Friday, November 21, 2014

Teaching mark-recapture with dor beetles

The key step in the planning of any good field course is to spend some time at the field site observing and asking questions. What is the habitat like, what lives there, what are the facilities, what are potential challenges or dangers to working there, etc? When I first went to do this at Svanninge Bjerge, the location of my zoology field course, I immediately started seeing big blue dung beetles all over the place. Bikuben Foundation, who operate the place, run cattle there. There is no lack of dung. These big plodding dor beetles (Geotrupidae) were all over the place, and it didn't take me long to decide I wanted to work them into the course. I wanted to introduce mark-recapture methods, and these seemed like perfect subjects. Mark-recapture methods involve catching animals, marking them in some way that would allow them to be recognized if re-sighted, letting them go, and then trying to recapture them. Such methods have a huge range of applications from tracking individual movements and estimating population sizes to monitoring growth and survival and studying behavior and sociality. To teach this in a field course, I wanted an invertebrate animal that wasn't too likely to leave the study area, that is easy to capture, mark and handle without damage, and that has enough charisma to capture students' attention. Dor beetles have all this. They are big and slow, and so easy to find and catch by hand. They don't bite or sting. They will collect in large numbers in pitfall traps baited with cow dung. They have big hard upper wings (elytra) that can be marked in any number or ways without harming them (we used this system with nail polish, but I've now got a battery-powered cautery). They are extremely numerous. They are shiny and blue. They can fly, but don't often do so.
Students mark a live beetle for release. Photo by Kim Lundgreen.
They make such an ideal intro to mark-recapture that I almost worry that I've given the student a false sense that this is easy, where in fact such studies are often very hard work. Still, if you want an efficient system for teaching mark-recapture methods and have beetles like this at your location, I strongly recommend them to you.

Wednesday, November 19, 2014

Why lightning talks work

Last week was the second annual meeting of the Evolutionary Demography Society. It was fabulous. Close to 100 people, over three days, at Stanford. Man there is a lot of good food around there. A friend and I were sitting outside, eating burritos when this dude from a farmers' market booth came over and started giving us samples of gluten-free baked goods. Delicious. Great weather, friendly people. Oh, yes, something else. What was it now? Ah! We talked about a lot of great science. Roughly 70 presentations. Post-reproductive lifespan, evolution of aging, all the topics I like best and every talk on a topic of at least some interest. Fabulous.

Many conferences (but not this one) have what are called concurrent sessions. In one room there might be a series of perhaps 15 minute long talks about matrix models, while in another they are talking about theoretical modelling, and in a third it could be all about field data on hunter gatherers. The benefits of this are allowing more people to give talks in a short period of time, and letting audience members pick and choose which topics they spend their time hearing about. At EvoDemoS, we address these same problems in a very different way. Most presenters give a lightning talk plus poster. The lightning talk is five minutes (plus five for questions), and then after each session there is a break for coffee and posters. But the posters are mostly from the same people who gave the lightning talks, on the same subject. So you get up, give a rapid intro to the work, answer a few questions, and then because there are no concurrent sessions, everyone at the conference knows who you are and what you are working on. If they are interested in it, they come talk to you at your poster. If you didn't bother to print your poster, they already know what you are working on and come talk to you anyway. If they aren't  interested, they don't have to sit through 15 minutes of you talking about it. The frequent and lengthy breaks (made possible by the shortness of the presentations) make it easier to stay alert through the talks, and let us achieve a much higher conversation-to-passive-listening ratio, and it is really the conversations that are the point of the conference for me.

Now the obvious downside is that many speakers are used to having more than five minutes. Some won't come because they can't have more time, use their connections and seniority to push for more time, or simply prepare the same talk they would for a much longer slot and largely ignore the warnings that their time is almost up. One speaker, to remain nameless, was on slide 4 of 26 when the one minute warning came and sped up only slightly. So the moderators need to be a bit firm in some cases. The more senior the speaker, the more likely an overage, in my experience. This is partly a matter of habit, but also that the more senior people often have more work to present. There were a few talks where the theoretical framing got almost completely cut to make time for more methods and results, and that was sometimes problematic. A is consistently greater than B, but what does that tell us? That said, the great majority of the five minute speakers were able to state the question clearly, say a word or two about methods, give a main result (or maybe two) and draw a conclusion or three before inviting us to see the poster. And almost everyone I talked to at the conference, both as speakers and audience, thought it worked well in this context.

For a conference with thousands of people, I'm not sure lightning talks would work. I'd be interested to hear from anyone who has tried it. But for anyone organizing a small conference like ours, I absolutely recommend it.

Wednesday, October 22, 2014

Asimov on Creativity

Isaac Asimov's essays have been favorites of mine since I was a teenager, and while I can't claim to have read them all (he was the most prolific writer in the history of the world, if one excludes 'writers' who have computers write for them) I have read a lot. So I was excited to hear that a previously unpublished essay of his, On Creativity. And like many of his essays, this is spot on.

To summarize his conclusions, intellectual creativity (creation of startlingly new scientific ideas in particular, but not only that) tends to occur when previously unconnected ideas are examined together by a person in a conducive situation. And, he argues, a key feature of that conducive environment is the freedom to be playful, to unabashedly look foolish, to pursue ideas that don't seem likely to go anywhere with people whose expertise has no obvious connection to one's own. He implies, and it is at least as true now as when he wrote it in 1959, that the structure and strictures of science-as-a-business (including in academia) tend to discourage this. Connecting previously unconnected ideas is less likely when everyone is a specialist in her own field, not only unaware of the big ideas in other areas of science, but obligated by the strictures of specialist journals, specialist department, etc. to not wander too far afield. In the world of reputation building and publish or perish,  things like playfulness, acceptance of foolishness, and exploration of uncertain goals is potentially fatal. Funding applications not only require that you know exactly where you will end up, but also that you already have a significant portion of the data needed to get there.

