Speaking of New Scientist:

They have an article about methane plumes found bubbling up from from methane hydrates in the Arctic Ocean near Svalbard, where warming water seems to be releasing (and then redissolving) large quantities of the greenhouse gas. First talking polar bears and now potentially catastrophic climate changing gasses.

Science News that isn't

Google news has a science/tech section which I occasionally glance at to see if there is any interesting science news. Of the 20 some stories on their main page at any given time somewhere between 0 and 2 are usually science. The rest are Tech, including video game reviews, prospects for the newest iPhone app, and other useless hogwash.

The New York Times online Science section is better, but they lump in technology, health and the environment, including stories with no science news involved.

BBC science news is still better, focusing on science (although they always have a few non-science environment stories mixed in). They also tend to get less of the science wrong than the American press.

The source I am starting to like more is New Scientist.

Your biggest misconception about science

Among the frantic madness of trying to finish a thesis, I've been thinking a lot about how we evaluate scientific evidence. This has brought me to realize what I see as the single greatest, most damaging, and potentially most widespread misconception held about science. I'm not talking about disbelief in evolution, or climate change, or the moon landing, or any of the other usual loony bin stories. The misconception I have in mind is at the root of, or at least facilitates, many of these more discussed fallacies.

Imagine if you will that you are an electrician. I ask you to install a solar power system, in which you have specific training, and then to run the power to batteries, outlets and appliances in various parts of a house I am building for my grandmother. You carefully chose the type, size and placement of the photovoltaic panels, figure out how to attach them securely to my roof, how to run the wires, how to ensure safety and consistency of power. You comply with various and sundry codes I've never heard of, use materials whose properties I'm not knowledgeable enough to appreciate, and otherwise exercise your expertise and skill.

I, as an intelligent well-educated person with some layman's knowledge of wiring should be able to ask you questions about your work, and if you know what you are doing, you should be able to explain your choices in ways that make sense to me. Why are you using the more expensive panels instead of these cheap ones my cousin bought? Why does the wire go through there instead of through here? But you would rightly think I was an idiot if I thought I could evaluate the soundness of the plan in all its intricacies. Other than getting independent opinions from other experts, assessing your reputation, or spotting huge obvious flaws like a lack of power to the kitchen, I would have no way of telling if you were really planning an ideal system, or screwing me because you secretly own stock in the company that sells that brand of battery. And if three electricians gave me three divergent opinions on the same design, I would not presume to know which was right without asking a fourth. The same would be true of work by almost any expert in almost any technical field. Non-experts should be able to understand, should be able to spot obvious flaws, should be able to ask multiple opinions, but should not assume they are qualified to assess the finest points. No one without training as an electrician can say if a complex wiring diagram is perfect or adjudicate a disagreement between master electricians.

You've probably spotted where the long analogy is headed. It is often said, quite rightly that any scientist who can't explain his work to an intelligent layman is a fraud (or at least very bad at explaining). I forget the original quote. This, and the general (and correct) view that scientists should feel obligated to explain our work to the public reinforce the view that any thinking person should be able to evaluate the correctness of a scientific conclusion. But if I, having worked as a carpenter and done some wiring, can't evaluate the optimality of a complex circuit diagram, why should I, as a biologist, expect to be able to assess whether the uncertainty is understated in a climate prediction model which took hundreds of person years to design and build, went through multiple iterations, been evaluated by independent experts and are so complex it would take me months of reading just to understand what all of the variables are? I shouldn't and neither should you, unless you have years of intense training in that sub-field. I can read the papers, get a sense of what the question and conclusion is, understand an outline of the methodology. But I have no hope of just stumbling upon a conceptual or methodological error. I have no hope of finding the climatologist's errors if what I read is not the primary paper, but an article written by a journalist who also has no training in climatology. This is the blind leading the blind in trying to find flaws in the color scheme of a digital drawing. If two climatologists with opposing viewpoints were to write a trade book in which they lay out their disagreements, present evidence for their views and question each other's evidence, I would understand the science much better than I do, but I would still not be qualified to say which one of them was right and why.

It is unfortunate that non-experts generally can't evaluate science. It leads to the view that science is esoteric, made up, snobbish, arbitrary, undemocratic, religious and most of the other negative things people believe about science. It is also unfortunate that people don't know, or won't admit, that they can't just sit down and by thinking hard decide whether a scientist's work is useful, novel and correct. But they can't. You can't. I can't either, except in fields where I have reviewed the literature, thought deeply about the issues for weeks or months, read more literature in tangentially related fields, discussed the issues with other scientists and then sat down and written out my objections and concerns. This is why PhDs take more than five years on average. Science is hard and requires masochistic attention to detail, not only for those making statements, but also for those evaluating it. If you could sit down read a few papers on a subject and make a novel, well reasoned and convincing argument showing that previous papers are substantially wrong, you could have a PhD in a few weeks. No one has ever done it (or if they did their was fraud involved.)

This misperception, that anyone can evaluate science is widespread. I know scientists who openly contradict conclusions which are long since the consensus in fields in which they have no particular expertise. I've talked to several extremely well educated non-scientists who claim to have evaluated the evidence for human-caused global warming and come to firm conclusions. My conclusion that humans are causing climate change is based not on my personal review of the arguments pro and con, but on the fact that the vast majority of people who are qualified to judge, including many who were originally skeptics, say that it is no longer reasonable to doubt. But many, perhaps most Americans feel qualified to personally cast judgment based on the evidence. I have seen no polling on this, but expect that a larger number of Americans would tell you they are capable of offering informed opinions of scientific controversies than on disagreements between electricians.

As an evolutionary biologist, I feel qualified to read a book by an "Intelligent Design" proponent and say exactly what is wrong with their argument. I can map the circular logic, find the flaws in their interpretation of the Second Law of Thermodynamics, and point out which references are being misquoted. I can describe exactly how their evidence fails to support their argument, and explain exactly why the argument fails to qualify as a science. A nonscientist, reading these books, and armed with the delusion that if there are flaws she will see them, is likely to believe or disbelieve based on religion, politics and predilection. The scientific soundness of the argument is tertiary. Before I was versed in evolutionary biology, I could see logical flaws in Intelligent Design. But had I been raised with as little knowledge of evolution as I have of climatology, I could have only trusted to expert opinion. Similarly, while conspiracy theories about the moon landing are grossly implausible, I am not qualified to judge the claim that the physics of the landing wouldn't work as NASA says they do. The fact that physicist say it works just as explained is good enough for me.

It is not the moral of this story that you shouldn't ask questions, be skeptical and challenge authority. It is not my intention to claim that laymen should never question the competence and motives of experts. Rather, I urge that we try to be realistic in judging our ability to evaluate complex arguments in fields we don't know much about. I am not an expert in whatever it is you studied, and I am not hubristic enough to think that I am.

Plagaism, homicide and Wyeth

In trying to understand why America's healthcare system is so much more expensive and so much less effective than in other rich nations, I usually blame the insurance companies. But as is common with problems of this magnitude, there is more than enough blame to go around. The New York Times today highlights another major problem: distortion of the scientific literature by moneyed interests, particularly the pharmaceutical companies. Corporate culture, and corporate law, effectively require officers of publicly owned companies to do everything they legally can to maximize profit. A pharmaceutical company, faced with the option of doing something that boosts profits but decreases health, has every incentive to do so, and predictably will do so in many cases. Americans end up spending money to decrease our own health.

The case described in today's article should be shocking, but due to a long standing pattern of this type of thing, is only disgusting and outragous. Pharma giant Wyeth, maker of among many of things, synthetic hormones for hormone replacement therapy, has been paying ghostwriters to write review articles highlighting the benefits and minimizing the dangers of hormone replacement for post-menopausal women. These review articles were then passed to respected medical researchers who published them in their own names (whether for money, or just to boost their publication records, I'm not sure). The ghostwriters are not mentioned. Wyeth used these articles to paint a false consensus that its product was safe, and thereby boost sales and stave of regulation.

"But the seeming consensus fell apart in 2002 when a huge federal study on hormone therapy was stopped after researchers found that menopausal women who took certain hormones had an increased risk of invasive breast cancer, heart disease and stroke. A later study found that hormones increased the risk of dementia in older patients."

Wyeth's behavior is certainly harmful and reprehensible, and may or may not be illegal; they are currently being sued by several thousand former patients or their survivors. What is absolutely clear is that the researchers who went along with this are some seriously sleazy people who should not be allowed anywhere near medicine, or research. One of the first things we tell students in freshman science classes is that you never ever ever put your name on something that someone else wrote. It is fine to quote people, it is fine to collaborate and have everyone involved in the collaboration listed as authors, but we have a name for taking something someone else wrote and claiming it as your own, even with the blessing of the true author: plagiarism.

