BLOG OF SCIENCE!

Can anyone think of model organism genera starting with I,J or Q?

2012-01-25T05:08:00.000-08:00

Arabadopsis

Bufo

Caenorhabditis

Drosophila

Escherichia

Felis

Gallus

Hydra

Klebsiella

Loligo

Mus

Neurospora

Oikopleura

Phodopus

Rattus

Saccharomyces

Trichoplax

Ustilago

Vibrio

Wolbachia

Xenopus

Yersinia

Zea

A, alligators all around

2012-01-05T13:43:00.000-08:00

They say that the distance in inches between an alligator's eyes and its nostrils is equal to the length of the whole animal in feet. This behemoth hangs out by the fishing dock in Loxahatchee National Wildlife Refuge feeding on discarded bait fish and who knows what else. My best guess is 14 inches nose to eyes, which would make it not unheard-of big but certainly exciting-to-canoe-past big.

It is amazing to think such an invulnerable top predator (at least within the refuge) started out nearby as a scared little snack for herons like this:

Authorship code

2012-01-05T13:34:00.000-08:00

I'm writing a paper with two of my students. Well, I'm writing it with one of them and another one did a lot of work on the statistics. But today we had to straighten out the order that the authors would be listed in on the paper. This can be a contentious issue, and I know of cases in which papers did not getting written at all because the authors couldn't agree on who got to be listed first. Some big multi-author papers simply list everyone in alphabetical order to avoid the fuss, but then Dr. Aardvark always gets to be first author. Some journals have a little section where each author's contribution is described, but they usually end up saying something uninformative and false like "all authors contributed equally."

I came up with most of the ideas in the current paper, put things together, decided who would do what, etc. My student did much of the lab work and is doing much of the actual writing. Given this, most biologists would propose what I did, and what my student objected to: She (as the person doing the writing) should come first, I (as the senior person on the paper) should come last, and everyone else (in this case meaning the statistics student) gets sandwiched in between. This was very counterintuitive for my student; she thought I was trying to minimize my own role by putting myself last. In fact, it is a step up for me to be writing papers in which I am in that last position. I remember this being counterintuitive for me the first time it was explained to me. I was a college student, and a boss said that he'd make me second author on a paper. I said something to the effect that I'd be glad to be even last author, which I thought was being humble, but he took it as me saying the paper had been my idea. We straightened out the miscommunication but I didn't end up being listed as author on the paper. That the last author spot (at least in biology) signifies the senior author is a code biologists internalize, and I had to think back a long way to figure out why my student objected to me being last author. I explained, she reluctantly believed, and now it is settled.

Oh give me a home, where the apple-snails roam

2012-01-03T11:32:00.000-08:00

Retirement communities are, by design, fairly sterile places. Much of south Florida is covered in huge gated spreads of nearly identical buildings with neatly trimmed lawns leading down to pleasingly curving shallow canals so that every apartment can have water views. It is uniform, controlled, boring. But all those networks of shallow canals catching lawn fertilizer and Florida sun provide habitat and highways for rapidly growing aquatic plants, which feed aquatic invertebrates and fish. With relatively few retirement community residents catching their own fish, this leaves the fish to grow as big as want.

Or at least it used to. When I was a kid visiting my grandparents in Century Village, I rarely saw any wildlife around the wide place in the canal (referred to as a lagoon because it increases resale values) behind their apartment.

When I was a teenager and my grandmother was widowed, the lawn by the water was occupied by a flock of Muscovi Ducks (plant eaters), Cattle Egrets (which eat mostly insects picked from lawns) and the very occasional Great Blue Heron, which eat only small to medium fish. My aunt inherited the same apartment, and my wife and I brought our baby daughter to visit her this winter. Our first morning there, jetlag woke us early. Standing by the lagoon was a flock of Wood Storks. Walking past them in the water's edge was a flock of White Ibis, trailed by a Tricolor Heron.

On the far bank an Anhinga spread its black wings to the sun. A few feet away lay a huge dead fish, heavily built and probably 80cm long, partly eaten by something. What could kill a fish that big, drag it up on the bank and eat only part of it? Walking the banks we found the shells of numerous Apple Snails, so named because they are as large as the fruit. Apple snails don't come up on land by themselves, so something must have carried them up, presumably to eat them. In back of the next building over, beyond the Great Egret and Little Blue Heron, I could just see something moving on the bank. I thought it might be a dog (not allowed in Century Village) but then I could see it was two long low animals chasing and wrestling with each other. They jumped in the water and swam as no dog could. River otters! A pair of very large river otters chased each other, making circles in the reflected condos. The remains of several large fish, each only partly eaten, attested to the successful hunting they had been having in the canal.

Four Turkey Vultures sat around one such plate of sushi as others circled and swooped, their wing tips almost brushing the screening of enclosed patios. We cajoled my aunt, her bad ankle throbbing, to come out onto the lawn with us for a closer look at the otters. We crept closer to them and the fish they were snacking on until they raised their heads and hissed at me, at which point we backed off.

All this wildlife, carrion, birds and their poo on cars, giant snails, etc. are pretty clearly not what the designers of Century Village, and south Florida's thousands of other retirement communities had in mind. Nevertheless, I think most of the residents are probably happy to have so much nature on their lawns. I doubt all those telescopes and binoculars sitting in the screened patios were for spying on the other retirees.

Is this all good for the wildlife populations? Clearly they would have been better off if the wetlands had not been made into retirement communities, but given that they were, I'd guess that learning to exploit those communities is to their advantage. The water in these canals surely has all sorts of runoff from lawns and parking lots, but if the birds feeding in it can still breed consistently, they are likely to have a feeding habitat that no one will drain, pave or burn. If things get too rough in the nearby Everglades, they will have a retirement home ready.

The end is neigh!

2011-12-18T06:05:00.000-08:00

When I start working on a project, it is always interesting and exciting, otherwise I wouldn't start working on it. Developing ideas is fun, narrowing down the question to just the core issue is challenging, building an apparatus or simulation or whatever feels productive and creative. But I also have to actually write a paper which frame the whole thing in a useful way, which means reviewing and summarizing the relevant literature, which is boring unless I actually have something novel to say about that literature, other than what my new experiment or analysis or whatever shows. And I have to make my paper, which is always interdisciplinary in some way, fit into a particular journal, most of which are tightly disciplinary. So I'm much better at starting papers than finishing them, and I have a tremendous backlog of papers to get out. It is therefore a great relief to have just sent out what was originally (three years ago) a response to another paper in which I saw some methodological shortcomings, that turned into a broad comparative analysis of human and primate demography, and ended up as a review article submitted yesterday to an anthropology journal. One of my co-authors is a bone fide anthropologist, so I feel confident that we at least refer to most of the right papers. I'm also confident that our points are valid and important and the paper generally well written. But mostly I just feel happy that if all goes well I will soon no longer have to work on this paper.

Undermining the Wall of Death

2011-10-26T01:19:00.000-07:00

Different fields of science often don't talk to each other, even when coming at the same problem from different angles. A stark example of this can be found in the literature on aging. I'm in the field of evolutionary demography, and aging is one of our central focuses. We ask why and how it happens by studying the demographic patterns of different species under different circumstances. The evolutionary demographic theory of aging is built around the idea that there are alleles that have effects at different ages and natural selection acts on these genes to sculpt the age-specific mortality at different ages. Because dying young (before you've had a chance to reproduce) is more disadvantageous than dying old (after you've already passed on some genes) natural selection acts more strongly to minimize mortality in early adulthood than later adulthood, resulting in a chance of dying that increases in age. There are decades of theory built up around this idea, and the idea is not without merit, but it does assume these age-specific gene effects, generally without bothering to say what the actual genes are or how they influence mortality.

Another field within biology that focuses heavily on understanding aging is biogerontology. Biogerontology focuses on understanding the mechanistic basis of aging at the cellular and molecular level. They describe aging as a process of narrowing of the homeodynamic space, often due to accumulation of damage. Homeodynamic space is a concept related to homeostasis (the tendency of organisms to push their physiological state back to some optimum), but with the recognition that the goal that the individual is pushing towards, and its options for pushing, change over time. For example, as the cells in an organism accumulate mutations, it becomes more dangerous to allow them to continue replicating, because this could spawn a cancer. So the cells are forced to turn down expression of genes that allow for cell replication. But if your cells are replicating less, then you should be more reluctant to allow apoptosis, programmed cell death, because cells that die can't as easily be replaced. But if you've down-regulated the genes involved in apoptosis, this means infected cells will be less likely to kill themselves, so you need to have a stronger inflammation response, so that white blood cells will be brought to areas of infection and kill the infected cells from the outside. But increased inflammation has all sorts of nasty side effects, which themselves need to be compensated for. Note that I am just making this chain up as an example. The point being that the organism, in order to deal with the accumulation of damage, has to adjust various aspects of its physiology, which can cause damage or challenges to the system, which requires further adjustments. The organism gradually loses wiggle room, paints itself into a corner as it were. When this homeodynamic space gets too small, the organism can't respond to whatever insults (internal or external) come along and gets killed.

Reading papers in biogerontology, I am struck by two things. The first is how naive and outdated their evolutionary assumptions tend to be. For example, they still will state that aging is not observed in the wild because no individual lives long enough to grow old in the wild, an opinion that evolutionary biologists began to reject in the 1960s and have now disproved with data from numerous species from plankton to humans and birds to aphids. But I am also struck by how naive they would think our assumptions about age-specific genes are. They state as one of the basic principles of biogerontology that are no genes whose roll it is to cause aging, or which act at a particular age to regulate the chance of death. You will remember I said that such age-specific gene effects, from unspecified genes, are at the center of much of the theory behind evolutionary demography. Yet biogerontologists know such genes not to exist. So our assumptions about the mechanisms are as naive and simplistic as their assumptions regarding the demography.

This lack of communication, with each field basing its thinking on ideas the other has long since rejected, is common in science. There are simply too many journals, papers, conferences, etc., too many fields that may produce important information, for anyone to keep a useful fraction of an eye on most of them. So the lack of communication between fields is to some extent inevitable, but it does have significant consequences.

This is obvious when we introduce the gerontological observation that gene expression is not highly age specific (at least not late in life) to the evolutionary literature on post-reproductive lifespan (PRLS). Much of the study of PRLS has been motivated by the idea that PRLS shouldn't exist unless post-reproductive individuals do something useful for their younger kin. This idea arises from the evolutionary demographic theory of aging I described above. If an individual has reached the age where it can no longer reproduce, the genes it is expressing at that age should be genes that selection doesn't care about at all, because whether she dies at that age has no effect on how many offspring she has. So mutations that kill post-reproductive individuals should accumulate rapidly, unopposed by natural selection. W.D. Hamilton, a preeminent evolutionary theorist of the mid-20th century, wrote in 1966 that “In the absence of complications due to parental care or other altruistic contributions due to post-reproductives, the [mortality] curve should be roughly asymptotic to the age of the ending of reproduction.” By this he means that as the individual approaches the end of her reproductive period, her chance of dying at each instant should approach 100%. This has been dubbed "Hamilton's Wall of Death." Hamilton's work is influential enough, and his basic logic sound enough, that many of my colleagues still believe we should find the Wall of Death. But in fact we can find PRLS in a huge range of organisms where there is no parental care or anything comparable, and the Wall of Death is nowhere to be found. Hamilton's prediction fails because his model is built around high age-specificity of gene expression, which we now know not to exist. Genes which are being expressed at and after the age of reproductive cessation are the same genes being expressed prior to that age, doing the same things they did prior to that age (except of course reproduction) and so they can't just suddenly cause all sorts of lethal effects. This represents a major constraint on the ways selection can shape the pattern of mortality over age, and we evolutionary demographers are just starting to come to terms with the ramifications of this. When I have time to write another longish post, I'll explain how this leads to a major question in evolutionary demography that I have been thinking about but don't yet have any plausible answer to.

Constraints

2011-10-10T05:35:00.000-07:00

The field of life-history evolution, into which the stuff I do roughly fits, spends a lot of time thinking about optimality. What is the optimal age to start reproducing? What is the optimal amount of time to spend foraging each day? What is the optimal body size for a creature in a particular niche? The factor being optimized here is fitness, usually measured by the rate at which a sub-population with a particular trait would increase in size. The trait value that leads to the fastest increase is the optimum. Quite often when we calculate an optimum value and then measure the actual values in the population, most individuals are fairly close to the optimum. But fairly often this does not happen, and then we start talking about "optimality with constraints." By this we mean that there are certain conditions that must be met, and the optimum we are looking for is the best value that is consistent with those conditions. The most commonly considered constraint in my field is the constraint of limited resources. If you have only 100 calories a day of energy to expend, you can't expend it all on growth and maintenance and all on reproduction, your reproduction is constrained by the need for maintenance, and vice versa. So we can calculate, given a set of biologically informed assumptions, what the optimal investment in reproduction is at each age. This kind of constraint makes sense to people, and yields many useful insights. That said, it is often the only type of constraint considered in situations where many other constraints potentially come into play.

One type of constraint that is particularly hard to build theory around is that natural selection can only favor those traits that exist. That is, a trait may be drastically suboptimal, but if all individuals in the population have that trait, and the genes which determine it cannot easily be altered by mutation such that they allow a higher fitness solution, the population will continue being far from optimal.

A classic example of this type of suboptimality is known as the 'obstetric dilemma.' This is the problem that humans have narrow pelvises and big heads, and the head has to pass through the pelvis during birth. In a (now somewhat out of date but still sound for our purposes) summary of one hypothesis of how humans diverged from our chimply relatives, Kristen Hawkes (the anthropologist behind the Grandmother Hypothesis) described (in 2003) the central role this obstetric dilemma played in human evolution thusly:

* Drying environments in the late Tertiary constricted African forests, making capacities to use alternative foods more advantageous among ancestral apes.
* Bipedalism was then favored because it freed hands for tool use, which
increased success at hunting big animals, and this put a premium
on larger brains.
* But the mechanics of bipedal locomotion limited pelvic width, so brain expansion created an ‘‘obstetrical dilemma’’ requiring most brain growth to be postnatal.
Consequently, children with developing brains were immature longer and were more dependent, for a longer time, on maternal care.
* The care requirements interfered with maternal hunting, so mothers relied on
provisioning from hunting mates. This help from fathers allowed mothers to produce more surviving offspring.
* Thus, parents formed lasting bonds and nuclear families became the fundamental
units of cooperation in which a sexual division of labor served familial goals of production and reproduction.

Now according to this story, variations of which are still supported by the scientific evidence,much of the distinctness of human life-history comes through:
1. The need for large brains and small pelvises
2. Which explains why our babies are so undeveloped
3. Which explains we take so long to mature
4. Which is an important part in explaining why we end up with our social system.
5. Which explains why we live so long.

So the optimality of a narrow pelvis, the optimality of a large brain and the need for
that brain to pass through that pelvis ends up being a central fact of human evolution. And why, we may ask, is it optimal for the baby's skull to pass through the mother's pelvis? The apparent answer is that if there is only one possible trait, that trait is the best of all possible traits.

The pattern of vertebrates expelling their young through their pelvis dates back to
before vertebrates actually had pelvises.

Note that this fish has its gonads above and in front of its pelvic fin. That is a common trait among fish, including the lobe-finned fish from which all terrestiral vertebrates are descended. The lobe-finned fishes had bony feet with which they could support themselves on the sea floor, and the bones in their pelvic fins would eventually be modified by evolution into the legs and pelvis.

Now the first terrestrial vertebrates were amphibians, and like most frogs and salamanders, laid small soft eggs, so it was probably no problem for them to continue having the gonads in front and running a tube through the pelvis to the cloaca. This system only became problematic when the eggs got large and hard, as they are in reptiles like turtles. Turtle people like to talk about "pelvic consraint" when they discuss why turtles don't make bigger eggs.

The only non-fish vertebrates to escape the need to run the babies through the pelvis are those that no longer have ana full pelvis, like whales and most snakes. To my knowledge nobody has managed to invent an alternative outlet, so everybody, including us, has to find one way or another to get through the pelvis. In fact, the only alternative is a human invention, the cesarian section.

This obstetric dillema is a very obvious contraint of the 'no alternative' type. Whenever I get a chance to write another longish post, I'll give an example of a constraint where the lack of alternatives is less obvious because it is genetic rather than anatomical.

More fun zoo photos

2011-10-08T15:05:00.000-07:00

Rostock Zoo, Oct, 2011

I like zoo photography. Click the caiman to see the slideshow.

Thoughts during a trip to a conference

2011-09-25T08:13:00.000-07:00

The Rostock main train station (Hauptbahnhof, Hbf) is an easy walk from our building, even when bedangled with a laptop bag, poster tube and backpack. I was amused to see that three other passengers getting on my same train also had the black plastic tubes which announce that one is going to or from a conference. None of them looked like ecologists, so I figured it wasn't the same conference. I tried to eavesdrop to figure out what topic two of them were discussing, but it was rapid and in French, and so instead I fell asleep as the train pulled out.

It took 34 minutes from the time we arrived at Hamburg Hbf until I was sitting in my gate at the Hamburg airport waiting for my flight to Manchester. This without any running, pushing or hurrying, and the airport is not particularly near the Hbf. A single S-Bahn trip stops directly under the security check, so up two escalators I got on one of the many very short lines, and didn't have to remove my shoes or belt, nor get molested. I like to complain about the fact that you can't get a flight from Rostock's small airport to anywhere, but if door to gate takes only two and half hours, this is still better than many trips to JFK I've made. It is frankly slightly disorienting for an American for a transit system to work this smoothly.

As I sat in the gate, two English gentlemen sitting just behind me recognized each other and began to make small talk. The one is the occasional patient of the other, and has an appointment to see him in late December. They kept up a lively conversation about not much of anything, without a single pause, for about 45 minutes. I have heard the English talent for small talk described before, but I must say this was really impressive. They moved purposefully from one genial topic to the next, always with a smooth transition. Football, Christmas Markets, vacation destinations, and so forth. I felt like congratulating them.