At previous jobs, and in previous stages of my life, I often felt (and was told) that my intellectual creativity was my greatest strength. As things now stand, I have surprisingly little space for creativity, and when I do come out with something really original, I get something along the lines of, "Huh. That's different. What about this other thing that we all know about?" So the question I must ask myself is, how (and where) can I find a place where my creativity is an asset, not only for me, but for science and the world?

Friday, October 03, 2014

Ear to Ear

Yesterday, two students came to my office. They asked me to help them organize a BioBlitz, a rapid assessment of what species are present, at Svanninge Bjerge, the site where I taught my field course this spring. One of these students was in that course, the other I have seen around but don't really know. I asked all the basic questions. What do you envisage? Where will you do it? When? How will it be funded? We had a good long conversation, and I offered what support I can, while making clear I may no longer be in Denmark when this all happens. They frowned. I asked, "Where did you get the idea to do this? Why do you want to?" They looked at each other. The one I don't know, smiled sheepishly. "Well, I couldn't take your course last year. And after the course, all the students who did take it made all of us who couldn't fell incredibly jealous. They talked about it endlessly, like it was everything they could ever want in a course. Like we would go to a bar and instead of whatever we were talking about, they would be all about pinning beetles. Rather than fight about it, we agreed to try to organize something similar for ourselves. And it would really be great if you could be involved." I needed a moment to focus on maintaining my composure.

Tuesday, September 30, 2014

Jeg kan aila dig!


My three year old has already learned that she can insult us in Danish with relative impunity.  Recently, when angry, she shouts "Jeg kan aila dig!" which means "I can aila you!" only we don't know what illa is, or what Danish word she is actually using there. She was calling us "superfalig" which means, "extremely dangerous" for months before we figured out what she was saying, at which point it lost its appeal.

Having our toddler speak the local language better than we do is a comic indignity, but my failure to learn Danish has more serious consequences. While three quarters of everyone we meet here speaks decent English, the culture, administration, government, commerce, etc. are mostly conducted in Danish, and my engagement in any of these is therefore quite limited. Iris's Danish is vastly better than mine, while still far from fluent. In a fairly open and engaging society we are bound by these linguistic barriers.

Why, you may justly ask, don't I just buckle down and learn Danish? A few reasons immediately come to mind. A more-than-full-time job and two young daughters don't give me a great deal of time for down-buckling. Danish is, even the Danes often say, an unusually difficult spoken language. The correspondence between what a work looks like and sounds like is even looser than in English. Many of the consonants are silent or nearly so, and I just can't detect any differences between some of the very many vowel sounds and stops that make up most of the spoken language.

Danish teacher: The first is Å and the second is Å.
Me: You just said the same sound twice, you said O and O.
Danish teacher: No, Ååååååå vs. Ååååååå. No, you are pronouncing too hard. Oooooo is a third sound, and has long and short forms.
Me: What do the long and short forms sound like?
Danish teacher: Oooooo vs. Ooooo.
Me: Maybe we should skip to grammar.

My students say that my attempts to pronounce Danish make me sound like a drunken Norwegian. I do understand a lot more spoken Norwegian than Danish, as Norwegian is a relatively phonetic sister of Danish and I can read simple Danish. If the Danes would agree to compromise on drunken Norwegian, I would learn it.

But when my department sends me scientific reports to grade (what they call censoring), I know my Danish is not nearly good enough to know if they make sense. My course descriptions all state prominently that the entire course will be taught in English. I Google Translate every email sent out to the department to find out if it is something I need to do something about. Google Translate is less good at Danish than it is at German, for example.

Another reason for my linguistic failing is the linguistic proficiency of the Danes. One look and they can tell that I am not Danish. They start speaking English before I even open my mouth. My daughter's three-year-old friends may not speak English, but their seven-year-old siblings do.

Finally, there is the broader motivation problem. Denmark is a wonderful country in which we do not want to spend the rest of our lives. We want to be closer to family, in a more familiar and diverse culture, in a place where we speak the language (and oh what I wouldn't give for a decent bagel, or a burrito with spicy black beans and nopales). Knowing that we don't want to stay makes it easy to not learn, which makes it easy to not want to stay.

This experience has reinforced my long-standing intolerance for the intolerance toward immigrants and linguistic minorities that is very much on display in many parts of the US and Europe. I could spend the rest of my life in Denmark, and actually apply myself to learning, and would never speak the language well. Those countries that have the harshest attitudes towards immigrants tend to be the ones that need immigrants the most urgently. And being an immigrant is hard enough, even in a relatively accepting culture like Denmark's.

Thursday, September 25, 2014

Wednesday, September 24, 2014

Rejection

Getting a paper rejection from a journal is always frustrating. So much time, effort and care goes into a paper that to have anonymous strangers say its no good can't help but hurt. I've just had a paper rejected, and it still hurts even though they had nothing bad to say about the paper.

