Wednesday, December 31, 2008

Field Guide to the Birds of whereever I am right now.

Planning a recent trip to Baja California, I decided to buy a field guide to the birds of Baja, only to discover that there is no such book. Ornithologist colleagues suggested I just bring a guide to the birds of Mexico, but that seemed much less than ideal. Mexico has more than a thousand species of birds. Somewhere around 300 of those 1000 have ever been seen anywhere on the peninsula of Baja, and maybe a 150 of those have a moose's chance in Texas of showing up where we where when we were there. I looked through my very old edition of Peterson's Field Guide to the Birds of Mexico (so old they don't even have pictures of all the species because of the cost of printing illistrations), and decided that almost every bird we were at all likely to see was in the much more usable National Geographic Field Guide to the Birds of North America (which in this case means the US and Canada), so I just brought that.
Of the 66 bird species we saw, only one wasn't in the Nat Geo guide, or at least only one I successfully identified, the Grey Thrasher.

But this system of having to have a different guide for each place one goes is just so cumbersome, especially when one goes to a place for which a guide is not available. It's time for field guide 2.0. What I want is an electronic guide that detects where I am and what season it is, then displays a list of species that could possibly be there. This could even be a fairly simple application for an iPhone or PDA. I click on the name of the species I want to see, or the group I want to explore, and I get that page. If I know I am looking at a booby, but don't know which one, I click on the genus Sula. Based on the fact that I am in Baja in winter, I get pictures of a Blue-Footed Booby and a Brown Booby of the brewsteri subspecies.

If I am an ambitious birder and hope to find birds that aren't normally found where I am, I tell the program to be less picky in the list it gives me. If I am a novice who will only notice the species that there are at least a thousand of all aroud me, I can get a more selective list and have an easier time IDing the Yellow-footed Gulls.

This would require no new technology, only someone from one of the several companies who make bird guides to take the data they already have and slap them in a program. But no, instead they want to sell us stacks of bound paper. How 20th century.

(EDIT: Just after posting this it occurred to me that someone might already bo doing this. The closest I can find are "Handheld Birds" from National Geographic and iBird Explorer. They don't yet have any more birds than what appear in field guides to the US and Canada, and they don't seem to have the capability to let your wireless device filter by your location and season, but I hope that will come soon. It is clear at least that bird guides are going digital.)

Here, by the way, is the unorganized list of bird species Iris and I saw on our trip:

La Paz, La Ventana & Puerto San Carlos, Baja California Sur, Mexico Dec. 15-25th, 2008

1. White-winged Dove
2. California Quail
3. Magnificent Frigate Bird
4. Brown Pelican
5. Turkey Vulture
6. Crested Caracara
7. Merlin
8. American Kestrel
9. Western Gull
10. Gila Woodpecker
11. Cassin’s Kingbird
12. Cactus Wren
13. Northern Mockinbird
14. Gilded Flicker
15. Phainopepla
16. Western Scrub Jay
17. Spotted Sandpiper
18. Royal Tern
19. Ring-Billed Gull
20. Orange-Crowned Warbler
21. California Gnatcatcher
22. Common Ground Dove
23. Common Raven
24 Costa’s Hummingbird
25. House Finch
26. House Sparrow
27. Pyrrhuloxia
28. Hooded Oriole
29. Great Egret
30. Sanderling
31. Bonaparte’s Gull
32. Lesser Scaup
33. Double-Crested Coromorant
34. Green Heron
35. Little Blue Heron
36. Great Blue Heron
37. Snowy Egret
38. Great Egret
39. Cattle Egret
40. Tricolored Heron
41. White Ibis
42. Osprey
43. Red-Tailed Hawk
44. Heermann’s Gull
45. Western Sandpiper
46. Rock Pigeon
47. Mourning Dove
48. Anna’s Hummingbird
49. Blue-Footed Booby
50. Caspian Tern
51. Forster’s Tern
52. Eared Grebe
53. Yellow-Footed Gull
54. Ash-Throated Flycatcher
55. Grey Vireo
56. Verdin
57. Rock Wren
58. Semi-Palmated Plover
59. Long-Billed Curlew
60. Black-Throated Sparrow
61. Belted Kingfisher
62. Ladderback Woodpecker
63. Willet
64. American Oyster Catcher
65. Grey Thrasher
66. Brown Boobie

