Saturday, January 31, 2009

Oldest old

Among my demography colleagues there is considerable academic interest in the 'oldest old,' the people who make 90 year olds seem positively youthful. I once heard a series of talks on "Sardinian Super-Centenarians" (a truly lovely phrase to hear repeated in an Italian accent). So first you're old, then you are really old, then you are a centenarian, then you are a super-centenarian, then, once having turned 100 is ancient history, you get to be oldest old. And once you are oldest old, having outlived many millions of your cohort, lots of people start taking an interest in you. Locals take it as a mark of pride to have someone so incredibly longevous living among them. People wonder what kind of yogurt you eat, and how often. Geneticists want blood samples to find all the things that didn't kill you. Demographers need data on you to know how the rightmost extremes of their graphs of anything over age should look. Is mortality rate higher among 115 year olds than 116 year olds, and what does that tell us about the possibility of increasing human lifespan generally? Is maximum longevity still increasing with improved technology?
It is hard to find very many data points for these questions, and significant resources have been invested in scouring the world for very old people whose ages can be positively verified.

Tuti Yusupova of Uzbekistan is a good example. According to her recently "noticed" birth certificate, she is 128 years old, by far the oldest living person ever recorded. But was the birth certificate really made in 1880, or was it slipped into a folder in 1920 or 2008? Could it be a clerical error? Some priest or bureaucrat may have written the wrong year for some reason. These things are surely being investigated.

And is she the original Tuti? A colleague told me of a case in which a potential oldest woman turned out to have adopted her mother's name, persona and possessions when her mother died. In the process she added 30 years to her age. She was old, but not oldest old. Publicity surrounding her apparent record brought the truth to light. So my colleagues are understandably dubious about the new record holder. If she is that old (which I hope is the case just because a real record is nicer than a fake one) some of my colleagues will have to (slightly) modify their thinking about how long a human being can stay alive.

Editing I know not what.

My wife often asks me to edit her writings in linguistics. This is an interesting exercise, as my knowledge of linguistics is probably sufficient to get me a D+ on a Linguistics 1A final. And most of that limited knowledge is derived from the works I have helped to edit. This makes me very good at finding sentences that are not crystal clear, but very bad at knowing whether the lack of clarity arises from my lack of knowledge. The result is that Iris's writing ends up being much clearer to the non-linguist (or at least to me) than most technical writing is to non-experts.
Perhaps all academics should be encouraged to have their work edited by a practitioner of an unrelated field prior to publication.

Saturday, January 24, 2009

Cephalic rotiferitis

I've been in the lab every day all day for the last week looking at rotifers. When I close my eyes, I not only see rotifers, I can count their eggs, see their teeth chewing and estimate their age.

Thursday, January 22, 2009

Rep. Boehner, Ludite

This morning on NPR, I heard an interview with Rep. John Boehner, the House Minority Leader. When asked about his reservations with President Obama's stimulus plan, he responded by saying that some of the spending did not seem wise to him.

"Remember, the goal of the stimulus package is to preserve jobs and help create new jobs in America," Boehner said. "And I don't know how giving NASA $400 million to study global warming is going to meet the goals."

It occurs to me to wonder if perhaps Rep. Boehner has so little conception of how science works that he truely doesn't know that when money is spent to study a problem, that money goes into the economy. NASA does not simply trassubstantiate the money into knowledge about global warming. NASA employs thousands of Americans on problems such as these; NASA contractors employ many thousands more. NASA advances technologies that help create new jobs.

My guess is that Rep. Boehner knows all this. It seems likely that Rep. Boehner knows that engineers and scientists are being laid off along with workers in almost every other field. Rather, I suspect the congressman is simly trying to rally his political base by warning them that the government is spending money on a problem they have been trained to think is a liberal hoax, global warming.

Which shows a certain level of consistency. Rep. Boehner is as derisive of the conclusions of science as he is ignorant of the process by which we reach those conclusions.

Wednesday, January 21, 2009

Text is a battlefield

I have spent a week of evenings trying to impose order upon this section on the measurement of post-reproductive survival. The document is littered with dead and broken bits of cast away paragraphs, sentence fragments, disembodied equations, references to tables that don't yet exist and citations of papers I remember reading a long time ago but need to check what they actually say. Multiple passages providing identical information vie to eliminate each other. Clean up is going to be long and ugly. Some concepts that don't make it will be scavenged for other papers. Others, too badly broken, will simply be left for dead.

After all this textual carnage, I finally have a good idea of how to ram all my multi-dimensional conceptual links into a single linear string of text. I even have most of it there. If I pretend I have a year more to finish than I actually do, I feel like I am making great progress, and greatly enjoying it.

