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.,
Clutton-Brock, T., Dobson, F.S., Festa-Bianchet, M., Gustafsson, L.,
Jensen, H., Jones, C.J., Lillandt, G., McCleery, R., Merila, J., Neuhaus, P.,
Nicoll, M.A.C., Norris, K., Oli, M.K., Pemberton, J., Pietiainen, H.,
Ringsby, T.H., Roulin, A., Saether, B.E., Setchell, J.M., Sheldon, B.C.,
Thompson, P.M., Weimerskirch, H., Wickings, E.J. & Coulson, T. 2008.
Senescence rates are determined by ranking on the fast-slow life-history continuum.
Ecology Letters.
Abstract:
Comparative analyses of survival senescence by using life tables have identified generalizations including the observation that mammals senesce faster than similar-sized birds. These generalizations have been challenged because of limitations of life-table approaches and the growing appreciation that senescence is more than an increasing probability of death. Without using life tables, we examine senescence rates in annual individual fitness using 20 individual-based data sets of terrestrial vertebrates with contrasting life histories and body size. We find that senescence is widespread in the wild and equally likely to occur in survival and reproduction. Additionally, mammals senesce faster than birds because they have a faster life history for a given body size. By allowing us to disentangle the effects of two major fitness components our methods allow an assessment of the robustness of the prevalent life-table approach. Focusing on one aspect of life history - survival or recruitment - can provide reliable information on overall senescence.
Keywords: Aging; comparative analysis; demography; generation time; metabolic rate; senescence
Comments: One of the authors is applying for a position here in the next few days.
Monday, October 26, 2009
The Meta-Journal of EvoDemo
I've often complained that there is no journal of evolutionary biodemography, or life-history evolution. I've decided to do something about this, sort of. I'm starting a new series here on Blog of Science! in which I post the abstract to published papers of interest and link to the online versions. If I get ambitious I may include some comments or criticisms. In part this will just make it easier for me to keep track of what I've read and what I thought of it. In part it will help motivate me to look for relevant literature. Perhaps it will even be useful to others. Posts like these will be tagged with EvoDemo.
Malards on my mind
My office here at the institute has a beautiful view of the unter-Warnow, the tidal harbor area just before the Warnow River flows into the Baltic. The city of Rostock and many of its suburbs are arrayed along both banks of the unter-Warnow, and the Institute is right above the banks, allowing marvelous views. There are some drawbacks to this for a person easily distracted by birds, as I am. I frequently find myself watching the gulls chasing each other, the swans terrorizing the mallards, or the rooks, hooded-crows and jackdaws playing in the wind.
The last several days I have noticed that the same two groups of mallards are always in the same two spots. In the river, near the institute there is a consistent group of six males and five females, always floating in about the same spot. In a drowned foundation on the abandoned port-facility just west of here, there are always four male and three female mallards, with one of the males showing the white splotching indicating it has some ancestry among the domestic mallards. These several birds always seem to be in the same two groups, in very similar spots, and I can only assume they have found something good to eat there, as they don't seem to move elsewhere to feed. I wonder if they will stay all winter. I wonder what I should have done in the time I spent censusing mallards.
The last several days I have noticed that the same two groups of mallards are always in the same two spots. In the river, near the institute there is a consistent group of six males and five females, always floating in about the same spot. In a drowned foundation on the abandoned port-facility just west of here, there are always four male and three female mallards, with one of the males showing the white splotching indicating it has some ancestry among the domestic mallards. These several birds always seem to be in the same two groups, in very similar spots, and I can only assume they have found something good to eat there, as they don't seem to move elsewhere to feed. I wonder if they will stay all winter. I wonder what I should have done in the time I spent censusing mallards.
Friday, October 23, 2009
Individuality
The central question of interest here in the Laboratory for Evolutionary Biodemography is: how does evolution determine demographic patterns (usually individual lifespan) and, secondarily, how do demographic patterns (again usually individual lifespan) influence the evolution of other traits? This questions leads to all manner of difficult sub-questions. One of these, that comes up surprisingly often is, "what is an individual in this case?"
One colleague has been pondering this question in the context of eusocial insects. Eusocial means that some individuals do all the reproducing, and others don't reproduce at all, they just work to increase the survival and reproductive success of the breeders. Queen ants and their workers are a good example. It seems pretty easy to count ants, they have separate little bodies and they are genetically distinct "individuals" but because they don't breed (usually) from the viewpoint of propagating genetic material, their only role is to perform their appointed task within the colony, in order to aid the queen. This has led some ant experts to refer to the ant nest as a super organism, with the queen functioning as the reproductive organ, and the workers, like the cells in our intestines, as merely the body that supports this reproduction. In many organisms reproductive cells can last the whole lifetime, which intestinal cells are disposable, and frequently replaced. Likewise, queens live as long as the colony does, greater than 30 years in some species, while workers usually last only a few weeks or months. So is the colony a single organism, and therefore the workers its sub-parts, or is each worker an individual, and therefore the colony a multiplicity?
Another colleague is studying the demography of hydra, small mostly sessile cnidarians. Hydra are among the most demographically bizarre organisms. For starters, no one has been able to prove that hydra age at all, despite multiple long term attempts. Second, their primary means of reproduction is through budding, where a bump on the side of the organism gradually elongates, grows tentacles, forms a digestive cavity and takes on the form of a fully formed and functional (but somewhat small) hydra before detaching and becoming a separate individual. Add to this that if you mash them up to separate their cells from each other, each cell has the capacity to grow into a new hydra. Yesterday, I spent a few minutes watching through a microscope as a hydra with a large bud sticking off the side, about half the size of the main body, wiggled in a perti dish. Both sets of tentacles, both digestive systems worked, like conjoined twins. As I watched, I wondered if I was looking at one individual, or two, or hundreds. Each cell had the capacity to found a new colony, build a new hydra, and therefore each cell was in a sense an individual. Each stem could be called an individual, by the loose analogy to humans. Or the whole genetically identical, physically attached, coordinated being could be an organism. Depending on what unit we call the individual, we get very different answers as to the lifespan.