Tuesday, December 30, 2008


Writing a paper with others, in the sense that we all have to agree to have our names on every bit of it, and publish it, is a difficult but rewarding process. The paper is surely improving because of it, and the disagreements have all been purely intellectual and cordial, but every step of the process has involved spirited discussion over a thousand details of fact, style and strategy. I have 'won' about as many of these discussions as I have 'lost' and I am satisfied with the outcome in pretty much every case. It will all be well worth it if we actually get the paper into print.

240 mile deep water?

Listening to NPR news this morning, I heard of a break in an underwater fiber-optic cable between Europe and the Middle East, just off the coast of Alexandria in "240 mile deep water."

It struck me as odd that this was such a minor news item. After all, the previous record for deepest water on earth was only seven miles (held by Challenger Deep, off the Marianas Islands.) NPR has just increased the deepest water on earth by 3328%, an astonishing accomplishment.

I am not sure what the message was supposed to be. Perhaps the water was 0.24 miles deep? The break was 240 miles from Alexandria? There are a great many plausible options.

To anyone to whom numbers communicate anything "240 mile deep water"just off shore in the relatively shallow Mediterranean should be instantly absurd. Unfortunately, basic competence in subjects such as science and math are not expected of those in the news business. If I were king...

Monday, December 29, 2008

A conjecture on the link between babies and lack of sex

I am told by those who have children that one of the many sacrifices couples make to raise a baby is opportunity for sexual intimacy. I don't have kids, so don't know from personal experience, but it certainly makes sense. Between exhaustion, vehement interruptions and company in the house, it can be hard for a couple to find the time, privacy and energy to maintain their pre-parental levels of activity. I have had friends say that it seems very much like the baby is plotting to destroy its parents' sex lives. It has just occurred to me that in a sense, this could be very true.

Evolutionarily, there are many ways in which the interests of the parent and the interests of the offspring are aligned. The fitness of both are improved if the baby grows, thrives and go on to produce its own offspring. They share many genes, and anything that is good for the one is at least a little bit good for the other. But some things that are good for the fitness of the parents are a net selective loss for the baby. Such as having another baby come along too soon. The parents of course are equally closely related to all their offspring, and therefore will tend to distribute care and resources between their children in a way that maximizes the number of future grandchildren. But the baby is twice as closely related to herself as she is to her full sibling; she is much better off monopolizing her parents' time and resources for longer than they might desire. The parents' fitness is maximized by having an interbirth interval just long enough to get a good return on their investment in this offspring, without unduly diminishing their opportunity to have more children in the future. The child's fitness is maximized by having the parents wait somewhat longer, until the diminishment of their future reproductive chances for each additional day waited is twice the per day increase in her own fitness gain. The technical term for this disalignment of interest, appropriately, is parent-offspring conflict.
At first glance, the advantage in the conflict over the length of the interbirth interval would seem to be distinctly on the side of the parents, rather than the sessile, pre-sentient, altricail lump of chub, digestive organs and breathing apparatus. But oh, those breathing bits can very easily be used to make sounds. Sounds that communicate desperate dire need to protect and nourish the baby. Sounds that cannot easily be ignored. What harm if one screams just a little bit louder, a little more frequently, screams and cries with slightly less provocation, and makes the parents increase their interbirth interval just a little while longer?

Before you label me a conspiracy theorist, let me be clear. I am not implying that the babies of the world are 'trying,' in any intentional way, to deprive their parents of sex. They don't have to try. It comes naturally to them.