The starfish paper I wrote with my students documents something that hasn't been documented before, but is certainly not the world's most important paper. It doesn't fit neatly into any field or derive from the pressing questions in any literature. So we sent it to a journal that explicitly says they don't care if it is important, so long as it is original, technically sound research. The reviewers agree that is passes these hurdles, but question its importance to their field. On this basis alone, the academic editor rejected it. I can't say I'm entirely surprised, as PLOS ONE has become a relatively high-impact journal. That type of success naturally brings them to function like a more traditional print journal competing for the flashiest papers. I filled out their feedback form to suggest that they update their stated criteria for acceptance, but won't otherwise protest.

There are two upsides to all this. The reviewers found the paper convincing and novel, with no technical or language faults. So we just need reformat for another journal and submit it there. Perhaps more importantly, this gives my student co-authors a window into yet another aspect of the scientific process that most of their peers never see.



Thursday, September 18, 2014

Unsolicited parenting advice


I have decided to share with you one of the big points of baby raising that Iris and I learned by hard experience.

We have a million books on baby care, Iris reads a bunch of "mommy blogs," and we know lot of people with babies; we felt quite confident in our baby skills before our first daughter was born. For the most part that confidence was justified, but there was one thing we just had no idea about. Once we figured it out, it transformed our parenting experience: helping a baby fart. One hears all about midnight feedings and how to deal with diaper rashes, but we had no idea it was necessary to help a baby fart. She would be crying inconsolably, and we would be going crazy trying everything we could think of to sooth her, and then at 3 or 4 or 5AM, she would finally fart, and immediately fall asleep. This happened repeatedly for weeks, maybe months, until we figured out that belly massage, light pressure on the belly, or alternatively pushing her knees up toward her belly would squeeze the fart out. With practice one can feel exactly where the gas bubble is and guide it up and around and down and out. We got good at this, and could make her fart almost immediately, bypassing the hours of gas pains and ear pains. 

P.S.  Another thing I found very useful, when woken up for the 14th time that night, was to have a posted list of things to try to help the baby. It seems like it would easy to remember to check the diaper, but when sleep deprived enough this can be quite hard. So here it is:

Belly Massage
Milk
Temperature
Wrap
Rock
Light
Sing/Hum
Diaper
Clean skin
Nose

In almost every case where she wasn't actually sick, one of those was it. Print it poster size and put it near a nightlight.

Picture show (in Danish)

This spring I taught a field course in terrestrial zoology at Svanninge Bjerge, a nature area owned and operated by the Bikuben Foundation. The foundation had Casper Tybjerg, a well known Danish photographer, join us and take photos. Bikubenfonden has featured the course on the Svanninge Bjerge website, including posting many of his photos (including the above). If you start here, and click to the right, most of the next several dozen photos are from our course, and all are beautiful. The accompany text is in Danish.

It makes me all happy and proud and sad-that-it-is-over to look through these and remember what amazing fun that course was.

Tuesday, September 16, 2014

Chocranut

Lightly-salted peanut wrapped in a sweetened dried cranberry, then covered in dark (>75%) chocolate.

Saturday, September 13, 2014

Student scientists study sea stars, produce plaudable publication

A good university science education should give students the opportunity to engage in scientific research. This is widely agreed upon, and most of the biology position announcements I consider state that the successful applicant's research should present opportunities for student participation. The general model is that the professor has the research program, and a question that needs answering, and a plan for answering it, and the student gets to see how research happens by carrying out, or at best refining, that plan. I'm all in favor of this, but I'd like to take it a step further.

My first publication, way back in 2003, was with one of my professors at Bennington College, based on work that she planned, and I, as an undergraduate, helped carry out. I made alterations to the experimental protocols, did a lot of lab work with minimal supervision, and chose to work on this project rather than others that were available, but I can take no credit for any of the ideas in the publication. In retrospect the one thing I would add to my own undergraduate education, if I was to be my own professor, was working through the entire process of generating a primary paper, from initial observations and idea generation to publication.

Implausible you say? Impracticable? If generating publishable science is so easy, why doesn't every professional scientist publish a paper a week? Well, I've just finished doing it with two of my students, and I'll tell you about it.

'Finished' is vague. We've submitted the paper, and I think it good, but we have to wait to hear if the reviewers agree. I'm not going to give you too much detail on what we found because you'll have to read the paper (or a future post) when it comes out.

It happened like this: At SDU, where I currently work, all natural science students in their second semester have to complete a group project. A group of students (four in my case) are assigned a faculty mentor who gives them a question to answer and guides them in answering it. In my case, the question was, "Can we use PIT-tags (like a vet puts in your cat) to mark starfish for a long-term demographic study?" We brought some starfish into the lab, talked about animal care and experimental design, showed them how to inject the tags and pretty much let them do their own thing.

They did great, but the tags just kept coming out. After a few weeks, all the tags were out. They answered my question with confidence: No, PIT-tags cannot be used to mark starfish long term. But the thing is, they didn't stop there. With no pay, no additional course credit, no requests for recommendation letters or such, two of the four students just decided to keep going. We met occasionally and I offered encouragement and comments, but little more.

They presented their results to the Evolutionary Demography Society, and long after the course was over they kept doing more experiments to figure out how the starfish were ejecting the tags. Notice that this is their own question. I asked, "Do the tags stay?" and my students answered this then asked, "How do they get rid of the tags?" And when we had an open house at the laboratory, they presented what they had learned to the public. Just by chance, one of the visitors they talked to had access to an ultrasound machine. This let them repeatedly image exactly where within the starfish the foreign body was moving. A year after they started, they convinced me that they had discovered, and had the data to back up, a previously unknown mechanism by which starfish can eliminate foreign objects from within their body cavities. "Okay," I said, "write it up for publication, and tell me now by what date you will have a finished draft." They missed their self-assigned deadline. They needed more help with data analysis than they expected. They put in all the wrong references in all the wrong places, and the flow of the article was terrible. English is not their first language. But not so long after they said they would, they sent me a draft that had most everything I needed to make it good. With the co-authorship of a couple of marine biologists (did I mention that I know next to nothing about starfish and have no other starfish research ongoing?) and with the continued input of these two students, we made a respectable manuscript out of it.