A final example I've been wondering about is the giant redwood tree. A single trunk of a redwood seems to the casual observer to be one huge individual. But redwoods bud prolifically from the base, and multiple trunks can grow out of the same stump, the same root system. Large groups of huge trees can be genetically identical, save for the mutations accumulated in their growing tissues over thousands of years of growth. If we consider one stem to be the individual, redwoods can live for thousands of years. But if we consider everything derived from one seed to be the individual, I don't know of any reason not to consider redwoods, like hydra, effectively immortal. Sequoia sempervirens indeed.
So I'm posing the question to you dear reader, what is an individual? What operational rule should be applied? How do we find the individual in a hydra, or in a redwood forest?
Sunday, October 18, 2009
Nuts with no squirrels
At my parent's home in New York State, the acorns don't last long. The deer, squirrels, chipmunks and turkeys quickly gobble up, hoard or bury the best nuts, leaving only the small and wormy nuts for the insects and mice. A forest ecologist I once worked for told me that oaks are reproducing poorly in the northeastern US, in part because the unnaturally high deer populations consume so many acorns.
Walking through the woods around Rostock is a stark contrast, despite the similar mix of trees. Here, it is nearly impossible to avoid stepping on piles of big, healthy nuts. Acorns, chestnuts, beechnuts, walnuts. All the trees seem to be dropping fantastic numbers of nuts, and nothing but insects and a few birds seems to be eating them. Here neither deer nor squirrels seem to be common in urban parks as they are in the US. In fact the only wild mammals we have seen around Rostock are Fledermäuse (bats) flying around at dusk and a jackrabbit or two. The ground in the parks is also full of mole tunnels (must be moles, as there are no gophers or other rodent tunnelers here). There are of course some mice and rats, but we haven't seen them and their numbers don't seem up to the task of disposing of all those nuts.
In North America, deer and gray squirrels have increased their numbers and expanded their ranges as humans have removed predators and made food available year-round. In western Europe, where the native animals have a far longer history of being persecuted by humans, where large wilderness areas are rare, and where there seem to be fewer native mammal species anyway (perhaps because of extinctions?) there just doesn't seem to be anyone to fill that urban nut-eater niche. There aren't even any turkeys or other birds big enough to eat nuts whole. Under such circumstances, I wonder if the nut trees do well because their nuts aren't all eaten, or do poorly because their nuts don't get buried, passed though germination-inducing digestive systems and dispersed.
Walking through the woods around Rostock is a stark contrast, despite the similar mix of trees. Here, it is nearly impossible to avoid stepping on piles of big, healthy nuts. Acorns, chestnuts, beechnuts, walnuts. All the trees seem to be dropping fantastic numbers of nuts, and nothing but insects and a few birds seems to be eating them. Here neither deer nor squirrels seem to be common in urban parks as they are in the US. In fact the only wild mammals we have seen around Rostock are Fledermäuse (bats) flying around at dusk and a jackrabbit or two. The ground in the parks is also full of mole tunnels (must be moles, as there are no gophers or other rodent tunnelers here). There are of course some mice and rats, but we haven't seen them and their numbers don't seem up to the task of disposing of all those nuts.
In North America, deer and gray squirrels have increased their numbers and expanded their ranges as humans have removed predators and made food available year-round. In western Europe, where the native animals have a far longer history of being persecuted by humans, where large wilderness areas are rare, and where there seem to be fewer native mammal species anyway (perhaps because of extinctions?) there just doesn't seem to be anyone to fill that urban nut-eater niche. There aren't even any turkeys or other birds big enough to eat nuts whole. Under such circumstances, I wonder if the nut trees do well because their nuts aren't all eaten, or do poorly because their nuts don't get buried, passed though germination-inducing digestive systems and dispersed.
Saturday, October 17, 2009
Rostock Zoo
We wanted to go for a longish walk today, and the Rostock Zoo is walking distance from our house, so we headed on over. We walked through only a few city blocks and then a large city park with oak/maple/chestnut/beech forest and playing fields. The zoo was blissfully uncrowded due to the cold and wet weather. Unfortunately, this also meant that many of the animals were inside or inactive. Walking into this zoo the differences in funding and history from the Copenhagen Zoo we so recently admired were painfully obvious. It is of course an unfair comparison, given the differences between the two cities, and the weather when we visited, but still striking. Many of the animals simply stood in small, relatively featureless enclosures. Iris commented that the people who designed some of the enclosures were following in the style of Soviet apartment blocks. The animals, with some notable exceptions, looked bored, and sat waiting to be fed. A couple of the fish tanks had dead fish at the bottoms. The lone elephant walked in a small circle, always clockwise. The orangutan clutched the bars of her cage.
Many of the animals were tremendously obese. We saw almost no zoo employees except at the cafe, the entrances and the store. There was a lot of the feeling of bad old zoo here.
At the same time, like much of Rostock, it was obvious that the Rostock Zoo is very actively trying to replace the run-down vestiges of GDR with new, modern and elegant. The otter habitat, clearly recently built, had the otter racing every which way through trees, ponds and tunnels searching for cleverly hidden bits of food. We watched from a small bridge over the enclosure or from a sunken room below water level, aquarium style. The otter's enclosure was beautifully thought through and built.