Saturday, December 06, 2008

Experts in a Lesser Known Phylum

Ask most people to name some phyla of animals and they will just look at you funny. Those who do know what you are talking about are likely to name Chordata, Arthropoda, Annelida, or maybe Mollusca. Most people will run out of Phyla long before getting to Rotifera. We humans tend not to pay a lot of attention to a Phylum whose members are mostly microscopic and don't cause any known disease. This is true not only among lay-folk, but among scientists as well. Web of Science, a catalogs of the scholaraly articles from about 8700 publications, lists fewer than 100 papers focusing on rotifers in the last year. Arthropoda, by comparison, gets more than 38,000 hits in the same period. So rotifers are not the best studied group in the world.
But those almost a hundred publications had to derive from somewhere. That somewhere is a scattering of experts across the globe. And it gets lonely being the only one in your city, state, country or continent with a strong interest in rotifers. (For example, I think I my lab is the only one in California which focuses on rotifers.) So what's a lonesome rotiferologist to do? Organize a conference, of course. Every two or three years there is a Rotifera conference somewhere in the world, and I have just found out that Rotifera XII is in Berlin, Germany next August. I very much plan on going, and hope to give a short talk on my work. They have about 60 slots open for presentations, which I think means almost everyone who studies rotifers will be there presenting. It should be interesting.

Le Deluge

I'm in a new place. For the first time in my career, I have gobs of data. Over the last couple of years, with the help of all my students, I have amassed a couple of enormous data sets. I've got this data-gathering thing down.

Faced with all these data demanding to be analyzed, written up and published, I have a new and different challenge. I need to decided which of the hundreds of different papers I could potentially write with all these data I actually will write. In some cases it is obvious that I need to write a particular paper. For other potential papers, it is fairly obvious that the opportunity cost would be higher than the benefit. This still leaves a vast middle ground.

I need to figure out how to think about how many, and which, papers to try to publish soon, which to present at conferences, get feedback, then publish, and which could be filed away in case I ever decide they are important.

Some of this last group I will use as motivational tools for my students, saying in effect, "I will put the time in to get the project you worked on published if you do a particularly good job moving the process along, and I will make you an author on the paper." Relatively few of my papers do I expect to be co-author on. Most I will need to include advisors, collaborators, students, or some combination thereof.

What is clear is that between now and next August (when I will move to Germany) I need to write about two papers a month, which is about two papers a month more than I am accustomed to writing.

Thursday, December 04, 2008

40,000 Senegalis or My Building

The building I work in has a yearly energy bill of over $1,000,000 dollars a year. That translates to about 10 Million Kilowatt-Hours per year, the same as about 100 average American houses or 40,000 Senegalis. Granted, it is a big building, with a greenhouse on the roof, four elevators, large water dionization systems, lots of -80C freezers, class rooms, laboratories and offices. Still, that seems like a lot of electricity for one building. The building manager emailed everyone to ask if we had ideas for cutting that down some. I suggested getting a smaller autoclave. The building has three autoclaves, each big enough to park a Mini in. Hundreds of different people use these, each setting them to their own specifications, usually to autoclave one or two bottles or one tray of equipment. A machine with 1/100 of the internal volume would work for most of these jobs, and get it done faster. I emailed to suggest installing a smaller autoclave, and the building manager wrote back that, "buying and installing one would cost over $50,000, which is about $50,000 more than is available at the moment." I am sure he is right, still I can't help thinking that if we saved even 0.1% of the building's energy usage, the thing would pay for itself in five years. Different budget line though.

Journal of Biodemography

Yesterday on the BART I sat down to write a list of papers I hope to publish based on my rotifer work. Most of them I had a pretty good sense of what type of journal they should go into. But one, the article in which I present a detailed human-style demographic analysis of my rotifer population, I just didn't know. It is a paper that I specifically want to write to an audience of demographers, to say, "Hey Look! Other species are good for demographers to study other than humans!" But I was not at all sure a demography journal would accept a paper on a species other than humans. I emailed my demography professor, and he said he had never sen such a thing in a demography journal. And frankly, most biologists aren't that interested in this type of analysis, and I'm not sure what biology journal I would send it to. I decided that since there is a journal for everything, there must be a Journal of Biodemography. But nope. I looked it up. Nothing even vaguely like that exist as far as I can tell. So either I'll have to found the journal myself (unlikely) or I'll have to shoehorn it in somewhere.

