Octopuses good, octopi non-existent.

Note to world: the plural of octopus is octopuses, not octopi. I have discussed this with more than one expert on octopuses, and they consistently report that 'octopi' is is just plain wrong. Octopus comes from Greek roots (octi=eight, pous=foot), not Latin. Greek does not pluralize words ending in -us by ending in -i. That is Latin. The old fashioned plural was octipodes, but that went out with dropsy and mammifers.

Will do math for chocolate

I don’t usually pay too much attention to the conversations in my office that are in German. My office mates both have many people coming in to talk to them and are both German, so speak in German with their German visitors. This particular conversation caught my attention primarily because it repeatedly used the work ‘Schokolade” one of the few German words I have no trouble with. Also there were four people involved. Eventually one of my office mates said, “Ask Dan, he is very interested in chocolate!”

So the conversation was about a simple demography puzzle, and my boss had offered a chocolate bar to whoever solved it first.
The problem is this: 100% of a population were alive at the beginning of a year. 60% were alive at the end of the year. Assuming that the mortality rate is constant throughout the year, what percentage of individuals were alive at the exact middle of the year?

Note that a constant mortality rate does not mean that the same absolute number of individuals die each day, but rather than the same proportion of those starting the day alive end the day dead.
Motivated by chocolate, and using one simple bit of algebra, I secured the Intense Orange Lindt dark chocolate bar.

So I can’t hang a chocolate bar in the comments section, but I can promise kudos if you can tell me what portion of individuals were alive after six months, and how you got that answer.

What I'm literature searching for now..

how does one tell if a fruit fly egg has died, other than waiting to see if it hatches, which doesn't tell me at what developmental stage it died, which is what I want to know.

So far I can't find any evidence that anyone has a method for this.

Brain melt.

I have been sick to various degrees, and with various different bugs, continuously for the last three weeks. Tonight I am developing a fever again.

It is very hard to get any science done while I am sick. Partly there is the general lack of energy, lack of focus and slow mental activity. But I also make the weirdest mistakes while I am sick. I send people emails with the same sentence three times in a row phrased slightly differently each time, without realizing I am repeating myself. I decide that I have accidentally deleted all my emails when in fact I am just looking at the wrong mailbox. I write a thought that pertains to one paper into a different paper, then have trouble figuring out which paper it is.

I understand that my body is scaling back on certain activities (such as cognition) so as to be able to go all out on others (immune response), but honestly given the quantity of lipids I am carrying around I would think a little bit of multitasking could be supported.

A fallacy in need of a name

At a party I attended earlier this year, one particularly vehement guest announced that, "Russia was justified in bombing civilian targets in Georgia because Georgia had killed ethnic Russian civilians in South Ossetia." I pointed out to the vehement fellow that neither Russian law, nor Georgian law, nor international law, nor moral reason allow for collective capital punishment based on ethnicity or nationality, and therefore of course it doesn't make any sense that if the Georgian military killed ethnic Russian civilians, the Russian military is allowed to kill Georgian civilians. Unable to refute this logic, he switched to another argument, using the same logical fallacy, claiming that we as Americans cannot object to the behavior of the Russian government, because the American government has killed so many civilians in so many countries. When I pointed out to him the possibility that the Russian and Georgian and American governments may all, simultaneously, be culpable for their own actions, and that we need not be apologists for any war crimes, despite the multiplicity of criminals, my wife suggested it was time we leave the party. This was a very sensible suggestion, so we did.

I've recently written about the importance of having names for common logical fallacies, and this got me wondering what the name for this guy's fallacy is. It is an extremely common one, and is in no way original to him. The fallacy is this: assuming or implying that if one side in a debate/argument/conflict is wrong/guilty the other side is therefore right/justified. This most often comes up in moral contexts, where the misdeeds of one party are used as a defense for the misdeed of the other party, but is also used in the context of disagreements about fact. For example when it comes out that an evolutionary biologists was wrong about anything, creationist make the leap to this being proof of Creation, rather than simply a flaw in the thinking of a biologist. One side is wrong, so the other must be right, even if the flaw is immaterial to the disagreement. Similarly, it is common in interpersonal disagreements to hear one party respond to an accusation of misbehavior only by pointing out a misbehavior of the other party without ever replying to the statement about their own behavior. This often goes well beyond "two wrongs make a right" to "my behavior is necessarily right because yours is wrong." This is also distinct (and almost opposite) from the idea of moral equivalence. In the Arab-Israeli conflict, for example, some people argue that the crimes committed by supporters of the two sides are morally equivalent, and therefore neither side can be held responsible. Each side often responds to this nonsense with the counterfallacy that our behavior, whatever it may be, is justified by their crimes. They are criminals therefore we are just. I would tend to assume that each party or individual is responsible for its own actions, and whether or not the crimes are equivalent is morally irrelevant.