Scientist Poitical Humor

me: Obama has appointed two Berkeley professors.
Karen: Who are the Berkeley professors?
me: Christina Romer and Steve Chu
Karen: Do you know them?
me: No, but I know people who know them, which is the square root of as good.

Tuesday, January 20, 2009

Why most scientists are not poets

As I try to write my thesis, I am coming to a realization. Writing complex scientific chains of thought in a way that is both clear and interesting is hard. Much harder than the natural history writing I have much more experience with. One of the many reasons this is so is because scientific writing must rely almost entirely on sentence meaning rather than speaker meaning. My wife, a linguist, has helped me to appreciate the difference. Sentence meaning is the information actually contained in the words of the sentence, accessible without knowledge of the thought processes or social context of the speaker. If a young man says, "Oh, I hate spiders!" the sentence meaning is simply, "I hate spiders." However, if the young man has just been asked to help clean out a garage, walks into the garage, looks around, then turns to the person who asked for his help and says, "Oh, I hate spiders!" much more is conveyed. The young man is not just signaling his dislike of spiders, but also that he has detected spiders in the garage, and is therefore reluctant to help with the cleaning. He may even be conveying that while he doesn't want to help he is a friendly person and therefore is reluctant to refuse outright, but please take this hint. This additional information, the speaker meaning, is nowhere in the text of his words, but is obvious to most humans who have healthy social comprehension skills. Much of the artistry of writing is in the careful crafting of speaker meaning. Beautiful writing, poetry in particular, generally conveys far more through speaker meaning than sentence meaning. But scientific writing by tradition and necessity relies almost entirely on sentence meaning. If any piece of information or logic is a necessary part of a scientific argument, the author has little choice but to state it outright. Likewise, if something has not been stated, scientific authors generally cannot assume the reader knows or agrees with it. This of course goes only so far. Scientists, as humans using human languages, are incapable of avoiding speaker meaning entirely. But the injunction is clear: thou shalt not ask thine audience to read between the lines.

Writing a complex chain of mathematics laced evolutionary thought in a way that is readable and elegant is a real challenge. I begin to understand why so many scientists over the centuries have largely let elegance and readability fall by the wayside. I very much hope to avoid following that clearly but unattractively marked trail.

Monday, January 19, 2009


One of the great things about having lots of students involved in my research over the last few semesters is that the ones who aren't that interested tend to drift away and the ones who are really interested and energetic keep coming back for more. It is like a distillation process where now, my last semester in grad school, I have this awesome group of highly motivated students and very few who are just along for the ride. It makes me happy.

Saturday, January 17, 2009

Very rough section of a very rough draft.

Today between 11 and midnight I wrote a very rough section of a section of a rough draft of one of the several papers that will go into my thesis. Feels like progress. I don't expect to have much time for blogging over the next few months, but I will try to post bits like this that are potentially interesting, and that show what efforts keep me from having time for blogging.

The Measurement of Post-Reproductive Lifespan
Advancement in the study of PRLS has been hampered by differences over terminology, the use of a wide range of non-comparable measures and the failure to put measures of the scale of PRLS in the context of the time scales on which the organisms live.

Some authors have used the term "post-fertile" rather than "post-reproductive" arguing that anything that an organism does that increases her genetic representation in future generations is a form of reproduction, and that "post-reproductive" is therefore an inaccurate term to apply to post-fertile individuals who are still caring for their young (REFS). Indeed Hamilton (1966) argues that, "if the organism practises parental care 'birth' should be considered to occur... at the age at which the offspring becomes independent." While not disputing the biology behind this argument, we feel that the term "post-reproductive" is deeply enough ensconced in the literature on this topic that the use of alternative terminology to convey the same concept may tend to muddy communication. For this reason we use the term "post-reproductive" to refer to life after direct reproduction (fertility), excluding indirect reproduction (care of young and indirect fitness benefits).
Beyond semantic disagreements, so many methods have been used to calculate the scale of PRLS that efforts at comparisons across species and studies have been few and confusing. For example, XXXX and ZZZZ (REF) present a table of PRSL for 12 primate species, all given in units of years, but calculated in six different ways. Disagreements exist as to how to define the end of reproduction, how to determine the end of survival, and which individuals to include. The measures vary because the type of data used vary, and the interests of the authors vary, figuratively leading to comparisons of the shelf-life of apples to the refrigerator hardiness of oranges. The effect of sample size on these estimates is generally not addressed.
Even when these drawbacks are not found, authors generally fail to correct for the overall longevity of the species in question. One should expect a species that lives 100 years to, on the average, experience more years of PRLS than a species that lives 20 years. Without a denominator related to the time scale of the organism's life history, the numerator of PRLS is fairly uninformative.