I'm just too interdisciplinary for my own good.

Wednesday, November 26, 2008

Binning Algorithms for Metagenomic Sequencing

One of my assistants, SM, who is at least as smart as me and twice as hard working, wrote to ask my advice.

SM: Do you know of any good binning algorithms for metagenomic sequencing?
DL: Huh? What does, "binning algorithms for metagenomic sequencing," mean?

SM has not given me an answer. Either she assumes I am joking, and actually do know (which I don't) or she assumes it would take far too long to explain it to me (which I will pretend to resent.) So now I shall try to reckon out what "binning algorithms for metagenomic sequencing" means on my own.

Metagenomics, according to my sources (Wikipedia) "is the study of genetic material recovered directly from environmental samples." So, you take a pinch of garden dirt, extract all the DNA in it and then set out to study it in some way. You are metagenomisizing.

Sequencing, in the context of genetics, means figuring out the sequence of DNA bases (A's, T's, G's and C's) that make up part of the genome of an organism. So metagenomic sequencing presumably is taking the DNA from your pinch of dirt, then trying to figure out the sequence of DNA bases that made up all the genomes of all the organisms whose DNA are jumbled together in that dirt. A pinch of dirt, I am guessing, has DNA from hundreds of types of bacteria, a huge number of types of fungi, various protozoans and whatever else has dropped seeds, pollen, poo, tissue or hair in that vicinity in the recent past. And much of that DNA isn't going to be whole chromosomes, but whatever bits and pieces are still mostly intact after all that pooing and shedding and biodegrading. You'll have a real mishmash.

This, I suspect, is where the "binning algorithm" comes in. Binning is any process where you have a large number of elements and you want to separate them into a smaller number of categories. A binning algorithm would be a set of rules one uses to make those decisions on categorization. In the context of metagenomics, I'm guessing that each bin represents a species. You have a snippet of DNA and you need to assign it to an organism, so you don't just think that every bit of DNA is another organism, and you want to get a sense of how much representation you have of each species. So the set of rules you use to assign snippets of DNA extracted from your pinch of dirt to different species is your Binning Algorithms for Metagenomic Sequencing. I think.
My friend DS works on this kind of stuff. I'll write to him and ask.

I wrote to SM and DS and asked:
Will one of you tell me what "binning algorithms for metagenomic sequencing" means?
I know what each word means, but I could come up with three or four very different guesses as to what the whole phrase means. What does each bin represent?

DS writes: [Bins represent] Taxa. In metagenomic sequencing, you get a soup of reads from all the strains of microbes present in your sample. "Binning" is the process of trying to guess which species each read comes from (or genus, or kingdom for that matter).

All methods in the literature so far are "supervised", meaning that you can only assign a read to a taxon bin if you know something about that taxon in advance (e.g., you have an isolate genome). However, environmental samples may contain previously unknown taxa: new bacterial divisions are still being discovered fairly rapidly, and at the strain level of course nearly everything is novel. A supervised binning process ought to throw up its hands at sequences from novel taxa, since they don't match any known bins. An "unsupervised" process would create new bins on the fly, in order to lump together reads that seem to be related to each other, independent of reference sequences. No published methods do that yet, though.

The accuracy of binning varies dramatically depending on the complexity of the community, the read length, the phylogenetic resolution you're asking for, and many other parameters.

Hope this helps,


Tuesday, November 25, 2008

Demographics of Science!

African Americans are generally underrepresented, both in the universities, and in the sciences. Berkeley is no exception in this case.

During my time in grad school I have interviewed well over 100 undergraduates who were applying to work with me, and taken on (as volunteers or paid workers) about 30 of them. Currently, I have 18 undergraduate collaborators. I've not given a great deal of thought to the demographics of this group, other than to notice that the great majority of my applicants (and therefore of my assistants) are female. A recent conversation (about Pres. Elect Obama) made me stop and think about the race and religion of this group. It is a very diverse group. I have had assistants who are Christian, Jewish, Hindui, Muslim and non-religious. Maybe other religions, I don't know. I have had assistants whose ancestors (or they themselves) came from East Asia, South Asia, the Middle East, Eastern Europe, Western Europe, Pacific Islands, Latin America and possibly other places I am not aware of. They have been male and female, heterosexual and homosexual. There are few places in the world where I could have ended up with a more diverse group, but I have no one of obvious African decent.