The depressing concrete and iron boxes that house the great apes have been retrofitted with glass fronts for warmth as well as branches and nets for climbing on, and big signs requesting donations to build a new ape house. I emptied my coins into the collection box. A large counter showed that they had raised most of the million Euros in donations they need for the new ape house. The old-world monkeys were in a new (although still somewhat cramped) exhibition hall that doubles as a gallery of large prints of the winners of a wildlife photography contest.
The most striking (and to me most disturbing) enclosure is the crocodile house. About the size of a two car garage, it has a couple of small crocs, some large soft-shelled turtles, brightly colored freshwater fish (all the fish at the zoo are freshwater, presumably because they lack the facilities for salt-water aquaria) and four free-roaming Black-mantled Tamarins. These little South American monkeys had the complete run of the place. They jumped over the crocodile tank, ran between the zoo visitors' feet, jumped on the visitors and scurried up and down the walls. They showed no fear of people, and while we were there were fed by hand by more than one young guest. One young lady took turns with a tamarin licking her ice cream.
All this with no zoo employee or volunteer in the building, and both doors to the house frequently open. It was thrilling to see these tiny (~1Lb) primates up so close, have them jump onto my shoulder, stick their noses against my camera lens to see what was inside, etc. But it also struck me as really quite irresponsible. It may be that the zoo simply has no other warm space to keep the tamarins, but my mind was filled with all the things that could go wrong here. Someone could step on a tamarin. One of the teenagers attempting to grab a tamarin's tail could succeed and get a nasty bite, or injure the animal. People could transmit diseases to our fellow primates. The monkeys could transmit diseases to people. Someone could stuff a tamarin in a backpack and take it home (this sort of thing has happened at other zoos). The tamarins could run out the door and wander into the nearby lion enclosure, or just die of cold. The crocs could get them. Petting zoos are supervised, and never contain primates or species of conservation concern. This broke every rule, and I can only hope it is a very temporary arrangement. That said, the tamarins were probably the most memorable and exciting part of the visit.
One other thing that struck me about this zoo is how much space they have for expansion. Many of their newer exhibits, and large fields for the ungulates, are in an area across a road from the main zoo, accessible through a separate entrance or via an underpass. Most of that added-on section is still just woods, waiting to be made into wooded homes for animals. They also have lots of old cages that are simply empty, ripe for replacement or creative reuse. What they seem to lack is not the will to improve, or the space, but funding. With the exception of the tamarins (which I think should be moved at once, even if it has to be to somewhere the public can't see them, or to another zoo) all of the animals are situated as well as they can be given the current enclosures available. If asked, I would probably advise replacing or significantly modifying 75% of the enclosures. I suspect the people who work there feel the same way. I very much hope that they find the funding and the will to make the type of transformation they need.
Due to poor weather and bad batteries I only took 150 pictures today. 20 of the better or more relevant ones are here.
 |
| From Rostock Zoo 10/17/09 |
Many of the animals were tremendously obese. We saw almost no zoo employees except at the cafe, the entrances and the store. There was a lot of the feeling of bad old zoo here.
At the same time, like much of Rostock, it was obvious that the Rostock Zoo is very actively trying to replace the run-down vestiges of GDR with new, modern and elegant. The otter habitat, clearly recently built, had the otter racing every which way through trees, ponds and tunnels searching for cleverly hidden bits of food. We watched from a small bridge over the enclosure or from a sunken room below water level, aquarium style. The otter's enclosure was beautifully thought through and built.
 |
| From Rostock Zoo 10/17/09 |
The depressing concrete and iron boxes that house the great apes have been retrofitted with glass fronts for warmth as well as branches and nets for climbing on, and big signs requesting donations to build a new ape house. I emptied my coins into the collection box. A large counter showed that they had raised most of the million Euros in donations they need for the new ape house. The old-world monkeys were in a new (although still somewhat cramped) exhibition hall that doubles as a gallery of large prints of the winners of a wildlife photography contest.
The most striking (and to me most disturbing) enclosure is the crocodile house. About the size of a two car garage, it has a couple of small crocs, some large soft-shelled turtles, brightly colored freshwater fish (all the fish at the zoo are freshwater, presumably because they lack the facilities for salt-water aquaria) and four free-roaming Black-mantled Tamarins. These little South American monkeys had the complete run of the place. They jumped over the crocodile tank, ran between the zoo visitors' feet, jumped on the visitors and scurried up and down the walls. They showed no fear of people, and while we were there were fed by hand by more than one young guest. One young lady took turns with a tamarin licking her ice cream.
 |
| From Rostock Zoo 10/17/09 |
All this with no zoo employee or volunteer in the building, and both doors to the house frequently open. It was thrilling to see these tiny (~1Lb) primates up so close, have them jump onto my shoulder, stick their noses against my camera lens to see what was inside, etc. But it also struck me as really quite irresponsible. It may be that the zoo simply has no other warm space to keep the tamarins, but my mind was filled with all the things that could go wrong here. Someone could step on a tamarin. One of the teenagers attempting to grab a tamarin's tail could succeed and get a nasty bite, or injure the animal. People could transmit diseases to our fellow primates. The monkeys could transmit diseases to people. Someone could stuff a tamarin in a backpack and take it home (this sort of thing has happened at other zoos). The tamarins could run out the door and wander into the nearby lion enclosure, or just die of cold. The crocs could get them. Petting zoos are supervised, and never contain primates or species of conservation concern. This broke every rule, and I can only hope it is a very temporary arrangement. That said, the tamarins were probably the most memorable and exciting part of the visit.