So this raises three sets of questions for me:

1. What is this fallacy called? If we want to describe a response as following this pattern, how should we refer to the pattern?

2. Why do humans do this so freely? On some deep level are we programmed by evolution to use this type of rationalization? Is this culture specific, or do all humans do this?

3. Why is this particular type of illogic useful/successful in arguments? Perhaps it is particularly effective because it allows one to move from being on the defensive to being on the offensive, to accuse rather than excuse (or to effectively do both at once)? Or maybe it is just very hard for people to find fault in both sides of a conflict at once, so by making them see the fault in the other side you make them forget about the fault in your own?

I'd appreciate hearing your thoughts on this, particularly what this type of fallacy should be called, or if it already has a name. I've checked Wikipedia's list of fallacies, and it ain't there.

The right's next big scare tactic

My office mate occasionally organizes a movie night, showing something or other that people at the Institute might want to watch in the seminar room. When he heard that there were two movies, called Demographic Winter and Demography Bomb, he figured they would be of interest to an Institute full of demographers, and he got a copy of the DVDs from somewhere.

Twenty or thirty of us came to watch. Now Demographers are a pretty staid crowd, but by ten minutes in people were chuckling, and within a half hour there was full-bellied, breathing-difficulty, rolled over in pain laughing going on. Clearly, people who actually think about demography were not the target audience.

These two documentaries, are based on the premise, which they take intensely seriously, that humanity (or at least the white section thereof) is at risk of economic ruin, political chaos, pain, suffering, homosexuality, the death of the traditional family and ultimate and total extinction because of a population control conspiracy by the UN, the EU, the Ford Foundation, Democrats, Liberals, Communists, UC Berkeley, Charles Darwin, Malthus, W.E.B DuBois, Gloria Steinem, Big Gay, Nazis, Feminazis, and most of all Paul Ehrlich. Dr. Erhlich, a professor at Stanford is a favorite punching bag of the right because he made many and varied dire predictions back in the sixties and seventies, and like most prolific prognosticators, many of his forecasts were wrong. His 1968 book, The Population Bomb, is identified as the driving source behind the idea that overpopulation might be a problem. In it he made various overly pessimistic predictions about the rate of population growth and the rate of food productivity growth, and concluded that we would see mass starvation of hundreds of millions of people by the 1970s or '80s. That this didn't happen is taken as proof that there are no possible ill effects of overpopulation, and that in fact humans are now heading toward population decline, which will by the end of the century see an under populated world dominated by geriatric patients, Muslims and Latinos. The same three or four animated graphics are shown incessantly, demonstrating that "westerners" (i.e., white people) are going extinct. "By the end of the century, there may not be any actual French people in France." They string together statements from representatives of various Teabagger interest groups and wildly out of context statements by academics (often repeating the same clip of the same academic to make it seem like they are agreeing with two very different ideas) with alternatively faux-reasonable and openly snarky narrators. The failure of the US auto industry, the housing bubble, immigration, homosexuality, terrorism, crime, feminism and the excesses of Wall Street are all shown to be symptoms of insufficiently rapid population growth. Demographers from all over the world hooted and guffawed and thought it was just the funniest damn thing they had seen.

Now like most vehemently presented lies, there is a grain of truth to the hysteria behind the movie. That grain is this: some, but not all, population forecasts predict that world population will cease growing some time around 2050, and may gradually decline for some decades thereafter, falling from maybe 9 billion to maybe 8.5 billion by 2100, and in the mean time the ratio of older people to younger people will temporarily increase. (Forecasts any further out than that are beyond the realm of speculation into pure fantasy, but one thing we can say with high confidence is that no population is likely to just stop breeding and go extinct.) This will pose some serious issues we need to think about over the next few decades. (I've written about this before, here.) Our markets, as currently structured, assume continuous population growth, and we don't yet have very clear ideas about how we need to adapt to population decline if it happens. Having lots of old people per working adult is a problem if you assume that it takes the same number of working adults to take care of each old person, and ignore that their will simultaneously be fewer children for those adults to take care of. The problem with the argument, even if you take out the hysteria, conspiracy theorizing, snarkiness, smear tactics and brain-washing techniques, is that overpopulation has known, current and disastrous consequences (see "Collapse" by Jared Diamond for several hundred pages on that, also a significant portion of the articles in Population and Development Review or Conservation Biology). I have never met a demographer who argues the problems of population decline are likely to be worse than those associated with population growth, or with trying to maintain a planet with more than 9,000,000,000 people on it. Second, I've never heard any demographer suggest that the cause of the eventual decline will be anything resulting from any policy of population control. Rather, educated, urban, mobile populations (and especially educated women) have fewer kids later in life, and that slows population growth. As the educational level and economic mobility of the world's women improves, and as people continue to move to cities, they will tend to reproduce less, no matter what the UN or Professor Ehrlich tells them. The clergy also have relatively little influence (see Italy).