African Americans are not represented in my lab for a simple but sad reason. I have had not one African American applicant (that I am aware of), out of maybe 120. It is striking that African American representation in this group is lower than among our nation's elected officials. I am not sure why exactly this is, what combination of bias, cultural factors and public policies to blame, but I know this is one area where African Americans don't yet seem to have made sufficient inroads.

Saturday, November 22, 2008

Reader JTE asks:

Q:What does

two individuals with the same genotypes, except for those genes determining sex (which is some species don't exist, where sex is environmentally determined),


A: I'm glad you asked.

It means that if I had one missing or dysfunctional gene on my Y chromosome (or was XX instead of XY), I would be phenotypically female, but the rest of my genome would be the same as it is now. A great many aspect of my physical, chemical, social and mental being (my phenotype) have been altered by the effects of this one gene, which acts as a sex switch. Switch on maleness, and a whole bunch of aspects of phenotype are altered. Don't switch it on, and you get a different phenotype.

In some species, there are no X and Y chromosomes, or anything equivalent, to act as a sex switch. Instead, whether an individual develops as a male or a female is determined by the environmental conditions which prevail at a certain point in development. In alligators for example, there is no genetic determination of sex. Instead, if the temperature around the egg is above a certain temperature at a certain point in development, the alligator becomes one sex (I think male, but I don't actually remember). If it is ?colder? than that temperature, you get a female alligator. Many of the aspects of the switch are the same, only the first step of the switch is very different.

So my colleague was pondering the fact that two individuals with similar, or even identical, genotypes can have importantly different phenotypes, based on the action of this switch. This means that whether this switch is on or off can greatly affect the actions of other genes, and therefore the effects those other genes have on the survival and reproductive success of the organism.

Thursday, November 20, 2008

Intersexual Correlation

A colleague wrote to ask me what I thought about an idea he'd had. He was thinking about the fact that one could have two individuals with the same genotypes, except for those genes determining sex (which is some species don't exist, where sex is environmentally determined), and end up with significantly different phenotypes. In some traits (e.g. Hair color) these two individuals would be expected to have very similar traits, in others (e.g. genital morphology) they would be expected to be very different, and perhaps in some cases uncorrelated or negatively correlated. He wondered if this might affect the ability of individuals to choose mates who would produce highly successful offspring. For instance, a female sizing up a male would have a better sense of what that male's sons would look like than what his daughters would look like. A big very masculine male might tend to have oversized and somewhat unattractive daughters. My colleage wondered if this might confuse things enough to slow down the action of sexual selection, and allow a greater genetic diversity to remain in the population than would otherwise be the case. I found htis a very interesting question, and wrote the following reply:

There is a body of literature on the degree to which natural selection on the traits of one sex will affect the traits of the other sex. People often use the term "correlated evolution" to describe this sort of thing. When there is a correlation (positive or negative) in a trait between the female expressed genotype and the male expressed genotype, I've seen the phrase "intersexual correlation." I am not terribly familiar with this literature, I'm afraid.

This recent paper is the closest thing I know of to what you are talking about.

Whether any of this would lead to a greater genetic diversity in the population, I am not sure. The effects of natural selection may be somewhat weaker, as traits that are expressed in one sex but not the other are less often expressed, and therefore less often subject to selection (an epistatic interaction in effect). In the case of sexual selection, my guess would be that as long as degrees of intersexual correlation in particular traits evolve more slowly than do what cues individuals use to choose mates, choosers should evolve to focus on characteristics that are good indicators of fitness in both male and female offspring. I think this will generally be the case, as there is clearly very strong selection against those who use misleading cues in mate choice. I am not aware of any reason to think there would be rapid change in the degree of intersexual correlation in a wide range of traits all at once. As long as there is any consistently reliable signal available, the family lines that use it should tend to do better than the population average.

