Sunday, December 18, 2011
Wednesday, October 26, 2011
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 The first is how naive and outdated their evolutionary assumptions tend to be.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.
Monday, October 10, 2011
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.
Saturday, October 08, 2011
Sunday, September 25, 2011
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.
Thursday, September 08, 2011
Tuesday, September 06, 2011
I am not generally given to violence, but do currently have the urge to break something.
Monday, September 05, 2011
Saturday, August 27, 2011
Tuesday, August 16, 2011
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.
Thursday, August 04, 2011
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.
Wednesday, August 03, 2011
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.
Monday, August 01, 2011
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.
Friday, July 22, 2011
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.
Friday, July 01, 2011
EDIT: May 2nd 2017.
The singular of hyphae is actually hypha. I just stumbled upon my own old blog post and said, "Whoa! That's wrong." I must have misheard that six years ago.
Friday, June 24, 2011
Thursday, June 23, 2011
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.
Monday, June 20, 2011
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.
Sunday, June 05, 2011
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.
Monday, May 30, 2011
Friday, May 20, 2011
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.
Thursday, May 19, 2011
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.
Tuesday, May 17, 2011
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
Various screws and bolts I had around the house
An old curtain rod
Total cost €90 spent last year
Thursday, May 12, 2011
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.
Thursday, April 14, 2011
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.
Tuesday, April 12, 2011
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!
Thursday, April 07, 2011
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.
Thursday, March 31, 2011
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.
Tuesday, March 29, 2011
Sunday, March 27, 2011
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.
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.
Friday, March 25, 2011
Will the culture shock ne'er end?
Tuesday, March 22, 2011
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?
Monday, March 21, 2011
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.
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.
Tuesday, March 15, 2011
Note to those applying for jobs: it is more efective to have and demonstrate interest than to claim it.
Monday, March 14, 2011
P.S. Yes, I know that they are actually beetles, not bugs, but who has ever heard of computer beetles?
Friday, March 11, 2011
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.
Tuesday, March 08, 2011
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.
Thursday, March 03, 2011
Summer Semester 2011
Introduction to Evolutionary Demography
|Start:||4 July 2011|
|End:||9 July 2011|
|Location:||Max Planck Institute for Demographic Research (MPIDR), Rostock, Germany|
- 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
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.
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.
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.
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.
Students will be evaluated on participation in class and on short presentations.
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 (email@example.com).
- Application deadline is 31 March 2011.
- Applicants will be informed whether they will be admitted by 15 April 2011.
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.
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.
A measure for describing and comparing postreproductive life span as a population trait
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.
Wednesday, March 02, 2011
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.
Sunday, February 27, 2011
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.
Friday, February 18, 2011
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.