But now that the lie is out there, no matter how laughable, it is a convenient tool for anyone who wants to argue against population control measures, family planning, contraception, feminism, etc. A friend pointed out to me a post on The Weekly Standard's blog stating that, "the discussion in demography circles isn't 'How do we cope with two extra China's?' Rather, it's "'How do we manage one of those extra China's disappearing?'" Living in a "demography circle," I can report that the Weekly Standard's unnamed source for that statement is a made-for-Fox-News propaganda special called "Demographic Winter" and its sequel (which borrows numerous lengthy sections from the first part) called "Demography Bomb." Type "population decline" into Google blog search and up come numerous posts on conservative blogs mumbling the same point.

So while my international colleagues were laughing their lungs out, I was exchanging dark glances with the only other American in the room. To those not familiar with the propaganda machine of the U.S. far right, the movie was pure, bizarre, hilarious fluff. Man-eating purple platypus stuff. One of my colleagues later asked me, "Republicans aren't idiots right? So they do not take that [compound expletive] seriously. Maybe a few nutballs? This is a joke?" But to me, it was clear this was yet one more battle being opened in the American right's war on science. As long as one is denying evolution, climate change and the moon landings, may as well claim that demographers don't see any possible drawbacks to overpopulation, and in fact that population collapse is just around the corner.

Expect to hear more of this particular lie in the years ahead. As the right touts the four biologists willing to deny the possibility of evolution, expect them to repeatedly trot out the few demographers willing to pretend that humanity's very existence is threatened by population control.

The climate tempest's teapot

You may have noticed the recent hullabaloo about the stolen email records from the Climate Research Unit at the University of East Anglia. The people who hacked into the system, and the climate-change-denier community generally, have taken the content of these emails as proof positive that climate science is all one big hoax. What they actually have is evidence that on one occasion one climate scientist informed his colleagues that he was doing some mildly misleading things to one graph to make it look prettier. Clearly he shouldn't do that, but this is proof of basically nothing beyond itself. I won't dwell on the point. Those who can't accept the global flood of evidence for anthropogenic climate change are not susceptible to logic or evidence, and none of the seven regular readers of this blog are among that crowd.

What I think is interesting about this is the extraordinarily high level of truthfulness we expect from our scientists these days. Journalists, politicians, doctors and lawyers are all expected to, in varying degrees, present pictures which are rosier, clearer, more advantageous or less illegal than the straight hard truth. A defense attorney is expected to find the most preferable interpretation of truth, rather than the straight up truth. Doctors need to make their patients feel comfortable and confident, even if that means overstating their confidence. No one is surprised when Republican appointed judges reach different decisions than Democratic appointed judges. Text-book writers are free to get as much wildly wrong as they want, usually for no apparent reason. Advertising is the art of misleading without directly lying in a provable way. But Phil Jones, the guy who fudged the graph, is resigning his appointment.

This is not to say that I think this level of expectation is a bad thing. Scientists don't have the excuses for bending the truth that lawyers or doctors or journalists have. We are supposed to fight desperately hard against our biases, against anything that prejudices our communications or thinking. Of course realistically many scientists fail to live up to this ideal, and there are (and should be) consequences when these failings are exposed. But one of the many things reactionary deniers of all sorts (moon landings, evolution, Holocaust, climate, HIV/AIDS, etc.) tend to refuse to see is that science also has powerful mechanisms for keeping any one person's malfeasance from making too much of a difference to our larger understanding. The more respected and influential a scientist is, the more people there are looking to poke holes in everything he does. The more enshrined an idea is, the more it benefits the career of a young researcher if she can point out a fatal flaw, an exception, a modification, even an unexplained corner. Every scientist that was ever great built his or her reputation and career by finding flaws, limitations or unanswered questions in the work of older, more established scholars. If I could produce convincing evidence that macroevolution doesn't happen, I would be the most successful scientist of the century (unfortunately for me, macroevolution happens, so producing that evidence is going to be hard). Under such a system, fakery may help get a single paper published, even help build a successful career, but it can't easily lead to a lasting consensus that is contrary to data that somebody else can go out and collect, because somebody is always trying to tear a hole in anything that could possibly be torn. The single best argument for anthropogenic climate change is that nobody has yet succeeded in blowing a hole in it.

"Possible to live forever"

Iris came to the Institute to have lunch with me. We were sitting and eating the tasty pasta dish she'd made when my friend passed by. He stopped to say hi. Iris picked up on the fact that he was excited about something before I did.

"What's new?" she asked.

"I have discovered that it is possible to live forever," he said, with no hint of irony.

"Oh?," I said, taking another delicious bite of pasta and doing my best to maintain a neutral tone.

He went on to describe how he had noticed that under a set of mathematical assumptions about the pattern of human aging, if one plugs in the right values for various parameters, one can get the result that life expectancy approaches infinity. I'm not going to give away his secrets, or try to explain the bit of calculus he uses, but the whole proof fit on one page including only a handful of equations. There, in black and white was mathematical proof that one could live forever. Well sort of. The math was impeccable, at least I couldn't peck it. The question is how relevant was the mathematical model, and how meaningful were the limits he was taking?