One of the many reasons plagiarism is illegal, and specifically forbidden in the ethics codes of universities and publishers, is to avoid exactly this kind of nonsense. We are trained to always question the motivation and bias of the author of anything we read. Why does this person take such a sunny view of the medicine? Why isn't that other study that showed increased risk of strokes mentioned? If the author is a well respected medical researcher with no apparent ties to the manufacturer, maybe the medicine really is that good, and the stroke study wasn't done well enough to be worth mentioning. But if the real author is an employee of Wyeth, with the specific goal of boosting sales, our interpretation might be different. This applies as much to the peer reviewers who were tricked into approving these fake reviews as to the average reader. Peer reviewers are supposed to evaluate conflicts of interest which cold make the article less valuable to the reader. Plagiarism makes it impossible to know the interests of the real author, which was undoubtedly the goal of Wyeth's scheme.

All researcher shown to be publishing articles written in part or whole by ghost-writers (a.k.a. plagiarists) should be publicly discredited by both their employer and their publisher. Furthermore, they should be held legally responsible for the harm and deaths caused by their unethical practices. Such sleazebags are bad for science, bad for medicine, bad for patients and bad for America. Although Wyeth is the most identifiable villain in this particular debacle, the "researchers" who shilled for them should lose the reputations they let Wyeth borrow. Laws should be enacted to make it clear that pharmaceutical companies may not produce deceptive scientific literature to boost sales, and are legally and financially liable both for the deception and for any harm that arises from it. Governments and insurers tricked in buying medicines through deceptive practices should be able to collect recompense and penalties from those perpetrating the fraud. If other pharmaceutical companies have been engaging in similar practices, they and their mouthpieces should also be exposed. It took decades and hundreds of thousands of lives lost to kill the Tobacco Institute. I hope that it will take less time to rid Pharma, which uses largely the same playbook, of their homicidal tendencies.

The plan

At the end of this month, I fly out to Berkeley, give a finishing talk, get my advisors to sign my thesis, spend a couple of days closing everything up, and then Iris and I fly to Deutschland. That is the plan. It is an ambitious one, in that only one chapter of the thesis is done, the second needs major revisions, the third my committee members have not yet commented on, and the fourth I am still struggling with analyzing my mountains of data. And two of my committee members, including my major professor, are doing fieldwork on other continents for most of August, meaning they won't be doing much editing and approving of thesis chapters.

But that is my plan, and I'm sticking to it, until I am forced to think of something more realistic.

Like most places in the northeastern US, Vermont has been having a very wet summer. It rains most days, and the ground rarely has time to dry out before the next rain. This is just how the slugs like it. They seem to be everywhere, doing all their usual sluggy things: eating leaves, devouring mushrooms, sitting on wet rocks, getting squished on the sidewalk. What else is there for slugs to do? This afternoon I saw a group of slugs doing something I've never seen slugs do, or even heard of them doing.

Yesterday, a couple of blocks from home, I passed a freshly roadkilled squirrel. By today, most of the carcass was gone, with only bits and chunks scattered on the shoulder. And on each little morsel sat a garden variety slug, chowing down. The bigger chunks had two or three slugs, each about an inch long, actively feeding (or at least that's what it looked like, it was hard to know for sure, as their mouthparts are underneath). There were a few slugs that had been run over as they fed, and others had come in to finish the job, and eat there recently departed kin.

I've watched slugs eat hundred of times, and it has always been on plant matter or fungi. It never occurred to me that they might eat meat. So of course I checked what Wikipedia had to say on the subject:

"Many species of slugs play an important role in ecosystems by eating dead leaves, fungus, and decaying vegetable material. Other species eat parts of living plants.
Some slugs are predators, eating other slugs and snails, or earthworms.
Most slugs will on occasion also eat carrion, including dead of their own kind."

Which makes me wonder if there was ever a B movie about giant radioactive predatory slugs.

God's bellybutton

Hubble Space Telescope finally answers that question about whether God has a navel.



NASA now planning to aim telescope slightly lower.

Ego boost of science.

There is a very flattering article in tomorrow's New York Times science section, by Natalie Angier, about our article on the definition of behavior. (There is also an online quiz associated with it.) It has, to be honest, many fewer errors than I generally expect from science journalism. The main one that will jump out at most of my peers is her statement that, "neither that textbook nor any other reference he consulted bothered to" define behavior precisely. We found lots of definitions, they just didn't agree with each other, or with what we or other biologists thought the word meant. That said, I think this NYTimes article is much better than most science reporting on the accuracy front. And of course, it is nice to have one's work described as "provocative and crisply written" in a large circulation newspaper.

She did neglect mention my two favorite things about the article; the title is, "Behavioral biologists do not agree on what constitutes behavior," and; in a biological article in a peer reviewed journal, we quote both Supreme Court Justice Potter Stewart's opinion on pornography and Conan-Doyle's Sherlock Holmes mystery of the dog that did nothing in the nighttime. I amuse myself heartily.

Studies in current evolution

Research Question:
To what extent is the number of children people choose to have in developed nations heritable (in the genetic sense)?

Importance:
If it is heritable, this is most likely the largest determiner of fitness outcomes, as the great majority of children survive to adulthood, no matter how many siblings they have. This implies potentially rapid Darwinian selection for those who choose larger families. Over the course of a few centuries this selection could have important impacts on human demography and population. Given an estimate of heritability, this effect could be quantified.

Method:
The old twins/siblings separated at birth databases?

Ethical considerations: many

Likelihood I will actually get around to this:
small

Long Term Prediction

Several thousand years from now, if there are still humans around, someone will look back and describe the last few thousand years as a time of extraordinarily rapid biological evolution for humanity.

A bit humbling

I pride myself in knowing something about a very wide range of topics, even if there are very few in which I could confidently call myself expert. I can converse intelligently on most topics in organismal and population biology, and have read bits and pieces in a large range of other fields. I like to tell myself that this will allow me to make important scientific advances, because I can draw together knowledge from disparate fields. But then when I compare my own writings on the co-evolution of longevity and the brain in primates (the paper I am currently working on) to this amazing detailed, readable and reasonable chapter:

Kaplan H, Gangestad S, Gurven M, Lancaster J, Mueller T, and Robson A. 2007. The evolution of diet, brain and life history among primates and humans. In: Roebroeks JWM, editor. Guts and brains: An integrative approach to the hominin record: Leiden University Press. p 47-81.

The various authors of this paper have each been working on a set of related questions for decades, and they bring together this acquired knowledge into a devastatingly clear and cogent argument. Where I have vague intentions to explore an idea, they have specific arguments and evidence to back them up. I can't help but feel a bit like a child building a pile of sand on top of the great pyramid, thinking I am making it taller when I'm just making a mess. Or maybe it is just past my bedtime.

Angst of science.

I get this terrible sinking feeling when I discover an error in my calculations, because it means there are probably more, and I might have to do a lot of analysis and writing over again, and frankly checking calculations for errors often takes longer than just doing it over. When I shortly thereafter discover that my original math was correct, and I was just having a brain fart, this does not greatly improve my confidence in my other calculations, so I go through and recheck everything else I've done. But part way through that, I realize there would have been a much more convincing way to design the analyses, so I do that, which takes all of today.

Hiking the Montshire

We're in Norwich VT for the summer, while I finish writing my thesis, and before we head off the Germany. Yesterday, the first rainless day since we got to VT, I headed to the Montshire Museum of Science, a mile out of town, to check out their system of trails. The price of admission ($10 for adults) to this cool little child-oriented hands-on science museum got me a map of their trails and permission to walk them. The map shows 0.4 miles of trail here and 1.2 miles there. Doing some addition I decided that an out-of shape scientist could walk all their trails in one afternoon, and set out to do so. The forests around the museum are fairly typical second growth northeastern forest, with a mix of hardwoods and softwoods. Nothing spectacular, but extremely pleasant to walk though on a hot bright afternoon.

The trails are well maintained and marked, and most are flat enough for strollers, although I met almost no other hikers once I was away from the main museum building. They follow the banks of the upper Connecticut river or follow low rambling ridge-lines. Sprinkled along many of the trails are scientific activities and displays. It was fun to stop at the solar-powered kiosk and push buttons to hear recordings of the local birds. When I pushed the button to hear the Black-throated Blue Warbler, a real BTBW responded from the trees overhead. Their scale model of the solar system is stretched out along one trail, with Pluto about two miles from the sun.

Behind the museum is a stream-fed water park/ science display packed with wet excited children learning about waves and currents. Inside the museum is a relatively quiet pandemonium of children running, watching, pulling, stretching and learning the word 'viscosity.' My cousins, three and five years old, incessantly demand to visit the Montshire, and everything seems to be well aimed at kids their age. None of it is profound, but all is well presented and designed to keep kids engaged and learning.