What lessons do I draw from this? Motivated undergraduates, with just enough guidance, can basically have their own successful research programs. The paper we produced still took a bit of my time to write up, and isn't the most important paper in the world, but they discovered something completely new (answering a question that someone who knew the literature would never think to ask), and they learned. They learned a lot. Refining questions. Starfish anatomy and function. Experimental design and practice. Ultrasound imaging. Cox regression in R. Scientific English. Literature searching and use. Collaboration. Communicating science to peers and the public. Preparing and submitting a manuscript for publication. Now they will get to see how peer review really works, or doesn't. These students, just starting their third year as undergraduates, have a fuller experience of what goes into making a scientific publication than I did when I started my third year as a doctoral student. Chew on that for a minute.

It is important here to think about these students' motivation. Judging by their grades, they are not academic stars. Neither of them has described a lifelong fascination with starfish. They did this, so far as I can tell, because it was their first chance to truly be scientists rather than just science students.

I told them early on that:
A) That they would have a strong say in the direction of the research and
B) that if they produced something publishable, I would help them submit it for publication.

These are not promises to be made lightly. Publishing things, especially things outside one's own central line of research, is time consuming. Giving first year undergraduates even this limited version of academic freedom in their research is, understandably, not common practice. But it seems to me to be damn good educational practice, and I plan to continue offering this type of opportunity to students when possible. Students will do much better, and more, work when they are exercising agency and following their own curiosity. Even if they don't choose careers in science, they know how science happens from start to finish, and that is surely something science students should be given the chance to learn.

Friday, August 15, 2014

Toddler naturalist

It was only 45 minutes until dinner and my girl was antsy. We decided to head out into the woods and see what we could see. We got on a bike brought along an almond and raisin snack, a water bottle, a doll, and stuffed orangutan. Five minutes later we were standing in the woods outside of town looking at this piece of wood. "This is a perfect cover object," I told Tigerlily. It was flat or even slightly concave underneath, it was on the soil but not in the soil, it was broad, and it was in the sunlight. "I want to look under it," she said. We lifted it up and found this shiny black toad.
We talked about toad poison and washing hands before eating. She hadn't finished her raisin and almond snack so only I held the toad.
Next we went for a little walk in the woods. She said she wanted to find insects. Instead, we found blackberries.
Or rather, she stumbled into them and I recognized what they were. I tried one just to make sure they were good, and they were. I didn't use my hands. Toad poison.
She left only the underripe ones. On our way back to our bike, she said, "what's this? An insect?" It was a beautiful dragonfly that I had walked right past. I couldn't get a good picture of it but you can get a sense of how colorful it was. 
Now it was dinner time and we walked straight back to our bike. My girl was tired and hungry but learning about the woods and was ready to come home.

Monday, August 04, 2014

To-write-list


I keep a running list of papers to write on my whiteboard.

This list currently has 15 entries.

Two of these have been accepted for publication this year but not yet taken off my list because it is nice to see them there.
 
Another was submitted, rejected, and is waiting rewriting.

Two have nearly complete manuscripts written and have been sent to colleagues for comments.

Five more are actively being worked on by me or co-authors and will hopefully be finished by the end of the year.

Four others are collaborations that are currently not moving. One of those is a project died for some specific reasons (like the data couldn't answer the question) and I just haven't entirely decided what to do about it. The others are things that neither I nor my collaborators are currently prioritizing that I hope we will get back to.

Finally, I have one project on my list that I want to write, but I don't even know exactly what data I need or the approach I want to take. I just know it is an important paper to write.

There are roughly a million other ideas I could put on my list, but I'm having a moratorium. I have decided I am not allowed to start on anything else until my list gets a lot shorter. As I have mentioned, I am applying for jobs, and I'd like to have most of this backlog cleared up before I go.

Thursday, July 17, 2014

Too consise?

I'm preparing a manuscript to submit to Nature. In addition to a low acceptance rate (8%), they have severe word limits. The 'main text' should be "about 1500 words" excluding introductory paragraph, references, methods, figure legends, etc. It is the intro, summary of results, and the discussion all in one. My main text, of which I now have a complete but not final draft, is 1138. It was not hard to make it this short. This is just how long I wrote it. This of course makes me think that there are all sorts of vital things that I should have said but left out. I will think about what these might be after my wife and daughter are asleep.

Monday, July 07, 2014

Nightly visitor

Hedgehog! We have a hedgehog picking up the seed under our feeder every night at 11. The feeder is just outside our bathroom window so when we hear it cracking seeds we creep over, open the window and watch. One night there were two of them, mating, being pretty loud about it. Europeans are mostly pretty blasé about hedgehogs, but to us they are cool and exotic (there are none, except pets, in the Americas).

Friday, June 20, 2014

So many reference to choose from, may as well alliterate

"Many different processes are commonly referred to as asexual reproduction and numerous authorities have set out systems of terminology dividing these up and labeling them (e.g., Schön et al. 2009; Schulz-Schaeffer 1980; Suomalainen 1950)."

Thursday, May 22, 2014

Field Course!