As the bus took us from our gate to the plane, we passed a taxiing airplane from Air Tunis. It wonder if flights to Tunis are cheep these days? I've heard they have trouble filling their hotels since the revolution.

As we pass up then down through layers of clouds, I notice how closely defined their surfaces are. The top of my window can be mostly in the cloud, and the bottom mostly out. I wonder vaguely what sort of fluid dynamics allow for such a sharp transition to be stable.

I hope I have the right ticket for this train.

An hour and a half into wandering around Sheffield looking for my accommodation, I'm standing on a corner with three young guys with tattoos on their massive biceps as one of them looks up Edgecliffe Crescent on his iPhone. The guy resting in front of the closed Pakistani restaurant next door says go to the roundabout, take a right, and straight to the top.

Breakfast in the cafeteria is much what you would expect from breakfast in an English University's dormitory cafeteria. The orange juice and eggs are from concentrate, but the sausage is fresh squeezed. I sit across from a young woman who has never been to a conference before. I briefly consider teasing her about the fact that she is nervous despite not having to do anything but listen to other people's presentations. She gives me good directions to the conference hall.

"You can't really understand anything in ecology without thinking about soil biodiversity," says the plenary speaker. I guess what I do isn't ecology.

A couple of people come up to question me further after my talk. One of them is a guy I once emailed for advice on keeping rotifers. I can't remember what the question was, but thank him for how quickly he responded.

There is no way I am going to stay awake through the whole poster session. I get slightly lost on my way back to my room and end up in an OxFam thrift store. I get lost again carrying some used books. I spot an expidition of ecologists and follow them home.

Waking up cold I pass by the Greek place and have peas panner with garlic nann. I happily chew the hard chunks of spices in the sauce. "I'm a womanizer!" announces the old, obese, bald and drunk puddle of English gentleman at the corner table with the off duty waiters. "Yes, Sir, you are!" one of them reassures him.

I consider rehearsing my poster spiel for tomorrow, but instead prepare by sleeping more.

We are joined at breakfast by a conference of dentists (there may be a better term of venery for dentists, but I don't know it). They are easily distinguished by their unecologist-like formalwear.

Lost of people ask questions about my poster, and most of them tell me that while interesting, it has nothing to do with anything they will ever work on. This interesting but not directly relevant feeling is largely mutual.

Typical

2011-09-08T02:32:00.001-07:00

In Rostock it is entirely unsurprising that the woman who answers the phone at the Fremdsprachendienst (Foreign Language Services company) proudly speaks nothing but German.

Dan SMASH!

2011-09-06T10:50:00.000-07:00

I've just spent six hours trying to convert a file (a poster I'm presenting at a conference next week) from one standard format to another for printing. After six computers and dozens of programs each of which is supposed to be able to do this conversion instantly, it finally converted, although it looks kind of crappy in its converted format. I've sent it to the printer because I don't care anymore. None of the other things I desperately needed to get done today got done.

I am not generally given to violence, but do currently have the urge to break something.

Irene reaches Europe

2011-09-05T00:05:00.000-07:00

The National Hurricane Center was remarkably accurate in predicting the track Hurricane Irene would follow up the East Coast of the US. Tropical Storm Irene made her way over New England pretty much as they said she would. They stopped updating that forecast when Tropical Depression Irene passed the northern boundary of Maine into Canada, and even the Canadian press largely stopped covering Irene once it passed out into the Labrador Sea. But now Post-Tropical Cyclone Irene, is forecast to bring gale-force winds to Wales over the next few days. Given that this storm started as a tropical wave over Africa, I wonder if she is just trying to find her way back home. Or maybe she wants to go around again? The only forecast I have seen on the future path of the remnants actually calls for her to come this way (towards the Baltic), as a fairly ordinary low-pressure wave and storm later this week.

Writing while sleep deprived

2011-08-27T10:44:00.000-07:00

I am about to submit another big funding application. This one has been a lot more work than the previous applications, as the required research statement, the largest of several sections, is 25 pages. I can't really complain. If I was going to give someone enough money to run a research group for five years, I too would want to know in some detail what they would do with the money. Further, sitting down and trying to put my plans into a single document makes me systematically consider how my various plans fit together, always a useful exercise. My only complaint really is that I should have done much more on this long before my daughter was born. It is hard to care too much about the details of the application while fighting to stay awake and get the baby to sleep.

Busy

2011-08-16T00:33:00.000-07:00

I am working on another big funding application. This one is a lot more work than the previous applications, as the required research statement, the largest of several sections, is 25 pages. I can't really complain. If I was going to give someone enough money to run a research group for five years, I too would want to know in some detail what they would do with the money. Further, sitting down and trying to put my plans into a single document makes me systematically consider how my various plans fit together, always a useful exercise. My only complaint really is that I should have done much more on this much earlier. Trying to finish everything up at the same time that my wife is preparing to deliver a baby and my family is visiting is an less than an optimal solution.

Taxonomically not what you eat

2011-08-04T05:25:00.000-07:00

One should be cautious in naming a taxonomic group for their ecological habits.

I offer you these examples:

1. Most turtles are amphibious; all are reptiles, not amphibians. Turtles have scales, lay hard leathery eggs, have the physiological and genetic makeup of reptiles. I often see phrases such as, "turtles and other Amphibians" in writing about biology by non-scientists. The taxonomic term 'amphibians' is not helpful in getting across to people that turtles are reptiles.

2. Consider the Carnivora. Most Carnivora are carnivores, but some, such as the giant panda, eat largely plants. Further, many carnivorous mammals are not Carnivora in the taxonomic sense. Unnecessarily confusing.

3. Pity the poor Insectivora. It turns out things are worse than just dietary nonconformity (not all the Insectivora ate insects, and not all insectivorous mammals were called Insectivora). The group called Insectivora no longer exists! Biologists had assumed that similarities in diet and morphology among the moles, shrews, tree shrews, golden moles, hedgehogs, moonrats, solenodons, tenrecs, elephant shrews and colugos were the result of common descent (they all had these traits because they were all closely related to each other). It is now clear that Insectivora was an ecological rather than taxonomic grouping. This is because modern molecular genetic and phylogenetic methods make clear that most of these Insectivores are not any more closely related to each other than they are to you, or to an elephant. Specifically, the moles, shrews, solodons, hedgehogs and moonrats form one group, whose closest relatives include the carnivores and hoofed mammals. The tree shrews and culogos (of southeast Asia) are more closely related to the primates. The golden moles, tenrecs and elephant shrews (all African groups) are related to larger mammals found in Africa such as the aardvarks and elephants.

4. The Caprimulgidae (Latin for goat suckers), do not suck goats. They were named for a feeding behavior falsely attributed to them. They are in fact insectivores.

Who's a demographer?

2011-08-03T10:47:00.000-07:00

I tend to find religious fundamentalists, whatever the religion, hard to listen to. One of the habits I find objectionable is the tendency for fundamentalists of a religion to argue that others who practice the same religion differently aren't really practitioners of that religion at all. This tendency has recently been popping up in the news as Christian fundamentalists in the US argue that because Mitt Romney is a Mormon, he isn't really a Christian. I have no fondness for Mitt Romney, and frankly suspect he would claim to be a Pastafarian if he thought it would get him elected. That said, the Mormons declare themselves to be Christians (they do talk about Christ a lot), and I can't see as anyone has the authority to tell them they aren't. It is just hubris to go around telling people that you can describe their religious beliefs better than they can.

This is all a roundabout way of getting to the question of who is a demographer. Ask a demographer what is the largest annual scientific meeting for demographers, and she will probably say The Population Association of America (PAA). I consider myself a demographer as well as a biologist, but I think most PAA members would say the stuff I do isn't demography. This is for the simple reason that I mostly study non-human populations, and the PAA defines demography as the study of human population processes. Studying the same processes in non-humans is, by this definition, not demography. Last year they had a session on evolutionary demography, but all the accepted papers were on humans. This year they don't even have such a session. I think that inserting the word 'human' into the definition of demography is roughly akin to saying that anyone who doesn't follow the teachings of a particular Rabii isn't really Jewish, so I call myself a demographer.

I was recently surprised to find myself in a conversation in which the tables were turned. A colleague was arguing that most PAA members are not really demographers, but sociologists. His argument was that many human-focused hard-core demographers feel out of place at the PAA. After their meetings this spring several colleagues complained that most talks at PAA meetings are really quantitative sociology rather than demography. The distinction is a fine one, but basically classical demography has a core set of questions and methods, and these have certainly been supplanted to a considerable degree by questions coming out of sociology, mostly approached with methods that don't require the quantitative machinery of formal demography. My colleague told me, "All the talks are full of regression tables, and most of the regressions aren't even done well."

So is it fair to say that my colleagues and I, who apply classical demographic methods to non-humans are more demographery than the quantitative sociologists at the PAA? I'm afraid not. We can no more revoke their demographer label than they can revoke ours. However, since the social demographers who control the PAA aren't interested in evolutionary demography, and most of their presentations frankly aren't that interesting to us (there really are a ridiculous number of regression tables, mostly demonstrating the relationship between fertility and female education for yet another population), I'm going to let my membership lapse. I'm thinking I'll join the British Ecological Society instead. They have lots of evolutionary demography at their meetings. I don't even feel the need to call myself an ecologist.

Why there are no whale-like birds.

2011-08-01T05:58:00.000-07:00

For my birthday, my parents sent DVDs of the Life series with David Attenborough, nature films from the BBC. These are wonderfully made, with amazing photography, and you will likely never hear me say that about any other films. One aspect of the photography that is amazing are the underwater shots. This has got me thinking about marine mammals and seabirds, and the differences between them.

There are five independent lineages of extant (extant is the opposite of extinct) marine mammals:
1. The Cetaceans (whales, porpoises and dolphins), relatives of pigs and hippos.
2. The Sirenians (manatees and dugongs), mildly related to elephants and hyraxes.
3/4. The Pinnepeds (walrus, seals and sea lions), descended from a dog-like carnivore.
3/4. The sea otter, an otter, which is an aquatic weasel.
5. The polar bear, bear.

I have ordered these in the degree to which they have become fully aquatic. The Cetaceans neither need to, nor safely can, leave the water. This is true of Sirenians also, but they tend to feed and birth in shallow water near shorelines, where whales wander the open oceans and dive to amazing depths. The Pinnepeds aren't so good on land, but they do haul up to breed and pup. The sea otter is in some ways more fully marine than the Pinnepeds, mating and usually giving birth at sea. But again, otters are more tied to the land than are Pinnepeds the rest of the year, living and feeding in coastal kelp forests and being capable of fast and efficient movement on land. The polar bear is marine in that it swims long distances, hunts at sea, and has structures that specifically help it do these things. But it still prefers to walk rather than swim, brings its food onto solid ground to feed, breeds and pups out of the water and so forth.

There are more independent groups of sea birds, even if you don't consider each transition from freshwater to saltwater. Penguins are perhaps the most fully marine, flying only in water, feeding entirely on seafood, having special mechanisms for dealing with high levels of salt. The Procellariiformes (albatrosses and petrels) are not far behind, spending about as much time at sea (although over rather than in) as penguins do. The Phaethontiformes (tropicbirds) spend most of their lives at sea, as do many of the Pelicaniformes (pelicans, frigatebirds, boobies, gannets, cormorants and shags). While many gulls live far from the sea, many Charadriiformes (gulls, terns, skuas, plovers, puffins, auks etc.) are extremely marine. Many Anseriformes (ducks, swans and geese), particularly the Merginae (sea ducks) are, well, sea ducks. It was recently discovered that gyrfalcons spend long periods hunting on and around sea-ice, although they probably don't actually swim. I'm sure I've forgotten other examples.

Why so many birds moving out to sea, but so few mammals?

The obvious first hypothesis is that the ability to fly is very useful at sea, while the ability to walk/run/hop etc. is not. The falcons are a pretty terrestrial group, but with few changes beyond the behavioral, gyrfalcons can spend extended periods at sea. Ospreys and eagles, relatives of falcons, use talons that evolved grabbing terrestrial prey to scoop fish. Even hummingbirds and warblers that can't forage or land at sea regularly spend long periods migrating over open ocean. Birds may have an easier entree than do mammals.

Given this, it may be surprising that the most fully marine descendent of terrestrial vertebrates are not birds. All birds lay eggs, and none have figured out how to make that work at sea, so all need to maintain the ability to be land animals. Almost all mammals give live birth, and three groups (Cetaceans, Sirineans and sea otters) can do that without ever leaving the water. The birds may have an easier time getting started down evolutionary paths that lead to a marine life, but they seem to have an inescapable constraint that keeps them from finishing that path: shelled eggs.

The marine reptiles show an interesting parallel to this. Marine iguanas, saltwater crocs and sea turtles all lay eggs, and all do so on land. Sea snakes, excepting one genus, birth live young, and do so at sea. That one genus lays eggs on land.

If some snakes have evolved the ability to have their eggs hatch internally and their hatchlings ready to swim the moment they emerge from the mother, why can't some bird do the same? Imagine how much better off an emperor penguin would be if instead of spending the Antarctic winter fasting in the cold, it could spend that time feasting in the ocean with it's chick developing internally.

Any answer I could offer would be pure speculation. One class of question that evolutionary biology is very bad at answering is "why didn't X evolve." Why hasn't any bird evolved live birth? Maybe it is something about their egg shells. Maybe they are in a habitat where that just doesn't work. Probably it just never happened.

37 weeks

2011-07-22T06:59:00.000-07:00

It is an obvious yet remarkable fact that a fetus, near the end of pregnancy, could as easily be a newborn baby. Whether through natural birth or c-section, removing the full term fetus from the mother is all that is necessary to transform it into a baby. One remarkable thing about this is that a baby is an air-breathing animal much like any other, and a fetus does all its gas exchange through a tube attached to its circulatory system through its belly button. I can’t easily imagine keeping a tortoise alive by sticking a tube into its belly, nor do I imagine one would have much luck doing so with an adult human, or even a child. But somehow it works for the fetus.

Another thing that is striking about the fetus being a nearly complete baby is that it is a nearly complete baby entirely inside the belly of the mother, upside-down, often with its head inside her pelvis. I don’t know about you, but I could not function for very long with a nearly full sized baby inside me and a skull in the middle of my pelvis. I think I wouldn’t last five minutes, but apparently this situation can go for weeks with little danger, and bearable discomfort, to possessor of either pelvis or skull.

A tremendous amount is now known about ontogenesis, the process by which a single egg grows and develops into a whole person. We have studied it on the scale of molecules, cells, tissues, organs and whole individuals and from the perspectives of physiology, genetics and evolution. There are still vast areas we know almost nothing about, but we can largely reject the hypothesis that there is magic involved. Never the less, things can feel like magic even when reason rejects it. This whole process, of self-directed growth of a single cell into a person, makes it easy to understand why spirits, gods and humunculi are so often invoked.

Hyphum

2011-07-01T12:27:00.000-07:00

I know a bit about a lot of organisms, but don't really qualify as an expert on any species. It is great fun planning experiments with people who know a lot about a particular organism. I can say, "if a hypha that is only 300 microns breaks in half, do you get two living 150 micron individuals, or two dead hyphae?" and get the immediate response, "The singular of hyphae is hyphum," followed by, "you would get two dead halves, so we don't have to worry about it." This way I can concentrate on designing the experiment and learn good Scrabble words.

33 weeks LMP

2011-06-24T10:35:00.000-07:00

There is a certain irony to being to a researcher who studies mortality risk early in life, and also a soon-to-be father. Sometimes I feel I know way too much about certain topics.

Decreasing population, increasing density

2011-06-23T04:33:00.000-07:00

The Institute where I work is built on land that used to be part of huge East German ship building facility. The facility folded shortly after the German Democratic Republic did. The buildings were, for the most part, left derelict. One of the former factory buildings has been converted into an indoor shopping center. Each store is its own single story box built into the bottom of the cavernous factory building, with walkways and cranes still hanging overhead. Most of the other buildings have been torn down, and ~15 waterfront apartment buildings have been built (or are being built) on the land, most just within the two years I have been here. Apartments in these new buildings are on the expensive side for Rostock, but are filling up fast. One or two huge windowless cement monstrosities (one holds a dance club called The Bunker) remain, as well as a couple of older brick warehouses that have been refurbished. One is being used as a temporary home for the Rostock Volkstheater (community theater) while their main hall is closed for fire-code violations. It feels as though a new, fairly fancy, neighborhood is simply sprouting from the root-system of the old shipyards, among the remaining shells, foundations and train tracks to nowhere.

The demand for housing that fuels all this building is a story of migration. Rostock is Mecklenberg-Vorpomern, the least densely populated state in Germany, and a state that has steadily lost population since reunification. Many of the outylying villages are dominated by abandoned buildings. Apartment complexes on the outer edges of Rostock, plunked down in the middle of fields by the communist planners, now offer multiple months of free rent to anyone who will move in and still are emptying out. Rostock is full of college students, who don’t want to be on the outskirts in half empty buildings, and an aging population of long-term residents, who don’t either. The more abandoned the outskirts get, the strong the incentive to move toward the city center. So the center of Rostock is becoming denser even as the state loses population.

A name but no face

2011-06-20T11:27:00.000-07:00

The first time I saw one? I was out in the rowboat, only a couple of hundred feet from our dock, and had, for whatever reason, dropped an oar over the side. I was probably 11, so there is a good chance I had dropped it on purpose, so as to be able to retrieve it. As I was reaching for the oar, I noticed a little white circle, mostly translucent, maybe the size of a dime, floating just under the oar. My hand retracted as the word 'jellyfish' formed in my brain. But I had swum in this lake many hundreds of times and never been stung, or heard that anyone else had. It wafted back and forth in the wavelets I created as I wiggled down in the boat to get a closer look. I held still and eventually so did it. Definitely a jellyfish, or something very similar to one. I watched it until it sank down into the dark silky water and out of view. I imagined it going back down to its secret world and hidden life. I imagined following it and learning.

