See no seagull

One advantage to living in the tallest building in town is that we can see who's sneaking around on the roofs of other buildings. That is in fact part of why our building was built so tall. Back when this was the German Democratic Republic (East Germany), this building was occupied mostly by the  Stasi (secret police) whose job it was to keep an eye on everyone all the time and their families. 

The building next to ours was the Stasi office building for the state. It has not only been taken over for university use, but there are Herring Gulls nesting on its roof. I spotted two big chicks wandering around yesterday. It is a great place for nesting: high up, with a rim so the chicks won't jump out, and fitted with the finest 1970's surveillance equipment. The roof is even roughly chick-colored, which is probably why until now I have seen no seagull.

lebenslauf

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

Will the culture shock ne'er end?

Cold and Fat

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

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

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

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

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

Rostock ten day forecast

Snow
Snow
Mostly Cloudy
Snow
Snow
Snow
Snow
Snow
Snow
Snow

I must really love science, as I don't know what else would keep me in this sun-forsaken place.

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.

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

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.

And it's off to Germany with us

I spent last week in Berkeley. My finishing talk was the first joint demography and biology seminar at Berkeley in at least 30 years, possibly ever. I closed with an appeal for the demographers and the biologists to talk to each other more. Evolution is the source of many ultimate explanations in demography, and demography has extremely important methods and insights for understanding evolution in age-structured populations. There was a good discussion, with the demographers and biologists both asking questions, and even talking to each other. Then I spent a couple of days fighting my way through the bureaucracy surrounding the filing of dissertations. I filed, cleaned out my office, packed up my stuff and missed my plane east. I went standby, got to my parents' house at 5AM the next day, spent a day with the family. Then we rushed to the airport only to find that our flight to Germany was canceled because the flight attendants are on strike. Air Berlin assures us we will get to fly today, but in the mean time we are in the JFK Holiday Inn. Being stuck here has given me my first chance to stop and reflect on the fact that:

1. I am now Dr. Daniel Levitis, Ph.D.
2. I am moving to Germany.
3. After nursery school, kindergarten, elementary school, junior high, high school, college and grad school, 22.5 years of schooling in all, I am no longer a student. Being a student was getting pretty old anyway.
4. I am starting a new job very soon, and don't know exactly what I will be doing.
5. I am on vacation for the next few weeks.

Time to go see if our flight will happen today. Posting may be sporadic until I am ensconced somewhere.

What I've been working on

Here is the last bit of my post-doc fellowship application:

Summary and Conclusion:
Evolutionary Biodemography has focused on explaining late-life mortality patterns and overall longevity. The evolutionary basis of early-life mortality has been studied more rarely and less systematically. My proposal boils down to four basic steps intended to firmly establish the field of early-life evolutionary biodemography:
1. Mathematically define and parameterize the age specific mortality patterns that characterize Human-like Early-life Mortality (HEM).
2. Compile, review and organize those evolutionary hypotheses potentially explaining HEM.
3. Use these hypotheses to predict life-history traits that may be necessary causative factors of HEM, and thereby predict which taxonomic groups are not subject to HEM.
4. Gather data to determine in what species or populations, if any, HEM does not occur, thereby testing my collection of evolutionary hypotheses.
Early life mortality has a tremendous effect on a wide range of populations, and our failure to date to understand its evolutionary basis is a major gap in our understanding of both evolution and demography. Working at MPIDR, I will begin to fill that gap.

Compresed Timeline

The Max Planck Society is a network of research institutes, mostly but not entirely in Germany. Many people consider it, to be the world's leading non-university research organization. The member institutes are more or less autonomous in terms of planning and executing research, as far as I understand, but all of them have the reputation for world-leading excellence.

A couple of years ago, at a conference on aging I had the pleasure of meeting the Executive Director of the Max Planck Institute for Demographic Research, Jim Vaupel. At the time, he and my professors, Ron Lee, discussed the possibility of me coming to MPIDR at some point. I was excited by the prospect. Here at Berkeley there is effectively no one outside of Ron's lab group who thinks much about the kinds of questions I do, while MPIDR has a whole Evolutionary Biodemography Lab, at which they think about and work on pretty much everything I do, plus a lot more.
But then I went off to PNG, and then I was injured, and pretty soon I figured the opportunity had passed. But then I got an email announcing that there was a fellowship available through the German Academic Exchange Service (better known by its German acronym, DAAD, for North American researchers to come work in Germany if they had the invitation of a German institution. The email conversation that followed was suprisingly short, spanning little more than 24 hours, and completely reorganized my timeline for finishing grad school. If I may paraphrase, it went something like this:

Me to Ron: Should I apply for a DAAD fellowship to work at MPIDR.
Ron to me: Do you want me to ask them?
Me: Yes, thank you.
Ron to Jim Vaupel: Dan is an excellent young biologist, should he apply for a DAAD fellowship to come work there?
Jim to Ron (to me): Yes, he should apply, but even if he doesn't get the fellowship he should come here as soon as is convenient, and we can support him.

Just like that, no application, no interview, I had a desirable post-doctoral position lined up at a time when the economy is tanking and most of my peers are wondering if there will be any positions for them at all. My deliberations consisted of describing the situation to my wife to make sure she didn't mind spending some time on the Baltic, and emailing Dr. Vaupel to make sure I understood him properly.

What this means for my grad-school timeline is that instead of 16 to 21 months, I have eight to ten months to finish. I was thinking I would finish December of 2009 or May of 2010. After the offer from MPIDR, I thought I would have to finish by August of 2009. Afer talking to my major proffessor today, it is clear I need to be pretty much done by May of 2009.

My department's commencment is May 23rd 2009, and I plan to walk then, if at all possible. I won't actually be finished at that point, but I will be finished enough to convince my faculty persons that I can file my disertation before the end of summer. My wife's graduation from UC Davis is mid-June 2009. That summer I will finish my dissertation, then we will pack up our lives, take the cat's to my sister's house, and fly to Germany.

That seems like a lot to accomplish in one year.

Yikes.