One other thing that struck me about this zoo is how much space they have for expansion. Many of their newer exhibits, and large fields for the ungulates, are in an area across a road from the main zoo, accessible through a separate entrance or via an underpass. Most of that added-on section is still just woods, waiting to be made into wooded homes for animals. They also have lots of old cages that are simply empty, ripe for replacement or creative reuse. What they seem to lack is not the will to improve, or the space, but funding. With the exception of the tamarins (which I think should be moved at once, even if it has to be to somewhere the public can't see them, or to another zoo) all of the animals are situated as well as they can be given the current enclosures available. If asked, I would probably advise replacing or significantly modifying 75% of the enclosures. I suspect the people who work there feel the same way. I very much hope that they find the funding and the will to make the type of transformation they need.
Due to poor weather and bad batteries I only took 150 pictures today. 20 of the better or more relevant ones are here.
 |
| Rostock Zoo 10/17/09 |
Wednesday, October 14, 2009
R
I was maybe 10 when I first hear of programming and decided that it would be a good thing to know how to do, and perhaps 16 when I first decided I would learn. I've been meaning to ever since then, and frequently aware that my work would be faster, more reliable and more repeatable if I just knew some programming. Somehow I never found the combination of time, motivation and opportunity until now. I've spent most of the last week laboriously writing a simple program in R. It is clunky and inelegant, it doesn't yet do everything I want it to, and what it does it does a bit slowly. But it does what is intended, produces useful answers and I wrote it myself. Well, with occasional help from colleagues. Time to check it off the "to do eventually" list. Given another several months of this I may develop a useful skill.
Thursday, October 08, 2009
The sleep is half full
In high school I and my friends built scenery for the school's shows. Fun with power tools. A couple of months before one show, the auditorium was temporarily condemned because it was full of asbestos. We were told that we would be able to get back into the auditorium only three days before the show was supposed to open. Installing a set, doing the wiring and the lighting and otherwise getting the theater ready for the show is a massive job, so we just decided we would stay up all night a couple of nights in a row and get it done. 5AM or so I fell asleep in one of the seats, then slept just an hour or two, only to be woken by a loud strange noise. I had no idea what it was. Crashing sounds and weird warped howling. I got up, looked around, couldn't figure out what the hell the noise was, but it came from the loudspeakers. Several seconds later, something in my brain 'switched on' and I instantly recognized the beat, the notes, the words. It was Sgt. Pepper's Lonely Hearts' Club Band. I knew the song well, but when I thought back on what I had heard moments earlier, I remembered it as atonal, arrhythmic, non-linguistic noise. My brain, unable to find the pattern, encoded it in memory as largely patternless, a snapshot grossly out of focus.
What this episode drove home to me is that saying that someone is half asleep, or only partly awake, is often literally true. Some parts of the brain may boot-up, come on-line, get in-gear, be hooked-in (etc.) more quickly than others. My ability to stand up and investigate the source of a sound may precede by several seconds my ability to process that sound. Or someone being read to at night may lose the ability to remember what is going on in a story long before she is asleep enough to not understand each sentence. Some bits of my brain don't seem to start working until after breakfast, and I don't even take caffeine. I've more than once had the experience of waking up and being totally unable to move for several seconds, with mobility then returning over the course of two or three seconds in different sets of muscles.
All this comes to mind because of an interesting article in New Scientist, on the non-monolithic nature of sleep. I recommend it, because it makes very clear how overly simplistic many models of human consciousness are, and how little we understand.
What this episode drove home to me is that saying that someone is half asleep, or only partly awake, is often literally true. Some parts of the brain may boot-up, come on-line, get in-gear, be hooked-in (etc.) more quickly than others. My ability to stand up and investigate the source of a sound may precede by several seconds my ability to process that sound. Or someone being read to at night may lose the ability to remember what is going on in a story long before she is asleep enough to not understand each sentence. Some bits of my brain don't seem to start working until after breakfast, and I don't even take caffeine. I've more than once had the experience of waking up and being totally unable to move for several seconds, with mobility then returning over the course of two or three seconds in different sets of muscles.
All this comes to mind because of an interesting article in New Scientist, on the non-monolithic nature of sleep. I recommend it, because it makes very clear how overly simplistic many models of human consciousness are, and how little we understand.
Crazy like a crow
I've seen a lot of birds doing a lot of bizarre things. But I couldn't figure out what the heck this crow was doing. Yesterday afternoon, as I was leaving work, I saw a hooded crow (one of the common urban birds hereabouts) flying in the most bizarre bouncy way. Flap hard to climb, drop sharply, pull up, flap upward, attempt to hover, sliding from side to side, drop sharply and repeat. It weaved and bobbed 30 meters above a road full of moving cars. All I could think was that it was playing (which was surprising because crows usually play when there are other crows around to impress, and this was the only one in my line of sight). Then I noticed it had something in its beak. A small ball on a string, or something such. It repeatedly, and obviously intentionally dropped it, only to dive downward and catch it again, then regain altitude for another drop. Several times I thought the what-ever-it-was would fall on one of the moving cars, but the crow always caught it before it could fall that far. After a couple of minutes of this, the crow changed position, flying high over the broad and mostly empty sidewalk on which I stood. After a couple of false starts it dropped its cargo, which plummeted to crash in the middle of the sidewalk, in a clear area with little leaf debris and no people within 20m . As the crow came in to land, I ran over to see what the thing was. It watched me, keeping maybe 5m back, but obviously not ready to take off. The something it had carried, dropped and broken was a large chestnut, now cleanly cracked in half, with the meat easily accessible through the shattered shell.
I backed off and let the crow enjoy its well-earned meal.
Language Learning
Today Iris and I are each trying to learn a language. Iris is out, walking around Rostock, investigating the various schools in town that offer German classes to auslanders. I am focusing on learning a much more broadly used language, R. Now Germany is certainly used by more people than is R, and R isn't really anybody's first language, but R is used all around the world, and by a surprising range of people. Yesterday a colleague who has been in Germany for a year and not yet learned German said to me, "I'm not staying in Germany forever, and German isn't going to do me a whole lot of good outside of a few countries, but R I will need for every job I might ever have."
