that occurs is that niche conservatism comes about simply because a trait works well with the way a population lives, and the other traits is has, and therefore some form of selection acts to keep the trait where it is. The trait is conserved because it is functional. Even if some other combination of traits would be more advantageous, that combination would require so many modifications that you can't get there from here. The population would have to go to far 'downhill' on the fitness landscape to get to that taller hill across the way. So selection, which tends to push the population 'uphill,' keeps it on the little local peak it is on. By keeping the population where it is, selection causes niche conservatism.

I'll call it a hypothesis. First I need to find out who has already said almost the same thing.

Sunday, April 19, 2009

A third way of seeing things

The paper I'm writing now is on sex-biased longevity in primates. I'm trying to understand why in some species the males live longer, and in others the females live longer. The story I'm trying to test goes like this:

The largest investment in primates' offspring is in the form of care, not eggs or sperm or pregnancy. In species where females provide all of the care, males need not stay with a single mate, so the operational sex ratio is male biased (i.e. lots of males are out looking for a mate, while most of the females are pregnant or nursing and therefore not looking to mate), reproductive skew is high for males (some males will father lots of offspring, others none), and the fitness rewards to successful male competitors are great. Larger males are more likely to win these competitions, resulting in an increase in optimal male size. These large belligerent males risk increased mortality through conflict, and through diversion of physiological and developmental resources away from longevity and into competitiveness. Simultaneously, selection for longevity in females may be increased by the need to stay alive until their young become independent (and in the case of humans, to care for grandkids). This leads to males who, relative to females, are non-caring, short-lived, large and conflict prone.

I have data (gleaned from the literature) for a bunch of primate species on how long males and females live, how much care the fathers provide in each species, how big males and females are and how frequently and intensely males fight with each other. Depending on how I analyze these data, I get two very different answers. If I treat each species as an independent sample, and look at the correlations between these variables, the data completely support the story. The species range along a continuum having short-lived belligerent large, uncaring males at one end and long-lived caring low-conflict small males at the other.

But most evolutionary biologists would say that is not the right way to analyze the data. I need to take into account the relationships among the species. Two traits might seem to be correlated not because the one makes the other selectively advantageous, but because a group related species all have the one and all have the second. Take the example of feathers and laying eggs. All birds have feathers and all birds lay eggs. Is this because something about feathers requires egg-laying (probably not) or because all birds are descendents of some ancestral birds that laid eggs and had feathers, and ever since no bird has arisen that didn't do both those things. That all birds have eggs and feathers is an example of what biologists call evolutionary inertia.

The question this poses for me in writing my paper on primates is whether the correspondence between sex-biased longevity and these other variables is because of the adaptive story I told you, or because of evolutionary inertia. So I look at the data a second way, and see that there is a great deal of evolutionary inertia in these traits. Most primate species are somewhere near the middle of that continuum I described. Ever species at one end is from one group of related monkeys. Every species at the other end of the continuum is either a great ape or from a different family of monkeys. Plugging my data into software designed to test for evolutionary inertia, I find that closely related species are very likely to have similar values for all the traits I am measuring, and that inertia is fully sufficient to explain the correlations between these traits. It is like eggs and feathers in bird.

As I am trying to write the paper to present all of this in a scientifically rigorous way, I am struggling with what to say about it. The easiest, and least interesting, conclusion would be to simply say that the correlations are purely illusions conjured by evolutionary inertia. What I'm attempting to find a way to argue it that it could just be inertia, but that the inertia might be because of selective effects. In other words, that both the inertia story and the selective story could simultaneously be true, and closely related species are similar not because they can't change, but because what was adaptive for their common ancestor is still adaptive for them. If a male from a very belligerent species was to grow in a way that made him not a good competitor, but able to live a long time and provide care to his young, this wouldn't fit with the way his species lives, so he wouldn't pass on his novel trait, and his species would stay like their ancestors had been. It is evolutionary inertia caused by adaptive mechanisms. I think my next step is to find out who has already written about adaptive evolutionary inertia, and what they said.

Saturday, April 18, 2009

Science-based do-gooding.