The oar by this time was far enough away that I had to jump in and get it. I did this with some reluctance, having been stung too many times before, by jellyfish at summer camp on the Chesapeake Bay, and the previous winter in Florida by a Portuguese Man-o-War. Like every swim in the lake before and since, no stings.

My mother afterwards told me that there were freshwater jellyfish in the lake, but only occasionally, and not as many as my grandfather described from when he was a boy. I’ve seen them occasionally since, usually only on really hot days, one or two at a time. I only recently learned their name, Craspedacusta sowerbyi, when they were suggested to me as a possible study organism. Looking them up, finding that they had been studied down to the molecular, I realized I already knew this organism, but only as scattered phantasms floating by on summer days.

name for a principle?

2011-06-05T02:56:00.000-07:00

There is a principle that I want to refer to in an upcoming talk, but I can't find a name for it. Someone must have named it after themselves by now. It is related to Ockham's razor, and to parsimony, but is distinct.

The principle is that an explanation for a pattern should preferably be applicable as broadly as the pattern is observed, but not more broadly. For example, an evolutionary explanation for group living that can be applied to all the group-living insects is preferable to an explanation that works only for one species of ant. The explanation should preferably not explain the pattern more broadly than it occurs. For example, an explanation for the fusion reaction of the sun merely in terms of the presence of hydrogen would also tend to predict fusion in many other contexts where it does not generally occur, making this explanation less desirable than a more complex one which also specifies the need for the physical conditions which encourage the hydrogen to fuse.

This is the sort of logical statement that is so obvious as to rarely need to be said, yet I need to say it for this talk. If you know what I should call it, please let me know.

Reproduction

2011-05-30T13:42:00.001-07:00

The ladybugs are successfully reproducing on our mint plant. Oh frabjous day! The larvae are crawling all over the plant scarfing down aphids like mad, and the adults are laying more eggs. It is exciting to see them doing so well.

Two offers out

2011-05-20T05:36:00.000-07:00

We have now interviewed two post-doc applicants. Both are extremely well qualified for their respective prospective positions. Both seem very easy to get along with, and both have been offered the positions. Neither, unfortunately, has yet accepted. The first because she is scheduled for a competing interview today, the other because she needs to make sure her partner can also get a job in Rostock. If we hire both of them, I will have a wonderful research team. With either one we could make real progress.

We still have one more candidate coming, next week, and if my bosses like him we could offer a position to him also. If we end up successfully hiring all three, I will be very happy.

Bedside ecosystem

2011-05-19T23:09:00.000-07:00

Most mornings I spritz the chocolate peppermint plant on our bedroom windowsill from a spray bottle of water. It loves to be damp. It is growing so well these days, is so juicy and luscious, that the aphids are maintaining a healthy population on it despite my best efforts to squish them and the depredations of the ladybugs. This of course leads the ladybugs to congregate on the mint, as the aphids, thrips and whiteflies have been picked clean off our other plants. And you know what happens when beetles congregate in the spring. This morning as I was spraying, I noticed one of the ladybugs laying eggs on the window frame!

There are about 30 eggs so far and she is still laying. The great thing about this is that labybug larvae are wonderful aphid predators, and don't fly away the way the adults do. So I'm going to transfer the eggs onto a leaf and hope they hatch.

Walking desk

2011-05-17T06:53:00.000-07:00

I'm one of those people who have trouble sitting still and working for any great period of time. I frequently find excuses to get up and walk to the other side of the building to talk to someone or check on something. I've occasionally seen articles like this one on NPR touting the health and productivity benefits of treadmill desks.

When I was in grad school I read such an article, then saw a treadmill for sale in a thrift store near campus. I stopped by the office of the acting director of the museum where my office was and asked if I could install myself a treadmill desk. She looked confused and busy but said yes. The next day maybe half an hour after I had moved the mill in, as I was just figuring out how to build a desk over it, she apologetically called me to her office and asked me to remove it from the museum. My wife kindly let me keep the machine in our tiny tiny Berkeley studio apartment until we sold it to a friend.

Now that I have a real job and we have a decent sized apartment, we are reorganizing that apartment to fit a baby and all the stuff that goes with modern babyhood. And it just so happens that I have both another used treadmill and a broken desk. Below are pictures of the result. It is not the world's prettiest construction (built while recovering from a tooth extraction using only materials I had in the room and without taking any measurements) but now I can walk and type at the same time. It will take a little bit of getting used to typing while rocking from foot to foot, but I think I am going to like this, and maybe it will help me remember to use the treadmill.

Here is my wife's shot of me typing this post:

And here's a view from the treadmill. We are in the tallest building in the state, so I have a nice view of Rostock from my desk.

List of materials:
Treadmill from thrift store
Broken desk
Various screws and bolts I had around the house
An old curtain rod

Total cost €90 spent last year

Spring is the season of interviews

2011-05-12T06:02:00.000-07:00

Spring has sprung and is sprinting toward summer here in Rostock. The horse-chestnut trees that line many of the parks and roads are covered in big spikes of flowers. There are fledglings all over the place, running around on the ground until their wings are developed enough to let them fly. (Many of them don’t make it and the curious eye will spot the occasional bit of carnage under a bush). In the shallow western end of the old city moat, newts are breeding among the sunken leaves and floating catkins. From one day to the next, the skies above the city have filled with squadrons of swifts, whistling incessantly as they outmaneuver any insect that dares take flight.

The days are rapidly getting longer. The sun might officially go down at 9:02 today, but the twilight stretches to well after 10 as the sun skims just below the northwestern horizon. Early this morning there was light streaming in our north-facing kitchen window.

The spring here brings more than just a physical thaw. Come to Rostock in the winter and you will think the population generally has forgotten how to smile. You will see few people on the streets, and often the only parts of them that are visible are scowling. Now the streets are full of summer dresses and shorts, and their occupants are reveling in sunshine.

This, frankly, is the perfect time to be bringing post-doc candidates to Rostock. Flowers, birds, smiling faces, warm breezes, so much sun. These interviews are as much about convincing people they want to come here as they are deciding which people we want to hire. Having the place at its best certainly helps in that regard. We won’t do any interviewing in February.

My very first robot

2011-04-14T06:40:00.000-07:00

We've just gotten a Roomba. For those of you who don't know, this is one of those vacuum-cleaner robots. It has some obvious advantages (and disadvantages) as compared to just using a normal vacuum. First, I can turn it on and then go back to my sickbed while it cleans the floors. Push a button on the top and it vacuums the whole room. It is low enough to get under and behind the couches and beds, picking up huge amounts of dust and hair in the process. It is fun to watch when one has a fever.
On the downside, the thing is an idiot. In theory it has various "robot behaviors" that help it to efficiently clean the whole room, but in practice it seems to pretty much bounce around the room at random, occasionally following a wall successfully. I should specify that the version we have (440) is probably not as good at navigating as the latest versions (610). It does eventually find its way to most corners of the room, although it took about 45 minutes of bouncing around to have covered our living room fairly well, even after I put up the chairs, trash-can, etc. It doesn't see, and doesn't seem to make a map of where it has and hasn't gone, so it will repeatedly miss clumps of dust sitting in the middle of the floor. Some of these it never got. It has a very small dirt compartment, so after one room it was completely full, although I admit most of that dirt came from under couches where I don't usually get.
On a single charge it did our living room, hallway, office and most of our bedroom, although it needed to be emptied after each room. I left it doing the bedroom while I took a shower. Half way through the shower it started making a rather pathetic beeping. It was under the middle of the bed and had picked up so much lint and hair that its brushes and wheels could not longer turn. I pulled it out with a broom and had to take the thing half apart to clean all the hair wrapped around everything. Oh the plus side, it hasn't looked so clean under our bed in months I suppose with regular Roomba-ing the dust won't accumulate to the point that it becomes a navigational hazard.

With time these things and their competitors will become more advanced and less clueless. In movies and books we always go straight to humanoid sentient robots, without the intermediate step of a self-propelled vacuum cleaner taking two minutes to find its way out from under the desk. This is like the Precambrian ancestor of R2D2.

Dunno

2011-04-12T09:11:00.000-07:00

I have called a lot of references for post-doctoral candidates over the last weeks. I always go into it wanting the reference to tell me how wonderful the candidate is. You would think the alternative would be for the reference to reluctantly express some concerns about the candidate’s appropriateness for the position, or something such. But I’ve now a few times had the experience of a third answer I didn’t really expect.

This answer is effectively, “Not qualified to answer.” The reference can’t really answer my questions, either because he didn’t work so closely with the applicant, or because she worked with him several years ago, before a great deal of professional development.

I can sympathize with the situation these references are in. Imagine that a student you like but don’t know extremely well asks you to be a reference for a job application. It can be hard to say, “Well, I don’t know you so well, isn’t there anyone else you can ask?” So you agree and then kind of hope not to wind up on the phone with some guy in Germany asking for insight into the applicant. Then I call. Doh!

Despair not!

2011-04-07T01:46:00.000-07:00

My prediction for hiring success has improved significantly over the past few days, for reasons both rational and irrational.

Rationally, I’ve started to receive more good applications, if not fewer spamly ones. I suspect that this is because the people who are preparing position-specific applications are taking their time to do it, as our deadline is not until April 30th. Also, it being spring, many graduate students are just finishing their thesis defenses and looking for positions.

Irrationally, I have been speaking to people’s references, and the references are of course enthusiastic about the applicants. I knew this was going to be so. I am well aware that the applicants wouldn’t have listed these references if they were going to say terrible things about them, and that the references feel a sense of obligation to say good things, but hearing great things about an applicant from a basically rational and honest colleague inevitably improves my view somewhat. It makes the applicant seem more like a person, and less like a CV. I don’t have any basic predilection to like CVs, but I like most people.

Skipping that hard middle part

2011-03-31T08:59:00.000-07:00

The part of science I like best is the coming up with questions part. The part where I ask something someone else has never asked before (or at least I don't yet know that they did) and brainstorm together a plan about how the question could be answered. But my second favorite part is writing rough drafts. I like the rough drafts in particular because I can let the ideas flow, without getting hung up on making sure I have exactly the right reference or my font is just the one the journal prefers. In other words, it is writing without the impeding mechanical details.

I can do lab work, I can program a simulation, I can edit bibliography formats in citation management software, and all those other jobs that require extensive attention to details beyond the scientific concepts. But by preference I'm really a concept guy. If I had collaborators who wanted to do every part of the process between the planning and writing the rough draft, I'd be thrilled.

This is why I'm writing a Forum piece, to submit to a journal that responded positively to my pre-submission inquiry. (A positive response means they are willing to look at it, not that they promise to publish it.) Their Forum section is designed for short papers of about a 1000 words, in which the author makes a relatively simple point or poses a question without a lot of new data. I've finished a rough draft of 1100 words in the last two days. Now comes the less fun part of editing it for clarity, making sure all the papers I cite actually say what I claim they say, getting feedback from colleagues and editing it again. A more adulterated and repetitive form of creativity. Still, I think I would be inclined to write more papers in this format, as it makes a nice compact project.

Fun with Photoshop: Hoofstock

2011-03-29T14:32:00.000-07:00

The pun is my wife's, the Photoshopping my own:

This, for the record, took 36 minutes, starting with a giraffe clipart.

What to do?

2011-03-27T13:12:00.000-07:00

I have an ethical situation here. I've received a fraudulent post-doctoral application. This applicant has, on his CV, listed quite a few publications in peer reviewed journals. Some of them are real. Others simply don't exist. There are no papers by this author in the listed journals. There are no publications with the listed titles in any journal. One of the imaginary papers is supposed to be in Nature, but the listed volume number doesn't even correspond to the listed year, and so on. I am very confident that the CV is fraudulent.

The question then is what, if anything, should I do about this? I don't really want to waste a lot of my time, but this is fairly serious misconduct. I could write to him and request copies of the papers, or an explanation of Figure 2 in the Nature paper. I could tell his boss on him, assuming he actually works where he says he does. I could simply reject the application. I'm not certain what, if anything, is the standard response to this situation. There are confidentiality rules that apply to job applications, even fraudulent ones, so public humiliation is out of the question.

Etymological challange: Evolutionary Demography

2011-03-27T12:47:00.000-07:00

I have a bit of a stomach bug this weekend, so I am thinking about things that don't require so much concentration. A colleague had raised the question of when the term "evolutionary demography" was first used in print, and said that the oldest example he could find was:

Caswell, H. 1985. The evolutionary demography of clonal reproduction. pp. 187-224. In: J. B. C. Jackson, L. W. Buss and R. E. Cook (eds.) Population Biology and Evolution of Clonal Organisms. Yale Univ. Press.

I, currently having more time than brain power, did a little bit of searching, and found this:

Wilbur, H.M. 1975. The Evolutionary and Mathematical Demography of the Turtle Chrysemys picta. Ecology, Vol. 56, No. 1 (Winter), pp. 64-77.

which uses the phrase "evolutionary demography," explicitly in the acknowledgements and implicitly in the title.

Can anyone find an older explicit recorded use of the phrase? If so, the commenter presenting the oldest confirmable example will win a prize: I will personally make a sculpture representing a species of your choosing (excepting diatoms) and send it to you in recognition of your etymological achievement. Comments will be accepted for one month from today, or until I get the first winning example, whichever comes last.

lebenslauf

2011-03-25T04:50:00.000-07:00

I'm a bit uncomfortable with some of these German CVs. The lebenslauf (life run) is the rough equivlent to a curriculum vitae, but it is a lot more personal. Many of the lebenslaufen I have seen contain not only educational and employment infomation, skills and other things relevant to qualifications, but also things that from my frame of reference simply don't belong. What legitmate reason would a potential employer have for wanting to know the applicant's religion, the name and employment of her parents and siblings, what primary school she went to and her photograph?

Will the culture shock ne'er end?

What is EvoDemo?

2011-03-22T08:38:00.000-07:00

The question has arisen how we should define Evolutionary Demography, such that we can decide if someone's work qualifies. I have offered 2 short definitions, into which I haven't yet put a lot of thought.

Short definition 1 : Scientific study which combines evolutionary biology and demography.

Short definition 2: The study of the evolutionary history, function, variation and relevance of demographic traits.

These are both broadly phrased. I don't like constraining definitions to the traditional terrain. A zebra found outside Africa is, in my opinion, still a zebra. As such, I haven't included anything about what traits, methods, etc. evolutionary demographers usually consider.

My question to you, dear readers, is: Can you think of anything that should be considered evolutionary demography that doesn't qualify under these definitions, or anything that shouldn't qualify that these definitions let in?

Propositioning journals

2011-03-22T07:23:00.000-07:00

I’m a great fan of the pre-submission inquiry. The way this usually works is I write an email to the editor of a journal saying, “Here’s this great idea for a paper, and I’d like to know whether I should write this up for your fine journal.” Usually within a few days the editor writes back and says yes or no. Some journals require this, but I’ve started doing it even for some that don’t. It is useful for everyone involved. The editor gets to spend a couple of minutes reviewing my email and telling me that my paper doesn’t fit that journal, or inviting me to submit, rather than dealing with a full submission. I get to not waste time preparing a submission to a journal that is entirely uninterested in my topic, or I get the encouragement to submit to a journal that I have been told is likely to be receptive. Writing the email also forces me to think about what I want to say, and at what length, which aids my thought process. Finally, while rewriting and reformatting a paper to send to another journal takes some days, redoing the pre-submission inquiry takes only minutes. This is very useful for an interdisciplinary researcher like me who often has to hunt around for an appropriate journal for each paper.

The demographics of evolutionary demographers

2011-03-21T09:40:00.000-07:00

A group of us considering organizing a new scientific society have been compiling a list of those we would like to invite to the initial meeting of the society, to be held here in Rostock, probably next year. We are up to 125 people (excluding people who work here, as everyone who works here will be invited). The group making this list is about half male, half female. The list is 100 males and 25 females.

Why this skew? We each listed people whose names came to mind, and in some of the subfields we are drawing from (e.g., mathematical ecology) almost all of the well known people are male. Higher level academics in general still skew strongly male, and the higher the level the stronger the skew, in most cases. This is both a cohort effect (older cohorts of scientists are both more well known and more male) and a selection effect (males find it easier to advance up the ladder). Being demographers, we are very much aware of this, and are very much interested in having a diverse society, but it is not clear what we can do about it. There is also a preponderance of Europeans, North Americans and East Asians; again this is unintentional and difficult to reasonably address.

Despite these skews, it is a wonderful list of researchers, and I hope we can get most of them to attend.

High r strategy in a high k regime

2011-03-21T06:14:00.000-07:00

I have thus far received 39 post-doctoral applications. Of these 29 were immediately rejectable on the criteria that the application did not include the documents requested. Most of the 29 I couldn’t even tell which position the applicant was applying for, or that they had read the ad. About half of these also contain a similar mix of muddled excessive politeness and jumbled frilly clauses, as though they are cut and pasted at random from the same absurdist form letter. I have no doubt that these are smart, competent people, and perhaps this broadcast spawning strategy of application works in some fields or some countries, but my experience suggests no circumstance under which it would be effective.

Whenever I am hiring, or reviewing applications, I ask myself if I am expressing any unintended biases. I was warned by a friend to expect a large number of irrelevant applications out of India and China (where indeed most of the applications have come from) and so now I force myself to consider in detail whether each of these applications may be more relevant than it at first appears. So far if there is any doubt I have refrained from putting them in my reject folder, meaning that the 10 applications I haven’t yet rejected outright contain a few that I probably should. They also contain a few well worth consideration.

We listed April 30th as the application deadline, so I hope most of the people particularly interested in our positions here are simply taking their time to prepare a high quality application.

keen but generic interest

2011-03-15T08:05:00.000-07:00

The cover letters of the post-doc applications I have received have included statements along the lines of, "I have been following the exciting publications from your lab with great interest." Which is generally hard to believe, as I don't yet have a lab. I have recently receiveced one that makes a statement like this, which begins, "Dear Dr. ," with a space left for the insertion of a name. I can't help but suspect...