R is a simple programming language intended for statistics and data analysis. It is rapidly becoming the standard for advanced data analysis, in the natural and social sciences, from advanced college students to statistics professors, and in every country where people with internet connections need to analyze data.
Back in the 1970s, Bell Labs developed a programming language called S (for "statistical") and somehow, in the mid '90s had the wisdom to release an open source version of it, called R. R had the wonderful property of being easy to extend. Any user can, invent new words for this language and tell the computer exactly what to do when users used those words. This is equivalent to English's allowance of the sentence, " From now on, let's use the word reflop to mean 'to flip something over, and then flip it back to its original position.'" Users can also find something they don't think works well, look at the underlying language, and tell the computer, "from now on, I want this word to mean X, not Y as it did before." Users have added and modified Graphical User Interfaces, make implementations that work inside other programs, and compiled packages for every major operating system.
These extensions and modifications can be uploaded to the R website, and other users can decide which bits and pieces they want. Every once in a while a pre-fab version is released, with all the most recommended bits and pieces, and with someone having checked that they all work well together. So every user is necessarily a programmer, and every programmer can fairly straightforwardly improve on the model. It is as though every user of an open source browser such as Firefox in learning how to use the browser also necessarily learned how to make improvements to the browser. By this model R quickly and clearly outstripped S and S+. I am sure there is someone out there who still uses S, but not many. R is more versatile, more widely used, has elegant add-ons in fields from architecture to phylogenetics, and is entirely free. It's the feel good statistics package of the decade, and a serious threat to the business model of anyone who makes money selling data analysis software (which can often cost hundreds of dollars for a single user).
At the Max Planck Institute for Demographic Research, where I've recently started working, everybody uses R. The simulations are in R, the data queries are in R, statistics are in R and the figures and graphs are created in R. R is more necessary than German for anyone at the Institute. Which is why I am dedicating the next couple of weeks to learning it. As with any language, the largest part of learning R is trying to using it, failing to be understood, and trying again. So I've given myself a task, outlining in English a simple simulation I need to perform for a paper I'm revising. Programming this requires about 50 steps. So far I've figured out the first three, and I'm stumped on the fourth. Even so, I think my R is already better than my German.
R is a simple programming language intended for statistics and data analysis. It is rapidly becoming the standard for advanced data analysis, in the natural and social sciences, from advanced college students to statistics professors, and in every country where people with internet connections need to analyze data.
Back in the 1970s, Bell Labs developed a programming language called S (for "statistical") and somehow, in the mid '90s had the wisdom to release an open source version of it, called R. R had the wonderful property of being easy to extend. Any user can, invent new words for this language and tell the computer exactly what to do when users used those words. This is equivalent to English's allowance of the sentence, " From now on, let's use the word reflop to mean 'to flip something over, and then flip it back to its original position.'" Users can also find something they don't think works well, look at the underlying language, and tell the computer, "from now on, I want this word to mean X, not Y as it did before." Users have added and modified Graphical User Interfaces, make implementations that work inside other programs, and compiled packages for every major operating system.
These extensions and modifications can be uploaded to the R website, and other users can decide which bits and pieces they want. Every once in a while a pre-fab version is released, with all the most recommended bits and pieces, and with someone having checked that they all work well together. So every user is necessarily a programmer, and every programmer can fairly straightforwardly improve on the model. It is as though every user of an open source browser such as Firefox in learning how to use the browser also necessarily learned how to make improvements to the browser. By this model R quickly and clearly outstripped S and S+. I am sure there is someone out there who still uses S, but not many. R is more versatile, more widely used, has elegant add-ons in fields from architecture to phylogenetics, and is entirely free. It's the feel good statistics package of the decade, and a serious threat to the business model of anyone who makes money selling data analysis software (which can often cost hundreds of dollars for a single user).
At the Max Planck Institute for Demographic Research, where I've recently started working, everybody uses R. The simulations are in R, the data queries are in R, statistics are in R and the figures and graphs are created in R. R is more necessary than German for anyone at the Institute. Which is why I am dedicating the next couple of weeks to learning it. As with any language, the largest part of learning R is trying to using it, failing to be understood, and trying again. So I've given myself a task, outlining in English a simple simulation I need to perform for a paper I'm revising. Programming this requires about 50 steps. So far I've figured out the first three, and I'm stumped on the fourth. Even so, I think my R is already better than my German.
Tuesday, October 06, 2009
Something's doing at the zoo
I can think of nothing that divides the opinions of animal lovers more than zoos. To some they are horrid spectacles where wild animals are locked in little cement boxes for the public to gawk at. To others they are a way to educate the public about wildlife while adding to our knowledge of each species and contributing meaningfully to conservation efforts. Some view zoo animals as living short boring lives of confinement, while others view zoos as predator, poacher and disease free shelters for species rapidly declining in the wild. Both groups are passionate in their support of animal welfare, and both are partly right about zoos. Zoos for a very long time were, and to some extent and in some places still are, places where animals are kept in very unnatural conditions for the gawking pleasure of humans. Zoological gardens originally cared little about the welfare of the animals, beyond the expense of replacing them. When most modern zoos were opened, animals usually were kept in small hard cages with no natural elements and nothing to do. It is still possible to find many zoos like this, and many cages like this even in the more modernized zoos. But many zoos, including most I have been to in the US, are actively and intentionally reforming themselves, and have been gradually improving for some decades. Rapid improvement is difficult while one has a large group of animals to keep. You can't simply bull-doze the whole place and start anew. Rather you must find what open space you have and build a new tiger habitat, then move the tigers there and rip up their old cages to build a large outdoor space (with winter quarters underneath) for the baboons. When that is done, and the baboons are safely outside, the monkey house can be rebuilt, and so on. In a few decades when all the old cages are gone, you will realize that the tiger habitat you built really isn't big enough for tigers, and you can start the cycle again. So changing from a bad old zoological garden to a new fancy new wildlife conservation and education center takes decades.