Last month as we drove up to her mom's house, Iris and I were talking about what sorts of non-profits we think really use their money well, in terms of achieving a lot of good with relatively little money. I said that the ones that usually impressed me were those very focused on a single type of action that did that one thing extremely well, rather than trying to save the whales and reduce teen pregnancy and sue the manufacturers and put out a great picture book of homeless homosexual redwood trees. Iris asked what kind of action I had in mind, and I said that ultimately, the step that seems to do the most good for the least expense is educating girls in poor countries where girls don't traditionally get educations. The list of things one can accomplish by educating girls is truly amazing. The level of education of the females in a country is the single best predictor of longevity increases, decrease in infant and juvenile mortality, decrease in rate of population growth, decrease in rate of infectious disease, increase in future education of both boys and girls and so on and so on. It is more important than how rich a country it is, how many doctors it has, the religious practices of the population or how well educated the men are. There are decades of studies comparing between nations, between regions, between villages and between individual families, and at every level having better educated women around translates into a healthier, more stable and less quickly increasing population. And the greatest gains in all these outcomes come from the first steps in educating the women. Whether women have a masters or a PhD doesn't affect the chance of their babies dying much. Whether they finished third grade or had no school at all has an enormous impact. Every additional year of schooling is helpful, but less so than the previous year.

When I read these studies, I feel like we shouldn't be spending development money on anything but educating girls. I feel like we've known about the development wonder drug for decades (and unlike most wonder-drugs, this one actually works) but haven't bothered to use it. Iris pointed out that in many countries, such as Niger, where she was a Peace Corps volunteer, there are cultural sensitivities that would keep a westerner from marching in and educating girls. The education of boys is considered more important, and many boys don't get educated for lack of funding. Post-colonial resentments exist, and must be treated carefully. Iris argued that if an organization wanted to educated Niger's girls, its organizers would have to have the kinds of insights and sensitivities to Niger's culture that only Nigeriens have. She lamented the fact that there was no such organization in Niger.

Imagine then our surprise and delight when (less than a week later) Iris found out that some of her Nigerien contacts were founding an organization to promote and fund the education of Nigerien girls. If we were superstitious people, we could draw all sorts of conclusions from the coincidence. Instead, we have offered to do what we can to help them get up and running. They don't yet have anything more official than a possible name and a board of directors. They aren't even taking donations yet (they still have to apply for tax-exempt status). Iris has been contacting her Peace Corps friends who have particular useful expertise, and I've been unwisely taking time away from my thesis to gather up and summarize the published research on the benefits of educating women. Perhaps it is naive, but I can't help but think that it would be useful to have a well documented statement on the benefits of educating girls to show to potential donors and government types. We expect to be helpful to them however we can. If they are able to do what they want to do, Niger (currently one of the world's poorest and worst educated nations) should be an amazing success story in a decade or two.

Thursday, April 16, 2009


In a couple of weeks I'll be attending the conference of the Population Association of America. It will be a bunch of demographers. Most of the conference is talks divided into topic-specific sessions. They don't have a session for biodemography, or really anything related to my research, but the poster-session is open to whatever topic, so I'm presenting a poster.

My title is, "Post-Reproductive Lifespan in Humans: Cultural Artifact, Widespread Primate Trait or Unique Adaptation?"

I've had fun making my poster, mostly because it is an excuse to play with Photoshop and Powerpoint instead of writing my thesis. For my poster I needed to find a compact easy way to display how the fertility and survival of a population changes with age, and simultaneously explain my methods. And I needed to be able to do that for several populations side by side in a small space. Now this is all tailored to make sense to the demographer, so it may not be that intuitive to anyone else, but I like what I've got. To clarify, in demographerese, lx means what portion of the individuals that survive to each age and mx means how fertile are individuals at that age.

By plotting mx and lx on the same graph I make it visually clear (to a demographer) that the population nears an endpoint to fertility (age M) long before it nears an endpoint of survival (age Z). I then go on to use some math and demographic methods to define good ways to measure post-fertile survival in ways that allow for straightforward comparisons between species. I call the two measurements G and S. But the fun part comes in when I use the graphical format established in Figure 1 to compare populations in Figure 2:

My hope is that having labeled and explained the parts of the graph in Fig. 1, the meaning of these graphs in Fig. 2 will be quickly obvious to the demography crowd. I'll leave you to interpret what these graphs say about post-fertile survival in humans and chimps in different environments. I can't give away everything.