Often when we use mathematical models of the world it is because we think they not only approximate the outcomes of the pattern, but actually describe something about the underlying process. An object fired up into the air will fall to earth in a parabola, a real, honest, no tricks involved parabola. The form arises just from the interplay of momentum and gravity, and the parabola arises, not as a fluke, but under a wide range of gravities and velocities. In other words, we think that sometimes the mathematical ideal is what the world is actually approximating. There is thinking that the mathematical forms my friend employs actually are the underlying form of human aging. They are our best guesses anyway. So maybe, just maybe, exploring the limits of that form tell us something about the limits of possibility when it comes to aging. Unfortunately, relationships that hold under a wide range of velocities often don't hold at the limits. Shoot the object at an improbably high velocity and it will escape Earth's gravity entirely, and likely end up orbiting the Sun, eventually making an ellipse. Shoot the object too slowly and forces such as viscosity, friction and wind become increasingly important, and the object will trace a good approximation of a line-segment to the ground. So while my friend's mathematical discovery is interesting and novel, I remain skeptical that he has found the possibility of immortality. Rather he has shown that if one makes extraordinary and unexpected assumptions, one can arrive at extraordinary and unexpected conclusions. Important, but hardly the key to eternal life.

Sorry to be such a downer.

Stupid Eustachian tube tricks

From Wikipedia:

Some people are born with an ability to voluntarily contract just these muscles called Voluntary Tubal Opening, similar to the ability of those who can wiggle their ears. Those who have this ability can hear "pop" or "click" sound in the middle ear when actuating these muscles, and are able to hold the muscle contraction (some refer to this as 'clicking your ears to equalize the pressure').[citation needed] Doing so will make one's voice sound louder to oneself. This ability allows such people to voluntarily equalize pressures at will when making rapid ascents or descents, typically in aircraft flights or large elevation changes in either tall buildings or mountainous treks.

I am one of these people, although clearing my ears without swallowing wasn't something I was aware I could do until I took SCUBA classes some years ago. When I do this it makes a click loud enough that my wife can hear it if she puts her head close to mine. Unfortunately this doesn't seem to help in clearing a lingering ear infection, as I can't currently get my left ear to click.

Constructive trashing

I very much wanted to like the first paper I peer-reviewed. Having gotten some negative peer reviews on my own papers, I didn't want to inflict the same upon whoever the authors might be. So when the journal sent me the manuscript, I was eager to see the good in it. I wasn't able to find much. The analysis was poorly designed, the questions not clearly framed and the writing somewhat loose and hard to follow. The topic was interesting, and the authors had the data to address it well, but failed to do so. I decided that if I couldn't write a positive review I could at least give detailed criticisms, so that if the authors do rewrite the paper they will have some guidance on what needs to be fixed. To the authors this will look like two pages of dumping, at least at first. I hope they do rewrite, as it has the potential to be a useful paper, and I hope that if they do, they find my comments helpful.

I had decided beforehand that whatever I wrote, I would keep the review anonymous. This means that the journal editors know who wrote it, but the authors do not. They give reviewers the option of signing their reviews, but I'm not sure why. The temptation of course is to sign the positive reviews only, but this is considered something akin to slimy. I prefer to be able to give my opinion without considering what the authors might think of me, or how they will review my papers in the future. Unlike online forums where people can be as abusive as they want because they are entirely anonymous, here the editors of the journal know who wrote what and can respond accordingly.

I'm happy to have been asked, by a well-respected journal, to be a reviewer. I've learned from the experience. Perhaps I should request that next time they send me a paper I'll like?

conflation

Word of the day: Conflate (v)- to mistake two or more separate things as being only one thing, generally in a way that leads to further logical flaws.

from Latin con- (together) -flate (blow, as in inflate).

I'll give you a few examples of conflation:

There was, some years ago, a debate as to what to call that portion of the American electorate who wanted the US government to be run according to the precepts of the right-wing evangelical clergy in the US. Should they be the Evangelical voters, the Christian Right, the Values Voters? It seemed to many on the political left that we should simply use the word which by definition means, "those who advocate for government according to the rules of a particular religion." This word of course is "theocrats.' Leaders of this movement for Christian government, when asked about the term theocrat would reply that this word comes from Greek theos, meaning god and kratos, meaning rule or regime, and therefore theocracy is direct rule by God, and so they weren't advocating for theocracy, merely rule in the name of and in line with their understanding of the will of God. It is a common trick by those who wish to redefine a word for political or rhetorical purposes to conflate etymology with denotation.