I love field courses. I loved taking them, love teaching them and even enjoy the logistics of preparing for them. What could be better than teaching excited students about animals by taking them out to see the animals where they live? Nope, not better. Try again. Nope, not that either.

Our five day field-trip starts on Saturday. Me, three teaching assistants, twenty-four students and a small house out in the woods. Beetles, birds, frogs, snakes, newts, mice etc. Stinging nettle, ticks,  mosquitoes, vipers. Out late to record bats, up early to hear the dawn chorus. I love it.

More about the course is here.

While you should regret that you are not taking this course, you should take solace in the knowledge that you would not have enjoyed it as much as I will.

Thursday, May 08, 2014

One way to avoid writing negative reviews is to decline to act as reviewer

"Please tell us why you have declined to review this article"

I am afraid I am unable to decipher the meaning of even the title of this paper, and the abstract implies a communicative style that could charitably be called idiomatic. I know all the words being used, (and am familiar with the probable subject matter) but couldn't tell you what most of them mean in this context. Were I to review a paper written in this manner I would spend an excessive amount of time on these linguistic issues, and might or might not ever get around to figuring out the embedded science.

Monday, May 05, 2014

Administrative Danglish

A few examples:

Censorship- Grading, examining
"Will this class require external censorship?"

Confrontation Hours- The time an instructor spends actually face to face with the students, contact hours
"You are responsible for 160 confrontation hours."

Critical Situation- Emergency
"A critical situation has occurred. A critical situation has occurred. A critical situation has occurred."

Dimensioning- Downsizing, rescaling
"The department will undergo dimensioning, as the government has determined there is too much competition for the jobs our graduates seek."

Economy- Accounting, bookkeeping, purchasing, etc.
"Mads handles our economy."

Licitation- bidding (as for a construction contract) or bid
"The licitation on the new station was higher than we expected."

Referent- The person who takes minutes at a meeting, secretary
"Are you the referent for this class?"

Taxameter- I have not yet figured out what this one means.  Something to do with fees or tuition.

Breaking a truly ancient tradition

"Modal age at death" means the age at which the largest number of individual deaths occur. The modal age at death is determined by the interaction of two factors, the increasing risk to each individual with advancing age, and the decreasing number of individuals still alive with advancing age. As a population of adults gets older, each person is at ever increasing risk of death, so at first the number of deaths at each age goes up. But eventually, even though individual risk is still increasing, the number of people experiencing that risk is going down so fast that the number of deaths at each age (what demographers call dx) goes down. So modal age at death is neither at the age with the most individuals or the age at the highest risk, but somewhere in between. And studying the modal age at death, how it varies between populations and over time can tell demographers many useful things that I'm not going to go into because I am more interested in subverting the paradigm.

The paradigm in this case is that modal age at death is some time in early old-age, when death rate is going up but not too many people have died yet. Except that often it hasn't been. If one looks at life-tables for historical populations of humans, the highest dx (by far) is often d0, the number of individuals who die before their first birthday. Put another way, far more people died between birth and their 1st birthday than during any other year of age. The Human Mortality Database (the world's premier source for data on this sort of thing) estimates that of the baby girls born in Sweden between 1751 and 1759, slightly over 20% died in their first year. To put in perspective how the resulting distribution of deaths over age looks, please glance at this graph:
If I asked you to guess at what exact age a random female had died, by far your best guess would be age 0. And surely the people living in such a population must have been affected in all sorts of ways by the frequency that babies die. To ask how this population would have adjusted to such a thing is to ask a misleading question, because adjustment would imply that this is something new. In fact, the modal age at death is almost always 0, and modern humans are highly unusual in having it be much later in life. In fact, even in the cohort of Swedes born in the 1920s, modal age at death was still 0. In some countries it may still be 0, although such places are generally harder to get good demographic data from.

How far back does this go? Well it is 0 for hunter gather populations. It is zero for wild primates. It is zero for other mammals. It is zero for.... As far as I can tell, modal age at death has been zero for almost every population of almost every kind of organism for the entire history of life on earth. Contemporary wealthy humans still suffer much higher mortality in our first year than at any other pre-adult age, but infant mortality has been gradually brought down over the last centuries, so far that somewhere in the 1930s and '40s, many of the world's nations unknowingly broke with hundreds of millions of years of tradition by having a modal age of death that wasn't zero. So the right question to ask may well be not, "how did they adjust to zero being the mode?" but rather, "how are we adjusting to zero not being the mode?" And my impression is that one important way that we have adjusted is by very gladly forgetting that things were ever different than they are now.

Seen another way though, we haven't changed the modal age at death at all. If one is willing to classify the loss of an embryo or fetus as a death, modal age at death has never been zero. It has always been, and remains, -1. Minus one because far more individuals are lost in the year prior to birth (even if only nine months) than the year after it, or any other age. Where before many cultures avoided naming newborns until a week or month or even a year had passed, we still often avoid it for those not yet born, for the same set of emotional (some say superstitious) reasons.

Will science progress to the point that we feel safe naming that recently implanted embryo, knowing that she will almost surely make it? Perhaps. If so, modal age at death will finally, at long last, be in the age range that my demographer friends like to consider.


Wednesday, April 02, 2014

Diana Levitis

T-Mobile is sending me emails about your wireless device. I think you may have mistyped your email address when you set up your account.

Monday, March 31, 2014

Lines 147-152 show great potential.