I went about 8 miles (including the road to and from Norwich) in a little over three hours of actual walking, and can now say I have hiked every trail the Montshire has. It is flat, short and simple enough to have made a great first hike for an old naturalist trying to get back into shape. Next I will try part of the Appalachian Trail, which comes right through Norwich. But first I will lay down and rest my aching muscles.

EvoDemo Poetry

A chimpess keeps the knack to breed
until she's not alive
But woman stops and then goes on
another forty-five

A hydra grows and buds and splits,
then does it all again
But man can live his life but once
before his certain end

A rotifer skips infanthood,
lays eggs on her first day
But humans grow and learn and find
all reasons for delay

You'll live your life as humans do
and never think it's odd
But redwoods still are saplings
when we're pushing up the sod.

H1: The universe is 96% aliens.

Most good scientists are deeply impressed by, and even excited about, how little we yet know, how much there still is to find out. Our science and technology are impressive accomplishments, but still very much in their infancy as compared to what is possible.

Imagine, if you will, a tremendously technologically advanced civilization, whose technology just continues to advance. What is the end point? What do they and their technology look like after billions of years of rapid technological advance? I think it is safe to say that we don't know. It clearly wouldn't be anything that we currently have the science or technology to understand. As Arthur C. Clarke wrote, "Any sufficiently advanced technology is indistinguishable from magic." We wouldn't understand this alien technology or what it did any more than Cro-Magnons would understand a wireless modem. This hyper-advanced civilization would presumably have explored ever nook, cranny and loophole in the physical laws that govern the universe and transformed their technology and themselves beyond recognition. We likely wouldn't even recognize it or them as technology or life. We might not even recognize them or their technology as normal matter or energy, although after billions of years they would likely have transformed large parts of the universe itself.

Which brings me back to how little we currently know. Modern cosmology assigns only 4% of the mass/energy in the universe to "normal" matter, the kind we know anything about. 22% is thought to be "dark matter" and the remainder, 74%, is "dark energy." We know little about dark matter and next to nothing about dark energy, except that they are necessary to make our equations work out. Putting to one side the plausibility that the equations are wrong, we are free to speculate on what is going on with that other 96% that we can't see but suspect is there. My preferred hypothesis is that the universe is 96% aliens. Which is a somewhat silly way of saying that other life-forms may have transformed some large portion of the mass and energy in the universe into forms we don't understand. Why should a civilization with the most advanced technology we can pretend to conceive of be expected to leave things as they found them? If conservation of mass/energy is one of the rules they can't get around, couldn't a big crowded universe of aliens be expected to convert a large portion of its limiting resource into whatever form allows them to use this resource most efficiently? Dark matter releases no detectable radiation, and as such leaks no mass/energy. This would also help to explain why SETI can't detect any aliens. A civilization that hoards mass and energy isn't going to go blaring electromagnetism all over the place.

Why under this hypothesis would 4% of the matter be left as boring old stars, dust, black holes and light? Perhaps these things serve some function for the dark aliens. Or maybe we, and everything we can see, are a designated nature preserve with strictly enforced limits on poaching. To try to answer this last question is to move from pure speculation to pure fancy, so your guess is as good as mine.

Benign Decline?

For many decades now intellectuals, policy makers, humanitarian organizations and environmentalists have put time, money and effort into worrying about the negative impacts of humanity's ever-increasing population. It is certainly a problem worth worrying about. Everything from food and water shortages to increased disease transmissibility to habitat destruction and global climate change are made worse by overpopulation. Jared Diamond, in his excruciatingly detailed and example rich tome, Collapse, explores how human societies can fail when their population outgrows the resource base on which they depend. World population projections estimate that we will top out at 9 to 12 billion some time between 2050 and 2075. That is a lot of people for this little planet, and the risks are real and enormous. But I've been thinking about the opposite problem, one we have thought very little about, but is predicted in the same forecasts, declining population.

World population is predicted not to level off and stay at 9 to 12 billion, but to begin declining. There are two main reasons for this. First, the fertility declines that have driven the demographic transitions in rich countries are predicted to eventually reach poorer and then poorest countries as well. There is good evidence that this is already happening, as education of females and availability of information have reached places like Iran and India, fertility rates in those places has dropped very dramatically and without Chinese style coercion. Fertility rates are declining almost everywhere, even if they are still quite high in some places. The countries that undergo this transition latest are expected to still get there eventually. If the whole world had fertility rates like what the Japenese have, world population would eventually decline.

The second reason population is expected to decline dramatically is what is called population momentum. A population that had a lot of babies 20-30 years ago inevitably has a lot of babies now, because of the large number of young women reaching their peak reproductive capacity. Iran is a perfect example of this. Iran is still producing an enormous number of babies, even though per-woman fertility has declined dramatically, because there are just so many reproductive age women who were born when fertility was extremely high 20-30 years ago. Americans are familiar with this effect from the "echo boomers" the large cohort of children born in the 60s and 70s as offspring of the baby boomers. Much of what is currently carrying world population upward is this type of momentum. Much of the world still has a very young (median age in Pakistan is about 16), and therefore reproductive, population. As fertility rates decline and longevity decreases, world population is aging dramatically. Median age in Japan is about 47 and rising fast. By 2050, the UN predicts that median age in Pakistan will be closer to 35 and Japan closer to 55.

Somewhere around there world population will begin to decline, slowly at first, and then more rapidly. That is the prediction anyway. The problem is that all of our models are predicated and tested based on increasing world population. World population has increased every year since before the advent of modern science. And it is not only our demography that is based on the assumption of ever increasing population. Our entire economic system is built around the idea of ever-expanding demand driven by ever expanding population. We know how to add new housing developments, houses, cities, businesses, banks and so forth. We know how to tear down small buildings to make space for bigger, taller ones. We have no system for dealing with declining population. How should a business respond if its potential audience gets smaller every year? How should a city respond if fewer and fewer of its housing units are occupied? How should a family respond if there is no one to take over the family business or farm? How should a government respond if there are too few people to pay its taxes or fill its military?

We do have case studies of this sort of thing. Flint, Michigan is talking about condemning and leveling not just individual homes, not just whole neighborhoods, but major portions of the city that are no longer viable because the population of that city has shrunk so fast. Japan, Germany and much of the former Soviet Block are experience population decline, and adapting to it with various degrees of success. The countries that do well despite population decline seem to be those that base their economies on exports to other regions where population is still increasing. If domestic demand declines but overall demand continues to rise, it may not be such a problem. But what will happen if population is declining almost everywhere? Will people or nations increase fertility in response? Will the general lack of children induce even more people to not have children, driving fertility even further down? Will we develop economic and development structures that thrive on population decline, as our current system requires population growth?

Michigan's population decline is directly attributable to collapse in demand for Michigan's main product. Population declines in Eastern Europe are similarly caused by politial, economic and social decline. The types of population declines Jared Diamond wrote about were caused by collapses of ecologies and socieites. If we manage to get through the population maximum of the 21st century without major collapses, we may be faced with the relatively novel situation of benign decline. That can only happen if we build systems that can function and thrive with declining populations. We don't yet know how to do that.

Behavio(u)r defined.

Published in this month's Animal Behaviour. British spelling.

Behavioural biologists do not agree on what constitutes behaviour

Daniel A. Levitis, William Z. Lidicker Jr. and Glenn Freund

"Behavioural biology is a major discipline within biology, centred on the key concept of ‘behaviour’. But how is ‘behaviour’ defined, and how should it be defined? We outline what characteristics we believe a scientific definition should have, and why we think it is important that a definition have these traits. We then examine the range of available published definitions for behaviour. Finding no consensus, we present survey responses from 174 members of three behaviour-focused scientific societies as to their understanding of the term. Here again, we find surprisingly widespread disagreement as to what qualifies as behaviour. Respondents contradict themselves, each other and published definitions, indicating that they are using individually variable intuitive, rather than codified, meanings of ‘behaviour’. We offer a new definition, based largely on survey responses:

Behaviour is the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal and/or external stimuli, excluding responses more easily understood as developmental changes.

Finally, we discuss the usage, meanings and limitations of this definition."

Demography of Islamic Extremism

The size of any population is determined by births, deaths, immigrations and emigrations.

Change in population= Births-Deaths+Immigrations-Emigrations.

This is one of the first facts mentioned in any class or text on demography, and is so obvious that we often simply take it for granted. But like many concepts which are obvious in context, this can be easily forgotten.