Note to those applying for jobs: it is more efective to have and demonstrate interest than to claim it.

Computer bugs

2011-03-14T00:56:00.000-07:00

We now have enough ladybugs in our window plants that the aphids and white-flies won't last long. However keeping the predators concentrated in the little ecosystem for that long requires some doing. We find these little red happy pills wandering all over the apartment, and occasionally find them congregating in some warm dark niche. They like to be in groups, as their defensive chemicals and colors work better that way. This morning I found them assembling a conclave on and in the wireless router. Warm. Dark. Dry. Connected. Perhaps it is time to supply some hidey-holes in the planters under the plants.

P.S. Yes, I know that they are actually beetles, not bugs, but who has ever heard of computer beetles?

March of the Beetles

2011-03-11T04:25:00.000-08:00

I like to have edible plants in the house. We have mint, basil and a Thai chili plant at the moment. We had oregano, but it didn't make it through the long sunless months. One of the drawbacks to having edible plants year round is that it means we also have aphids year round. All winter long I have been keeping them in check by spending a few minutes each morning squishing them or wiping them off the plants, but it is impossible to eradicate them this way.

So you can imagine my excitement and disappointment when on my way to work this morning I saw that wonderful eater of aphids, a ladybug, squished on the sidewalk. This is practically the first outdoor insect I have seen this spring, and just the one I wanted to catch and put on my plants, but it had been stepped upon.

Knowing that the ladybugs were waking from hibernation, I kept an eye out for them on the rest of my walk, and at lunch time. I collected a dozen, and am prepared to offer advice on the finding of ladybugs on cold spring days. Look for them climbing out of dense vegetation (evergreen shrubs, tall dead grass) upon which the sun is shining in places sheltered from the cold wind. If you see one, look closely for more nearby, as they tend to overwinter in groups. Ladybugs are poisonous to most things that might want to eat them, and will come out of cover into the sun even when they are too cold and slow to fly or escape, and are therefore easy to catch. Generally a slightly moist finger touched to the wing covers will adhere enough to lift the beetle into a jar without risk of squishing them. Once you have handled them they will arouse quickly, and attempt to climb to the top of whatever container you have but them in. Apply them liberally to plants infested with aphids, whiteflies or other pests, and expect to find them crawling around your apartment.

Acronymic Challenge

2011-03-08T12:20:00.000-08:00

As a grad student, I operated independently enough, and had a large enough group of undergraduate assistants, that I decided to pretend I had my own institute. I named it the Dissertational Institute for Evolutionary Demography, and believe me, I worked for that acronym.

Some colleagues and I are now discussing starting an actual scientific society for evolutionary demography, and it needs a good acronym. I suggested Society for Ecological and Evolutionary Demography (SEED) but was shot down on the grounds that I had added Ecology to the society just for the acronym. So I'm still thinking here, and wonder if you have any good ideas.

It has to have the words "Evolutionary Demography" in it and some word that means society or association. It can have the word "International" if the I helps. Keep in mind that this is going to be an actual scientific society, so nothing ridiculous, scatological or overtly jocular will do.

Now, I should clarify I'm not actually in charge here, so I don't necessarily get to pick the name, but if you propose something sufficiently clever, appropriate and memorable, I'll propose it, and you may have the honor of naming a scientific society.

Excited to teach again

2011-03-03T14:33:00.000-08:00

Summer Semester 2011

IMPRSD 189
Introduction to Evolutionary Demography

Start:	4 July 2011
End:	9 July 2011
Location:	Max Planck Institute for Demographic Research (MPIDR), Rostock, Germany

Instructors:

Daniel Levitis, MPIDR
Hal Caswell, Woods Hole Oceanographic Institution
David Thomson, University of Hong Kong
Annette Baudisch, MPIDR
Alexander Scheuerlein, MPIDR
Oskar Burger, MPIDR
Maren Rebke, MPIDR

Course description:

Understanding survival, reproduction and other life-history events is central to the study of both demography and evolutionary biology, and each field has developed methods and concepts to observe patterns and elucidate principles. The growing field of evolutionary demography treats demographic variables (patterns of survival, reproduction, and development) as properties of organisms that reflect evolutionary processes, just as morphology, behavior, and physiology do. It draws on both disciplines to search for evolutionary explanations of demographic patterns in terms of adaptation, genetics, phylogeny, and the environment. Further, it applies demographic methods and reasoning to answering evolutionary questions. Demography and evolutionary biology are conceptually unified and inextricably linked, so the questions we want to answer can best be tackled by traversing traditional disciplinary boundaries. This course is intended to introduce early career researchers from both fields to the concepts, methods, challenges and questions of evolutionary demography.

Course structure:

We will begin with an introduction to classical evolutionary demography and the motivations for combing evolution and demography, incorporating enough basic evolutionary theory and demographic theory to get everyone on the same page. We will then focus on current topics in evolutionary demography, including:

Aging across the Tree of Life: Measures and Patterns
Sex-specific differences in mortality patterns: Evolution in action
Modes of adaptive explanation of demographic patterns: a survey
The pace and shape of aging
The evolution of mortality of the young
Age specific reproduction in the wild
Life-history allometry and Charnovian invariants

Finally, pairs of students will be asked to spend the afternoons of the 7th and 8th preparing short presentations, to be presented on July 9th. Each pair will discuss the evolutionary basis of a different demographic trait or phenomenon, what is known about it and how it can be investigated.

Organization:

For July 4-8, each morning will consist of two lectures (one hour each) and each afternoon will have a one hour lab. Then the afternoon of July 9th will be occupied with short presentations by pairs of students.

Prerequisites:

Students should be familiar either with the basics of demographic life-table methods, or with evolutionary theory. Familiarity with Stata or R software will be very helpful.

Examination:

Students will be evaluated on participation in class and on short presentations.

Financial support:

There is no tuition fee for this course. Students are expected to pay their own transportation and living costs. However, a limited number of scholarships are available on a competitive basis for outstanding candidates.

Recruitment of students:

Applicants should either be enrolled in a PhD program or have received their PhD.
A maximum of 16 students will be admitted.
The selection will be made by the MPIDR based on the applicants’ scientific qualifications.

How to apply:

Applications should be sent by email to the MPIDR. Please begin your email message with a statement saying that you apply for course IMPRSD 189 - Introduction to Evolutionary Demography.

You also need to include the following three documents, either in the text of the email or as attached documents. (1) A two-page curriculum vitae, including a list of your scholarly publications. (2) A one-page letter from your supervisor at your home institution supporting your application. (3) A one-page statement of your research and how it relates to course IMPRSD 189. Please indicate whether you would like to be considered for financial support.
Send your email to Heiner Maier (office@imprs-demogr.mpg.de).
Application deadline is 31 March 2011.
Applicants will be informed whether they will be admitted by 15 April 2011.

Readings:

The course will make use of readings from:

Baudisch, A. 2011. The pace and shape of ageing. Methods in Ecology and Evolution. DOI: 10.1111/j.2041-210X.2010.00087.x
Caswell, H. 2001. Chapter 11, Matrix population models. Sinauer.
Jones, O. R., Gaillard, J. M., Tuljapurkar, S., Alho, J. S., Armitage, K. B., Becker, P. H., Bize, P., Brommer, J., Charmantier, A. & Charpentier, M. 2008 Senescence rates are determined by ranking on the fast-slow life history continuum. Ecology Letters 11, 664-673.
Levitis, D. A. 2011 Before senescence: the evolutionary demography of ontogenesis. Proceedings of the Royal Society B: Biological Sciences 278, 801-809.
Metcalf, C. J. E. & Pavard, S. 2007 Why evolutionary biologists should be demographers. Trends in Ecology & Evolution 22, 205-212.
Rebke, M., Coulson, T., Becker, P. H. & Vaupel, J. W. 2010 Reproductive improvement and senescence in a long-lived bird. Proceedings of the National Academy of Sciences 107, 7841-7846.
Vaupel, J. W., Baudisch, A., Dolling, M., Roach, D. A. & Gampe, J. 2004 The case for negative senescence. Theoretical Population Biology 65, 339-351.

Additional reading material will be provided at the beginning of the course.

A reviewer's lot is not an'appy one

2011-03-03T05:32:00.000-08:00

Suppose you are a scientist, and suppose you get an email asking you to peer-review a paper. This email contains the abstract of the paper, so that you can assess whether you are qualified to review the paper. Reading the abstract, you find that you are qualified, as the topic is one you know well. You also notice that you are deeply skeptical of the argument being made, and that you are very likely to recommend that the article not be published. What is your professional duty? Should you try to read the article with an open mind, despite your misgivings, or should you simply decline to review it out of fear of being biased?

In this situation, I did the former, reasoning that if we only review article we are sympathetic to, many terrible articles will be published simply because skeptical reviewers eliminated themselves, and some good articles with unpopular claims will be rejected for lack of qualified reviewers. I read the article, found it irreparably flawed in several major respects, and suggested that the journal reject it. I looked hard for nice things to say about it and didn't find much. While I'm confident my review was accurate, I'm glad these things are anonymous.

Finally out

2011-03-03T01:12:00.000-08:00

This is the first of my dissertation chapters to be published. It is good to have it out. It is in a new Journal called Methods in Ecology and Evolution. It seems like it will be a very good journal, but it is too soon to know for sure.

A measure for describing and comparing postreproductive life span as a population trait

Summary:
While classical life-history theory does not predict postreproductive life span (PRLS), it has been detected in a great number of taxa, leading to the view that it is a broadly conserved trait and attempts to reconcile theory with these observations. We suggest an alternative: the apparently wide distribution of significant PRLS is an artefact of insufficient methods.
2. PRLS is traditionally measured in units of time between each individual’s last parturition and death, after excluding those individuals for whom this interval is short. A mean of this measure is then calculated as a population value. We show this traditional population measure (which we denote PrT) to be inconsistently calculated, inherently biased, strongly correlated with overall longevity, uninformative on the importance of PRLS in a population’s life history, unable to use the most commonly available form of relevant data and without a realistic null hypothesis. Using data altered to ensure that the null hypothesis is true, we find a false-positive rate of 0·47 for PrT.
3. We propose an alternative population measure, using life-table methods. Postreproductive representation (PrR) is the proportion of adult years lived which are postreproductive. We briefly derive PrR and discuss its properties. We employ a demographic simulation, based on the null hypothesis of simultaneous and proportional decline in survivorship and fecundity, to produce a null distribution for PrR based on the age-specific rates of a population.
4. In an example analysis, using data on 84 populations of human and nonhuman primates, we demonstrate the ability of PrR to represent the effects of artificial protection from mortality and of humanness on PRLS. PrR is found to be higher for all human populations under a wide range of conditions than for any nonhuman primate in our sample. A strong effect of artificial protection is found, but humans under the most adverse conditions still achieve PrR of >0·3.
5. PrT should not be used as a population measure and should be used as an individual measure only with great caution. The use of PrR as an intuitive, statistically valid and intercomparable population life-history measure is encouraged.

One of my goals in this paper was to show how badly some evolutionary questions need demographic methods. I think we accomplished that.

Places where I may post postdoc ads

2011-03-02T04:47:00.001-08:00

As a public service, here is the list I have assembled so far of places where post-doc ads may be placed (given of course the particular types of specialists I am looking for):

http://www.evolutionsociety.org/jobs.asp
http://www.sdbonline.org/archive/SDBNews/JobsIndexPostdoc.html
http://www.newscientistjobs.com/jobs/browse/biology.htm
http://www.sicb.org/jobs.php3
http://www.benthos.org/Classified-Ads/Jobs-offered.aspx
http://www.eseb2011.de/sponsoring.htm
http://www.evolution2011.ou.edu/sponsor_exhibition.html
http://www.thesciencejobs.com/category/fellowships
https://careers.chronicle.com/webbase/index.jsp
http://www.smb.org/jobs/index.shtml
http://www.math-jobs.com/?nav=employers&nav_sub=post_a_job
http://botany.org/newsite/employment/index.asp
http://www.postdocjobs.com/jobs/jobs2.php?subcatid=37&catid=2
http://evol.mcmaster.ca/cgi-bin/my_wrap/brian/evoldir/PostDocs/
https://listserv.umd.edu/archives/ecolog-l.html

Advertising

2011-03-02T04:26:00.000-08:00

While I am sure there are Americans who consume fewer advertisements than I do, I'm sure there aren't too many. I don't watch TV or listen to commercial radio, I don't get the print versions of any magazines or newspapers and when I use the internet I use AdBlock, which pretty much means I see no online ads. I walk past a couple of billboards on my way to work, but they are in German, and generally for products or services I don't recognize, so I'm not sure I could be said to have consumed. Further, my opinion of the advertising industry hovers between my opinions of the fashion industry (inherently ridiculous and basically harmful) and the tobacco industry (murder for profit).

It therefore strikes me as somewhat ironic that most of my time this week seems to be consumed with advertising. I am advertising positions available and a summer course in evolutionary demography we will teach here at the Institute. So I write ads, consider how best to appeal to my target audiences, edit them, figure out where to place them, and so forth. Granted, these are very different kinds of ads than the one calibrated to make young women feel bad about wearing any shoes that don't draw blood, but it is still somewhat outside my core competency.

Recruiting

2011-02-27T06:14:00.000-08:00

I need to recruit some post-doctoral fellows. This sounds fairly simple at first glance, given the general state of the economy and the good reputation of the Institute, but there are a few complicating factors.

First, there is the possibility (depending upon my application) that I, and therefore these positions, will be moving to a different institute in a different part of Germany. I should know by mid-April, but until then I need to be somewhat vague as to the location.

Second, my boss is also recruiting, and effectively has first dibs on any of the candidates except those I independently recruit. So there are a couple of interesting candidates coming through the Institute's training courses, but he plans to offer them positions. In so far as there is a pool of local talent, I can't readily draw on it.

Third, although quite a few people have now seen my review article, I am still not widely known. This means no one is going to be just looking me up to see if I have positions available.

Fourth, I need to recruit some people with fairly specific and distinct skill sets and interests. A statistical demographer, a experimentalist to work with small aquatic invertebrates, and a developmental geneticist to start with. Good candidates for these three positions are likely to be reading three different sets of journals, going to three different types of meetings, and so on. Further, what I will ask them to work on is a bit outside the purview of each field, meaning candidates with specific plans for what research they want to do would have to change those plans considerably to fit within the bounds of the project.

Fifth, Rostock as a location is not a big draw. While not a bad lace to live for a few years, the place doesn't add anything to the appeal of the job for most potential applicants.

Finally, while my Institute is very well known to Demographers internationally, most biologists don't know of it and the biology that goes on here, and may be turned off by applying to a demographic institute.

Post-finally, I've not recruited anyone more senior than an undergrad before, and so I'm learning as I go.

Which all goes to say I am going to have to put some time and work into getting the word out. I frankly doubt I will fill each position in the near future, but I sure will try.

news

2011-02-18T05:26:00.000-08:00

First the bad news:
I will not get the grant. The interview went well, but the Human Sciences committee included no one with knowledge of my field (either of my fields, really), and my claims that no one else is focusing on this important topic, while true, were not entirely believed. Out of >60 applicants, I am told they interviewed 10 and will fund three.

Second, the good news:
I have been encouraged to apply for a nearly identical grant in the Biology section, deadline this Monday. If I don’t get that, I have been generously offered enough funds to recruit a couple of grad students and a post-doc, while keeping my current position. So one way or another I will have a research group, although not necessarily one as well funded or official as I would have had.

Focus

2011-02-11T01:51:00.000-08:00

We turned the living room into a seminar room for the night, all the couches and chairs facing the blank white west wall, onto which we projected my PowerPoint slides. The audience was diverse: in addition to a dozen adults from several professions, I spoke to two little girls (neither of which understand English), an eight month old baby and a big old shaggy dog who curled up by my feet. Before I had gotten through my introductory slide the dog was snoring loudly under the table I was using as a podium, one of the little girls was raising her hand wanting to go to the bathroom, and the baby was waving at me with both hands and saying, "bob bob bob bob bob bob bob bob." As I described the success of my laboratory experiments to date, the dog woke up and began snuffling in the trashcan next to me, and at some point one of the little girls came and tried to sit behind the podium. Despite these disruptions (or perhaps because of them?) the presentation went well, the assembled nonexperts seemed to think the presentation clear and convincing, and their comments, while helpful, require only minor changes to the talk.

I hope that the distinguished scientists I am to present to on Wednesday will be somewhat more decorous. If they are not, it may give me an unfair advantage over the other applicants.

My morning walk

2011-02-09T03:42:00.000-08:00

Most mornings as I am walking to work I try to think through what I have to do that day, what was left undone the previous day, and other science related things. Today, instead, I made up this song:

No you can’t make a soup for your belly from your head,
No you can’t make a soup for your belly from your head,
No you can’t make head soup, for you’d surely wind up dead,
No you can’t make a soup from your head.

No you can’t make a soup for your mommy from your head,
No you can’t make a soup for your mommy from your head,
Tell your mom you want soup, she’ll see that you’re well fed,
No you can’t make a soup from your head.

No you can’t make a soup for your wedding from your head,
No you can’t make a soup for your wedding from your head,
If you served self-head soup, then you probably would not wed,
No you can’t make a soup from your head.

No you can’t make a soup for your belly from your head,
No you can’t make a soup for your belly from your head,
No you can’t make head soup, for you’d surely wind up dead,
No you can’t make a soup from your head.

It may be a sign of stress, or just plain silliness.

All I have to do in 15 minutes...

2011-02-08T09:45:00.000-08:00

according to my boss, is convince the committee that I am brilliant, that my work is revolutionary, and that I am a natural leader.

I have now completely reworked my talk, put the phrase "path breaking" in there, redone all my figures to make them more non-specialist friendly, and made all the font real big in case anyone of the ≤ seven audience members is sitting way at the back of the room. My next task is to run through it several times before my next practice talk this Thursday.

This is why we give practice talks.