I hate writing negative reviews of people's manuscripts. I really hate writing negative reviews when I know the authors. But one has to be honest in these things, and honestly, this one needs to be tossed out and maybe even not started again. I put it nicer than that in the review. I really worked to find nice things to say about this manuscript. I'm not sure I entirely succeeded.

Sunday, March 30, 2014

The Case of the Incomprehensibly Big Super Volcano

The Yellowstone Super Volcano is every American's favorite geological Apocalypse-in-waiting.* Every 700,000 years, give or take a few hundred thousand, this buries a significant portion of the western US in various astounding superlatives. But this article on the recent 4.8 earthquake at Yellowstone has the biggest (and silliest) superlative I've come across in a while. The article states that,
"Late last year a new study into the enormous super volcano found the underground magma chamber to be 2.5 times larger than previously thought — a cavern spanning some 90km by 30km and capable of holding 300 billion cubic kilometers of molten rock." 
Now, 90*30=2700, and 300 billion over 2700 is 111,111,111.1111, or a bit more than 110 million. So for the volume of the cavern to be 300 billion cubic kilometers, the cavern would have to be 110 million km deep, or roughly 8700 times the diameter of the earth, about 2/3 of the distance to the sun. That is one deep hole. With the utmost respect to the Ragnarokian prowess of the great and powerful Super Volcano, I question whether its magma chamber is roughly one third of the entire Earth. Rather, I suspect that this is another case of innumeracy (or at least i-unitacy) on the part of a reporter. 300 billion cubic kilometers of molten rock is not likely, but 300 billion cubic meters of molten rock is quite plausible. A cubic kilometer is a billion cubic meters, so 300 billion cubic meters is 300 cubic kilometers, which is about how big you would expect a 90*30 km cavern to be. Still figuratively, but not literally, astronomical.

The fact that reporters often don't understand units and don't do the basic arithmetic to check numbers is nothing new, but it has only just occurred to me that there is a systematic bias in this. As when NPR casually mentioned the "240 mile deep water" off Alexandria, or when I heard on the radio that a local bank was receiving a bailout in the hundreds of trillions of dollars, reporters always seem to get the numbers wrong in a way that grossly exaggerates the claim. If the magma cavern was stated to be 300 billion cubic millimeters (equal to 300 cubic meters) instead of 300 billion cubic kilometers, a reporter or editor probably would have found that unsatisfying and therefore caught the mistake. If it was instead 300 Sextillion cubic meters, it would look sexy and nobody would likely question it. But there is probably another bias at work. Once a number is really big, substituting another really big number generally doesn't change the impression much, and if one doesn't understand what the numbers mean, it is therefore equivalent. Incomprehensibly Big = Incomprehensibly Big. So overstating your case by a factor of a billion isn't go to raise nearly as many alarms as understating it and thereby eliminating the hugitude.


*You only think you prefer that tired old tectonic fault.

Thursday, March 20, 2014

. . . by any other name . . .


I'm sure it makes a difference to the worms, but to me 'cattle manure,' 'cowdung,' 'cowshed manure' and 'cattle solid waste' are all the same experimental growth medium.

Wednesday, March 19, 2014

Apozygotic agamospermic apomictic agamospory

I'm making a table. Not the tisch, bord, tavolo, mensa kind. I'm making a table of comparisons of offspring viability between sexually and asexually produced offspring. This is polychallenging. Part of it is that the literature is scattered, so it takes a lot of hunting around, but that is a usual and interesting sort of challenge. Part of it is that I want to include lots of different kinds of organisms, and find basically comparable comparisons for each, and the measure one might use for offspring viability for a lizard is necessarily different than that used for an insect, plant or mold, but this is arises from the real diversity of biological process, and so is also interesting. The part that I am finding frustrating and difficult is the choking miasma of obfuscatory terminology. Some terms, like amictic, are used to mean different things by different authors. Clear concepts (e.g., what portion of seeds open and something live comes out) are referred to by a dozen different terms. Frequently a single author or group of authors will have a term that does not seem to be defined anywhere and isn't used by anyone else. Apozygotic, for example, seems to be used only by eastern European sugar beet scientists to mean agamospermic, which is a term botanists use to describe reproduction via diplospory, apospory or nucellar embryony, which are all (I think) non-automictic kinds of agamospory, which is close to what a zoologist would call apomictic parthenogenesis, which basically means that offspring are coming out of eggs (or seeds or spores) produced without any genetic recombination or changes in chromosome number along the way. There are various places in the literature or on the web where good intentions have tried to straighten all of this out and discard the duplicate or ambiguous terms, but of course they come to different conclusions and are frequently ignored.

Saturday, March 15, 2014

Knee deep in the fetid pools of evolution


I am, as I may have told you before, an evolutionary biologist at heart. And one of the things I love about evolution is how messy, random and complicated it is. Evolutionary outcomes aren't just survival of the fittest, but also reproduction of the luckiest and replication of the not overly deleterious. Natural selection often doesn't get its way and the optimal trait often doesn't exist or can't quite win out. Evolution is a box of dirty tooth-marked mismatched Legos with no instructions all in clumps from previous projects, and that is how I like my Legos

So I always enjoy talking with colleagues who really think about evolution in depth, not as a nice neat optimization process (which it isn't) or a collection of family tree (which it can be, but this misses the forest) but rather as the beautiful mucky anarchic tangled mess of genes, lineages, mutations and highly fallible biology that it is. Sure, there is a lot of phylogeny in there, and a bunch of natural selection, which to an extent can optimize things, but it is like optimizing the design of a boat when all you have to work with is coconut husks, maple syrup and a swarm of fire ants. It isn't so much optimization with constraints as a bowl of constraints with optimized sprinkles on top. To really capture the beauty of it you have to do away with the basically creationist notion that organisms are perfect for their niches and the anarchic view that biology follows the rules we write in text books. Organisms only breed with members of their own species, except when they don't, and clones are genetically identical to each other, unless you look closely.  Only changes to DNA are heritable, except those non-DNA heritable traits. Rules, broadly defined, do not apply to fungi. The dissertation that was defended from me this week showed that in real wild populations, genetic drift is sufficient to speed aging and shorten lifespan. These populations aren't short lived because there is something optimal about it, but rather because drift isn't letting selection have its own way. I'm oversimplifying, and you'll have to wait for the details to come out, but it is a wonderful example of evolution in its slip-shod Rube Goldberg glory.