I am thinking here particularly of the population President Obama refers to as "Islamic Extremists." What determines the global population of these extremists? We can assume that no one is born as a violent extremist, so it isn't births. The Bush administration tended to assume the population of extremists was a declining stock, whose numbers would be determined primarily through deaths. We saw how well that worked out. What the Obama folks seem to understand, and what I believe to be the goal of much of the US's redirected foreign policy and rhetoric, is that the number of violent extremists in the world is determined primarily through immigration (recruitment) and emigration (defections, retirements, going homes, laying down of arms).

Let's assume, again that no one is born a violent extremist. Let's further assume that 1% of the world's 1.5 Billion Muslims have the backgrounds and personality traits such that the proper circumstances could push them to violent extremism. We estimate 15 Million potential extremists. What proportion of those will turn to violent extremism at any one time? The answer is clearly a very small. Depending on how we define our terms, maybe there are 150,000 violent Islamic extremists in the world today. That is if we add together the Taliban forces, al Qaeda, al Shabab, Hamas fighters, Hezbolah fighters and so forth. It is a rough estimate, but will do for now. We estimate that 1% of 1% of the worlds' Muslims are violent extremists.

What if, instead of 1% of potential extremists becoming actual extremists, 2% were? Then we double the number of extremists, to 300,000. If only 0.5% of those with the potential for extremism experienced circumstances causing them to act on that potential? Then we have 75,000 extremists, and our problem of eliminating extremists is half solved.

Nothing the US does is going to kill 75 thousand extremists, or 150 thousand extremists. Not that the US military isn't still trying to kill as many violent extremists as possible, but we seem to kill maybe five thousand a year, if we are lucky. Let's look again at our equation and start plugging numbers into it.

Change in population= Births-Deaths+Immigrations-Emigrations.
Change in population= 0-5000+Immigrations-Emigrations.

Let's plug in numbers for the two scenarios we outlined above.

Change in population= 0-5000+150,000=145,000
Change in population= 0-5000-75,000= -80,000

The number of extremists killed is largely irrelevant in these two scenarios. If we kill 15,000 instead of 5,000, we end up with
Change in population= 135,000 or -90,000

The potential fluxes through immigration and emigration are just so much bigger than the number we kill. Nor are these numbers necessarily independent. One can easily imagine that if brother A has the capacity to be a violent extremist, brother B is more likely than average to have the same capacity. Killing A may increase deaths by one, but it may also increase immigrations by one. If there is a brother C, it may increase immigrations by two.

The point of all this is to say that the most effective way to manage the population of violent extremists is decrease their recruiting and increase the number of their colleagues who go home. Killing them is useful in limiting the damage they can do, reducing their moral and providing alternative opportunities to those who could join them. But the number killed is far less important than the effect that that killing has on recruiting and defections.

I could get into a long discussion of what I think will ultimately influence that (Immigration-Emigration) term, but I won't, as that would stray too far from anything I have any scientific basis for considering. Rather I will simply say that I think the US government has finally caught on that the conditions determining (Immigration-Emigration) are far more important than the number killed, and I think this is a key insight.

Scientific publishing after paper

Yesterday I submitted a paper to the Proceedings of the National Academy of Sciences. Like most high profile journals they have strict page limits, and my paper was carefully planned to be just under the limit. I got an email from them today saying that they had recently changed the format in which references are given in the journal, and I would have to use the new, longer, format, and resubmit. I had 65 references, so the longer format made my paper half a page too long, which means I have spent the morning making the paper shorter again.

All this has got me thinking about the future of publishing, as fewer and fewer people read their journals on actual paper. The traditional justification for page limits, and a lot of the other rules journals have, was that it cost the journal money to print the extra pages, or the color, or figures above a certain size. Several journals, including PNAS, have even offered authors the option of going over the page limit or adding colors, but paying the extra printing costs. What happens to these limitation as fewer and fewer subscribers bother with the paper edition, and almost everyone goes straight to the digital version?

We are not near abandoning the paper journal yet. Even journals that start out as internet only, as PLoS did a few years back, often end up printing a paper edition because libraries and some readers (especially the older and more established) really like have a paper journal to thumb through. But this is changing. I, and most researchers my age, read almost everything from a digital copy. Some people print out the individual articles they want to read, others read from a screen. It is rare to see anyone my age or younger reading from a bound print journal, unless of course it is one of those rare journals that isn't available online. It is becoming increasingly common for libraries, to save shelf space and money, to provide access to only the digital copies of the less frequently read journals. There are journals which can only be found online, and I suspect their number will increase rapidly over the next decades. These journals (e.g. JoVE) can be far more multimedia than the old ink on rectangle.

So far, this seems to be having relatively little effect on the page limit. Journal editors want authors to get to the point, even if they don't have to worry about the cost of paper and ink. Journals are increasingly offering the option of accompanying the paper with supplemental online material. Those experimental protocols, that video sequence, the large table and the mathematical appendix can all be posted online, with the permalink listed in the main paper and hyperlinked directly from the digital versions. PNAS allows up to ten such files, and the length of all these add-ons often surpass the article itself, but without busting the page limit.

Annoying as it is to have to go through and find three more lines of text to cut to get down to that page limit, I suppose I should be happy that the page limit will be around long after the page itself has gone the way of the mimeograph. I don't want to have to read as much as all those people would write.

I do think the journals themselves will last, even if only online. Someone has to organize the peer review, and everyone needs to have a limit on the number of places they need to look to find relevant papers. I doubt I will see the day when one can be a successful scientist just by uploading my own work onto my own website and inviting people to read it.

A lack of enemies

I am working on submitting a paper to the Proceedings of the National Academy of Sciences. They ask that I suggest editors and reviewers who are qualified to evaluate my paper. They also give me the option of listing a few people who I want to not be given the chance to peer review my paper. I assume this is so that if two authors have written on the same topic, and clashed on that topic, one can't keep the other from publishing by writing very negative reviews. It is a way to ask that your paper not be sent to your rival and then treated unfairly.

There are people whose previous conclusions I disagree with, but nobody I can think of who I have any reason to believe would treat my paper unfairly. I haven't been in the field long enough or published enough papers to make enemies yet. Something to look forward to, I guess.

The University that Was

The University of California at Berkeley has long claimed, with reasonable justification, to be the world's top public University. The University of Massachusetts has some very good campuses, but they have never been any challenge to Harvard. The University of Connecticut is no Yale. But Berkeley and Stanford have often been considered on equal footing (or rather people at Berkeley thought Berkeley was clearly better and people at Stanford held the opposite opinion). In terms of prestige of faculty, Nobel Prizes won, National Academy members, number of important scientific publications, number of top-ranked programs and so on, Berkeley has long been among the US's top universities and far and away the best among the public institutions. California, historically a big wealthy state with a high standard of living and strong emphasis on education, made Berkeley the jewel of its enormous system of public education.

Berkeley now has this wonderful global reputation, amazing arsenal of high-powered faculty, several former faculty in high positions in the Obama administration and world-class facilities. It also has a crushing budget shortfall coming on top of several years of budget cuts, pay for grad students and many staff that is well below what the university considers a living wage, the expectation of massive staff layoffs in the near future, vanishing budgets for maintenance, supplies and support and deep sense that things are going to get a lot worse before they get any better.

The voters of California, in their wisdom, have used the state's mechanisms for direct democracy to require spending increases, but forbid tax increases. They have amended the state constitution to dictate budget items and make it enormously difficult to pass a budget. They have elected politicians based on looks and swagger and reacted with petulance when those politicians had more looks than brains. The state government has deteriorated to the point that most state spending not mandated by ballot initiatives will need to be completely cut. The budget for higher education is expected to be cut by about $1 Billion for the next school year. Similar shortfalls are expected until the global economy has rebounded, or the state constitution has been scraped and more workable one written.

Berkeley, I think it is safe to say, will not retain its reputation for excellence if this goes on for long. For some years now, as the budget has worsened, Berkeley has had a tougher time attracting the most competitive faculty. Many faculty searches have been canceled, and those which weren't often ended up offering positions to researchers who went for much better deals at private institutions. Berkeley has also been having trouble recruiting grad students. My department this year had six first year grad students enter and 17 PhDs graduate. Administrative departments are being eliminated or combined. Journal subscribtions are being scalled back. Phone lines are being turned off. Scholarships are being eliminated. It's ugly, and likely to get uglier fast.

I suspect that given a few years the economy will improve, and the budgetting process in California will be reformed, and Berkeley's budget will start to improve. I fear that by the time that happens Berkeley will have lost its global reputation, many of its most famous faculty, and its culture of intellectual greatness. UC Berkeley may from now on be just a very good public university.