2011-02-04T06:23:00.000-08:00

I gave my practice talk yesterday. About 25 people came, including my bosses, my students, and most of the people I collaborate with in the Institute. The talk went well, I presented lots of cool results, I answered all the questions comfortably, and then asked for suggestions on how to fix/improve the talk. The audience gave me so many helpful comments that I pretty much have to start from scratch. It was a great talk for presenting my work to others in my field, but not so much for communicating with an audience of non-biologist non-demographers. So the beautiful Lexis Diagram has to go. The bar graph has to be chopped down. The definitions have to be less precise in order to be more clear. I need to have less detail on my research process and more on why the question is original. The slides should be prettier. And so on. It is sort of exhausting.

I am giving another practice talk next Thursday, this time to complete non-experts. By then I hope to make it comprehensible to that audience.

Hydra bud

2011-01-27T06:56:00.001-08:00

To reproduce asexually, hydra bud. A bump grows on the lower stem of the adult, elongates, grows tenticles, develops a seperated body cavity, and finally releases from the mother to be a perfect little clone. This particular bud needs another few days of growing before it can detach, but its tenticles are already armed with poison stingers, and it can catch prey, or eat plankton passed to it by the tenticles of the mother. I've only seen this food-passing a couple of time, and it could even be coincidental, but it is nice to think that even cnidarians get tasty treats from their mommies.

Blame the vehicle

2011-01-26T14:19:00.000-08:00

I'm on a medicine that helps tremendously with the neuropathic pain associated with Levitis Syndrome. It is often prescribed for neuropathies associated with diabetes, and while there apparently no similarity between the two disorders other than the peripheral neuropathies they cause, this stuff seems to help with both. I recently went to my doctor for a refill, and she prescribed the tablet form, where I had been taking the slow-release capsule in the same dosage. Two days after switching to the tablets, I suddenly started getting these sharp distinctive pains in my hands and wrist again, and the surgical scars on my palms are looking angry. So this morning I went back to my doctor, and this being Germany got to see her within 20 minutes. I am back on the capsules, and I hope the problem is solved. I really would love to understand what is going on with my neurophysiology that the difference between a tablet and a capsule makes such a difference. I don't think it is even understood why neuropathic pain happens, or why some compounds interfere with it, so I don't have much hope of understanding the pharmacokinetics. I just hope the stuff keeps working.

Science picture of the month: Hydra hatchling

2011-01-24T07:44:00.001-08:00

I've talked her before about hydra and their reproduction, so I thought I should post a few out of the thousands of pictures I have of them. I particularly like this one, and have a copy o up on the wall in the lab. It is a hydra hatchling, right out of the shell. The three bumps at the lower end of the picture are it's stubby little baby tentacles. The diameter of that shell is a bit under half a millimeter.

Innervation

2011-01-24T07:33:00.000-08:00

I have an almost complete first draft of the PowerPoint slides for my job talk. I have a week and a half until my practice talk, and two more weeks after that before the interview. It has just occurred to me that I’ve never actually given a job talk before. I’ve heard lots of other people’s job talks, and practice job talks, and I’ve given lots of non-job talks. I am not generally nervous about public speaking, and I don’t find myself too nervous about this. I wonder if I should be more nervous than I am, and if thinking of this as my first job-talk, instead of my hundredth talk, is a good way to accomplish that.

There is perhaps good reason for concern. The other applicants I’m competing against are likely to be an extraordinary group. I have no indication of what fraction of us they're likely to hire. I have the bare minimum professional experience necessary to apply. I'm a biologist interviewing in the Humanities Section. What to an American seems an appropriate level of self recognition can strike many Germans as immodest boasting. My slides are currently a bit too wordy and dense.

All that said, I don't feel nervous yet; they don't expect me to describe my work in German. Just the idea makes me sweat.

Linguistic injustice; it's good to be a native Anglophone

2011-01-16T03:32:00.000-08:00

The English language is good to me. Much of my success in science to date can be attributed to my English skills. The quality of my writing and my speaking attract the praise of my peers at least as frequently as the originality or soundness of my ideas. (I am not such a good speller, but at this point that has very little effect on me.) Further, my wife’s work is very much based on her English skills; she teaches English as a second language and edits scientific articles to improve their English.

All this came to mind when I saw this letter
“Awkward wording. Rephrase”: linguistic injustice in ecological journals

and this response
‘Linguistic injustice’ is not black and white

in the journal Trends in Ecology and Evolution (TREE).

TREE is a high profile journal, publishing mostly excellent review articles, but unfortunately most of its content is not free to the public.

I will quote; the letter’s author, Miguel Clavero, begins,

International scientific communication is monolithically dominated by English, particularly within natural sciences. The professional career of individual scientists relies on their ability to publish in internationally relevant journals, and writing in English is the only way to achieve this. Non-native English speakers (NoNES) seem to be clearly disadvantaged with respect to native English speakers (NES) when trying to get their work published. In fact, English language proficiency has been shown to be a strong predictor of scientific output...

This argument makes sense to me. I have colleagues who are both smarter and harder working than I, who are quite fluent in conversational English, who take much longer to write a paper than I do. Writing crisp, clear, precise, flowing science while staying within word limits is hard, and frankly I’ll never learn a second language well enough to pull it off in anything but English. If Greek, Latin, French, Chinese, Arabic or German were the dominant language of science, I would be in deep trouble.

The response published in TREE points out that other disadvantages (e.g., being from a developing country) are vastly harder to overcome than being NoNES. A Swede has a much better chance to succeed in international science than an Anglophone African. A Swede may even come to speak and write English which is better than that of some Anglophones. It also points out that most English language journals won’t reject a paper because of language problems, so long as the science is sound and the writing is comprehensible and reparable. Both of these things are surely true, but don’t negate Clavero’s point. Bad English may not be a huge disadvantage, but skilled beautiful English is, it seems to me, a big advantage, and native speakers are much more likely to speak a language beautifully. This is particularly true, I think, when it comes to job applications. When one is being evaluated not only on the quality of one’s work, but also on one’s presentation skills, ability to answer complex questions clearly and leadership potential, language skills are important. I have seen application talks at the Institute given in such poor English that I had trouble following them; these people were not hired. The graduate students and post-docs I work with are mostly NoNES; a larger portion of the Research Scientist and lab heads are NES or have lived for extended periods in English speaking countries. This is not because of hiring decisions beeing made inappropriately. Rather, those fluent in English tend to be more successful in those tasks on which hiring decisions are legitimately based.

I doubt that English will cease to be the dominant language of science in my lifetime, and for this I am glad. That said, I take Clavero’s point, and I suppose we should add NoNES to the list of groups disadvantaged in scientific careers (females, underrepresented minorities, the disabled, citizens of developing nations, etc.). I am not sure what is to be done about it. Clavero argues that journals should cover the costs of language editing by charging a fee to all authors, whether they need language editing or not, spreading the costs. They would have to waive this fee for those without sufficient funding to cover them. Some journals in fact already do this, paying in-house language editors from author fees. This has not obviated the linguistic injustice. I am not sure what will, short of sci-fi quality automatic simultanious translation technology. I would love to have this technology, if for no other reason than because then I could stop struggling to learn German.

Weasel words

2011-01-14T11:39:00.000-08:00

I always thought the term "weasel words" derived from the idea that some words are inserted into speech or writing to allow the speaker to weasel out of saying something directly. It turns out it comes from the false belief that weasels suck the insides out of eggs, but leave the shell almost intact, so they appear to have more substance than they do. So in the statement, "I've heard it said that maybe half of your ancestors were kangaroos, just sayin'," the weasel words "I've heard it said," "maybe half," and "just sayin'" suck the hard meaning out of the actual statement "Your ancestors were kangaroos." The speaker, if challenged, can disavow responsibility for the statement, but has still said it.
After reading the Wikipedia article on this, I happened to sit down to edit an application essay by a brilliant, but very shy, student of mine. I found it full of phrases like, "I wanted to," "Although I was," "I believe," "I began to," "I had the opportunity to," and "I helped to." These aren't weasel words mostly, but they serve a similar function. They allow her to say what she accomplished without it seeming like she is saying that she accomplished things. "I designed and carried out the research" reads a lot better than, "I was offered the chance to gain experience in designing research and gathering data," and takes up a lot less space.
The really successful scientists I know not only can say a great deal in very little space, they can squeeze in praise of their own work. I have several times seen, in scientific publications, people describe their own work as startling, revolutionary or subtle. For purely professional reasons, I aspire to this level of unabashidness. For the truly shy, classes in hubris might be in order.

Two talks at once!

2011-01-14T08:37:00.000-08:00

My task, apparently, is to give a talk to both audiences simultaneously. Those viewing my job talk will include “a specialist in your field” as well as committee member representing the breadth of backgrounds of the Human Sciences Section of the Max Planck Society. That Section consists of the following Institutes, which I have casually categorized:

Anthropology:
MPI for Evolutionary Anthropology, Leipzig
MPI for Social Anthropology, Halle/Saale

Psychology:
MPI for Human Development, Berlin
MPI for Human Cognitive and Brain Sciences, Leipzig
MPI for Psycholinguistics, Nijmegen, Netherlands

Economics:
MPI of Economics, Jena
MPI for Research on Collective Goods, Bonn

Law:
MPI for Foreign and International Social Law, München
MPI for Intellectual Property, München
MPI for Comparative and International Private Law, Hamburg
MPI for Foreign and International Criminal Law, Freiburg
MPI for Comparative Public Law and International Law, Heidelberg

Sociology:
MPI for the Study of Religious and Ethnic Diversity, Göttingen
MPI for the Study of Societies, Köln
MPI for Demographic Research, Rostock

History:
MPI for Art History, Florence, Italy
MPI for the History of Science, Berlin
MPI for European Legal History, Frankfurt/Main

You will note that I put my own institute, Demography, under the heading of sociology. Demography is in many way rooted in sociology, despite my belief that it should be a branch of biology. You will also note the preponderance of topics such as Law, Economics and Psychology, which have little theoretical overlap with evolutionary demography.
This is, in a way, a brilliant way of evaluating an applicant. Anyone who can describe their topic in a way which is simultaneously comprehensible and exciting to experts in one’s own field and experts in distant fields is at least a talented communicator. If they threw in some toddlers, who also had to like my talk, and maybe a few Tea Partiers, then it would be a real challenge.

The dead blackbird thing.

2011-01-05T05:25:00.000-08:00

Much has been made of the news that 5000 dead blackbirds fell from the sky onto a small Arkansas town at the turning of the year. ~11:30PM on New Year's Eve. Conspiracy theories and omens abound, but I will propose my own theory: a conspiracy between fireworks and the migratory behavior of blackbirds.

There are several species of blackbirds in North America (e.g. Red-winged Blackbirds, Grackles, Starlings), that tend to migrate in large mix-species flocks. And when I say large, I mean blot out the sun, river in the sky, ornithophobe's nightmare large. Frequently in the hundreds of thousands, not rarely in the millions of birds. I was working at the Long Point Bird Observatory (in southern Ontario) one day in late November when one of these blackbird flocks went by, too thickly to count, for an hour and a half. As soon as we saw them we rushed out and closed the mist-nets we had put up to catch birds. While these nets work well for catching a flock of a dozen chickadees (which we would then measure, band and release), a thousand blackbirds hitting the nets all at once will collapse them, potentially killing large numbers of the birds. Many of the nets had several dozen blackbirds in them within the first minute, and it was a struggle to free them faster than new birds got caught. We couldn't close the nets until they were empty, and we couldn't stop catching them without closing the nets, so thick and fast they came, despite the fact that the main stream of birds was far above our heads, and despite each bird tending to avoid places where humans were standing. We put brightly colored cloths in the nets to make them more visible, but still we couldn't keep up. The nets began to sag under the weight of birds, each of which weighed only a few ounces. Only when the course of the avian river shifted significantly to one side were we able to empty and close the nets, and then stand and gape at the immensity of the flock. That night they all settled in a nearby wetland, densely and within a surprisingly small area.

Now by New Years Eve, these flocks would not be in Ontario, but in places more like Arkansas. It is reported that a wooded area in Beebe was being used as a nighttime roost for several hundred thousand blackbirds. My guess is that somebody was setting off fireworks near that wood, and scared the bejesus out of at least half a million blackbirds. Fireworks are used in agriculture to scare blackbirds out of fields, and to uninitiated birds, they are quite terrifying. So this river of blackbirds leaps into the air whirl around and around as the rockets and fountains go up. Now blackbirds, like most songbirds, have very poor night vision, and frequently smack into things if startled up at night. So maybe one in a thousand in the whirling disoriented mass smacked into a lamp, a sign, a building, each other. They go quite fast enough to kill themselves crashing headlong into hard objects, and can rebound several feet. The birds seemed to have died of blunt trauma, as from a crash.

Or it could be a sign of the end times.

A Frigorific New Year!

2010-12-31T04:55:00.000-08:00

For the first time in about a month, there is not a cold wind blowing through Rostock. The temperature started going up late last night, as announced by the sound our chunks of ice and snow falling 24 stories off the of our building onto the street below.

The temperature of course can't get much above freezing with all this ice all over everything. Looks like a frigorific new year.

Passed round one

2010-12-23T02:24:00.000-08:00

They said they would get back to me in December, but I was starting to doubt, as today is effectively the last working day of the year for those few Germans who aren't already on vacation. But I got the email this morning.

I've been invited to give a short talk on my research to the committee deciding which applicants will be invited to form Research Groups. The interview will be mid-February in Berlin, and I should know very shortly after that if my application was successful.

This means I have a month and a half to write a talk, make impressive figures and graphs, and so forth. The hardest part for me in writing the talk is figuring out who my audience is. The committee that wants to interview me is from the Human Sciences Section. This includes institutes focusing on anthropology, economics, art-history, law, religious and ethnic studies, linguistics, sociology, the history of science and the study of cognition. It also includes demography, evolutionary anthropology and a fair bit of other natural sciences. I can't simply give the same talk to a group of biologists and demographers that I would give to a committee of lawyers and ethnographers. I don't yet know if the committee as a whole will be judging my talk, in which case I have to assume a great diversity of background, or if they will have a smaller group of specialists assigned to each talk. I can give a good talk either way, but not both simultaneously. I've got some thinking to do.

Christmas Party of Science

2010-12-17T07:48:00.000-08:00

I was Santa Clause at the Institute’s X-mas party this year. I asked everyone if they had been good, and handed out presents and chocolate. I made small children cry. I got chocolate in my long white beard. It was great. I think it speaks to how far Germany has come that no one thought it odd to have a Jewish Santa.

My favorite part of the party was the Powerpoint Karaoke. This is a game which could be popular only with academics. Each player gets up to give a talk with power-point slides, which sounds boring, until you consider that he has never seen these slides before, and they are on a topic he likely knows nothing about. There were three contestants, including Santa, and each of us prepared a set of slides another one of us had to speak on. We were not kind to each other. My friend Jon spoke first, on a set of slides I had made, on sesquipedalianisms. I had the longest and most complicated words in several languages under the bright red heading “SAY THESE WITH ME!!.” He made a valiant attempt. Next I got up, in costume, and my slides were entirely in Greek. I recognized the alphabet, but had no idea what any of the words said, and there were no pictures. Lucky for me, most of my audience also didn’t read Greek, so I pretended that I knew exactly what the slides said, and that they were designed to correct common misconceptions about Santa (e.g., Santa does not in fact employ any reindeer, as their odor offends his sensitive nose.) The talk went quite well, and only afterwards did I find out that it was a presentation in Greek on numerical modeling. Finally, my friend Mikko got up and gave a talk on obscure economic phenomena he knew nothing about. He did a creditable job of pretending he knew what he was saying, or rather of being so precise in his vagaries that it was a believable if entirely uninformative talk. It was the first time I’d played this game, but I think it will not be the last.

Frohe Weinachten! Ho Ho ho!!!

Could be good

2010-11-27T03:02:00.000-08:00

A reporter has sent me a couple of questions about my review article. It hasn’t come out yet, but the Royal Society makes these things available to reporters on condition that news stories not come out before the actual article does. So anyway, I have somewhat mixed feelings about this particular email. I have written in the past about my low opinion of the general state of science journalism. The journalists generally fail to understand the science, oversimplify that misunderstanding to make it accessible, add in unrelated stuff to make it interesting and then compress it all into a few hundred words. The resulting news article is often nearly pure misinformation. I should say here that when the NYTimes covered a previous paper of mine, it was pretty well done, and some science news outlets are of course better than others, and this particular reporter is from one of my favorites, which gives me considerable confidence. The content of the questions did not. They gave me the distinct feeling that the reporter either hadn’t read, or hadn’t understood the article. He said in his email that he had read it, so that leaves the possibilities that he hadn’t understood, or that he was trying to provoke quotable explanations by pretending not to understand.

If he ends up writing about my work it will bring my mother great bragging points with her cousins whether he gets it right or not, but I would be greatly annoyed if he slaughters it.

Competing by not competing

2010-11-27T02:23:00.000-08:00

I am an expert in evolutionary demography. I am not an expert demographer, in that my knowledge is primarily on topics relevant to, but not central to, demography as it is currently practiced. I have friends who have detailed well informed opinions on the relative merits of the various hypotheses purporting to explain the Second Demographic Transition. I by contrast have no idea what the Second Demographic Transition is. I can't fit a Gamma-Gompertz model of senescence to age-specific mortality data without the help of a statistical demographer. I don't know the literature on pretty much any topic in human demography well enough to write a demography paper without having to first do a great deal of slow background reading.

Despite this, I am setting out to write a human demography paper, with little if any evolution in it. I can do this with some confidence because, as far as I know, I am working in an area that has been almost completely overlooked, and therefore I have no competition. Most anyone with a solid demography background could do a better job of what I want to do than I can, and I really couldn't compete. But because they haven't bothered, I don't have to compete. I can do a decent job and hopefully publish in a good journal without worrying about the competition, because I believe there to be none.