In this study, we use a type of data that allow for broad comparability: age specific mortality and fertility figures as calculated in standard demographic methodology. Because the form of the data is highly standardized, the same measures can be calculated across taxa, for males and females, and in a wide range of environments. The use of data sources as information rich as are age specific mortality and fertility tables allows for the use of multiple measures which illuminate different aspects of PRLS, but which need not be falsely compared to each other, because we can calculate every measure for each population for which these data are fully available. Furthermore, the use of age-specific demographic tables allow us to put our measures of PRLS in the context of the reproductive and actuarial longevity of the organisms, allowing for meaningful comparisons between populations with very different lifespans.

Friday, January 16, 2009

New York's Geese are exploding in another way

The Christmas Bird Count is one of the great success stories of Citizen Science. Every year in late December, tens of thousands of volunteers across North America brave snow and sleet and Christmas Shopping traffic to go out and see how many birds they can see. Everyone writes down how many individual birds they see of each species, and where they were looking, and all these data are collected into a central database. The Audubon Society's scientists know how many people were looking, and where, and they have large numbers of observers, so they can calculate pretty reliable winter range maps, and calculate rates of population change in each area.

Looking at their data for Canada Geese, a pretty remarkable number emerges. The number of Canada Geese in New York State in December has, for quite a while, been increasing by 22% per year! At that rate of increase, population would double about every three and a half years (1.22^3.5=2), and the population doubled at this rate starting about 1955 and leveled off about 1990, so it had time to double about 10 times. 2^10=1024. So for every goose in New York in late December before the 1950s, there is now a kilogoose in the same area at the same season. To put it another way, most CBC observers in NY in the first half of the 20th century saw not one geese. The average NY state observer these days sees 50 or 60 geese.

Here is a graph from the CBC historical query page.

There is a lot of noise in the data, but the trend is very clear.

So why are there so many more geese in NY in the winter? Partly, there are just more geese everywhere. Humans have been good to Canada Geese. Lawns, golf courses and grain stubble are all feasts for geese. We've killed off a lot of the natural predators, and we don't hunt them ourselves as much as we used to. And New York winters aren't nearly as cold and snow-buried as they used to be, especially around the city, which means fewer of the geese bother migrating any further south than New York.

In considering the causes of the bird-plane collision that caused yesterday's much publicized crash, we should keep in mind that a few decades ago, there would have been no geese to hit in January above the Bronx.

Plane-Strike, not "Bird-Strike"

Yesterday a plane that had taken off from New York City was forced to make an emergency water landing shortly after take off. The reason given? "Bird-strike" on both engines minutes after takeoff. It seems quite likely that the cause was truly a collision between a flock of birds and the plane. But does it really make sense to call it "bird-strike?" Canada Geese, the type of bird mostly likely to have been involved, fly about 40 mph. The takeoff speed of an Airbus 320 is 170mph, its cruising speed above 500mph, and the plane was presumably somewhere between these two speeds when the collision happened. So the plane was probably going five to ten times as fast as the birds.

So saying that the birds "slammed into the plane" as some news sources have done is akin to saying, "the pedestrians slammed into the speeding tanker truck." The birds were relatively stationary and the plane plowed through them. All the humans survived. The birds got the worst of it. Not to imply that the people on the plane were at fault. Perhaps the pilot's instruments don't even register anything as small and dispersed as a flock of geese. But really, does it make sense to blame the geese?

Wednesday, January 14, 2009

Can't live with'em can't live without 'em.

Biologists and Ecologists have (mostly) learned to give at least some forethought to the consequences of introducing non-native species. The problems invasive species cause are often most sever on islands, where the native species often have limited evolutionary experience dealing with the relative of the invaders. For example, many island endemic bird species were flightless, as there were no land based predators to need to fly away from, so why bother building all that expensive escape equipment when there is nobody to escape from. Other island nesting birds, like those on Macquarie Island can fly (except the penguins) but don't seem to have the right tricks in their behavioral repertoires to escape from introduced predators.

A recent attempt to help these birds is making ecologists aware that one has to be very careful not only about introducing invasive species, but also about removing them. A commentary in Nature describes the story:

Cats were introduced to the Macquarie Island in 1818; sealers introduced rabbits 60 years later.

The rabbits tore through the island's vegetation. In 1968, the rabbit flea was introduced. Once that had established the lethal myxomatosis virus — which the flea spreads — was introduced in 1978.