In another example from the news, a large species of Atlantic ray, the flapper skate, has been fished nearly to extinction. It had been conflated with the blue skate, a smaller, faster breeding distinct species, such that for several decades we thought the two species were one, with the flapper skates merely being the larger individuals. As the number of larger individuals declined, no legal protections were put in place, as the relatively numerous smaller individuals indicated reproduction was still sufficient to maintain the population. Oops. Now that the two species have been deconflated, we know that the flapper skate is all but gone.

Finally, on this thanksgiving day, let us not conflate sweet potatoes, which are commonly eaten in North America, with yams, which are not. Whether orange or white, they are sweet potatoes.

So what, you might ask is the difference between conflation and confusion? The answer is that conflation is a specific type of confusion, one that is worth being aware of in its own right. Having a name for a logical flaw, in my experience, makes it easier to spot it.

Extinction is evolution

I often enjoy Olivia Judson's science blog on NYTimes.com. She has an actual science background, and gets the science badly wrong far less often than most other reporters of science.

Her most recent post is more in line with what I expect from science journalism. Without recapping her whole argument, she writes, "But if [evolution] has that much potential — how come organisms keep going extinct in nature? In other words, why does evolution keep failing?"

She then goes on to make a big deal about how evolution fails each time a population fails to evolve. But in so doing she fails to admit the distinction between evolution on the one hand and adaptation on the other.

Evolution is genetic change in lineages with time. Adaptation is the process by which the genetic makeup of a population is altered in a way that helps individuals of that population be more successful in their environment. Adaptation is one mechanism, and result of, evolution. It happens to be the best known mechanism, and the one that in the popular imagination defines evolution. But evolution has lots of other mechanisms. Genetic drift for example. Imagine you have a small population of squirrels on an island, some gray, some black. A disease comes through and kills a significant portion of the squirrels, and even though they are all equally susceptible to the disease, through the randomness of epidemiology more grays than black catch it and die. After the disease, the population has a higher proportion of black alleles than before. The population has evolved, because the proportional genetic makeup of the population has changed. But this is not an example of adaptation, because the genetic change was not caused by one version of the color gene conferring a selective advantage over the other. The allele frequencies "drifted" without being pushed by selective considerations. The next time the disease comes though more black squirrels could happen to catch it, and the allele frequencies could drift back.

So adaptation is not the be all and end all of evolution. Much of the evolution that happens is non-adaptive. And another important mechanisms of evolution is extinction. Imagine now that the disease killed not just some, but all of the squirrels on the island. That population is extinct. They are no longer represented in the genetic diversity of squirrels more generally, of rodents more generally, of mammals more generally. The remaining diversity, through the removal of that population, has changed. The extinct population has ceased evolving, but through their removal the larger group is left genetically less diverse. The genetic makeup of the larger lineage has changed, so evolution has occurred. It is also possible that the residual populations are more fit than the pre-epidemic average, because they are resistant to that particular disease. Whether or not this qualifies as adaptation depends on the fine details of the definition of adaptation you prefer. There is no standardly accepted definition, or rather different groups of biologists prefer different definitions. But all evolutionary biologists, save those who have crossed over into journalism, agree that extinction is an example of, not a failure of, evolution.

Return on Investment in Higher Education

One of the major debates in US politics is usually framed like this: Should we spend more on things that are worth doing, or should we maintain balanced budgets by spending less. The underlying assumption of this type of argument is that spending more necessarily worsens the budget outcome. If the budget outcome income minus spending, doesn't it make sense that spending more worsens the outcome? Only if we can assume that the spending does not spur more income. In other words, only if we assume that investment is impossible. Investment is spending intended to increase income.

After reading Mike Hout's recent article on the importance of public higher education, I was left wondering how public expenditure on higher education compared to other investments in purely budgetary terms. Mike points out that education leads to higher personal incomes, higher rates of entrepreneurship and other good things that increase tax revenues. At the same time education leads to lower rates of things that cost the state money, like imprisonment and needing public assistance through social security/unemployment/health expenditure. So I wondered, how does the expenditure function as a investment. If the state of California could either spend an extra Billion on education, or invest that money in the stock market, how fast would the market have to rise to give better returns than the education (ignoring the non-fiscal benefits of education)?

I wrote to Mike to ask him, and it turns out he is scheduled to give a talk on that very subject here in Rostock some time soon. He sent me a copy of a 129 page report he and colleagues wrote on the subject in 2005. A pdf of that report (or a draft of it) is here.


The concluding summary of the report says:

The state devotes a substantial portion of its budget to supporting education in
California. That support is not wasted: the costs of neglecting education are
high, and the return this investment brings to the state is equally high. Laudable
though it may be, California’s investment in higher education is insufficient. If
things stay as they are now, that is, if future students progress through their
educational careers at the same rates as their ethnic counterparts did in 2000, the
state will suffer a net loss, and that loss will increase as years pass. With no other
changes, the state will forgo revenues from the increased earnings that education
encourages, and pay more to support a population in a situation of increased
poverty and incarceration. If, rather than maintaining the per-person level of
educational support and access, the state were to limit capacity, the situation
would become even more dire.
However, based on existing trends in educational demand, we expect that high
school graduation rates and college going rates will increase, and demands on
state support for education will climb commensurately. California will have to
invest in community colleges and universities in the short run, but both the state
and its residents will benefit handsomely from this additional support in the long
run. Our calculations suggest net savings to the state will exceed the additional cost by three-fold or four-fold, while its population will enjoy lower levels of poverty, crime, and dependency, and higher levels of average income and political participation.