In my recent grant application, I wrote, "My work falls between demography and evolution, outside the well explored territory of either. Work within evolutionary demography tends to focus on senescence and reproduction; I have intentionally eschewed these to seek the question others have avoided. This is a high risk strategy; my work does not fit neatly into any one topic-specific journal or discipline. However this unconventional approach has the opportunity to found a new direction of study and investigate the most important questions therein." This is a polite way of saying that I intentionally avoid competition by seeking out the questions others have ignored, or deemed less interesting. Most successful scientists are successful because they look for opportunities to do what others aren't doing. I don't know to what extent other seek out whole areas that others haven't bothered with. I also don't know how successful or sustainable a strategy this is likely to be in the long run. After all, the success of the work will ultimately be measured by how many other people get interested in it, and try to improve upon it. Successful work, by definition, must therefore attract competition. So if I want to be successful, but continue not having competitors, I’ll need to move on to some other under-appreciated topic fairly quickly. As I rather like the topic I’m currently seeding, I may just have to put up with some competition, and try to stay ahead of them. having my own research group would be a great help in this. Not being an expert demographer is less of a problem if you have an expert demographer on staff.

More Tardigrades

2010-11-21T11:27:00.000-08:00

On my way to work today (Yes, I go to work on Sundays. Thus are the requirements of lab work.) I pulled up a few square centimeters of moss from a crack in the parking lot. I put it in a petri dish, sprayed some water over it and plunked it on the microscope to see what was floating around. So much! The sinusoidal thrashing of nematodes is unmistakable, and immediately jumped out at me. Several kinds of ciliates wobbled and spun through the water. I have spent far too much time looking at rotifers, so I quickly registered three kinds; two of these swam and third crawled. The crawler would move to a spot on the base of the dish, anchor its back, then do an excellent imitation of a vacuum cleaner, extend and contracting itself in each direction to pass its cilia over the whole surface of a small circle. There was something I think was a tiny annelid, maybe some kind of earthworm. There were tardigrades, so many tardigrades. I was able to get better pictures this time, as there were so many to choose from, it wasn't hard to find them in photogenic poses. I found myself wondering if every scrap of moss around here has so many tardigrades, and if so how many trillions there must be per square kilometer.
Anyway, here, by popular demand, are a couple more pictures.

Note the long curved claws at the ends of the toes, much like a bear has.

Fussy Hydra babies

2010-11-20T09:25:00.000-08:00

Hydra babies come in two types, buds and hatchlings. Buds grow like tree branches out the side of the main trunk of their parent. Eventually the branch is almost as big as the trunk, and they separate, and you have two hydra. Eggs also grow on the sides of their mothers, but they need to be fertilized by free-swimming sperm that are released by male hydra. Then they make a hard shell, detach from the mother and settle down to wait some weeks or months before a tiny hatchling wiggles out. Where the buds are like small copies of their parents, the hatchlings are tiny and genetically novel individuals. They are too small to easily eat the crustaceans we usually feed the adults and buds (Artemia) so we feed them mashed Artemia, except they like their food alive. I have ordered rotifers to see if they will eat those, as they are smaller and softer than the Artemia.

I find myself looking forward to having rotifers in the lab again. They are just so familiar at this point.

The Royal Society has informed me

2010-11-19T08:32:00.001-08:00

my review article will be published online on December 1st. This is very fast. Considering how long such things usually take, this is effectively instant gratification.

Focus

2010-11-19T08:07:00.000-08:00

Science, like most complex tasks, is much easier to make progress on if you know exactly what you are doing, and you have everything you need to do it ready. Over the last couple of months, I got a lot done because I focused on finishing my grant application, and on getting out the two papers I needed to finish to go with my application. Now the application is in, the review paper is accepted, and the methods paper is submitted, and I must find a new focus to guide me. Over the last couple of days I have been scattering my time and thoughts between a dozen projects, and not really making any progress on any of them. I am giving myself until Monday to decide what the new plan is.

Tardigrades!

2010-11-18T06:33:00.000-08:00

If one were to rate animals on two scales, how well known they are, and how well liked they are by those who know of them, tardigrades would be near the bottom of the first scale and near the top of the second. Very few non-biologists know what a tardegrade is, but people who know about them almost universally describe them as cool, cute and amazing. There is a very silly tardigrade song that makes the rounds of laboratory email lists. I count myself amoung those who have trouble not grinning when tardigrades are mentioned.

What is so cool about tardigrades? They can survive total dehydration, exposure to vacuum, radiation, freezing, extreme heat, conservative radio personalities, you name it. They can persist for a decade dried out with no signs of life, then just add water and they reanimate themselves. They are rolly and round and shaped kind of like six-legged teddy bears with two more legs growing out of their tails. This appearance has earned them the nickname ‘water bears.’

This afternoon I wanted to see if the hydra I am keeping in the lab would eat rotifers, because the Artemia I am giving them now are a bit too big for them, and rotifers a tiny. I found some in a puddle outside the institute, and in the same puddle, I found tardigrades. I had never knowingly seen a live tardigrade before, so I took a good long look at them under the microscope. These ones were well under a millimeter long, but I tried to get pictures.

They are small enough that really good photos would require a different microscope, but here are two.

This is a tardigrade from above. You can't really see how cute they are from above.

This is the shed skin of a tardigrade.

Just as snakes have to shed their stiff skins occasionally, many animals with exoskeletons molt that shell occasionally. All the arthropods (insects, spiders, crustaceans, crabs etc) will shed their skins, and so will tardigrades. Tardigrades are not arthropods, but are their closest realtive except for the velvet worms. This skin is head-end down. You can clearly see the six legs on the left side, and the two-legged tail at the top-left. I will try to get better pictures of a live critter tomorrow.

Jon Asks: 2

2010-11-14T06:32:00.000-08:00

In the Laura Ingalls Wilder book The Long Winter, Laura's father says that you can predict the severity of a winter by observing the thickness of muskrat nests in the summer. Muskrats, he says, will build thicker nests during the summer if the following winter is going to be relatively colder, and vice versa with thinner nests and relatively warmer winters. Has this folk wisdom been investigated? Is it true? And if so, where can I get my own muskrat colony?

I can't find anything on Google Scholar or Web of Science indicating that anyone has published anything about muskrats and weather prediction, other than this:

Man's natural craving for advance knowledge of coming weather extends thousands of years back of any attempts at scientific weather forecasting. Realizing that he has not the necessary foresight himself, he has imagined animals to be endowed with some peculiar sense which enables them to know, weeks or months ahead, what the weather will be. Thus a large group of animal weather proverbs has come into existence. Millions of people believe that the thickness of fur on a muskrat, or the number of nuts stored by a squirrel, or a supposedly early migration of certain birds, indicates a severe winter. Yet it is certain that animals have no such foresight.

from: Robert DeC. Ward. 1926. The Present Status of Long-Range Weather Forecasting
Proceedings of the American Philosophical Society,Vol. 65, No. 1, pp. 1-14

He provides no evidence to show that they don't, he is just certain. Note that the version you mention has to do with the thickness of the wall of the house, while the version Ward mentions has to do with the thicknesss of their fur. The fur hypothesis would be easier to test, if you were a muskrat hunter. I am frankly doubtful whether he or anyone else has done the work that would be needed to convincingly either story. You would have to measure the wall thickness of bunches of muskrat houses (or the pelt of many muskrats) in the summer. You would have to do this every year for quite a few years in order to make a convincing analysis of the relationship between wall thickness and hardness of winter. You would probably also want to measure various features of the microclimate, the muskrats behavior and physiology, and the local ecology, in order to get some sense of what the mechanism was. You probably would want to measure the pelts and the houses, just to make sure you were measuring the right thing. This is one limitation to testing folk-wisdom. There are often several versions, and it is hard to know if you are testing the right one unless you test all of them, and then you increase your chances of finding a strong correlation just by chance. My best guess is that there is some, but not a lot of, truth to either version of the story. Certainly they could pick up on whatever cues are available that the winter is going to be hard. But like most weather prediction, they probably aren't very accurate, at least not months in advance.

Jon Asks: 1

2010-11-14T06:23:00.001-08:00

I've read that fungi are the only organisms that can degrade the longer-chain fibers in wood, such as lignin, and that without saprobic fungi the world would be blanketed in dead, undecayed trees. I see on Wikipedia that it is not literally true that no bacteria can degrade lignins, however, by Wiki's account, it does seem that no known bacteria are very good at it. (http://en.wikipedia.org/wiki/Ligninase) So why would that be the evolutionary case? Bacteria have evolved to break down pretty much everything else on the planet (roughly speaking), and wood has been around for something like 350+ million years. Why would they be such second-rate degraders when it comes to lignin?

This is an interesting question, but not one I can give a very satisfying answer to. Explanations of why something didn't evolve are always fairly speculative. Why no six legged tigers? Why no live-birthing birds? Why no Ents?

So why no lignin devouring bacteria? If they can do it poorly, why not well? Maybe it isn't worth their while to invest in that capacity, as they are always outcompeted by the fungi who can already do it? Maybe they can rely on the fungi to make the enzymes, and then they can just mooch. Perhaps the process of making the necessary enzymes requires separate cellular compartments, which bacteria lack. Maybe the necessary mutations just never occurred, and so couldn't be selected for. Certainly I don't know.

Winter

2010-11-12T04:12:00.000-08:00

This morning as Iris and I sat and ate breakfast, we watched a mixture of leaves, rain and snow swirl upwards past our 18th floor (19th by American counting) window. If the winters here were only as windy as Chicago, or cold as New York, or dark as southern Alaska, or damp as Seattle, or foggier than San Francisco, I wouldn’t mind so much. But they are all of these things. The wind howls through everything, bringing cold and wet to each cranny.

I have found that the best strategy for keeping my bad hip from minding the weather is to make sure I am absurdly over-dressed. This morning I walked to work, in temperatures above freezing, wearing high insulated shoes, long-underwear, lined pants, a heavy over-shirt, a down parka and thick gloves, hat and scarf. I was sweating the whole time, but my hip felt fine.

All of this does not endear the city to my heart, and yet I hope I will be here another five years. The grant application that is taking most of my time is to establish a research group of my own, funded by the Max Planck Society for five years. There are three responses they could make to my application. They could say no, they could say yes and let me form the research group here, or they could say yes but tell me to form it at a different Max Planck Institute, in a different city (i.e., Cologne).

I indicate in my application that my first choice is to stay here (at MPIDR), not out of love for the climate, but because of MPIDR’s, “strength in evolutionary demography would be a great benefit to me. I have ongoing collaborations with several MPIDR researchers, including members of the Research Groups on Lifecourse Dynamics and Demographic Change, and Modeling the Evolution of Aging, and of the Laboratories of Statistical Demography, Survival and Longevity, and Evolutionary Biodemography. As my project draws on evolutionary and demographic theory, on MPIDR's Human Mortality Database and Biodemographic Database, on laboratory experiments and survey data, MPIDR’s mixture of social science and biology is the ideal environment for me.”

Add to that that we have good friends, Iris enjoys teaching at the University here, we like our colleagues, we have a great apartment, and moving (which we have done far to much of) is a pain in the rear, and I am very much hoping to stay here. That said, if they offer me a group in Cologne, we will certainly go, in the spring.

Good news

2010-11-11T14:03:00.000-08:00

As I have mentioned here before, I am applying for a big grant. (I may have more time to post here after that grant application is in.) My chances of getting that grant, or at least my personal estimation of my chances, have just gotten a lot better. This is because the review article, in which I do my best to lay out the whole field I plan to focus on, has been accepted for publication by the Proceedings of the Royal Society B. The B is for biology, as they split the journal into topics some decades back. Still the Roy. Soc. is a most venerable publisher. They published Darwin. They published Newton. They have published, well, tens of thousands of authors by now. It is the 350th anniversary of the society, But still, it is a very prestigious journal, and basing my application on a paper in press with them is a hell of a lot better than basing it on the same paper when it hadn't been accepted for publication anywhere. I wrote to a few journals (lower impact ones) who didn't even want to look at it. Having a single author, 10 page review article published with Proc. Roy. Soc. one year after I finished grad school is certainly going to improve my chances. I hope. The timing is good, as the application is due on Wednesday, and I only sent it to them three weeks ago. Most journals take months to give authors an answer. The two anonymous reviewers they sent it to had only very minor suggestions for edits (the first pointed out three typos and stopped at that), so it should be in print, or at least online, very soonish.

The point of a review article is to give an overview of the field. What is know, what is hypothesized, what are the important questions, where is the field going. I have been thinking about the topic of this one on and off for perhaps seven years, but if you put together all the time I specifically spent on it, it would be about six months of work, most in the last year. Perhaps half of that was spent just searching out the relevant literature. I must have read several thousand article titles, perhaps 500 abstracts, and maybe 200 full papers and book chapters. 91 sources made it into the final paper, and 18 more into the appendixes. The reason I had to do so much preliminary literature searching is that no one has ever written a review on this topic before, and perhaps four of the authors whose ideas and data I draw on had this general topic in mind.

Now, part of publishing with them and most other journals these days is that the paper is embargoed until they say it ain't. Embargoed means I can't tell the press what I found out, or even what the article is about, before the journal has a chance to publish it. But for the curious and bored, I can share the list of articles I reference. Just looking through them gives a sense of the range of journals I was searching in. Archiv fur Hydrobiologie, The American Journal of Tropical Medicine and Hygiene, Entomol. Exp. Appl, American Statistician, Obstetrical & Gynecological Survey, Can. J. Fish. Aquat. Sci., Experimental Gerontology, The Auk, Annals: New York Academy of Sciences, Biol. Reprod, Maturitas, Administrative Science Quarterly, J. Herpetol., Ophelia, Genetica, Journal of the Institute of Actuaries and so on. I am lucky in that I didn't have to actually scan the tables of contents of the several thousand journals that could potentially have had relevant papers. I used Google Scholar, Web of Science and other literature searching tools. I have no idea how they did this sort of thing before the internet.

Like a good playbill, in order of appearance:

Main Article:
1. Medawar, P. B. 1952 An unsolved problem of biology. London: HK Lewis.
2. Metcalf, C. J. E. & Pavard, S. 2007 Why evolutionary biologists should be demographers. Trends Ecol. Evol. 22, 205-212.
3. Wachter, K. W. 2008 Biodemography comes of age. Demographic Research 19, 1501-1512.
4. Vaupel, J. W. 2010 Biodemography of human ageing. Nature 464, 536-542.
5. Moorad, J. A. & Promislow, D. E. L. 2009 What can genetic variation tell us about the evolution of senescence? Proc. R. Soc. Lond., Ser. B: Biol. Sci.
6. Péron, G., Gimenez, O., Charmantier, A., Gaillard, J. M. & Crochet, P. A. 2010 Age at the onset of senescence in birds and mammals is predicted by early-life performance. Proceedings of the Royal Society B.
7. Young, H. 1963 Age-specific mortality in the eggs and nestlings of blackbirds. The Auk 80, 145-155.
8. Deevey, E. S. 1947 Life tables for natural populations of animals. The Quarterly Review of Biology 22, 283-314.
9. Jones, O. R., Gaillard, J. M., Tuljapurkar, S., Alho, J. S., Armitage, K. B., Becker, P. H., Bize, P., Brommer, J., Charmantier, A. & Charpentier, M. 2008 Senescence rates are determined by ranking on the fast–slow life-history continuum. Ecol. Lett. 11, 664-673.
10. Pike, D. A., Pizzatto, L., Pike, B. A. & Shine, R. 2008 Estimating survival rates of uncatchable animals: The myth of high juvenile mortality in reptiles. Ecology 89, 607-611.
11. Carey, J. R., Liedo, P. & Vaupel, J. W. 1995 Mortality dynamics of density in the Mediterranean fruit fly. Experimental Gerontology 30, 605-629.
12. Pletcher, S. D., Macdonald, S. J., Marguerie, R., Certa, U., Stearns, S. C., Goldstein, D. B. & Partridge, L. 2002 Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster. Curr. Biol. 12, 712-723.
13. Rose, M. R. 1984 Laboratory evolution of postponed senescence in Drosophila melanogaster. Evolution 38, 1004-1010.
14. Tatar, M., Carey, J. R. & Vaupel, J. W. 1993 Long-term cost of reproduction with and without accelerated senescence in Callosobruchus maculatus: analysis of age-specific mortality. Evolution 47, 1302-1312.
15. Bauer, G. 1983 Age structure, age specific mortality rates and population trend of the freshwater pearl mussel(Margaritifera margaritifera) in North Bavaria. Archiv fur Hydrobiologie 98, 523-532.
16. Styer, L. M., Carey, J. R., Wang, J. L. & Scott, T. W. 2007 Mosquitoes do senesce: departure from the paradigm of constant mortality. The American Journal of Tropical Medicine and Hygiene 76, 111.
17. Sarup, P. & Loeschcke, V. 2010 Life extension and the position of the hormetic zone depends on sex and genetic background in Drosophila melanogaster. Biogerontology, 1-9.
18. Caughley, G. 1966 Mortality patterns in mammals. Ecology 47, 906-918.
19. Barlow, J. & Boveng, P. 1991 Modeling age-specific mortality for marine mammal populations. Mar. Mamm. Sci. 7, 50-65.
20. Spinage, C. A. 1972 African ungulate life tables. Ecology 53, 645-652.
21. Bruderl, J. & Schussler, R. 1990 Organizational mortality: The liabilities of newness and adolescence. Administrative Science Quarterly 35, 530-547.
22. Yang, G. 2007 Life cycle reliability engineering. Hoboken, NJ: John Wiley & Sons Inc.
23. Holliday, R. 2006 Aging is no longer an unsolved problem in biology. Annals: New York Academy of Sciences 1067, 1-9.
24. Hamilton, W. D. 1966 The moulding of senescence by natural selection. J. Theor. Biol. 12, 12-45.
25. Williams, G. C. 1957 Pleiotropy, Natural Selection, and the Evolution of Senescence. Evolution 11, 398-411.
26. Baudisch, A. 2008 Inevitable aging?: contributions to evolutionary-demographic theory: Springer Verlag.
27. Kirkwood, T. B. L. 1990 The disposable soma theory of aging. In Genetic effects on aging (ed. D. E. Harrison), pp. 9–19. Caldwell, NJ: Telford Press.
28. Holman, D. J. & Wood, J. W. 2001 Pregnancy loss and fecundability in women. In Reproductive ecology and human evolution (ed. P. T. Ellison), pp. 15–38. Hawthorne, NY: Aldine de Gruyter.
29. Woods, R. 2009 Death before Birth. Oxford: Oxford University Press.
30. O'Connor, K. A., Holman, D. J. & Wood, J. W. 1998 Declining fecundity and ovarian ageing in natural fertility populations. Maturitas 30, 127-136.
31. Kruger, D. J. & Nesse, R. M. 2004 Sexual selection and the Male:Female Mortality Ratio. Evolutionary Psychology 2, 66-85.
32. Bonduriansky, R. & Brassil, C. E. 2002 Senescence: rapid and costly ageing in wild male flies. Nature 420, 377.
33. McDonald, D. B., Fitzpatrick, J. W. & Woolfenden, G. E. 1996 Actuarial senescence and demographic heterogeneity in the Florida Scrub Jay. Ecology 77, 2373-2381.
34. Roach, D. A., Ridley, C. E. & Dudycha, J. L. 2009 Longitudinal analysis of Plantago: age-by-environment interactions reveal aging. Ecology 90, 1427.
35. Nussey, D. H., Coulson, T., Festa-Bianchet, M. & Gaillard, J. M. 2008 Measuring senescence in wild animal populations: towards a longitudinal approach. Funct. Ecol. 22, 393-406.
36. Sheader, M. 2009 The reproductive biology and ecology of Gammarus duebeni (Crustacea: Amphipoda) in southern England. Journal of the Marine Biological Association of the UK 63, 517-540.
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Appendix 2
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8. Bloom, S. E. 1972 Chromosome abnormalities in chicken (Gallus domesticus) embryos: types, frequencies and phenotypic effects. Chromosoma 37, 309-326.
9. Forstmeier, W. & Ellegren, H. 2010 Trisomy and triploidy are sources of embryo mortality in the zebra finch. Proc. R. Soc. Lond., Ser. B: Biol. Sci.