I'd like spend more time with colleagues who think deeply about the gorgeous multi-layered sub-optimality of evolution. That's where the fun is.

Thursday, March 13, 2014

Cetacean eustachian excitation citation

1. Ridgway SH, Carder DA, Kamolnick T, Smith RR, Schlundt CE, et al. (2001) Hearing and whistling in the deep sea: depth influences whistle spectra but does not attenuate hearing by white whales (Delphinapterus leucas)(Odontoceti, Cetacea). Journal of Experimental Biology 204: 3829-3841.

A favor


If I ever propose to gather another dataset for other than educational purposes, please point out to me that I already have more data than I am likely to analyze in the next several years, and ask me why I need to spend time beating the bushes for data when my hands are already full.  Thanks.

Tuesday, March 04, 2014

Hear Ye

I've created a website for myself.

There are already sites* about me and my science, but these are boilerplate formatted things that are not really useful in communicating what I do and why. Sensible suggestions on improvements or additions to the new site are welcome.

*such as:
http://findresearcher.sdu.dk:8080/portal/da/person/levitis
http://www.demogr.mpg.de/en/institute/staff_directory_1899/daniel_a_levitis_2233.htm


Ceremony of Science


I am going to Switzerland for a day next week, to a dissertation defense. I have never been to one before, as UC Berkeley, where I got my Ph.D., does not conduct them. So I am curious to see how it works. I've been told where and when to come, and I've read and given comments on the dissertation, but I don't have any clear conception what we will actually do. I imagine the defender will present her results, we will ask questions, she will answer, then we will go off in another room for a period of time sufficient to make her nervous before coming back to warmly congratulate her. Since we have all already read the dissertation and any problems we pointed out have been fixed, I have trouble thinking of the event as other than ceremonial. Her university is paying for my travel and hotel, so if they want to fly me in for a solemn ceremony, I will not complain over much.

Saturday, February 22, 2014

Gloom and Doom from the happiest country on Earth


I will say first that I find it difficult to imagine any rich modern country taking climate change more seriously, or being more eager to take concrete actions to oppose it, than does Denmark. Danish individuals, society and government, including every political party, acknowledge the reality of anthropogentic climate change and the very real dangers it poses to (very flat) Denmark and the world. Danes know that Denmark is too small for a drop in its emissions to make much of a difference, but they seem more than willing to do their part by reducing energy use, subsidizing alternative power sources (etc.) and applying what limited diplomatic influence they have. Denmark is economically comfortable enough to really invest in these things and has both a highly functional government and a populace willing to implement the policies that their leaders decide upon. I am sure there are people in Denmark who disagree, but I haven't met (or even heard of) them. Unlike most countries, they have made their emission reduction targets law (although how such a law is enforced is unclear to me).

Because of the above, not despite it, Denmark convinces me that humanity will rush headlong into global ecological disaster. I say this because if any country has the willingness and ability to implement the policies needed to avoid disaster, it is Denmark, and they are not there. For while Denmark invests in weaning itself off fossil fuels, it also invests very heavily in the fossil fuel industry, notably North Sea oil and gas exploration. The Danish government surely believes, probably correctly, that the will does not exist in the populace to give up on the profits of involvement in the scramble for hydrocarbons. So while Denmark is trying hard not to burn those fuels here in Denmark, it is trying hard to sell them to someone else who will burn them, doing every bit as much to submerge the Danish lowlands (aka Denmark). Danes know this, but like the rest of the world (I'm looking at you Canadian Tar Sands) they seem to feel  (again probably correctly) that if they don't do it someone else (Norway, UK, etc.) will.

So I can imagine a possible future in which all countries have become as convinced as Denmark is that humans are hurtling into climate disaster and need to hit the breaks, and that would be great, but I have trouble imagining that even in such a world this peculiar form of the tragedy of the commons would be escapable. As long as there is demand for fossil fuels, there will always be others who will extract and sell them because if they don't do it someone else will. And there will always be countries who, even if they fully understand the global situation, need inexpensive fuel and will burn those hydrocarbons. And as long as that is the case, no amount of individual turning down of heat and biking to work is going to make a big enough difference to matter. The problem is structural and that structure is disastrously profitable.

Unless, of course, and this is me looking for that ray of hope, other sources of energy rapidly become so much cheaper than fossil fuels that there is just not much profit to be made in extracting oil, coal or gas. In which case, we will be able to say that all those solar panels installed in the gloom of Denmark were not in vain, but were a vote of confidence and a wise subsidy for the development of alternative energy

Tuesday, February 11, 2014

And while I'm on the subject...


In contrast, last week I turned down a request to review.

I replied honestly, "Judging from the abstract, this article is on topics that I know nothing about, and both it and your journal have nothing to do with the subjects of any of my publications. I am surprised you would send it to me. Please don't waste people's time with fake peer-review."