(Emphasis mine)

The report also specifies in great detail the time scale on which these returns occur, and the majority of returns are "realized in the first ten years after investment because the benefits it buys -- lower welfare, less crime, and healthier children -- are problems/ benefits that disproportionately affect 18-34 year olds."

Now this suggests that we are getting 300% return within the first ten years. So let's just say our $1Billion turns into $3Billion by the end of ten years. That is about 11.5% annual return on investment (1.115^10= 2.97), better than the 11% average rise in the Dow Jones from 1926 through to its pre-dot com bust peak in 1999.

I am a strong believer in the value of education, and would gladly quadruple expenditure on education, but I find this purely monetary claim incredible. This is such an extraordinary claim that we are forced to consider the background of the person making it. The only one of the authors I know is Mike, and what I know about him is that he is the Chair of the best Demography graduate program in the Western Hemisphere, a member of the National Academy of Sciences and a careful scholar. Mike does not go around spouting grand pronouncements. If he makes a claim like this it is because his analysis tells him it is true. There really is a strong argument to be made that in purely fiscal terms, investment in higher education pays off better and more consistently than investment in stock.

In that light, two things surprise me. First, that I haven't heard that argument made before. I hang around with a lot of people distraught about the direction American (and particularly Californian) higher education is going, and no one has ever mentioned this. Second, I'm amazed that Wall Street hasn't tried to securitize this yet.

I'm eager to hear what new work on the subject Mike will be presenting at his talk.

Finally, and sadly, I've just heard that Berkeley's demography department won't be able to accept any new graduate students this year. The lack of funding makes it impossible for them to hire faculty to replace those who have retired or left for better funded institutions. If this does not improve in the next few years, I would guess the department will have to close its doors.

Urg.

I just got back a paper I submitted last month. They didn't reject it, but they want major revisions. I'm currently too sick to think through exactly what needs to be changed, or rather how little reanalysis and rewriting I can get away with doing. I want it to be a good paper, but I also want to be done with it so I can write other papers. And of course I want it to be published.

Iris also has rewriting and resubmitting to do, so we can be grumpy as a family.

Education, hippies and commies

Iris: This guy is writing about a pipe dream:

Me: True, but it is a good pipe-dream. A well reasoned and researched pipe-dream with a firm empirical basis and deep social wisdom.

Iris: You mean he's a hippy.

Me: Actually, he's the Demography Department Chair at Berkeley.

Iris: Difference?


Prof. Mike Hout's recent piece on Rationing College Opportunity is timely and worth a read. One question he doesn't address, but I will likely write to him and ask: How long does it take for government investment in college level education to budgetarily* repay the government through taxes and avoided expenditures due to all the economic benefits he discusses? I would guess someone has made such an estimate, and if they haven't they certainly should.

The piece was published in The American Prospect. The subtitle of The American Prospect is "Liberal Intelligence" which Iris takes as further proof that only hippies or possibly communists** write for it.

Anyway, Mike writes well and I suggest you give his pipe-dream a read.


* Yes I know that budgetarily isn't a word, but my Grandma Esther, one of the finest kindergarten/1st grade teachers New York City has ever known, told me that because the English Language does so much for us, we have to do what we can for it. Therefore, to her thinking, we have the responsibility not only to use it well, but to give it new words that it should have but somehow doesn't have yet. 'Budgetarily' for example.

** Note that Iris was raised among hippies, and is the only person I know who waxes poetical about Soviet architecture, so she means the terms "communists" and "hippy" in the fondest possible senses. Further note that my Grandma Esther was a socialist with strong communist leanings, and would have agreed with Iris that Prof. Hout sounds like some kind of commie.

Emails from the Chancelor

UC Berkeley is having a bad day:

From: Robert J. Birgeneau, Chancellor
to "Academic Senate Faculty, Staff, All Academic Titles, Other Members of the Campus Community, Students,"
date Fri, Nov 20, 2009 at 9:02AM
subject URGENT: Wheeler Hall


The campus police are working to resolve a protest action that is occurring in Wheeler Hall. Staff, faculty and students who would normally be working in Wheeler Hall are asked to remain out of the building until further notice. Employees who can contact their supervisors should talk to them if possible to determine whether telecommuting or relocation to another work area is an option. Those in the building right now are advised to leave until the situation has been resolved.

Employees who remain on campus may check in at Dwinelle Plaza at 10am. for further information.