Monday, April 13, 2009

Diurnal Activity Cycles

My wife and I (both writing theses this spring) and two cats share a very small studio apartment. One way we make maximum use of the space is by having different sleep-wake schedules. I do my most effective writing between 9PM and 1AM. Iris gets the most done from 6AM to 10AM. I have the easiest time concentrating at that time, and only partly because everyone else is asleep. FeLion, our older cat, does some of her best suckling on inanimate objects in the middle of the day. Tigrinum, the kitten, expends most of his energy from 2AM to 6AM, charging around the house and leaping from the top of his cat-tree onto his sleeping humans. Come to think of it, it makes a pretty lousy system.

There is a well established pattern of individuals of different ages waking and sleeping at different times. Older adults and young children tend to go to sleep early and wake up early. Teenagers tend to stay up late and go to bed late. People in all the ages in between are pretty variable. These patterns are well known to most people, but I'm not sure we understand their evolutionary basis. Why did humans evolve to have sleep schedules that vary individually and with age as much as they do? My guess is that it had to do with avoiding competition within groups for space and forage. The old people and the little kids left the cave or the hut early in the morning and foraged before everyone else was up. In the evening, after everyone else was asleep the young people would stay up and try to impress potential mating partners. That was probably the easiest time to find some privacy without straying too far from the village. One thing I wonder about, do other primates have similar variation in their diurnal activity cycles? That right there is a good evolutionary biodemography question.

Sunday, April 12, 2009

Why I can love chocolate

The conversation usually goes something like this:

Me- I'm allergic to caffeine. It makes me get a terrible headache, then get really sleepy and sleep for 12 hours and then I still have a terrible headache.

You- Um, but I see you eat chocolate all the time. You're always talking about chocolate and writing about chocolate. You are a total chocolate adict.

Me- Yeah! I love chocolate. It's my main drug.

You- Um, but chocolate has caffeine.

Me- Well, it has a tiny bit, but mostly it has other closely related chemicals.

I've had this conversation with enough dozens of people that I figured I should look up what was in chocolate. And it turns out I actually did know what I was talking about (for once). According to this article in the journal European Food Research and Technology, cacao beans have three main kinds of very similar chemicals in the group called methylxanthines. These are theobromine (named for the Cacao tree, Theobroma cacao), caffeine, and theophylline. Raw fermented beans straight off the cacao tree have lots of theobromine, very little caffeine and almost no theophylline. In the various preparation steps between then and when I actually eat it, much of the caffeine is lost. The concentration of these various chemicals depends a lot on the strain of cacao, the growing conditions and the processing, but most chocolate has 20 to 100 times as much theobromine as caffeine. A cup of hot cocoa has about half as much caffeine as a cup of decaf coffee.

The fact that chocolate doesn't make me have a terrible headache and put me to sleep is likely (likely meaning I am speculating) either because there is too little caffeine in it to matter or because it has so much theobromine. Theobromine could be counteracting the caffeine, or it could be competitively excluding the caffeine from the neuroreceptors it normally binds to. Basically this means that theobromine and caffeine are so similar that they stick to the same spots on my neurons, and if the theobromine gets there first, the caffeine may not be able to stick, and therefore not affect me. But the moral of the story is I can eat chocolate without worrying about the caffeine making me sick.

Elastic replacement

I've been thinking on an off for several years about the concept of 'elastic replacement.' That is term I made up to mean when the rate at which new things arise increases in response to the effort to remove old things. The example that got me started thinking about this was a political one. For the early years of the US occupation of Iraq, the Bush administration frequently cited statistics on how many terrorists had been killed or captured as a result of US action in Iraq. What they never seemed to consider was that US action in Iraq might also be increasing the replacement of terrorists by making it easier for terrorists to find and recruit young people who might have otherwise been non-violent. The size of any population is determined by not only the number leaving, but also the number entering, and by measuring only one portion of our effect, the US government necessarily got a biased picture of our effect. The CIA has confirmed that the number of active terrorist in Iraq rapidly increased rather than decreasing through the first years of the Iraq war.