Forthcoming paper

The paper I wrote with two colleagues on how biologists define the word behavior should be coming out in Animal Behaviour in June or July. I am guessing it is the first article to appear in that journal to reference both a supreme court decision and a Sherlock Holmes mystery. I am certain it is the first one to tell behavioral biologists that they don't agree on what they mean by 'behavior.' I am very curious to see how it will be received.

Adaptive male lactation?

It has long been known that male mammals, including male humans, are physiologically capable of lactating. Screw with a man's physiology by giving him the right hormones, or the wrong series of starvation and then plenty, and he may start to produce milk. No one, as far as I know, has ever suggested that this is adaptive, that this capacity exists because men gain some reproductive advantage through lactation. Rather, it is usually seen as a result of the fact that we share almost all of our genetic material with females, who do make good use of their lactational prowess. Male lactation across the mammalian world is largely thought to be a side effect of intersexual correlation, the tendency for the two sexes of a species to have similar traits.

I am therefore skeptically excited to read that males of two species of fruit bats, one in Malaysia, and one in Papua New Guinea, are said to have "well-developed lacteriforus ducts and underlying mammary tissue similar to that found in lactating females" and that milk has been "expressed" from a large number of male bats.

It is not actually known whether these males are feeding young, and if so how commonly and to what effect, but this is the closest suggestion I have yet seen of the possibility of adaptive male lactation.

Hobbits had big odd looking feet.

Well, duh...

Next they'll discover that Homo floresiensis were fond of tea cakes and lived in holes with circular green doors.

The Free Encyclopedia and 'Hairless' Apes

Without having done extensive checking, I would guess that Wikipedia is the only encyclopedia in the world in which the section on primate taxonomy includes nude photos of male and female humans with all their body-hair removed.

I suppose one could argue that body hair would obscure some portion of our typically primate anatomy, or make the photos appear less clinical. That said, none of the other primates pictured are shaven, so why the humans? And honestly, human's body hair doesn't hide that much anyway. As humans are naturally the least hairy of any primate, the clean shaven models seem to me to unduly exaggerate our distinctness from other primates. I don't approve.

On further consideration of the nature of Wikipedia, the inclusion of these photos could be intended purely to annoy social conservatives who object on religious grounds to the placement of humans among the primates. In that case the hairlessness would presumably be intended to emphasize the nudity of the models.

Wherefore art thou, niche conseratism?

"Niche conservatism is the tendency of species to retain ancestral ecological characteristics." (PDF)

But why do species have this tendency, or more particularly, why do ecological traits not change more rapidly than they do as a lineage evolves? Wiens and Graham state that, "We refer to niche conservatism as a process, although it may be caused by more than one factor at the population level," but don't say what those factors may be, or provide a reference to someone who does.

So what causes niche conservatism:

Two basic mechanisms occur to me. The first is that new traits simply don't arise, and therefore can't be selected for or against. Why don't we have rats that can eat iron? There is lots of elemental iron around these days, and it is very high in energy. Surely a rat that could eat iron and extract all that energy would do very well, and make lots more iron-eating rats. But that trait has not occurred (and is not likely to do so) and as such there is no way for natural selection to favor the iron-eating rats. But for traits like sexual mass dimorphism, this type of constraint seems unlikely. We know that closely related species sometimes have very different mass dimorphisms (compare gorillas to humans). But closely related species usually don't have wildly different mass dimorphisms, so there is conservatism in the trait even though it is pliable.

The second possibility that occurs is that niche conservatism comes about simply because a trait works well with the way a population lives, and the other traits is has, and therefore some form of selection acts to keep the trait where it is. The trait is conserved because it is functional. Even if some other combination of traits would be more advantageous, that combination would require so many modifications that you can't get there from here. The population would have to go to far 'downhill' on the fitness landscape to get to that taller hill across the way. So selection, which tends to push the population 'uphill,' keeps it on the little local peak it is on. By keeping the population where it is, selection causes niche conservatism.

I'll call it a hypothesis. First I need to find out who has already said almost the same thing.

A third way of seeing things

The paper I'm writing now is on sex-biased longevity in primates. I'm trying to understand why in some species the males live longer, and in others the females live longer. The story I'm trying to test goes like this:

The largest investment in primates' offspring is in the form of care, not eggs or sperm or pregnancy. In species where females provide all of the care, males need not stay with a single mate, so the operational sex ratio is male biased (i.e. lots of males are out looking for a mate, while most of the females are pregnant or nursing and therefore not looking to mate), reproductive skew is high for males (some males will father lots of offspring, others none), and the fitness rewards to successful male competitors are great. Larger males are more likely to win these competitions, resulting in an increase in optimal male size. These large belligerent males risk increased mortality through conflict, and through diversion of physiological and developmental resources away from longevity and into competitiveness. Simultaneously, selection for longevity in females may be increased by the need to stay alive until their young become independent (and in the case of humans, to care for grandkids). This leads to males who, relative to females, are non-caring, short-lived, large and conflict prone.

I have data (gleaned from the literature) for a bunch of primate species on how long males and females live, how much care the fathers provide in each species, how big males and females are and how frequently and intensely males fight with each other. Depending on how I analyze these data, I get two very different answers. If I treat each species as an independent sample, and look at the correlations between these variables, the data completely support the story. The species range along a continuum having short-lived belligerent large, uncaring males at one end and long-lived caring low-conflict small males at the other.

But most evolutionary biologists would say that is not the right way to analyze the data. I need to take into account the relationships among the species. Two traits might seem to be correlated not because the one makes the other selectively advantageous, but because a group related species all have the one and all have the second. Take the example of feathers and laying eggs. All birds have feathers and all birds lay eggs. Is this because something about feathers requires egg-laying (probably not) or because all birds are descendents of some ancestral birds that laid eggs and had feathers, and ever since no bird has arisen that didn't do both those things. That all birds have eggs and feathers is an example of what biologists call evolutionary inertia.

The question this poses for me in writing my paper on primates is whether the correspondence between sex-biased longevity and these other variables is because of the adaptive story I told you, or because of evolutionary inertia. So I look at the data a second way, and see that there is a great deal of evolutionary inertia in these traits. Most primate species are somewhere near the middle of that continuum I described. Ever species at one end is from one group of related monkeys. Every species at the other end of the continuum is either a great ape or from a different family of monkeys. Plugging my data into software designed to test for evolutionary inertia, I find that closely related species are very likely to have similar values for all the traits I am measuring, and that inertia is fully sufficient to explain the correlations between these traits. It is like eggs and feathers in bird.

As I am trying to write the paper to present all of this in a scientifically rigorous way, I am struggling with what to say about it. The easiest, and least interesting, conclusion would be to simply say that the correlations are purely illusions conjured by evolutionary inertia. What I'm attempting to find a way to argue it that it could just be inertia, but that the inertia might be because of selective effects. In other words, that both the inertia story and the selective story could simultaneously be true, and closely related species are similar not because they can't change, but because what was adaptive for their common ancestor is still adaptive for them. If a male from a very belligerent species was to grow in a way that made him not a good competitor, but able to live a long time and provide care to his young, this wouldn't fit with the way his species lives, so he wouldn't pass on his novel trait, and his species would stay like their ancestors had been. It is evolutionary inertia caused by adaptive mechanisms. I think my next step is to find out who has already written about adaptive evolutionary inertia, and what they said.

Science-based do-gooding.

Last month as we drove up to her mom's house, Iris and I were talking about what sorts of non-profits we think really use their money well, in terms of achieving a lot of good with relatively little money. I said that the ones that usually impressed me were those very focused on a single type of action that did that one thing extremely well, rather than trying to save the whales and reduce teen pregnancy and sue the manufacturers and put out a great picture book of homeless homosexual redwood trees. Iris asked what kind of action I had in mind, and I said that ultimately, the step that seems to do the most good for the least expense is educating girls in poor countries where girls don't traditionally get educations. The list of things one can accomplish by educating girls is truly amazing. The level of education of the females in a country is the single best predictor of longevity increases, decrease in infant and juvenile mortality, decrease in rate of population growth, decrease in rate of infectious disease, increase in future education of both boys and girls and so on and so on. It is more important than how rich a country it is, how many doctors it has, the religious practices of the population or how well educated the men are. There are decades of studies comparing between nations, between regions, between villages and between individual families, and at every level having better educated women around translates into a healthier, more stable and less quickly increasing population. And the greatest gains in all these outcomes come from the first steps in educating the women. Whether women have a masters or a PhD doesn't affect the chance of their babies dying much. Whether they finished third grade or had no school at all has an enormous impact. Every additional year of schooling is helpful, but less so than the previous year.