A botanist once told me...

2010-11-08T02:06:00.000-08:00

"Sedges have edges, rushes are round, and grasses, like asses, have holes."

Botanists have to make up dirty rhymes because they can't just take fecal samples the way zoologists do.

Halloween, diversity, and the left-leaning scientists

2010-11-01T04:33:00.000-07:00

The popular view that scientists tend to be politically liberal has, despite the many counter examples, a pretty good basis in fact, at least as a trend. I don't want to give the impression that I have no conservative colleagues (I have several) or that these people are ostracized (they aren't), but simply that they are in the minority. None of them perhaps would pass a Republican purity test, but they certainly wouldn't pass the Democratic purity test either.

One could easily suggest several possible reasons for left-lean. The liberal might say that scientists are people trained to think carefully about ideas, and liberal ideas stand up to careful thought better than their conservative counterparts. She could add that conservatives, particularly the United States, tend to engage in a great deal of anti-intellectualism, which is not a good way to win the support of scientists and that conservative leaders and movements twist scientific conclusions and ideas more frequently and more disastrously than do liberals. A conservative could argue that as a big-spending liberals tend to support science funding, scientists have a direct interest in supporting liberals. I think all of these things are at least sometimes true.

Another hypothesis occurred to me last night during our Halloween party. Looking around our apartment, I saw not only several Americans (tiger, mime, fisherman, pirate, little girl/trick-or-treater, scarecrow, frog, Dorothy, lumberjack, but no tricorn hats) and Germans (lizard, clown, flapper, schoolgirl, bus stop, Little-Red-Riding-Hood, ninja, and a little boy dressed as a little boy), but also friends from Italy (a mouse and a mummy), Hungary (bank robber), Austria (ghost and witch), Australia (tin man and geisha), Poland (burglar, witches and a ghost), Latvia (witch), Spain (ghost and sorceress) and Finland (clown, penguin, bear and ladybug). We had 34 people from 10 countries, and had invited people from at least a dozen more (Japan, Taiwan, China, Mexico, Brazil, the Netherlands, Denmark, England, Russia, Bulgaria, Turkey and New Zealand). This sort of national diversity is common at gatherings of Institute researchers. I had a similar experience at Berkeley, with colleagues from all over the world.

Conservatives in many countries are nationalistic, or at least view the traditional ways of doing things in their part of the world as best and most correct. So perhaps the conservative hoping to build a career in science finds herself in many uncomfortably international situations, where her assumptions are challenged or potententally unpopular. If so, such people may tend to either revise their opinions (or pretend to, which often eventually leads to an actual change) or avoid such situations. Such avoidance would make a successful career in science difficult, at least at the prestigious institutions which tend to have international research staff.

The Ivory Tower's relative lack of political diversity may partly result from its high demographic diversity. It is hard to condemn witches when your living room is full of them.

Cold Season

2010-10-18T00:18:00.000-07:00

"I woke today and found the frost perched on the town
it hovered in a frozen sky, and gobbled summer down."
-Joni Mitchell

Rostock has its first real frost this morning. In anticipation of this event, the first bad cold of the year has been going around. I think about half the Institute has gotten it so far. I have been sick to varying degrees for a week now. Without having actually looked at the relevant research, my understanding is that we get so many more colds when it gets colder because the airborne viruses break down much more slowly when the areas cold and dry and sunlight is weak. I've also heard somewhere that the cold air makes mucous membranes more susceptible to viruses. This all makes sense, and helps explain why that other common airborne virus that spreads every year, the flu, also concentrates in winter, but it leaves me wondering this: is the pattern the same in species that are adapted to highly seasonal climates? Humans are basically a tropical species that construct tropic-like microclimates for ourselves wherever we go. Our ancestors a few thousand generations ago would not have experienced the yearly cold season as we do today. Moose on the other hand have been living in cold climates forever. Their bodies should expect high virus conditions every winter and prepare accordingly. I speculate that the immune systems of such animals are seasonal, being better at fighting airborne viruses in the winter, and perhaps skin fungus is in the summer. I wouldn't personally want to do the experiments to find out, but I would read the paper if somebody else wrote it.

Not buying a PC

2010-10-16T07:56:00.000-07:00

The paper I recently submitted was written almost entirely by dictating to my computer at work. I've been finding it hard to do any work, or other writing at home. I am dependent on dictation software, and the best available dictation software for Macs was okay but not nearly as good as the PC version. I had started to toy with idea of buying a PC for home use, despite already having a couple of good Macs, just so I could dictate easily and quickly. But now they updated the Mac software, and it is in theory the same as the latest PC dictation software. I'll wait for the reviews to come out, but I'll probably buy the $40 upgrade instead of a whole new computer.

The LPU

2010-10-15T05:50:00.000-07:00

This big grant on applying for, to lead my own group, requires me to do all sorts of things beyond just completing the grant application. I need my CV to look as good as possible when I submit, and that doesn't just mean checking for typos. A lot of the work that I've done recently is not yet in the form that goes on a CV, so I need to get it in that form. A paper that is written but just sitting on my computer is not a publication. So last week I submitted a draft to a high-profile journal is very rapid turnaround time, hoping to have accepted before my application deadline. I am now working on what is called an LPU.

The Least Publishable Unit has a long and proud history in science. It is often the case that one can either toil for months over a very long paper, or chop that up into several smaller papers which will come out faster, often in lower profile journals. The quality of the work is not necessarily any lower, but the step is more incremental and the CV filled out faster. This particular LPU is a simple reanalysis of some data from my doctoral work. I started writing it today, and expects to have completed draft by sometime next week. I will submitted to a low-profile journal with rapid turnaround and hope to have an answer from them before I send in my CV.

I do not feel at all bad about this, my first LPU, for several reasons. First, looking through the CVs of most of the very successful scientists I know, there are quite a few little papers among their giant publications. Second, I can think of several papers which seem to me to have started out as LPUs but which turned out to be tremendously important and widely cited. Third, experience and mentors have told me people are more likely to read a short paper. Fourth and finally, writing short papers is a hell of a lot easier when one has to dictate everything.

There is one way in which this paper does not really meet the classical definition of an LPU: there are lots of data behind it. The true LPU should have just enough data to make a publishable paper. In this case, the sample being analyzed is fairly enormous, although not much bigger than is needed to answer the question.

All in all, writing a little paper seems a good change from the massive review article I've just submitted. I hope it turns out to be as easy as I think it will.

Big grant, small grant application

2010-10-08T07:51:00.000-07:00

Applying for a grant is nothing new, but this one is big, at least by the standards of the grants have applied for previously. The Max Planck Society sponsors Independent Research Groups, headed by a promising young scientist to explore some innovative and important niche. My task is to convince them I am promising and young, and that my work is innovative and important. They don't actually say young, they say "early career," for which I qualify, as I just got my PhD last year. I'm also fairly confident that my work is innovative, as everyone I tell about my work tells me that nobody else has thought about the question. The problem is, "nobody else has thought about the question," can be taken to mean, "who could possibly be interested in that?" So I am young and innovative, and my challenge is to seem promising and important.

Assuming I can convince them of these things, more so than the many other applicants, it will be a pretty sweet deal. They will not only give me a significantly increased salary for five years and enough funding to get my experiments going, they will pay for me to hire a couple of graduate students and a postdoc or two. Frankly, this is more of a career advance than I think I am likely to receive at this point.

The nice part, other than the generosity of the award should I get it, is how little work they ask of me for the application. They want only a one-page statement of my Scientific Accomplishments (I'm not sure what these are yet) plus 2 pages of Research Plans. I could give them 20 pages of research plans with little difficulty if my hands worked well, but under the circumstances I'm much happier to give them 2.

How my health issues will work into this whole application is an interesting question. There is no doubt that I would have been more productive this year and in grad school had been healthy, but I doubt that they can or should take this into consideration. The best I can hope for is that one of my letter writers will mention something about dedication to science or gumption or the fact that I just keep coming back, like a bad case of poison ivy.

On a more philosophical level, I can ask this question: if someone has a disability which interferes with their productivity, and is likely to continue interfering with their productivity, should an employer consider how productive the worker would be without the disability, or should they simply asked of each candidate, "how productive is he/she likely to be?" I would like to say the former, but from the employer's point of view, it's hard to make the case against the latter.

On the other hand, my joint problems potentially make me better qualified to think of the questions and tell other people to gather the necessary data to answer them than I am for actual data gathering and analysis. The higher they promote me, the more qualified I may be.

The news from me

2010-10-01T02:48:00.001-07:00

I've just started using Dragon 11, the latest version of the dictation software I've gotten used to over the last few months. I was on version 8, and over some months of using it fairly intensively it had gotten pretty good at recognizing my voice and words. This new version does about as good a job as the old one did, maybe a bit better, but without the months of training. I haven't yet tried out how it works with other applications, in Excel, PowerPoint, Firefox, etc. but at least word it seems to work surprisingly well for never having heard my voice before.

I had carpal tunnel surgery on my left hand about a month ago and am pleased to report that had very little numbness or tingling since then in that hand. I still have pain around where the incision was and some of the internal cuts but they assure me that will fade with time. I'm having the same surgery on my right hand on Monday. I'm supposed to be on sick leave for all of next week, but I suspect I'll end up coming in to use the dictation software, as I don't have it at home (I have a Mac it works on PC.) I hope that by the end of the year I'll be able to use my hands fairly normally again.

I also just found out today that a large grant application I need to submit is due on November 17. This may interfere somewhat with my plans to post here more regularly.

Fall

2010-10-01T02:00:00.000-07:00

Sunrise splashes across autumn-spangled tree tips. A hooded crow, black and gray and flapping methodically, meanders between the swaying, glowing, multicolored peaks. Wingtip sweep up, flashing into horizontal sunlight, and down, into shadow and raucous foliage.

experimentation

2010-06-16T13:58:00.000-07:00

I have discovered that it is actually less effort to unlock the door to my apartment with my pocket knife than with the key. Perhaps it is time to change the lock.

Look Ma, ...

2010-05-27T06:28:00.000-07:00

I find myself unable to use my hands for very much of anything, and wondering how to be a productive scientists given this peculiar handicap. The problem is not that I lack hands, I have them and they looked perfectly complete, if slightly blue. The problem is not even I can operate them, I have full control and enough strength to do most simple tasks. Rather my problem is that I mustn't use my hands, for a fight to the swell up become quite painful and remain so for some time. It's not yet entirely clear why this is, so for the time being the blame Levitis Syndrome.

There are many jobs for which not using one's hands would be a greater problem than they are for me as a scientist. A carpenter, a cellist, or a cashier would be much less able to work around this problem and I am. Furthermore, there is extremely little short-term pressure for me to get anything done. In the long term, I have to publish papers to keep my job and move to better jobs in the future. In the short term I want to get things done simply because it is too frustrating to not do so.

I'm using dictation software which, now that I've used for some time, is quite quick and accurate for creating text. Not quite as fast as typing, but a hell of a lot faster than I thought dictation software was before I started using it. I have students to do my lab work for me, I'm not doing any field work, and I have access digitally most of the literature I need. Given all this, why should a small matter like hands make much of a difference?

In practice, there are all sorts of things that I find myself unable to do. The dictation software supposed to make it possible to use many different programs, for surfing the web, analyzing data, sending e-mails and so on; in fact many of these thing are quite difficult to do without moving the mouse or touching the keys. Writing code is extraordinarily difficult. Reading heavy paper books is quite hard. Many software tools are simply inaccessible.

My latest stratagem is to order a mouse controlled by foot. The ability to point and click should solve many of my problems, in combination with this dictation software.

The other challenge of being productive despite my hands, is one of concentration. Doing things so differently requires a lot of thought about how I do them, which distracts me from the ideas and tasks to concentrate on. In addition to that, my hands hurt, tingle, throb and otherwise distract me. I am frankly not so good at ignoring it to the point that I can think deeply.

Ultimately, my hands will probably get better with time and coddling. When that happens, I can add dictation software and foot-controlling a mouse to my long list of random and not particularly useful skills. Until then, I'll be studying the list of available voice commands and wearing slip ons.

Planeless sky

2010-04-18T04:07:00.000-07:00

The unpronounceable Icelandic volcano has left my place of work quite empty. This last week was the largest demography conference of the year, and a large portion of my colleagues flew to Dallas for it. They have not been able to return.

This map (from the NYTimes) shows which European airports are currently closed. Rostock is right in the middle of the gray area, half way between Berlin and Copenhagen. The closest operating airports right now are Madrid (2500km), Rome (1700 km including crossing the Alps) or St. Petersburg (2 days by ferry), and they are all booked up. So I may not have many coworkers around until this dust blows over.

The sunsets have been colorful the last couple of days, and the horizon looks hazier than usual, but other than that and the lack of airplanes flying over, I can see no smoke. Also, the grocery stores are out of bananas.

The airlines are starting to question the science behind the flight ban. I am doubtful myself. The concentration of particles (which hasn't actually been measured in most places) must be pretty minute, as the emissions from a small eruption are dispersed over perhaps 100,000,000 cubic kilometers.

I come to that rough estimate because the effected area is about 5000km east to west, 5000km north to south and the cloud is about 4 km top to bottom. I've not seen an estimate for how many tons of ash are up there, or what concentration is dangerous, but I'm guessing the concentration of particulate matter up there is no higher than that over LA or Houston in the summer.

Die Fledermaus

2010-04-14T10:55:00.000-07:00

It was only the second warm evening of the year and a Friday no less, so I came home at 5. Iris, having also noticed the weather, was up at Warnemunde, strolling the beach line of the still frigid Baltic with a couple friends, so I decided to go for a walk myself. The riverfront in town, which as been transformed from port to shops and restaurants, had been surrendered all winter to the ice and wind. The brick walkways and cement steps along the riverfront were still strewn with New Year's Eve firecrackers and beer bottles. The ice that had covered the Unterwarnow was gone, and the only remaining snow was nubbins of the huge piles the city had dumped in a parking lot. I strolled along the waterfront, enjoying the presence of other people in a place that for six months had been abandoned, and watching the grebes bring up small wriggling bits of silver from the river. The Institute is on the waterfront and I came to it as the sun went down. I thought about going inside to see if any colleagues wanted to stroll with me, but decided instead to wander through the unoccupied lot next door. That whole section had been a major port and while much of it has been built over, much, including the peace next to the Institute has gone to grass and the occasional tree. A two-story heap of dirt and rocks, dug up to make space for some building's foundation, is all that distinguishes the lot from a small unmaintained park. As I gazed up at this heap in the fading light, something fluttered over and around it. The silhouette of a tiny bat flitted and floated, gliding and diving after nothing I could see. I tried and failed to detect any insects it could be after. yet it repeatedly visited the same spots, just under those exposed tree roots, just over the top of the dirt pile, just past that lighted window of the Institute. closing my eyes and concentrating, I could just barely hear its wings and a rapid ticking at the upper end of audibility, the lowest notes in its echolocation. I could hear no insects flying, calling or crawling. Watching the lightest part of the sky, I spotted a single midge flying a few feet from my head. Moments later it had disappeared into the hunting bat. This qualified me to be added to its circuit; on each subsequent round of the lot, it would make a small circle around me, perhaps a meter way, checking what other insects I may have attracted. I watched it past when I could see anything, and will return on subsequent dusks.

little posting

2010-04-14T02:15:00.000-07:00

I"ve been posting not at all for a while; I have carpal tunnel syndrome, and can't easily type. However, over the next several days I will be posting several thing either dictated using dictation software, or copied and pasted.