It raises an interesting set of questions, I am not sure how many of them there is any literature on.

Does this answer your question? If you want more expert answers we could ask Monty Slatkin, who I am sure has thought about this in some detail at some point.

Tuesday, November 18, 2008

Misquotes of Science!

Science is the least precise way of describing the world, except for all those others that have been tried.

Sunday, November 16, 2008

Cannabalism, entropy, economics and consumerism.

Among the millions of species of organisms out there, you can find a species that specializes in eating almost anything. There are lion-poo specialists, feather-barb specialists, lichen specialist, you-name-it specialists. There are also lots of generalist species, and many of these generalists engage in cannibalism. But no species is a cannibalism specialist. I can say this with confidence, even though we don't know what most species eat in any detail. A species of dedicated cannibals would quickly run out of energy. Everything an organism does burns energy that cannot be retrieved. Thermodynamics and all that. If a population is to withstand the ravages of entropy for any time at all, there has to be a sizable inflow of concentrated nutrients and well-ordered energy. A population of cannibals has outflows but no inflows, and quickly changes food supply or goes extinct. Engaging in cannibalism can be beneficial for short periods under specific circumstance, but you can't eat all conspecifics all the time. That way lays rapid extinction. Similarly, an ecosystem cannot persist for any period of time without massive inward fluxes of organized energy. Sunlight, geothermal chemicals or organic detritus from one of these two are necessary inputs to every ecosystem we have ever come across. Without that, organized energy in the system quickly declines until life can no longer be supported.

This same logic applies in economics. Pyramid schemes and speculative bubbles ultimately must collapse, because there is no underlying production of valuable stuff to support the outflows of capital of those involved in the speculation. Extending the analogy only slightly further, we see why a "consumer services based economy" cannot long persist. We import the carpet-cleaning machine from China, but we cannot export the carpet-cleaning service. We import the yoga mats but can't export the yoga lessons. We bring in coffee beans but can't export the latte. The consumer services part of the US economy (the biggest part) sends money out but brings effectively no money in, feeding instead on money that is already in the system.

The fact that our consumer economy lasted as long as it did/has is a testament to why economics is a social science, rather than a natural one. Humans are inherently illogical, and economics needs an understanding of that as much as it needs equations to understand the ways in which we are logical. Economic theory worked out for any other species would perform terribly for humans, meaning economics is by necessity anthropocentric, and therefore a social science. This has allowed an economy with few inflows to persist by inventing imaginary inflows, known as international borrowing. Americans may not be able to give you anything back for your stuff, but if you lend us the money to buy it from you, we will promise that at some point in the future we will borrow more money from someone else to pay you back with interest. Stated this way, it is an obvious pyramid scheme. But we have preferred to think that because our economy is large, because it has been dynamic, we soon would no longer need to borrow. Instead, I hope, we have figured out that we have to consume at a level closer to the level at which we produce. Otherwise we are just eating our children's future earnings, which is a bit too close to cannibalism for my taste.

Saturday, November 15, 2008

Tough Love

A few months back, one of my first and best lab assistants, LZ, was graduating. We were at a ceremony/lunch for her and the other students who had received an undergraduate research fellowship.
I said to her, "now that you are graduating, I want honest feedback on how I can improve as a mentor, and what things I should think about changing." She copped out, going into a long list of all the things I do right, then asking me what things I thought I needed to work on. She's a clever one, if overly tactful.

I said, "that's a total cop-out answer." She persisted in answering without answering, and in pushing me to answer my own question, so I did.

I told her that there are two main things I feel I really needed to figure out better. First was the balance between autonomy (allowing students to do what they want in their own projects, even if it might not work) and direction (giving students a project that is very likely to work, even if it is not exactly what they want to do). Second, I thought I was pretty good at picking good students, and at mentoring good students, but not so good at knowing what to do about the disinterested students who I mistakenly hired and couldn't really motivate. I tend to assume everyone on my team is competent, interested and motivated, and when any of these assumptions is violated, it takes me a while to convince myself that there is little doubt to give the benefit of, and a longer while to figure out what to do about it. In typical LZ fashion, she consented without actually stating agreement.