This general idea carries over into all sorts of arenas. When a giant old tree falls, it makes space for hundreds of seedlings. When I comb my cat to remove loose hairs, I loosen lots more hairs and possibly even stimulate increased hair growth. WWII caused far fewer deaths of US soldiers than the ensuing baby-boom caused births of US babies. Eating all the chocolate so that my wife won't be tempted by it inspires her to go out and buy more chocolate. Responding to all the emails I should have responded to a long time ago brings in even more emails that need to be responded to.

Elastic replacement seems to be an extremely common class of unintended consequences. Humans don't seem to be good at considering it, but we should try.

Saturday, April 11, 2009

Making progress

Writing a paper is an iterative process. Figure out what my point is, start writing, change my point, adjust my writing, repeat. The process of rewriting the methods makes me realize it would be better to analyze the data a different way, so I do the analysis over which makes me realize that I need to modify not only my methods but also my conclusions. The new conclusion requires an additional analysis and therefore a further modified conclusion. Writing is very much like sculpture in that it is not so much a question of getting it perfect as getting it good enough that it isn't worth changing.

Friday, April 10, 2009

Fertility v. Fecundity

Fertility and fecundity are two closely related concepts.

One means the physiological state of being able to have offspring, the other means the state of actually producing offspring. In a population of 26 year old human females, 95% might be physiologically capable of giving live birth, while perhaps only 10% might actually have a baby that year. So fertility and fecundity are different. The problem is, which is which?

Demographers refer to the ability of have babies as fecundity, and the rate at which women actually have kids as fertility. Biologist do the opposite, saying that fertility is the capacity and fecundity is the realization.

This is just a quaint fact in academic linguistics until one tries to write papers and give presentations that will sit well with both demographers and biologists. Biologists think it is totally unreasonable to adopt the linguistic oddities of the social scientists, and demographers are not happy about people reversing the meaning of these terms. I usually go with the demographer's lingo. They are the ones who employ me.

Sex-biased longevity

Ive spent much of the last couple of weeks working on a paper on sex-biased longevity in primates.

Here is a draft of a portion of an introduction to said paper. Any similarities between this and the final published paper are purely coincidental:

The difference in longevity between the sexes of a population depends upon the selective forces each sex experiences, as well as the degree to which common genetic material limits independent demographic evolution. Sex-biased longevity has been proposed to arise from difference between the sexes in selective forces as diverse as reproductive physiology, care of offspring, parasite risk, mortality associated with reproduction, genomic stability and late-life support from kin. But measurements of sex-biased longevity have been made for relatively few species, and we have little sense of the degree to which sex-biased longevity is constrained by shared genetics or phylogenetic conservatism.

Most organisms, and likely all mammals, experience an evolved rapid increase in mortality and decrease in fertility at advanced ages, limiting longevity. The force of selection against mortality at a given age depends upon the likelihood of surviving to that age, and the mean remaining reproduction of individuals who do survive that long. Reproduction and survival are expected to drop to zero at similar ages, but reproduction can be direct (fertility) or indirect (care of offspring and kin effects).

Captive populations, the source of most demographic data on non-humans, will reflect sex-differences in evolved capacity for longevity more so than do wild populations, which tend to die younger (there are exceptions). For understanding the influence of experienced mortality patterns on evolved capacity for longevity, it is useful to make the distinction between extrinsic and intrinsic mortality. Extrinsic mortality is generally said to be that caused by the environment, while intrinsic death is driven by a failure of the organism's internal processes. In practice this distinction is difficult to make, as all environmental risk is influenced by the organism's characteristics and behaviors, and the timing and risk of intrinsic failure is inevitably influenced by an organism's history and environment. None-the less, much of our theory on the evolution of longevity is based on this intrinsic/extrinsic distinction. In general higher extrinsic mortality will lead to increased intrinsic mortality. However increased extrinsic risk at age x will influence evolved mortality at many ages, and not necessarily lead to a spike in intrinsic mortality centered at age x. This leaves overall sex-biased longevity as our best measure of sex-biased mortality when employing data from captive populations. Sex-biased longevity in captivity is highly correlated with sex-biased longevity in the wild even though the causes and timing of mortality may vary between species.