I recently had the pleasure of visiting one of the most advanced and impressive zoo I've been to, the Copenhagen Zoo. In overall appearance and plan it reminded me very much of the Bronx Zoo, where I worked for a short time. In fact it was so similar I have no doubt many of the same people were involved in planning the individual habitats in the two zoos. The two are so similar that I could say to my wife, "this looks just like the place in the Bronx Zoo where they have the crocodiles and river turtles," only to turn the corner and find the crocodiles and river turtles in nearly identical enclosures.
Almost all of the enclosures were state of the art, made to look and feel as much as possible like habitat, with places the animals can go to get out of the weather, and out of the view of tourists, or where they lay in the sun if they so choose. They had a large display (in Danish, so I couldn't read any of it) on the bad old way of doing thing, set up so that the viewers actually walk through a series of cold cement cages with giant steel bars where rhinos and hippos used to be kept. But what impressed me most was the attention paid to making sure the animals had something to do. The anteater ate not from a trough, but from a rotten log with numerous holes drilled in it and food stuffed into each hole. This gave it something to do with its improbably long tongue and impressive curved claws. Rather than laying around looking bored, it spent its time ripping open logs and licking food out from inside them.
Inside the impressive new elephant house the elephant also has to work for its food. I spent half an hour watching an elephant attempting to extract its food from a large barrel hung 5 meters off the ground. The barrel hangs from a rope, such that the elephant can barely reach it with its trunk. By repeatedly whacking the barrel with the tip of its trunk it can make it swing enough that eventually some of the food inside spills out on the ground. The elephant then eats this and goes back to whacking the barrel. By the time the meal was over, the elephant looked honestly tired, a rare and precious thing for a zoo animal.
The bears spent enough time digging in their enclosures (with enough magpies and starlings closely following them) that I can only assume there was food buried somewhere in there, with the location changing from day to day. Over and over throughout the zoo we saw animals doing something.
The term in the zoo community for this is behavioral enrichment, and it turns out to be incredibly important not only for the animal's mental state, but for their overall health, their longevity and the satisfaction and education of the viewing public. Crowds these days don't just want to see an elephant standing there, they want the elephant to be happy, and they want it to be doing something. In the Copenhagen Zoo, the animals are doing something, and usually it is something similar to an actual behavior observed from the wild. Wild elephants really do whack and grab overhead food with their trunks. Anteaters really do tear open rotten logs. Behavioral enrichment takes a lot more thought, and a lot more work, than dumping food in a trough, but it makes for a wonderful zoo. (A recent episode of the NPR show Radio Lab focuses on Zoos, and talks a lot about the importance of behavioral enrichment.)
We spent about eight hours walking around the Copenhagen Zoo, and saw most but not all of it. I strongly recommend it to anyone who loves animals, whether or not you love zoos. I took about 500 pictures that day, 60 of the better ones are linked to below.
 |
| Copenhagen Zoo |
Demographic Decline
There are no national rankings for departments of Demography in the US. If there were, UC Berkeley would certainly be near the top, and would likely rank first. Four of the five core faculty members have been elected to the National Academy of Sciences, and the last is relatively young. (The entire Academy has about 2100 members, out of perhaps a million PhDs who could potentially have qualified). I had the good luck to stumble into association with this department, benefited greatly, and was tremendously impressed.
This department contributes tremendously not only to Berkeley, and the field of Demography, but to our civilization's progress in understanding how populations function, how populations are likely to change in the future, and what effects these changes have on our economy, society and environment. Methods developed at Berkeley are at the core of the United Nations' understanding of population trends and their importance. Alumnae of Berkeley's rather small program in Demography can be found in almost every important institution making use of demographics, from the US Census Bureau to every major branch of the UN, to departments of Economics, Sociology, Anthropology and Epidemiology at most major universities, to think tanks, research organizations, and major corporations. The people that come out of this program are predictably smart, creative, quantitatively talented and know how to ask important questions and answer them convincingly. It is everything that graduate education should be. There are not many rooms full of people in which I feel slow, but discussing research with a bunch of Berkeley demographers required me to manufacture a fair bit of bravado. Among Berkeley's graduate programs, so many of which are at the top of their field, Demography stood out to me as a bastions of professionalism and brilliance.
Unfortunately, like so many of Berkeley's programs, Demography is in clear and present danger from the current fiscal crisis, and several of its students have hinted to me that it could easily cease to exist in a relatively few years. This happened once before. The following is an excerpt from a 1991 interview with Albert H. Bowker, Berkeley's sixth chancellor (1971-1980):
Demography was brought back by a group of faculty who are themselves now of an age where even many dedicated academics retire. The Demography department is, as a professor in another department put it "highly age structured." Beyond this older group, they brought in a few younger faculty, shared with the Department of Sociology. One of these recently left for a better offer in Texas. The department is unable to replace her because of the budget crisis. Another scheduled faculty search was cancelled. If recruitment remains frozen for longer than the faculty's more senior members care to continue teaching, (which is quite possible) the department could easily be back to one or two professors. One of these has already said that if this were to happen he could simply join another department. The current administration, may or may not remember what Demography is, or care whether it is important, and is unlikely to make any particular effort to save the department from attrition.