Rabbit numbers crashed, but then the cats, which had previously eaten rabbits, switched their attentions to the island's birds.

But once the cats were gone, the few hardy rabbits that had survived both the cats and the myxomatosis emerged and began doing what rabbits do best — breeding and eating.

So the island has cats, rabbits, rabbit fleas, rabbit viruses as well as rats and mice, all introduced. The cats were bad for the birds because they ate them. The rabbits were introduced and were bad for the birds because they destroyed the vegetation, but good in that they distracted the cats. And the cats were at least partly good for the birds, because they ate the rabbits. Some kind of unstable plateau was reached. And then disease was introduced to reduce the rabbit population, leaving a whole bunch of hungry cats, which were bad for the birds. But then the cats were killed off, which was bad for the birds and everything else (except the rabbits, rats and mice) because for the first time there were rabbits without cats on the island. The rabbits, unchecked, ate through most of the island's plants. And this, of course, is a vast over simplification.

The Australian authorities who run Macquarie Island are now trying to figure out how to exterminate the rabbits, rats and mice without harming other native populations, such as the seals and sea lions that breed on the island. They estimate it will take tens of millions of dollars, and that may be optimistic. Few efforts to irradicate rodents from any land mass of decent size have succeeded. Macquarie Island, at 128 km², offers a lot of hiding places big enough for a rat. Miss one pregnant rat and in just few years you are back to square one. And who knows what effect the rats would have without rabbits around harboring disease and eating potential cover? Rats eat bird eggs, and have been known to finish off large bird colonies in just a few years.

The lesson learned is that just because introducing species is generally bad, removing those introduced species from an ecosystem that has started to adjust to their input isn't always good. At least it has to be done very carefuly.

Tuesday, January 13, 2009

If this science thing doesn't work out.....

As I've mentioned before, my cousin David is the National Sales Director at Ozone Socks. Ozone has a yearly sock design competition. I submitted three designs themed around (what else?) science.
I just got the call from David. He had to recuse himself from much of the judging, in order to avoid bias. He didn't even tell them I was his cousin, he claims. But my oceanic drawing, "30000 Feet" won second place. Iris will be so excited. We get 12 free pairs of socks.

Oh, and by the way. It is not at all certain they will actually make this sock. They have in effect purchased rights to my design for the price of 12 pairs of any socks they already make. If you want to see this sock made, and would purchase a pair, please and tell them.

Tuesday, January 06, 2009

Just like old times, only with more world-savingness

My freshman year in college, my neighbor down the hall, the fellow in the picture above, was building a contraption that looked very much like this one, only much more home-made looking with various colors of extension cords, duct tape and PVC pipe. One end face the door of his room. The other pointed out his window, like a cannon out the gun port of a ship. I asked him if he was a pirate. We became friends anyway. He eventually explained that it was a sort of cannon, a "linear inductance accelerator." It used electrical current to induce electrical fields that accelerated little aluminum rings down the length of the gun and shot them out the window. They didn't shoot very fast or very far, but Stephen built the thing while he was in high school, mostly from stuff he scavenged from his parents' basement. When the campus security guards would do their once a semester safety checks of the dorm rooms, Stephen would put Christmas lights and stuffed animals all over it and tell them it was a sculpture project.

Stephen is one of those people who is instantly recognizable as brilliant. Walk into a room where Stephen is and try not to get knocked over by the slightest meanderings of his enormous brain. But in addition to intellectual brilliance, Stephen is incredibly tireless, multi-talented and helpful. He was known as the "campus super hero."

It was therefore with very little surprise then that I watched as Stephen got degrees in mathematics, physics, electrical engineering, plasma physics, then went to work for a company whose goal is to save the world by producing cheap clean electricity from hydrogen fusion. And the company Stephen went to work for is of course going to do it much sooner, cleaner and at 1/100th the cost of anything any government or university could think to try. The picture above is of Stephen working on a piston he designed for that fusion reactor, and is from an article in this month's Popular Science. The similarity to the linear inductance accelerator is mostly in my mind. I can tell the photo is posed, though, because Stephen is not grinning, which he normally would be when fine-tuning one of his machines.

Stephen, by the way is Stephen Howard, who has occasionally posted to this blog. These days he is too busy saving the world.

Friday, January 02, 2009

A tiger does not declare his tigritude, nor live in Africa.

Last night Iris, reading a book on French linguistics, came upon the word "tigritude." She asked me what it meant, and I Googled it. I came upon several references to a "Nigerian Proverb" stating that, "Un tigre ne proclame pas sa tigritude." (A tiger does not declare/proclaim/shout his tigritude.)

