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


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 a year."

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

Referent- The person who takes minutes at a meeting, secretary
"Every class needs a chairperson and referent?"

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.