This department is of course just one casualty of the budget cuts to the University, which is in turn only one portion of the destitution of California's public education system, which is in turn only one piece of the general collapse of governance in California. To me, of course it means more than that. I wasn't actually a student in the department, but I spent enough time there to know I was surrounded by the best humanity can produce finding out things that humanity desperately needs to understand. This department is one of the best pieces of the best school in what was once the most ambitious public education system in the world, and it hurts to see it left to atrophy. This abandonment of greatness symbolizes for me what ails California, and America.
This department contributes tremendously not only to Berkeley, and the field of Demography, but to our civilization's progress in understanding how populations function, how populations are likely to change in the future, and what effects these changes have on our economy, society and environment. Methods developed at Berkeley are at the core of the United Nations' understanding of population trends and their importance. Alumnae of Berkeley's rather small program in Demography can be found in almost every important institution making use of demographics, from the US Census Bureau to every major branch of the UN, to departments of Economics, Sociology, Anthropology and Epidemiology at most major universities, to think tanks, research organizations, and major corporations. The people that come out of this program are predictably smart, creative, quantitatively talented and know how to ask important questions and answer them convincingly. It is everything that graduate education should be. There are not many rooms full of people in which I feel slow, but discussing research with a bunch of Berkeley demographers required me to manufacture a fair bit of bravado. Among Berkeley's graduate programs, so many of which are at the top of their field, Demography stood out to me as a bastions of professionalism and brilliance.
Unfortunately, like so many of Berkeley's programs, Demography is in clear and present danger from the current fiscal crisis, and several of its students have hinted to me that it could easily cease to exist in a relatively few years. This happened once before. The following is an excerpt from a 1991 interview with Albert H. Bowker, Berkeley's sixth chancellor (1971-1980):
Q: I don't want to skip over some of your other activities with various departments, if you'd care to pick up on that again. Let's see, we had Department of Demography.
Bowker: Demography was a small group, and it had a lot of trouble recruiting faculty, largely because it was dominated by Judith Blake. I just decided to abolish it, largely because it was just one person, really, on permanent position. It's just something you can have or have not, not an important subject. There are some subjects that every university must have-- mathematics, physics, chemistry, biology, history, English, philosophy, some of the languages, and others. Demography is not one of them, and criminology is not one of them. If you have it, it ought to be good and large. They kept bringing it back, and apparently that was not so much on intellectual grounds. It's a silly subject and the group there couldn't be very effective. Then Judith left, and somebody revived it, not in my day.
Q: Do you remember the Department of Design?
Bowker: Vaguely. Yes, we abolished that for the same reason, I guess. I've forgotten now what design was.
Demography was brought back by a group of faculty who are themselves now of an age where even many dedicated academics retire. The Demography department is, as a professor in another department put it "highly age structured." Beyond this older group, they brought in a few younger faculty, shared with the Department of Sociology. One of these recently left for a better offer in Texas. The department is unable to replace her because of the budget crisis. Another scheduled faculty search was cancelled. If recruitment remains frozen for longer than the faculty's more senior members care to continue teaching, (which is quite possible) the department could easily be back to one or two professors. One of these has already said that if this were to happen he could simply join another department. The current administration, may or may not remember what Demography is, or care whether it is important, and is unlikely to make any particular effort to save the department from attrition.
This department is of course just one casualty of the budget cuts to the University, which is in turn only one portion of the destitution of California's public education system, which is in turn only one piece of the general collapse of governance in California. To me, of course it means more than that. I wasn't actually a student in the department, but I spent enough time there to know I was surrounded by the best humanity can produce finding out things that humanity desperately needs to understand. This department is one of the best pieces of the best school in what was once the most ambitious public education system in the world, and it hurts to see it left to atrophy. This abandonment of greatness symbolizes for me what ails California, and America.
Monday, October 05, 2009
The Jellyfish of Copenhagen
Unlike French toast, Danish pastry is actually a specialty of the country it is named for. So while visiting friends in Copenhagen, we had little choice but to make frequent visits to the "Lagkagehuset," pronounced "La-Kay-Who-set" and meaning "The Layer Cake House." Our friend Nisha assured us that this was the best bakery in Copenhagen, and judging by their pastry this seems likely. (Broader sampling may be necessary at some point.) Lagkagehuset is next to one of the many canals that crisscross Copenhagen, and one morning as we sat eating our pastry, I noticed something floating by, maybe a plastic bag. The way it moved caught my eye because it didn't seem entirely passive. I went to take a closer look, but it was gone, moving quickly downward in the water. Too quickly to be a plastic bag, unless there was a sudden and sharp down current. Watching for a moment more, another floated into view, and it was a jellyfish! A big one, as big around as a dinner plate, but with tentacles only a hand long. As we stood and watched dozens more gradually floated by, apparently feeding on the numerous small silver fish moving in schools through the canals. I was surprised to find so much active, apparently healthy sea life in the middle of a major metropolis. Over the next few days every time I glanced into the canals there were jellyfish. Copenhagen's water seems to support lots of little fish, and the jellyfish seem to be their main predators. I've heard that in at least some cases (e.g. where the Mississippi's nutrients spill into the Gulf of Mexico) jellyfish thrive in polluted waters. The water in the canals of Copenhagen look pretty clear, but it is a major metropolis, so I'm not sure if the jellyfish in this case indicate dirty water or a healthy ecosystem. Either way, it is cool to see them floating by.
Friday, October 02, 2009
Wadden Sea
Imagine if you will a big flat muddy seabed. Various rivers and ocean currents deposit mud, silt, and sand onto it for ages. Currents may dig a slightly deeper part here, cause a raised area to form there, but basically its flat. Next, suppose global sea level drops. The top of the water is about equal with the top of the accumulated sediment at the bottom of our flat sea. Where the sediment is piled high, it might stick a meter or two above the water. Where the sediment is low water will remain, but not be very deep. And everywhere there will be mud.