Thank you to all of the members of the campus community for your patience in this matter.

And at 10:42AM California time:

Campus police continue to work to resolve the protest action at Wheeler Hall. Campus police are striving to end the occupation of Wheeler Hall with the safety of our campus community, including all those involved in this action, as an uppermost priority.

Wheeler Hall will remain closed until further notice. Instructors who teach in Wheeler Hall will be contacted shortly by e-mail.

And at 11:30 local time:

Approximately 200 protestors are continuing to demonstrate on the south side of campus in the area around Wheeler Hall. Wheeler Hall is occupied by protestors and the building remains locked.

All classes at Wheeler are suspended until further notice and employees who work in Wheeler Hall are advised that they should plan on not being able to enter the building for the remainder of the work day. Employees should confirm alternative work arrangements with their supervisor, as possible. Instructors who teach in Wheeler Hall are being contacted by e-mail.

Fire alarms have been intentionally set off in several buildings including Barrows, Dwinelle, and Sproul Hall. The fire department is verifying that these are false alarms and will allow people to reenter buildings when it is safe to do so.

The safety of our campus community, including those involved in this protest, are an utmost priority of our police as they work to resolve the situation.

Thank you to all members of the campus community for your continued patience in this matter. Please check for updates throughout the day on the Berkeley home page http://berkeley.edu

Concepts in the evolution of senescence about which I am increasingly skeptical:

Intrinsic vs. Extrinsic mortality
Optimality hypothesis
Mutation Accumulation hypothesis
Agonistic Pleiotropy hypothesis
Disposable Soma hypothesis
Caloric Restriction Effects
"Rate of living" hypothesis

This list includes most of the theoretical basis for the field

Business trips

I'm being sent for three days in Paris next week. Most of it will be spent touring a laboratory and meeting with the potential collaborators who run it. Still it will be nice to see Paris.

A couple of weeks later I may be going for a meeting in Cologne, to talk with another potential collaborator. Again, it will mostly be work, but it will be nice to see Cologne.

Iris isn't coming with me on either of these business trips, but she may well get a baguette and some cologne out of it.

Hard to know what she will get this weekend on our trip to Hamburg, given that we are vegetarians.

Lunchhour at the Institute

A table full of scientists. Biologists, applied mathematicians, sociologists and demographers. Graduate students and post-docs working for the Institute. Maybe 20 of us, each eating a lunch brought from home. The several conversations are mostly in English, with some German and Italian thrown in for emphasis or clarification. The concert she went to where there were five bands but only four audience members. The hallucinogenic properties of toads and banana peels. The upcoming Kristmasmarkt. The worm in my pear. It takes me several minutes to realize I am the only native English speaker at the table. These several scientists, about half from Germany, have no common language but the language of international science, English. I'm sure glad it isn't German, or I'd be in a different line of work.

More musings on individuality and Hydra

It was a trick question. I admit. Well not a trick exactly, but a question to which science does not have a right answer. Even when the question is defined fairly exactly, it isn't clear what unit we should be looking at.

I've already talked a little bit about the hyrda, but I want to give you more detail, because they are such an interesting and bizarre case. There are at least four levels at which we could define the individual in hydra. The smallest is the individual cell. Most cells in a hydra are capable of turning into any kind of hydra cell, producing a whole new hydra, and moving on their own. People have turned a whole hydra body inside out, and the cells that were on the outside just become inside digestive cells, and the cells that were on the outside become skin cells, and the community of cells goes on about its business. Second, the polyp, that thing with the tentacles and digestive system we classically think of as the individual animal. It looks like a little animal. It acts like a little animal (in most ways). It hunts, it reproduces itself, it has different cells doing different jobs. Third, there is the physically attached cluster of hydra. Through budding (growing a new hydra-shaped organism off the side of the old one) hydra reproduce asexually, but the buds get to be a fair portion of the size of the parent before separating, and are generally of almost full complexity while still physically and physiologically attached. One or two or occasionally more buds can be growing off the main polyp at the same time, and one could easily see this mass of genetically identical connected cells as one individual, despite the fact that it has multiple sets of tentacles feeding multiple digestive systems. Finally, one could consider that these genetically identical groups of cells remain part of the same individual even after physical separation. The genetic individual could after a short time encompass many thousands of polyps.

At which of these four levels does senescence occur? We know from experimental evidence that the risk of death by individual cells increases with age, so we have senescence in level one. In level two, the polyp, the experimental evidence points to no senescence, and the same goes for level three. At level four we don't have experimental evidence, but Mueller's Ratchet implies that there would be slow senescence of the genetic individual. Without going into details, Mueller's Ratchet is a line of genetic reasoning which makes clear that the number of harmful mutations in an asexually producing population almost always increases with time, where the number could decrease with sexual reproduction. So as the genetic individual of the hydra keeps producing more polyps, the newer polyps on the average will always have more harmful mutations than those of earlier generations. And remember, just because the polpys don't age doesn't mean they are immortal. They still die, in large numbers, from causes such as being eaten. As the polyps are reproducing and dying, we end up with more polyps from more recent generations and fewer from older generations. The mutational load of the genetic individual increases, and over time this should lead to increased risk of the extinction of the genetic individual. So the genetic individuals, like the cells, senescence, but the two layers of organization in between, the polyps and the clusters, don't.