Recently, I have been trying to tackle the second problem, approaching students who I didn't feel were getting it done and letting them know where I thought they needed to improve. The results so far have been quite positive, and I am hopeful that despite LZ's concerted effort to be unhelpful, my conversation with her has helped me improve my mentoring.

So there.

Thursday, November 13, 2008

On a related note:

University of California's endowment loses $1Billion in value.

"UC Berkeley spokesman Dan Mogulof said that if the financial markets continue their downward slide in coming years, there could be future reduction in endowment support for scholarships, research and funding to recruit and retain faculty, among other things."

Graduating into a Depression

The number of professorships in the country does not vary much from year to year. Usually the number of positions opening up approximately equals the number of professors dying, retiring or moving to other jobs. Occasionally a new campus opens or there is a major expansion of enrollment, and a bunch of new positions are created. Other times the economy sucks (to use the technical term) and as a cost-cutting measure positions are retired or left vacant for a few years. As an example, the budget problems California has been having ever since the dot com bust have caused UC Berkeley to greatly increase the average time between one professor leaving and another being hired.
Right now, professorships are hard to get and I fully expect them to get harder. Somebody or other, a housing economist I think, was on NPR today predicting that the housing market will hit bottom in another three years. I expect the academic job market to hit bottom around the same time, or possibly a year or two later.

Which brings me to me. I will be getting my PhD in a little under a year. I then expect to spend two or three years as a Post-Doctoral researcher in Germany. That should have me searching for an assistant professorship just about the time there are no professorships of any sort to be had.

President-Elect Obama, I think an investment in our nation's universities and research institutes would be a great way to stimulate the economy, improve education and develop the technologies we need to deal with environmental issues and health care. Sooner is better than later. I have this three-year plan.

Monday, November 10, 2008

Team of Science

We attempted to get me and my entire team of undergraduate rotifer wranglers into our tiny lab space all at once. Two people couldn't make it, but 12 of us plus a photographer jammed in. The room is 12m^2 but about half of space that is occupied with counters, furniture and large equipment. Hopefully at my next job I will have a larger lab space, a smaller team, or both.

Sunday, November 09, 2008

Population Doubling

As I am preparing for my talk, I am doing some intense demographic analysis of my rotifer data set. One interesting factoid I have calculated is that the population doubling time, assuming I could keep an infinite number of rotifers and didn't have to get rid of any, is 28 hours.

A related calculation: If I started with one newly hatched rotifer and let the population grow (with my average age-specific reproductive rates and death rates), after one month I would have 159 million rotifers.

The average volume of a rotifer is about .001 cubic millimeters. A million of them pressed together makes one milliliter. A billion makes a liter. 10^27 would be a cubic kilometer. Earth's oceans have a total volume of 1.347*10^9 cu km, meaning I would need 1.347*10^36 rotifers to fill them completely with no space between rotifers. At the demographic rates they maintain in my lab, assuming I didn't cull any, this would take 138 days.

I only have time, container space and staff to keep track of 450 rotifers at a time, so I end up culling a significant portion of my population every day.

Rotifer Demography Talk Wednesday

I'm a biology grad student, but my funding and my fellowship are all through the Demography department. One service I return to the Demography department is to attend their weekly seminar and who ever the speaker is, suggest biological literature relevant to her topic of study. Some demographers take better to this than others. Most seem to appreciate the new perspective, even if they are not really interested in thinking about humans in a biological context. (For the record, I also go to biology talks and bring up demographic concerns.)

The next speaker I will have to deal with differently, because the speaker this coming week is me. I'll be presenting on demographic aspects of my rotifer research. Age specific mortality and reproduction. Effect of food supply on longevity. Infant mortality. I'll get into the biology a bit too, but mostly they'll want to hear about the demographics. If I was in my audience, I would suggest more of a focus on the biology.

Wednesday, November 05, 2008

Whose next?