When I read these studies, I feel like we shouldn't be spending development money on anything but educating girls. I feel like we've known about the development wonder drug for decades (and unlike most wonder-drugs, this one actually works) but haven't bothered to use it. Iris pointed out that in many countries, such as Niger, where she was a Peace Corps volunteer, there are cultural sensitivities that would keep a westerner from marching in and educating girls. The education of boys is considered more important, and many boys don't get educated for lack of funding. Post-colonial resentments exist, and must be treated carefully. Iris argued that if an organization wanted to educated Niger's girls, its organizers would have to have the kinds of insights and sensitivities to Niger's culture that only Nigeriens have. She lamented the fact that there was no such organization in Niger.

Imagine then our surprise and delight when (less than a week later) Iris found out that some of her Nigerien contacts were founding an organization to promote and fund the education of Nigerien girls. If we were superstitious people, we could draw all sorts of conclusions from the coincidence. Instead, we have offered to do what we can to help them get up and running. They don't yet have anything more official than a possible name and a board of directors. They aren't even taking donations yet (they still have to apply for tax-exempt status). Iris has been contacting her Peace Corps friends who have particular useful expertise, and I've been unwisely taking time away from my thesis to gather up and summarize the published research on the benefits of educating women. Perhaps it is naive, but I can't help but think that it would be useful to have a well documented statement on the benefits of educating girls to show to potential donors and government types. We expect to be helpful to them however we can. If they are able to do what they want to do, Niger (currently one of the world's poorest and worst educated nations) should be an amazing success story in a decade or two.

Poster-time

In a couple of weeks I'll be attending the conference of the Population Association of America. It will be a bunch of demographers. Most of the conference is talks divided into topic-specific sessions. They don't have a session for biodemography, or really anything related to my research, but the poster-session is open to whatever topic, so I'm presenting a poster.

My title is, "Post-Reproductive Lifespan in Humans: Cultural Artifact, Widespread Primate Trait or Unique Adaptation?"

I've had fun making my poster, mostly because it is an excuse to play with Photoshop and Powerpoint instead of writing my thesis. For my poster I needed to find a compact easy way to display how the fertility and survival of a population changes with age, and simultaneously explain my methods. And I needed to be able to do that for several populations side by side in a small space. Now this is all tailored to make sense to the demographer, so it may not be that intuitive to anyone else, but I like what I've got. To clarify, in demographerese, lx means what portion of the individuals that survive to each age and mx means how fertile are individuals at that age.

By plotting mx and lx on the same graph I make it visually clear (to a demographer) that the population nears an endpoint to fertility (age M) long before it nears an endpoint of survival (age Z). I then go on to use some math and demographic methods to define good ways to measure post-fertile survival in ways that allow for straightforward comparisons between species. I call the two measurements G and S. But the fun part comes in when I use the graphical format established in Figure 1 to compare populations in Figure 2:


My hope is that having labeled and explained the parts of the graph in Fig. 1, the meaning of these graphs in Fig. 2 will be quickly obvious to the demography crowd. I'll leave you to interpret what these graphs say about post-fertile survival in humans and chimps in different environments. I can't give away everything.

Diurnal Activity Cycles

My wife and I (both writing theses this spring) and two cats share a very small studio apartment. One way we make maximum use of the space is by having different sleep-wake schedules. I do my most effective writing between 9PM and 1AM. Iris gets the most done from 6AM to 10AM. I have the easiest time concentrating at that time, and only partly because everyone else is asleep. FeLion, our older cat, does some of her best suckling on inanimate objects in the middle of the day. Tigrinum, the kitten, expends most of his energy from 2AM to 6AM, charging around the house and leaping from the top of his cat-tree onto his sleeping humans. Come to think of it, it makes a pretty lousy system.

There is a well established pattern of individuals of different ages waking and sleeping at different times. Older adults and young children tend to go to sleep early and wake up early. Teenagers tend to stay up late and go to bed late. People in all the ages in between are pretty variable. These patterns are well known to most people, but I'm not sure we understand their evolutionary basis. Why did humans evolve to have sleep schedules that vary individually and with age as much as they do? My guess is that it had to do with avoiding competition within groups for space and forage. The old people and the little kids left the cave or the hut early in the morning and foraged before everyone else was up. In the evening, after everyone else was asleep the young people would stay up and try to impress potential mating partners. That was probably the easiest time to find some privacy without straying too far from the village. One thing I wonder about, do other primates have similar variation in their diurnal activity cycles? That right there is a good evolutionary biodemography question.

Why I can love chocolate

The conversation usually goes something like this:

Me- I'm allergic to caffeine. It makes me get a terrible headache, then get really sleepy and sleep for 12 hours and then I still have a terrible headache.

You- Um, but I see you eat chocolate all the time. You're always talking about chocolate and writing about chocolate. You are a total chocolate adict.

Me- Yeah! I love chocolate. It's my main drug.

You- Um, but chocolate has caffeine.

Me- Well, it has a tiny bit, but mostly it has other closely related chemicals.

I've had this conversation with enough dozens of people that I figured I should look up what was in chocolate. And it turns out I actually did know what I was talking about (for once). According to this article in the journal European Food Research and Technology, cacao beans have three main kinds of very similar chemicals in the group called methylxanthines. These are theobromine (named for the Cacao tree, Theobroma cacao), caffeine, and theophylline. Raw fermented beans straight off the cacao tree have lots of theobromine, very little caffeine and almost no theophylline. In the various preparation steps between then and when I actually eat it, much of the caffeine is lost. The concentration of these various chemicals depends a lot on the strain of cacao, the growing conditions and the processing, but most chocolate has 20 to 100 times as much theobromine as caffeine. A cup of hot cocoa has about half as much caffeine as a cup of decaf coffee.

The fact that chocolate doesn't make me have a terrible headache and put me to sleep is likely (likely meaning I am speculating) either because there is too little caffeine in it to matter or because it has so much theobromine. Theobromine could be counteracting the caffeine, or it could be competitively excluding the caffeine from the neuroreceptors it normally binds to. Basically this means that theobromine and caffeine are so similar that they stick to the same spots on my neurons, and if the theobromine gets there first, the caffeine may not be able to stick, and therefore not affect me. But the moral of the story is I can eat chocolate without worrying about the caffeine making me sick.

Elastic replacement

I've been thinking on an off for several years about the concept of 'elastic replacement.' That is term I made up to mean when the rate at which new things arise increases in response to the effort to remove old things. The example that got me started thinking about this was a political one. For the early years of the US occupation of Iraq, the Bush administration frequently cited statistics on how many terrorists had been killed or captured as a result of US action in Iraq. What they never seemed to consider was that US action in Iraq might also be increasing the replacement of terrorists by making it easier for terrorists to find and recruit young people who might have otherwise been non-violent. The size of any population is determined by not only the number leaving, but also the number entering, and by measuring only one portion of our effect, the US government necessarily got a biased picture of our effect. The CIA has confirmed that the number of active terrorist in Iraq rapidly increased rather than decreasing through the first years of the Iraq war.

This general idea carries over into all sorts of arenas. When a giant old tree falls, it makes space for hundreds of seedlings. When I comb my cat to remove loose hairs, I loosen lots more hairs and possibly even stimulate increased hair growth. WWII caused far fewer deaths of US soldiers than the ensuing baby-boom caused births of US babies. Eating all the chocolate so that my wife won't be tempted by it inspires her to go out and buy more chocolate. Responding to all the emails I should have responded to a long time ago brings in even more emails that need to be responded to.

Elastic replacement seems to be an extremely common class of unintended consequences. Humans don't seem to be good at considering it, but we should try.

Making progress

Writing a paper is an iterative process. Figure out what my point is, start writing, change my point, adjust my writing, repeat. The process of rewriting the methods makes me realize it would be better to analyze the data a different way, so I do the analysis over which makes me realize that I need to modify not only my methods but also my conclusions. The new conclusion requires an additional analysis and therefore a further modified conclusion. Writing is very much like sculpture in that it is not so much a question of getting it perfect as getting it good enough that it isn't worth changing.

Fertility v. Fecundity

Fertility and fecundity are two closely related concepts.

One means the physiological state of being able to have offspring, the other means the state of actually producing offspring. In a population of 26 year old human females, 95% might be physiologically capable of giving live birth, while perhaps only 10% might actually have a baby that year. So fertility and fecundity are different. The problem is, which is which?

Demographers refer to the ability of have babies as fecundity, and the rate at which women actually have kids as fertility. Biologist do the opposite, saying that fertility is the capacity and fecundity is the realization.

This is just a quaint fact in academic linguistics until one tries to write papers and give presentations that will sit well with both demographers and biologists. Biologists think it is totally unreasonable to adopt the linguistic oddities of the social scientists, and demographers are not happy about people reversing the meaning of these terms. I usually go with the demographer's lingo. They are the ones who employ me.

