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:

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

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


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,

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?"