This stuck me as a useful saying, but something about it wasn't quite right. It took me until just now to remember. There are no tigers in Africa. Haven't been for at least a million years. Either that saying was handed down from before the time Homo sapiens existed, or it isn't a traditional saying from Nigeria.

I looked it up again, in more detail, and it is actually a quote, from the Nigerian author Wole Soyinka, whom Iris of course has read but I had never heard of.

It is funny how many people, including "proverb dictionaries" have labeled various versions of it as traditional Nigerian wisdom. Is "Happy families are all alike; every unhappy family is unhappy in its own way," an ancient Russian proverb?

Parameterization of the Damned

I have had a headache for the last two days trying to figure out a theoretical problem related to my work. My best attempt to explain the problem, and the closest to a solution I have thus come up with, can be found in the email below, written to one of my research assistants. This is the kind of symbolic thinking that makes my forehead tie itself in a knot. Tell me if what I wrote means anything to you, 'cause it doesn't say a whole lot to me.

Hey Nik-

I have another favor to ask. I've been wracking my brains trying to figure out a problem, that we have no null hypothesis for what G should be. I try to explain the problem and what I'd like to do about it below.

Post-Reproductive Lifespan as measured by G cannot be negative, in that an individual cannot invest in reproduction after her death. G cannot even meaningfully be zero unless every individual dies at age M, the age at which fertility drops of to 5% of its former maximum. If even one individual in the study population lives past age M, G is non-zero. This has left me struggling to figure out what a meaningful null hypothesis for G could be. The answer seems to be that there isn't one. G is a parameter designed for a quantitative, rather than qualitative distinction. Human G is very different from G of non-human primates, but it isn't meaningful to ask if G of non-human primates is different than zero, because we know without knowing anything about the populations that it will be.

The relevant question is: is senescence in fertility offset in age/time from actuarial senescence? If M, is the parameter we use to demarcate the end of fertility, we can use the exactly analogous measure, Z, to demark the end of meaningful survivorship. Z is defined as the last age for which p(x)≥0.05*max(p(x)). ( By the way, in case we don't have p(x) in the data you have, p(x)=1-q(x))
So then the question becomes, how much different is M from Z? Z-M is the post reproductive period, and (Z-M)/(Z-B) is the portion of the adult lifespan that is post reproductive. If we define S=(Z-M)/(Z-B), then S gives us a decent measure of how much reproductive senescence is offset from actuarial senescence. And one that I can at least imagine being zero, in that the rates of survival and fertility can drop simultaneously, even if each individual reproduces only before she dies.

Would you be so kind as to have Access calculate Z and S for the populations we have in the database, and then send me a spreadsheet with B, Z, S and M for each population? I'd like to get a sense of how these variables behave.


Thursday, January 01, 2009

Evolution in the Great Pacific Garbage Patch

Put some sand grains in a round bowl of water, then twirl the water neatly, so that the water rotates cleanly around the inside of the bowl. You will observe most of the sand settle out of the water in the center of the bowl. Do the same thing with tiny bits of floating plastic, and you will get the same result. Now do the same thing to the Pacific Ocean with all the floating trash we throw into it, and you get the Great Pacific Garbage Patch. A large portion of the North Pacific naturally rotates in a current called the North Pacific Gyre. Take a boat to the center of rotation, and you will find enourous quantities of floating junk, especially plastic. Wave action and UV gradually break this plastic down into microscopic bits, which become part of the local ecosystem along with the water, plankton, fish and so forth. But nothing eats plastic, right?
This is where my current pondering comes in. Imagine that one of the hundreds of billions, maybe trillions, of plankton in the Great Pacific Garbage Patch had a mutation that allowed it to gain some slight advantage from plastic. It would surely find some tiny scrap of plastic, and would have a slight advantage over its competitors. If that helps it reproduce successfully, and its offspring carry that same mutation, then we have more plankton who gain a competative advantage from plastic. At the rates plankton reproduce, it is not long before the GPGP is full of plankton who can make some use of plastic. Now suppose another mutation in one of those plastic-loving plankton makes it even better at using plastic. Able to slowly digest some component of it or incorporate it into its protective covering. The larger plankton that eat those little plankton will also have to evolve to deal with plastic. Sooner or later, in the crazy fast generations of open ocean plankton, someone is going to start evolving down a path that leads to the ability to digest plastic. And when that happens, when the plastic in the North Pacific Gyre starts myseriously disapearing, don't expect the little plastic eaters to stay there. There are far to many ecosystems with far to much plastic available for plasticovores to be contained. Plastic is, after all, an organic substance with a high energy content. Sure it isn't biodegrable. Not yet.