Sex-biased longevity

Ive spent much of the last couple of weeks working on a paper on sex-biased longevity in primates.

Here is a draft of a portion of an introduction to said paper. Any similarities between this and the final published paper are purely coincidental:

The difference in longevity between the sexes of a population depends upon the selective forces each sex experiences, as well as the degree to which common genetic material limits independent demographic evolution. Sex-biased longevity has been proposed to arise from difference between the sexes in selective forces as diverse as reproductive physiology, care of offspring, parasite risk, mortality associated with reproduction, genomic stability and late-life support from kin. But measurements of sex-biased longevity have been made for relatively few species, and we have little sense of the degree to which sex-biased longevity is constrained by shared genetics or phylogenetic conservatism.

Most organisms, and likely all mammals, experience an evolved rapid increase in mortality and decrease in fertility at advanced ages, limiting longevity. The force of selection against mortality at a given age depends upon the likelihood of surviving to that age, and the mean remaining reproduction of individuals who do survive that long. Reproduction and survival are expected to drop to zero at similar ages, but reproduction can be direct (fertility) or indirect (care of offspring and kin effects).

Captive populations, the source of most demographic data on non-humans, will reflect sex-differences in evolved capacity for longevity more so than do wild populations, which tend to die younger (there are exceptions). For understanding the influence of experienced mortality patterns on evolved capacity for longevity, it is useful to make the distinction between extrinsic and intrinsic mortality. Extrinsic mortality is generally said to be that caused by the environment, while intrinsic death is driven by a failure of the organism's internal processes. In practice this distinction is difficult to make, as all environmental risk is influenced by the organism's characteristics and behaviors, and the timing and risk of intrinsic failure is inevitably influenced by an organism's history and environment. None-the less, much of our theory on the evolution of longevity is based on this intrinsic/extrinsic distinction. In general higher extrinsic mortality will lead to increased intrinsic mortality. However increased extrinsic risk at age x will influence evolved mortality at many ages, and not necessarily lead to a spike in intrinsic mortality centered at age x. This leaves overall sex-biased longevity as our best measure of sex-biased mortality when employing data from captive populations. Sex-biased longevity in captivity is highly correlated with sex-biased longevity in the wild even though the causes and timing of mortality may vary between species.

Much of the discussion of sex-biased longevity has focused on the idea that if one sex provides extended care to descendants, that sex should gain greater selective benefit from increased longevity. Allman et al. suggest that in primates, males who are the primary caregivers tend to live as long or longer than their females, while in species with little paternal care females tend to live longer. The Grandmother Hypothesis and its derivatives use indirect reproduction by post-menopausal women to explain their post-reproductive lifespan and therefore their tendency to live longer than men despite earlier decline in fertility. The Patriarch hypothesis instead argues that women's post-fertile survival is explicable based on late-life reproduction in males and the non-independence of male and female longevity.

Sex-biased longevity can also result from differences in mortality risk between the sexes. Trivers proposed that in species with frequent or intense male-male conflict, males incur significant mortality risk and therefore don't live as long as females. Alternatively, if females experience increased mortality in producing or rearing young, males should be expected to live longer. If either sex is the predominant disperser, and mortality risk during dispersal is high, this too could cause inter-sex differences in capacity for longevity. Finally, a variety of hypotheses have been put forward arguing that either the larger sex, or the smaller sex, should tend to live longer.

Using comparative primate life-history data, we examine the variability of sex-biased longevity in primates. We further examine the degree to which level of paternal care, grandmaternal care, male-male conflict, and mass dimorphism predict sex-biased longevity. Finally, we examine the patterns of correlated evolution among these variables in a phylogenetic context.

Tour of Science!

Walking back to the Valley Life Sciences Building this afternoon, I passed a large tour group of high-school students and their parents being led by an undergraduate. One mother, snickered into her cell phone, "they have an heeeeerb lab. They study herbs. This place is crazy. Crazy! No, no, no, the tour guide said they had a whole museum of herbs. I'm like what, parsley?!"

It took me an instant to figure out that she was talking about the University and Jepson Herbaria, a research museum dedicated to the study of plants generally, not culinary herbs in particular.

I emailed this story to the other grad students in my department. Many of them responded that they had heard the tour guides telling the tour groups all sorts of misleading and false information, including that a herbarium is a museum for studying cooking herbs.

Here are some other examples of overheard falsehoods made up by university tour guides to impress their tour groups and relayed to me by other grad students. Several of these things were independently reported by more than one observer:

- The Cretaceous display in front of the Herbaria contains extinct plants... Berkeley scientists rediscovered their ancient DNA, amplified it, germinated seedlings, and planted them there for museum visitors. (The display is of plants of types similar to those which existed during the Cretaceous, none of which have ever been extinct)

- The T. rex may be as many as 5 million years old. (It is at least 65 million years old)

- The T. rex came to the paleontology museum in a giant puzzle
box and when it got here, the paleontologists didn't know what to do with
it. One of the employees was about to get fired but he was able to figure
out how to put it back together so he was able to save his job. This man
is now the assistant director of the museum. (A complete fabrication, truth here)


- The T. rex is named "Osborn". (Sue)

- T. rex (the species) was discovered by Berkeley paleontologists. (False)

- Most of the UCMP fossils are actually in the Campanile. (False)

- UCMP geologists discovered asteroids. (False)

- The giant ammonite in the first floor south hallway is from a time on
Earth where everything was giant, even the snails. (Hilarious and false)

- The Herbaria is home to the world's largest pinecone, but they don't put
it on display because they are worried someone will steal it. (Goofy and false)

- The Herbaria has one example of every plant species known to man. (They wish)

- The plants outside the herbaria went extinct around the time T. rex went
extinct. (False)

- MVZ scientists save stem cells from each animal they capture in order to
help genetically engineer new animals to save endangered species from
going extinct. (And then we take over the world!)

- The Eucalyptus tree is native only to Berkeley, Australia, and New Zealand. (actually only Australia, New Guinea, eastern Indonesia and the Philippines)

- The Eucalyptus grove is protected by an Act of Congress and can never be
cut down for any reason. (Pure fabrication)

- Strawberry Creek used to flow all the way to the Ocean but then they
built roads over it and then there wasn't enough water so all the
strawberry plants that used to grow next to it died off. (A large portion of Strawberry creek between campus and the bay has been undergrounded. The rest is false.)

- The pterodon skeleton is hanging above the T-rex because they always flew over the T-rexes to keep them in view so the T-rex couldn't sneak up on them. (Awesomely hilarious)

Decide what your point is before you write

I have spent most of my time recently writing papers for publication, and I have come to a realization. It is one of those realizations where I knew it all along, but had forgotten, or had never considered how important it was. What I realized is this: every paper should have a point, expressible in a sentence or two, and everything in the paper should be relevant to understanding and evaluating that point. Analyze the data, read the literature, analyze the data some more, but before one actually starts writing, one should have a pretty good sense of what one's point is. I've taken to making the point of the paper also be the title of the paper. Here are three titles I've written recently:

• Post-fertile survival in comparative perspective: humans are qualitatively different
• Behavioral biologists don't agree on what constitutes behavior
• The grandmother hypothesis is supported, but only in humans

I don't know that these will be the titles these papers actually have when they get published, but they serve to remind me that there is a point I am trying to make, and I'm not just spilling out everything that I've done or found out or thought. In many cases the point changes somewhat once I start writing the paper, and then I change the title. But in those cases where I start writing not really having a point in mind, I end up in a morass, casting about, writing several pages and then deleting them because they don't really say anything, the bits don't go together into a single logical argument.

The null assumption of many paper writers is that one starts writing at the beginning of the paper, writes until one gets to the end, then stops. In some forms of writing, (e.g. writing a short essay for one's blog) this is probably the most reasonable approach. I have heard it suggested that in writing a scientific paper, one should write the sections in revers order. Compile the list of references one needs to mention, write the conclusion, then the discussion, the results, the methods, the intro and only very last the abstract. I am think that what works well for me in creating a first draft is more like this: Reference, title, abstract, decide what journal I hope to submit to, methods, results, discussion, conclusion, add more references and then re-write the abstract and then write the introduction last, putting in only that information necessary for readers to understand the rest of the paper. These are arranged into the document in the order the journal demands, but I write them in the order that I feel leads to an efficient writing process. Of course I then end up going back and reading it in the final order to make sure the document does not read as disjointed.

Now that I've come to this realization, and begun to implement it in my writing, I need to also impress it upon my students. I have more than one very talented student struggling somewhat in writing a paper for publication, and in some cases I think what the papers lack most is a clear and central point. We need to rectify that. New rule for the lab: decide what your point is first, then continue writing after that.