They replied, "Could you suggest a replacement reviewer?"

I replied, "No."

Coming home now




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I have been asked to review another paper. It is for a very good journal. I have published with them and thought their editorial office did a good job. It is on a topic I am very interested in and know the literature on quite well. It is a professional responsibility.

I have no time. I have a million projects and papers I am behind on. I have a bunch of papers I could get out relatively quickly if only I had the time, and I really need to get papers out. When I was a kid and my father came home late every night, I swore I would never "accept a bunch of extra work responsibilities just because my colleagues relied on me." My daughter is so damn cute and changing so fast. Every time I see her she says, "I need you Daddy, I need you!" (actually more like, "I ne-Jew Daddy, I ne-Jew!!!"). How can I ignore an adorable two year-old who not only needs me, but tells me so? I can't.

I said yes to the review, because that is what I am supposed to say. I will do it, and do it right. Sigh. But not tonight.

Tuesday, February 04, 2014

Revisiting the treadmill desk

I am very fond of my home-built treadmill desk, but basically never use it any more. Working at home with a toddler running around is hard enough. Working at home with a toddler attempting to run on the treadmill with me is impossible.

Now that I have had one for a while, and before I get rid of it, a few thoughts on the desirability of treadmill desks.

Pluses: I really could stand and work longer than I can sit without taking a break, and it is surely better for me to stand than to sit most of the time. When I used it for actually walking, rather than just standing, the health benefits surely increased and I found it easy to walk very slowly for hours at a time. Another, somewhat off topic, benefit is that when one needs to run one's toddler and the weather outside is Denmark, toddlers can easily be convinced to run on a treadmill for long enough to get some energy out. (Always hold the toddler's hand while she is on the treadmill so that you can prevent falls.) Before I started biking to campus, there were times when this was a useful tactic before my bedtime also.

Minuses: Achieving a deep focus on a topic is not as easy when walking on a treadmill (at least my cheep treadmill) as when sitting or even walking around. Some part of my mind always has to monitor my position on the treadmill so I don't slide off the back, and the slight bouncing makes both typing a reading a bit slower. I occasionally play a game of chess against the computer in the evening, and I can beat it at a much harder setting if I turn the treadmill off. Editing manuscripts, I inevitably end up turning the treadmill off when I get a point I really need to focus on. As a result, I rarely ended up walking, rather than standing, when doing any task that required speed or more than half a mind.


Sunday, February 02, 2014

ZIGLMM

I do not know nearly as much statistics as I would like. To put it another way, the marginal benefit of increasing my knowledge of statistics is greater than that of learning more of most other potentially relevant subjects, like chemistry or biophysics. I was therefore very pleased this last week, working with a very good collaborator, to finally understand generalized linear mixed models (GLMM) well enough to be confident that we were building and interpreting our model correctly. That it was a zero-inflated GLMM (ZIGLMM) only added to the fun. And in case you want to ask me anything about GLMM, the best I can tell you is to read lots of things by Ben Bolker,
http://ms.mcmaster.ca/~bolker/

On a potentially more useful note, finding smart capable kind people to collaborate with makes all the difference.

Friday, January 10, 2014

Quoth the tiger

Tiga: Kiga makes shopping list, go stoa.
Me: What is on your shopping list, Tiga?
Tiga: Oh, oh, oh, Kiga needs more, mmmm, uh, uh, uh, mmmmmmmmmm, bunny rabbits.


"Baba blackseep, abu any ul?"

Thursday, January 09, 2014

The Evolutionary Demography Society has a website

I spent a lot of time figuring out that I could very quickly and easily make a website that would suit our needs. I used SeaMonkey but frankly for what I made I could have used anything, down to and including any text editor. Now that I know how simple it is, I could do it again in a day.

The logo I designed for the society probably won't last, as there are far better designers than I involved, but it does the job. 

At some point I will add some pretty pictures of animals and plants.

Oh yes, the url:
http://www.evodemos.org/

Friday, January 03, 2014

A persistent problem

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I have a particular fondness for condors, so when I see an article about California Condors published in The Condor (a major ornithology journal), I usually take a quick look.  The look in this case was very short, because I am on my way to other things, but I found it interesting enough to mention to you.

Captive bred condors have over the last couple of decades been reintroduced to both southern (Ventura county) and central (Bug Sur) California, and young birds in both places have begun nesting. Their success has been limited, especially around Big Sur, where many of the egg shells have been extremely thin, leading to dehydration of the egg, fragility, etc. Why, you may well ask, should the eggshells be so thin around Big Sur? The suggested answer is that these condors do a lot of feeding on dead sea lions that wash up on the nearby beaches, and those sea lions do a lot of their feeding off southern California, in an area where an old DDT factory used to discharge its wastes into the ocean. DDT, and its breakdown product, DDE, are extremely persistent toxins, and biomagnify. So even though DDT was banned in the US in 1972, the marine ecosystems in that area are still quite contaminated. Algae pick up the DDE, small fish eat many times their weight in algae, bigger fish eat many times their weight in small fish, etc., up the food chain through sea-lions and eventually condors, who get a highly concentrated dose from their picnic on the beach. The Ventura condors don't often eat sea lion, and so don't get so much DDE. The Big Sur condors can see sea lion beaches from their majestically placed release area, and get enough DDE to seriously impair their reproduction. This of course is not the first time they have had this problem, but it is a reminder that DDT, while banned, is far from gone.