This is a real problem without a clear solution. Do hydra tell us something important about the evolution of aging, because unlike almost all other animals, they don't age, or are we just looking at the wrong scale?

A more useful way to phrase the question may be to ask why the cell and genetic individual age, but the polp and the cluster don't. The first answer that comes to mind is that both cells and genetic individuals accumulate damage in ways that they can't fully repair, while the polyp and the cluster can easily repair any damage that comes along because any one piece can completely rebuild the whole. In this context, aging occurs when organism are built in a way that doesn't allow for easy repair. At some point this idea will combine with some other idea to form something useful. Or it won't.

Big obvious idea

I've had a big idea. Actually, its an idea I a couple of years ago, but didn't have the time or resources to pursue. Being at the Institute, where the director can make most anything he want happen, I presented this idea to him, and he wants to make it happen. It is in many ways an obvious idea. When I tell people about it many wonder aloud why they didn't think of it, or think about it's ramifications. My boss says we have to be a little bit careful who and how we bring in collaborators to test and publish this idea, as it is simple and important enough that someone could in theory quickly publish it without us. I'm not used to having to worry about that, and we do need collaborators to test this idea, so I'm checking out potential collaborators' web pages and publications rather than contacting them directly. It is all at a level I'm not used to, and I'm glad to be where I am with the organization I'm in, because they do know how to work this out just right. I'm meeting with the director again on Monday.

And no, I'm not going to tell you what this idea is right now. It combines some blatantly obvious and therefore little examined facts from biology with similarly obvious and under examined facts of demography to come to a surprising (and in retrospect self evident) conclusion of (I hope) great relevance to both fields. The experiments will take some months of pre-organization, and then a few more months to actually do.

ixNay on the ifeLay istoryHay volutionEay

I have been doing a lot of reading of the life-history evolution literature. It turns out there is a lot of it. About 1200 papers are published each year in journals followed by Web of Science using the phrase "life history evolution." These are in a hugely wide range of journals. What I am coming to realize is that the phrase has been overused and broadened to the point that it is nearly meaningless. A study of egg size relative to adult size can be labeled life-history evolution. A study comparing daily activity patterns between males and females can be labeled life history evolution. A study of age at first reproduction can be labeled life-history evolution. Perhaps more troubling for the field, life-history evolution has come to be viewed very much as natural history is. Natural history, the basic facts about what a species does, what the individuals and groups are like, what their habitat is and so on is tremendously important to know when studying a species, but it doesn't get grants, citations or jobs because it is often only relevant to those studying that particular species, and the methods and conclusions are rarely ground breaking. Life history evolution has come to be seen in the same way, likely explaining why there is no journal society or regular meeting for Life History Evolution.

This stigma may help explain why so few biologists wade into the deep rich pools of unasked questions lining the boundaries between evolutionary biology and demography. Such work is quickly labeled as life-history evolution, and despite being novel, important and of general interest, suspected of having the same failings as the rest of the field. The name demographers prefer for this intersection, evolutionary biodemography, does not on the face of it sound like a task for biologists. As I learned from Crayola, green-blue is a type of blue, not a type of green. Evolutionary biodemography is by extension part of demography, not part of biology. This thinking applies despite the fact that many of the publications in evobiodemo are from biologists rather than demographers.

I briefly mentioned some of this to my boss, who is a demographer by training, but one of the leading advocates of the idea that demography and biology need to learn from each other more. He suggested I organize a small conference at the institute, inviting both biologists and demographers. The institute has had these types of meetings before, mostly inviting established people who already blend the two fields, and interesting papers and collaborations have come out of it, but little lasting progress. The people who were already aware of both fields remained aware of both fields, and those who weren't continued not to care. So my thought, now that I've been invited to organize a small conference, is to invite biologists and demographers early in their careers, who work on similar topics, but within their own fields. A few biologists who work on juvenile dispersal patterns, and a few demographers who work on juvenile dispersal patterns, each of which may have little awareness of the fact that other people in the other field wonder about remarkably similar questions. Other sets who work on infant mortality, population responses to natural disasters, cohabitation, etc. Let them present their work, let them make the explicit case of what the other field can learn from them, and then let them present on what they would like to know or get from the other field. A workshop on demography and evolution for early career scientists. I'll add it to my to do list.

EvoDemo: "Senescence rates are determined by ranking on the fast-slow life-history continuum"

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.

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.

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?

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.

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

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.

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.

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.

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):

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.

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.

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:

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.