Much of the discussion of sex-biased longevity has focused on the idea that if one sex provides extended care to descendants, that sex should gain greater selective benefit from increased longevity. Allman et al. suggest that in primates, males who are the primary caregivers tend to live as long or longer than their females, while in species with little paternal care females tend to live longer. The Grandmother Hypothesis and its derivatives use indirect reproduction by post-menopausal women to explain their post-reproductive lifespan and therefore their tendency to live longer than men despite earlier decline in fertility. The Patriarch hypothesis instead argues that women's post-fertile survival is explicable based on late-life reproduction in males and the non-independence of male and female longevity.

Sex-biased longevity can also result from differences in mortality risk between the sexes. Trivers proposed that in species with frequent or intense male-male conflict, males incur significant mortality risk and therefore don't live as long as females. Alternatively, if females experience increased mortality in producing or rearing young, males should be expected to live longer. If either sex is the predominant disperser, and mortality risk during dispersal is high, this too could cause inter-sex differences in capacity for longevity. Finally, a variety of hypotheses have been put forward arguing that either the larger sex, or the smaller sex, should tend to live longer.

Using comparative primate life-history data, we examine the variability of sex-biased longevity in primates. We further examine the degree to which level of paternal care, grandmaternal care, male-male conflict, and mass dimorphism predict sex-biased longevity. Finally, we examine the patterns of correlated evolution among these variables in a phylogenetic context.

Thursday, April 09, 2009

Tour of Science!

Walking back to the Valley Life Sciences Building this afternoon, I passed a large tour group of high-school students and their parents being led by an undergraduate. One mother, snickered into her cell phone, "they have an heeeeerb lab. They study herbs. This place is crazy. Crazy! No, no, no, the tour guide said they had a whole museum of herbs. I'm like what, parsley?!"

It took me an instant to figure out that she was talking about the University and Jepson Herbaria, a research museum dedicated to the study of plants generally, not culinary herbs in particular.

I emailed this story to the other grad students in my department. Many of them responded that they had heard the tour guides telling the tour groups all sorts of misleading and false information, including that a herbarium is a museum for studying cooking herbs.

Here are some other examples of overheard falsehoods made up by university tour guides to impress their tour groups and relayed to me by other grad students. Several of these things were independently reported by more than one observer:

- The Cretaceous display in front of the Herbaria contains extinct plants... Berkeley scientists rediscovered their ancient DNA, amplified it, germinated seedlings, and planted them there for museum visitors. (The display is of plants of types similar to those which existed during the Cretaceous, none of which have ever been extinct)

- The T. rex may be as many as 5 million years old. (It is at least 65 million years old)

- The T. rex came to the paleontology museum in a giant puzzle
box and when it got here, the paleontologists didn't know what to do with
it. One of the employees was about to get fired but he was able to figure
out how to put it back together so he was able to save his job. This man
is now the assistant director of the museum. (A complete fabrication, truth here)

- The T. rex is named "Osborn". (Sue)

- T. rex (the species) was discovered by Berkeley paleontologists. (False)

- Most of the UCMP fossils are actually in the Campanile. (False)

- UCMP geologists discovered asteroids. (False)

- The giant ammonite in the first floor south hallway is from a time on
Earth where everything was giant, even the snails. (Hilarious and false)

- The Herbaria is home to the world's largest pinecone, but they don't put
it on display because they are worried someone will steal it. (Goofy and false)

- The Herbaria has one example of every plant species known to man. (They wish)

- The plants outside the herbaria went extinct around the time T. rex went
extinct. (False)

- MVZ scientists save stem cells from each animal they capture in order to
help genetically engineer new animals to save endangered species from
going extinct. (And then we take over the world!)

- The Eucalyptus tree is native only to Berkeley, Australia, and New Zealand. (actually only Australia, New Guinea, eastern Indonesia and the Philippines)

- The Eucalyptus grove is protected by an Act of Congress and can never be
cut down for any reason. (Pure fabrication)

- Strawberry Creek used to flow all the way to the Ocean but then they
built roads over it and then there wasn't enough water so all the
strawberry plants that used to grow next to it died off. (A large portion of Strawberry creek between campus and the bay has been undergrounded. The rest is false.)

- The pterodon skeleton is hanging above the T-rex because they always flew over the T-rexes to keep them in view so the T-rex couldn't sneak up on them. (Awesomely hilarious)