The following is from the

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Discuss

Evolutionary models of evolution

2010-03-14T04:48:00.001-07:00

I've been asked to attend an upcoming workshop on modeling the evolution of aging. Modeling in this sense means building a computer model that provides insight into a process. Most of the people who will be there have some experience in modeling, which I don't. So I decided my roll, as the participant most focused on evolutionary theory, should be to make sure that they are doing evolution right. We were asked to each produce a seed, or opening idea, to get the conversation going. Following is a draft of mine. Note that while you can figure out what most of this means, it was written for other scientists and so includes a smattering of jargon and techniquese.

As an evolutionary biologist, I would like to encourage those modeling the evolution of aging to include in their models actual evolution. Optimization models and even Markov Chain models, while very useful, are not evolutionary. By this I mean that they do not include populations changing through descent with modification. To meet a biologist's definition of evolution, a process must include individuals who are reproducing and the offspring must be modified copies of the parents. This requires a population of individuals with heritable traits and mutation rates which modify the parents' traits in the offspring. In order for adaptive evolution to occur, these heritable traits must also influence how many copies of its genome each individual passes on to the next generation.
Markov-chain models, while somewhat closer to evolutionary, still lack the aspect of a population, which is essential for evolution. In many cases the outcome of evolution will depend on having competing or interacting sets of genes within the same population. This cannot be meaningfully understood if the whole population is assumed to have only one set of genes at any one time.
A truly evolutionary model of aging must therefore be fairly complex. It must simulate individuals, who have age-specific mortality and fertility probabilities. These age-specific schedules must be determined by a set of genes. These genes in turn must be determined by a process of inheritance and a process of mutation.
Using such a method, we can address questions that are difficult to get at through optimization. For example, suppose we would like to know why closely related populations have similar patterns of aging, even when they live in different habitats, or occupy different niches. This pattern has been observed in comparative data and comes under the heading of phylogenetic inertia. With an evolutionary simulation, we can impose environments which mediate the relationship between the genes and the demography. We can then ask what characteristics of the environment or what characteristics of the relationship between environment and demography would allow the starting point (that is the initial genes and demography of the population), to influence the ending point (that is the genes and demography the population ends up with).
To take another example, optimization models generally lack any information on the structure of the genome or the process by which that genome changes. However, genomic structure and mutation process are not irrelevant to what demography the population evolves. An evolutionary simulation will allow for modification of the genomic structure or the mutations process. Compare for example, two populations, each of which has a genetically controlled pattern of investment in various tasks such as reproduction, repair, growth or immune function. In population A, as many genes control this at the beginning of life as at the end. In population B, many genes control the pattern of investment early in life, while relatively few are still influencing late life investment. In both populations the genes affecting these investments are subject to mutational pressure and to selection. In each a mutation-selection balance will emerge, but these mutation selection balances will differ between the two populations. The two populations living in the same environment will arrive at different demographies, each nonoptimal.
These are but two of the many complicating factors which can be explored using an evolutionary simulation and are difficult to get at in a model that does not include explicit evolution. Of course models should be simple enough that one can figure out what factor is influencing what outcome. A model cannot include every complicating factor biologists might like to throw in. As such, I propose a modular evolutionary simulation. By this I mean we start with as simple a model as we can which still has real evolution going on and we write it in such a way that one can add more complicated processes. For example, the basic model could have an extremely simple process of mutation, but could be written such that that this process is easy to remove and replace with a more complicated mutational process. Reproduction could be clonal, but again that process of inheritance could be coded such that it could be pulled out and replaced with sexual reproduction by someone who is interested in what effect the mode of reproduction would have on the evolved demography. The environment could be extremely simple and replaceable with a more complicated environment. I am a slow and inexpert programmer but I imagine that it would not be impossible to write such a simulation in a way that genome, inheritance, mutation, environments, and demography are interacting pieces which can be replaced as one replaces the batteries, bulb, wire, switch and casing of a flashlight. One need not modify the casing to replace acid batteries with rechargeables, or replace rechargeables batteries with lithium rechargeables. One can swap a white bulb for a yellow one without modifying the wires or switch. A properly designed base simulation would allow each of us to experiment and still be able to compare our results without any one model becoming unnecessarily complex.

Kudzu Power

2010-03-06T11:42:00.000-08:00

For several years I've mused that if only we could find some efficient way to make ethanol from Kudzu (the incredibly fast growing invasive weed that has taken over much of the southeastern US), we could stop importing petroleum, vastly improve many ecosystems and tremendously improve the US economy, all in one swell foop. I didn't take this idea very seriously. It appears that somebody else has. Consider the following abstract from a recent volume of the journal Biomass and Bioenergy:

We determined the amount of standing biomass of kudzu (Pueraria montana var lobata) in naturally infested fields in Maryland and Alabama, USA. At each site, we evaluated the carbohydrate content of roots, stems, and leaves. For a third site from Georgia, we evaluated the carbohydrate content of kudzu roots of varying diameters. Belowground biomass in Alabama exceeded 13 t ha⁻¹, and contained an average of 37% fermentable carbohydrates (sucrose, glucose, and starch). Roots from Georgia of all size classes contained over 60% fermentable carbohydrates. Biomass and carbohydrate levels in roots from Maryland were low compared to plants growing in Alabama and Georgia, producing 5 t ha⁻¹ of roots with 20% non-structural carbohydrate. Stems from Alabama and Maryland contained 1–3% carbohydrates. Based on the yield and carbohydrate content, we estimate wild kudzu stands in Alabama and Georgia could produce 5–10 t ha⁻¹ of carbohydrate, which would rival carbohydrate production from maize and sugar cane fields. If economical harvesting and processing techniques could be developed, the kudzu infesting North America has the potential to supplement existing bioethanol feedstocks, which could be of significance to the rural economy of the southeastern USA.

Further consider this economical processing technique, from next month's PNAS:

Abundant plant biomass has the potential to become a sustainable source of fuels and chemicals. Realizing this potential requires the economical conversion of recalcitrant lignocellulose into useful intermediates, such as sugars. We report a high-yielding chemical process for the hydrolysis of biomass into monosaccharides. Adding water gradually to a chloride ionic liquid-containing catalytic acid leads to a nearly 90% yield of glucose from cellulose and 70–80% yield of sugars from untreated corn stover. Ion-exclusion chromatography allows recovery of the ionic liquid and delivers sugar feedstocks that support the vigorous growth of ethanologenic microbes. This simple chemical process, which requires neither an edible plant nor a cellulase, could enable crude biomass to be the sole source of carbon for a scalable biorefinery.

This will, of course, take longer and be more complicated than anyone currently expects, but I'd be surprised if we don't eventually have industrial scale application of this technology, using many sources, including kudzu.

neologistic challenge

2010-03-05T05:19:00.000-08:00

In demography, we spend a lot of time thinking about how the risk of dying increases with age. Economics calls itself the dismal science, demography is the morbid science. Anyway, we call the increase in mortality risk with age in adults "senescence", from the Latin root senex (old). I prefer to think and write about the fact that mortality rate decreases with age in those who are not yet adults. My problem is that there is no word equivalent to senescence that mean this, so I have to invent one.

So I want a word that can be defined as "the decline in mortality risk with age from conception to maturity." A root that means improvement, growth, blossoming, development, growing up, or something along those lines would be best. Twelve points for whoever comes up with the best term.

Cold and Fat

2010-02-06T03:33:00.000-08:00

Cold places tend to have fatty cuisines. The usual explanation for this, although I know of no rigorous test, is that cold weather requires us to burn lots of energy to stay warm, and our bodies respond to this greater demand by causing us to eat more rich foods.

This simple idea has several profound implications that I will now proceed to invent.

The first implication is that " burn lots of energy to stay warm" means something very similar to "increase metabolic rate." So people in colder environments should have higher metabolisms. This matches with the current experience of myself and my wife. For the past months the temperature outside our apartment has rarely gotten above freezing, the wind is always blowing and it is generally damp. Our apartment is somewhat difficult to heat, so it is generally cool and sometimes downright cold inside. We have been eating a very rich diet, and rather than gaining weight, I think we are both loosing a bit. And although the short days cause a degree of lethargy, I have been generally quite productive, with fewer problems of concentration than usual.

There is good reason to think, in fact, that colder climates lead to greater productivity. Colder countries are systematically more economically productive than hotter countries, air conditioning raises productivity considerably, and hot countries experience more economic growth in cool years than in warm ones. My preferred speculation is that this is because the experience of coolth induces greater physiological throughput, allowing for greater activity. If one needs to expend energy to keep oneself warm, why not put that energy to some good use, such as thinking, building, or working. Why shiver when I can use the same energy sharpening the knives or generating a hypothesis?

Allow me one further observation and conjecture. Germans, who eat very heavy diets but on the average are less heavy than Americans, are in the habit of opening all the windows whenever it gets warm inside, even if it is below freezing out. Two apparently unrelated stereo-types of modern Americans, both of which have some basis in fact, may in fact be causally related. These are, we are very fat, and we keep our houses very warm in the winter. Perhaps the miracle diet so many have been searching for should include turning down the thermostat. If we burn more calories when we experience cold, and we want to burn more calories, perhaps we should experience more cold.

A month of snow

2010-02-03T04:52:00.000-08:00

A cubic meter of fluffy freshly fallen snow weighs about 80kg, while a cubic meter of water weighs a metric ton, 1000kg. This implies that a meter of fresh snow will melt into a paltry 8cm deep layer of water. Enough to make the ground very soggy, but not nearly as impressive as a meter of snow. As ice is slightly less dense than water (about 92% as dense) a meter of snow will squish down into a slightly thicker layer of ice, almost 9cm. A third possibility is to catch a plane to someplace warmer, where the snow never fell at all.

Sprouting collaborations

2010-01-29T04:54:00.000-08:00

In the last week I have agreed on two major collaborations (with a Harvard professor and the Director of a Max Planck Institute) ordered some tens of thousands of Euros worth of equipment for my own experiments, hired two lab assistants for those experiments and promised my boss that I would perform a significant reanalysis of a set of data I already have in collaboration with another member of the lab. My wife and I also made some very tasty Brussels sprouts with garlic, soy sauce and lemon juice.

Here's the recipe:

Wash the sprouts, peel off any out leaves that don't look good, and cut each sprout in half.

Cut up a head of garlic.

Juice 2 lemons.

Heat a large cast-iron skillet or other frying surface, large enough to fit all the halved sprouts in a single layer. Put on a fair bit of oil and bring to very hot. Pour in the sprouts and use a spatula or fork to flip them over so that the flat side of each is down. Slide them around some so they all cook evenly. Cook them like that until they are somewhat charred on the bottom. Then flip them over and roll them around so that the other surfaces get cooked. They will still be somewhat too hard inside, so pour in a scant cup of water and cover while the water rapidly boils off, steaming the insides. Once the water cooks off, taste a couple of sprouts and if they are still too hard inside, pour on a little bit more water. Once they are done, remove them to a large bowl and put the garlic on to fry. After a minute, pour some splashes of soy sauce over the garlic, and let it cook down a little bit. Mix this with the lemon juice, salt and pepper, and pour it over the sprouts. Serve hot.

The flapper in winter

2010-01-27T12:14:00.000-08:00

It was -10C this morning, and fresh snow on ice made an unbroken expanse of flat whiteness where the harbor usually is. The small ferry constantly crossing back and forth kept one thin line open, and the water birds congregated around that oasis; compared to sub-freezing air, freezing water is relatively warm. A few birds seemed not to have gotten the memo and instead made lumps in the snow at random points on the ice. One large lump the color of dirty ice seemed bird shaped, and I looked at it on and off seeing if it moved. It was the right size and about the right shape and color to be a juvenile swan, but it could also be a pit of trash or a chunk of refrozen slush someone slid out onto the ice.

My colleague, who also watches birds came into my office to ask if I had noticed it, and if so what I thought it was. He said there were footsteps in the fresh snow near it. He was right. Through my binoculars I could see swan prints leading to where it sat. And that lump on top might be a bit of neck leading to a head tucked entirely under a wing. But it must be dead I thought, why else would it sit so still for so long in such a windy spot on the ice?

I glanced at it occasionally though the morning, and it didn't move. Then some people walking their dog passed by, and the dog made like it was going to run out onto the ice to get the swan. A long gray neck snaked out from under the wing and looked straight back at the dog. The dog must have realized the ice was too thin to hold it. As soon as the dog was gone, the head disappeared under the wing again, and there it stayed.

In the early afternoon a fire department rescue truck pulled down the road to the harbor near the swan. Two guys, one holding binoculars, got out and looked at the swan for a while. I wondered if they thought it was a child. They drove away and came back with a third guy, who threw snowballs near the swan and yelled at it until it got up and walked a few steps. They left again, and the swan sat back in its usual spot, head under wing. The snow got heavier and started to pile up on the windward side of the swan, but it stuck to its spot, and still was there when the sun went down.

Almost finished

2010-01-25T13:07:00.000-08:00

I'm about ready to submit this paper, and I have very mixed feelings as to its chances of acceptance. I've shown it to two people who told me they thought it was quite good and that I should send it to the high end journal I'm sending it to, and to a third who said he didn't think it would make it past any reviewer without major rewriting including changing which variables I was analyzing and the whole point of the paper. I've worked the paper over so many times I no longer have any idea if is it brilliant and revolutionary or a pile of misconceived hackary. What I do know for certain is that I am not going to start rewriting it at this point, and I'm going to hope that my friend who suggested I needed to do so just missed the point that the other two saw. The paper is methodologically sound, whatever its other flaws, and if the first journal rejects it I'll send it to lower profile journals until someone thinks it is important enough to print.

I really didn't want to get into discussing testis size.

2010-01-22T05:08:00.000-08:00

I'm writing a paper on the choice male primates face between caring for the young they already have, and fighting other males for access to mates so they can have more young. There are, of course, other reproductive strategies they could also be investing in, like trying to impress the ladies without fighting, or impressing the ladies by being such good carers. I didn't want to get into all of these, because it just gets to big and complicated, and the relationship between the variables I have is already complicated and interested enough. But my colleague who read the paper for me thinks it is important to include something on investment in sperm competition. Sperm competition occurs when a female mates with more than one male, but only one of them will end up being the father of each baby she produces. The male with the strongest, fastest, healthiest, most numerous sperm will tend to be the father, and as such will tend to pass on his genes for big healthy sperm to the most sons. And to make lots of big healthy sperm, a male needs big testicles. Testicle size turns out to be closely correlated with how much multiple mating the females do, and in highly promiscuous species, males may dedicate a significant portion of their body mass to testes. And this is how I came to be typing search terms like "bush baby testis mass" and "monkey sperm competition" into Google Scholar. You would be amazed what Google is willing to label as a scholarly article.

Lovers in the snow

2010-01-11T07:58:00.000-08:00

The UnterWarnow is frozen, and snow is building up on the ice. Sunset will come 7 hours and 45 minutes after sunrise today. The crows and blackbirds are digging in the snow looking for food, and the birds that usually haunt the harbor all winter are gone, perhaps to the south, perhaps out to the Baltic where the water isn’t solid.

But in the tree in front of my office window, two magpies are carrying fresh twigs into a crook between three branches. There is only one reason I know of why they would be doing this: they are building a nest. Most birds, including magpies, only build nests to lay eggs in, and now is not the time to lay eggs. It is too cold for the eggs to develop (even with mom sitting on them), and if they did hatch , there would be nothing to feed them. Any nest built now isn’t even likely to still be in good enough shape to use come spring. The spot where they are putting the twigs is near the top of the tree, on the branch closest to the river, and shakes whenever the wind blows, which it does frequently.

This raises the question of why? When other birds in the neighborhood are struggling just to keep from freezing or starving, why are the magpies wasting their time and exposing themselves to the cold building a nest they can’t use? Perhaps the cold has driven them mad? Maybe they are pulling food out of the dumpster of the near by grocery store, and having plenty of food, think it is time to breed? A genetic disorder?

There may be some perfectly good reason for this (pair-bonding activity?) but I’m not sure I buy that.

When my colleagues and I were writing a paper on the definition of behavior, many of previously published definitions we came across specified that behavior is adaptive, that it will tend to increase the fitness of the individual performing the behavior. We omitted this from our definition, because there are so many behaviors whose adaptive significance is uncertain, or which seem maladaptive. It is certainly true that most behaviors are adaptive, some, like building a nest in a snow storm, probably are not.

BLOG OF SCIENCE!

Can anyone think of model organism genera starting with I,J or Q?

A, alligators all around

Authorship code

Oh give me a home, where the apple-snails roam

The end is neigh!

Undermining the Wall of Death

Constraints

More fun zoo photos

Thoughts during a trip to a conference

Typical

Dan SMASH!

Irene reaches Europe

Writing while sleep deprived

Busy

Taxonomically not what you eat

Who's a demographer?

Why there are no whale-like birds.

37 weeks

Hyphum

33 weeks LMP

Decreasing population, increasing density

A name but no face

name for a principle?

Reproduction

Two offers out

Bedside ecosystem

Walking desk

Spring is the season of interviews

My very first robot

Dunno

Despair not!

Skipping that hard middle part

Fun with Photoshop: Hoofstock

What to do?

Etymological challange: Evolutionary Demography

lebenslauf

What is EvoDemo?

Propositioning journals

The demographics of evolutionary demographers

High r strategy in a high k regime

keen but generic interest

Computer bugs

March of the Beetles

Acronymic Challenge

Excited to teach again

Summer Semester 2011

IMPRSD 189Introduction to Evolutionary Demography

A reviewer's lot is not an'appy one

Finally out

Places where I may post postdoc ads

Advertising

Recruiting

news

Focus

My morning walk

All I have to do in 15 minutes...

This is why we give practice talks.

Hydra bud

Blame the vehicle

Science picture of the month: Hydra hatchling

Innervation

Linguistic injustice; it's good to be a native Anglophone

Weasel words

Two talks at once!

The dead blackbird thing.

A Frigorific New Year!

Passed round one

Christmas Party of Science

Could be good

Competing by not competing

More Tardigrades

Fussy Hydra babies

The Royal Society has informed me

Focus

Tardigrades!

Jon Asks: 2

Jon Asks: 1

Winter

Good news

IMPRSD 189
Introduction to Evolutionary Demography