A little praise goes a long way

I gave a draft to one of my mentors, and it came back covered in red. Comments, suggested edits, deletions, additions, objections, pointing out "wordiness," "bogging down" and opportunities to make it "more fun to read." However the comments start with the statement, "this is a very valuable paper, and I expect it will be widely cited."

A teaspoon of sugar does in fact make the medicine go down in the most delightful way.

Academic constipation

The NYTimes has a recent article about the current academic job market. In two words, it sucks. Professors who thought they could afford to retire are staying on, so positions aren't opening. Even when they do retire, hiring freezes are leaving their positions vacant until the economy improves, so post-doctoral researchers aren't likely to find a tenure-track position, and remain in underpaid temporary jobs. This means there are extremely few positions (as faculty or post-docs) for recent grad-students, and the usual routes out of academia, industry jobs, also aren't available. But while the routes out for grad-students are limited, recent college graduates who can't find real jobs are apply to graduate programs in record numbers.

While the situation is bleaker for the humanities, which have long been in decline economically, the scientific community in the US is keenly aware that however this turns out will have effects that will be felt for generations. The closest comparison I can make is the tremendous expansion of enrollment in colleges in the 1960s and '70s. As the students flooded in, colleges hired large numbers of professors right out of grad school. By the 1980s there were extremely few positions opening up, almost every professor had been hired in the previous two decades, and there were almost no retirements. A whole generation of academics had almost no chance of finding a professorship. I know several people of that era whose careers were permanently put onto alternate tracks because they simply couldn't find a professorship. Then, just in the last decade, that flood of professors hired to teach the baby-boomers have been retiring in droves, and many people were expecting a new wave of hires. More than one person has told me, "When I finished grad school, there were no jobs. When you finish, there will be openings everywhere." Now, given the economy into which I am graduating, I feel lucky to be in a sub-field that has some post-doctoral positions for a few years. Perhaps in three or four years universities will start filling all those vacant positions, and a new wave of young faculty, hopefully including me, will be an impediment to the career aspirations of our younger colleagues.

Evolutionary challenges to gene engeneering a better human

My friend Terry is a bioengineer, as well as a part time futurist. Much of what people in his field work on (as judged by what Terry talks about when he puts on his futurist hat and has a couple of glasses of wine) is thinking about how to modify the human genome to increase our lifespan and healthspan (I just made up the word healthspan, but I bet someone out there is already using it). Much of my work is to understand how and why we evolved to have the lifespan and healthspan we currently do. My understanding of my work is not promising to my understanding of this part of Terry's colleagues' work. In my view, bioengineering a much longer lived human will be extraordinarily difficult for several reasons.

First, we have a great many systems that seem to fail at about the same age, and there are good evolutionary reasons why this should be. Why bother building a femur that last longer than your heart, or your brain, or your pancreas? So to engineer a much longer-lived human, one has to be prepared to make a large number of changes to see a small effect. Terry counters that there will inevitably be some low-hanging fruit, and I concede this point. Simply by editing out some of the purely harmful mutations in the human gene-pool, we can probably extend average life span by a few months or maybe a couple of years. But because so many things fail at similar ages, no one or two or 100 changes could give us healthy 150 year olds.

Second, many individual genes have an enormous number of different effects in a wide range of systems, tissues and traits. When a gene has more than one effect, this is called pleiotropy, and we are chock full of pleiotropies, most of which we don't yet know about or understand. DNA is not like a blueprint, where you can just erase one wall, re-route a few wires, and draw in a new door. It is more like a vastly sprawling and disorganized system of interacting computer applications, add-ons, duplicates, and operating systems (only without any comprehensible order, annotation or easily understood compartmentalization). Something which functions as part of an unnecessary application may also be used in several disparate parts of the operating system. Modify a line of code and all sorts of unintended things can happen. Evolution has fine-tuned this system of interactions through millions of generations of trial and error, with emphasis on the error. Our best computer simulations are barely able to comprehend the folding of a single amino acid string into a protein, let alone a whole cell or organ or human, and animal models only go so far. So the process to modify evolution's optimization would not be fun, fast or clean. Our various bits are tuned to work together, and most potential single modifications can only move us away from that local optimum.

Terry counters that in many cases what evolution was tuning was utility in the form of health/strength/life vs. cost in the form of calories. A large part of the theory of life-history evolution is based on models where developing organisms have limited nutritional resources to invest in important tasks like growing, healing and reproducing. If one assumes unlimited calories are available, one can theoretically grow, reproduce and heal maximally all at the same time. And in Terry's view (which I can't help but see the wisdom in) anyone who can afford to play with the human genome can also afford plenty of potato chips. For the relevant population, calories are no longer limiting. In fact, we go out of our way to burn extra calories now. Spending calories lavishly to buy a few extra years of life or more garish secondary sexual traits is a win-win. The bioengineers of the future will have the advantage over evolution, because they won't have to worry about one of the main constraints evolution was dealing with, calorie restriction. So we may have to change a few things at once to make it all work well together, but we can do that. We can, in my imagining of Terry's thinking, reengineer the organism to its new environment.

It occurred to me last night that there is third, bigger and more insurmountable barrier to re-tuning. One that is not just a technological limitation: Breeding. Humans have been known to breed with each other, and in doing so they mix their genomes. You have half the genome of your biological father and half the genome of your biological mother. Imagine if your uber-mench father had a carefully altered suite of genes, and your mother was a good old-fashioned non-GMO woman. What do you get? You get half a carefully altered genome mixed with genes they were never designed to interact with. Chances are, you have all sorts of wacky health problems, and greatly reduced longevity. It would be like taking half the code of Mac OS 9 and half the code of OS X and expecting a stable operating system.

This means that every change and group of changes would have to be carefully designed to be back-compatible. The alternatives are gene altering the entire human population (which would never ever ever ever work (and I very rarely use that many "ever"s in a row)) or engineering the longevous new humans to be incapable of interbreeding with the old model. They'd have to start by separating off one population as a seperate species, Homo terrii, and only thereafter get serious about reengineering.

So suppose the engineers decide they want to make everything back compatible?
I'm not convinced this would work either. Most mutations are bad for you not only because they break a piece of the system, but because they make a new piece that doesn't work with what is already there. Requiring back compatibility means we have to have every piece work with not only the old set of genes and the new set of genes, but every possible combination of old and new. Evolution, largely free from constraints of time, funding and ethics, accomplishes this by letting those individuals who have bad combinations die out until there are very few harmful combinations possible. To extend the computer code analogy, this would be like trying to write OS XI in such a way that if one blended the code with OS X, it would still work. It is possible to do, but XI would end up looking an awful lot like X, too similar to be more than a service update.

This leaves only the option of creating a population incapable of breeding with normal humans and altering their genes extensively to try to overcome a large number of age-limiting factors at once. Again my understanding of evolution suggests a major difficulty. To do this successfully, one would need a large population all gene-altered simultaneously, to avoid inbreeding effects. One can't start a new population with just a few individuals and expect that species to have a decent chance of surviving well. Even if the species does make it through, there is likely to be an extended period of decreased lifespan and healthspan while the inbreeding kinks work themselves out and the population increases in size and genetic diversity.

Without doubting that bioengineers will continue to make things that seem impossible become projects of undergraduates, I consider it highly unlikely they will achieve any very significant advances in human longevity in the next few decades.

(NOTE: I sent this to Terry for comment or objection some time ago but he has been busy with 'job' and 'editing the book.' I take his failure to offer a substantive reply as evidence that in some basement deep under campus, his department is already failing to build an immortal human.)

Moving the last rotifer

For much of the last year my life and schedule have revolved around daily rotifer census. How often I go to campus, at what times, when I have time for anything else and the energy and time I have for anything else have all depended on lab work. When I could rely on my students to take care of it, I could do other things. Frequently, very frequently, my supply of dependable students was not up to the demands of taking data on and caring for several hundred animals each day. Even when my students are scheduled to do everything, it is rare for a day to go by without questions, problems or scheduling issues. If I am not in lab for a day or two both the quality of the data and the survival of the animals begins to decline.

So it feels like a big deal that my lab work will be done this week. Thursday. I've told my students that after that they are free to continue working on their side projects, but I'm not going to be in the lab. I'm not going to spend hours moving rotifers. I'm not going to be harassing them about keeping the lab organized and the rotifers' containers clean. I'm not going to be on campus six or seven days a week. I'm going to be at home, writing a thesis, and will come to campus on Wednesdays and Thursdays. And I'm taking my desktop (the lab's erstwhile main computer) home.

I like my students, and the rotifers are fascinating, and microscopes are fun. But I really like the idea of not needing to be in the lab every morning at 8. And the prospect of being able to have whole days to work on writing my thesis is positively thrilling.