Something very much like this has, over the eons, repeatedly occurred in what is currently the Wadden Sea area. Wadden Sea is the Anglicization of the Danish 'Vadehavet' which means mud-flat sea. In southwestern Jutland (the part of Denmark on mainland Europe), down through northwestern Germany and west across the northern Netherlands, simple daily tides still move the shoreline in and out by some miles. In between are extensive mudflats. As was done in Holland, the people of southwest Denmark gradually, over centuries, drained much of this tidal area with dikes, building walls over which the tide cannot climb (except during large storm floods, which throughout the middle ages would occasionally overcome the dikes and drown thousands of people). Despite the dikes, and the normally small tides of ~1.5m, the inter-tidal zone is many km wide in this area.
Iris and I spent a day on Mandø, an island in the Wadden Sea. The Danes long ago surrounded the island, which is only a few kilometers across, with dikes, and most of the interior is grazing land for cows and sheep. There is also a village of about 50 people, and an environmental education center/hotel, where we stayed. Outside the dikes, which are basically just 3-5m high slope-sides earthen walls grazed by sheep, there are wetlands surrounded by huge areas which daily alternate between being land and sea. At low tide one can drive to Mandø, or go for long walks on the mud-flats. At high tide it is water on every side for miles.
100m or so outside the dikes most of Mandø's shoreline (if it can be called that when it is often miles from the water) is ringed by fences that are about knee high. Each fence is made of two rows of sticks driven vertically into the mud, with thinner sticks, bits of brush and whatever else tied into bundles and wedged into the space between the two lines. Iris and I were mystified as to what function this short fence could perform, other than giving homes to billions of barnacles and perches to the preening shorebirds. It turns out these funny little fences, over generations, wrest land from the sea. At high tide water with sand and mud in it pours through, over and around the fence. As the tide recedes, much of its sediment gets caught in the bundled brush, like krill in the baleen of a whale. The area within the fence eventually fills with soil up to the top of the fence, and another fence is built further out. Repeat for 1000 years and add sheep.
Danish policy, now that they finally have the technology to seize the entire mud flats in years rather than centuries, is to let the boundary stand where it is. Let the shellfish, the shorebirds, the mud worms and the crabs keep what they have, and let the farmers keep their hard-won dry land. This summer Nationalpark Vadehavet became the largest national park in Demark. (Germany has also made large portions of its piece of the Wadden Sea into national parks.) It is bizarre, mysterious and wonderful to visit, and a glorious piece of wildness on the edge of all too tamed northern Europe. Global climate change may well doom the Wadden Sea to return to just being a flat seabed, so I suggest a visit sooner rather than later.
Here are a few photos:
Something very much like this has, over the eons, repeatedly occurred in what is currently the Wadden Sea area. Wadden Sea is the Anglicization of the Danish 'Vadehavet' which means mud-flat sea. In southwestern Jutland (the part of Denmark on mainland Europe), down through northwestern Germany and west across the northern Netherlands, simple daily tides still move the shoreline in and out by some miles. In between are extensive mudflats. As was done in Holland, the people of southwest Denmark gradually, over centuries, drained much of this tidal area with dikes, building walls over which the tide cannot climb (except during large storm floods, which throughout the middle ages would occasionally overcome the dikes and drown thousands of people). Despite the dikes, and the normally small tides of ~1.5m, the inter-tidal zone is many km wide in this area.
Iris and I spent a day on Mandø, an island in the Wadden Sea. The Danes long ago surrounded the island, which is only a few kilometers across, with dikes, and most of the interior is grazing land for cows and sheep. There is also a village of about 50 people, and an environmental education center/hotel, where we stayed. Outside the dikes, which are basically just 3-5m high slope-sides earthen walls grazed by sheep, there are wetlands surrounded by huge areas which daily alternate between being land and sea. At low tide one can drive to Mandø, or go for long walks on the mud-flats. At high tide it is water on every side for miles.
100m or so outside the dikes most of Mandø's shoreline (if it can be called that when it is often miles from the water) is ringed by fences that are about knee high. Each fence is made of two rows of sticks driven vertically into the mud, with thinner sticks, bits of brush and whatever else tied into bundles and wedged into the space between the two lines. Iris and I were mystified as to what function this short fence could perform, other than giving homes to billions of barnacles and perches to the preening shorebirds. It turns out these funny little fences, over generations, wrest land from the sea. At high tide water with sand and mud in it pours through, over and around the fence. As the tide recedes, much of its sediment gets caught in the bundled brush, like krill in the baleen of a whale. The area within the fence eventually fills with soil up to the top of the fence, and another fence is built further out. Repeat for 1000 years and add sheep.
Danish policy, now that they finally have the technology to seize the entire mud flats in years rather than centuries, is to let the boundary stand where it is. Let the shellfish, the shorebirds, the mud worms and the crabs keep what they have, and let the farmers keep their hard-won dry land. This summer Nationalpark Vadehavet became the largest national park in Demark. (Germany has also made large portions of its piece of the Wadden Sea into national parks.) It is bizarre, mysterious and wonderful to visit, and a glorious piece of wildness on the edge of all too tamed northern Europe. Global climate change may well doom the Wadden Sea to return to just being a flat seabed, so I suggest a visit sooner rather than later.
Here are a few photos:
Iris on the mud flats
Disintegrating coastal fence encrusted by shellfish
Oystercatchers like this one are extremely numerous in the Wadden Sea. Their long stout bills are perfect for wrestling invertebrates out of the mud.
Subscribe to:
Posts (Atom)