Of the thirteen students working with me in on rotifer work, only one is white Christian heterosexual male. This never occurred to me before yesterday, when we were sitting around the lab, talking about the fact that should Obama win, he would be the first POTUS who was not a straight white Christian man.

I asked my students if they thought, now that we were getting a non-white president, we would have a female president, a non-Christian president or a homosexual president first. Some said we would have a woman soon, others said America would elect a Jewish president before a woman. Everyone agreed that there is still too much bias against homosexuals to have an openly gay president any time soon. I asked them if they thought Americans would ever elect a scientist as president. They all said no, and a couple of them said that was probably a good thing.

Three of my students a naturalized citizens, and therefore are barred by our constitution from running for president. But the other ten, in my opinion, should all have equal shots at the White House. The fact that they are all science students studying evolution at Berkeley means that this chance is zero is bearable, so long as it is an equal and unbiased zero.

Thursday, October 30, 2008


In science, as in most anything, it pays to know your strengths and weaknesses.

I am about as good as anyone I have known at understanding, remembering, integrating and evaluating biological concepts. I am terrible at calculus. I am very good at recruiting, evaluating and training assistants. I am hopelessly slow at learning programming. I have very steady hands for lab work and a hip that is bad enough to keep me from doing much field work. I am a gifted improviser and a mediocre follower of protocols. I am the king of scrounging and am pretty good at applying for funding, but I struggle with remembering to do the accounting or keeping track of receipts. I am a great teacher but a disinterested disciplinarian. I am unrivaled in my ability to start research projects, but need serious improvement in my ability to finish them. I have great fun with ideas but no fun with spelling. I collaborate well but self-motivate poorly. I am good at being blunt and bad at being not-blunt. I am a good scientist, but need improvement as an academic.

Saturday, October 18, 2008

What I've been working on

Here is the last bit of my post-doc fellowship application:

Summary and Conclusion:
Evolutionary Biodemography has focused on explaining late-life mortality patterns and overall longevity. The evolutionary basis of early-life mortality has been studied more rarely and less systematically. My proposal boils down to four basic steps intended to firmly establish the field of early-life evolutionary biodemography:
1. Mathematically define and parameterize the age specific mortality patterns that characterize Human-like Early-life Mortality (HEM).
2. Compile, review and organize those evolutionary hypotheses potentially explaining HEM.
3. Use these hypotheses to predict life-history traits that may be necessary causative factors of HEM, and thereby predict which taxonomic groups are not subject to HEM.
4. Gather data to determine in what species or populations, if any, HEM does not occur, thereby testing my collection of evolutionary hypotheses.
Early life mortality has a tremendous effect on a wide range of populations, and our failure to date to understand its evolutionary basis is a major gap in our understanding of both evolution and demography. Working at MPIDR, I will begin to fill that gap.

Saturday, October 11, 2008

Writing to the audience

One of the most basic pragmatic points of writing is tailoring the language one uses to one's intended audience. I would use different words in a text book for first graders than in a paper sent to a scientific journal, even if the exact same concept was being communicated. I have to estimate the assumptions, interests, background knowledge, tolerance for jargon and a host of other parameters about my readers in order to write in the most useful voice and tone.

This becomes a problem when I don't know who my audience is. I am applying for a DAAD research grant, and while I know I need to submit four copies of my proposal, I have no information on the four people who will be reviewing it. They may be four evolutionary biologists, in which case I would like to write a fairly detailed and technical proposal, using all the appropriate terminology, so as to show that I know my topic and have detailed plans. They may be four non-biologists, but still natural scientists. They may be social-scientists, or a mix of academics from all fields. They may be (although I doubt it) four German first-graders, in which case I would write a very different proposal. But as I don't know who they are, I have been trying to write a proposal which is appropriate to all of these groups, and finding it nearly impossible. How does one write an audience-neutral grant application?

Friday, October 10, 2008

All global warming is local

I got home from the lab late last night and turned on NPR. There was a voice I instantly recognized, my major professor, and the director of the MVZ, Craig Moritz. What, I wondered, was Craig doing in my radio at this late hour? Being interviewed by All Things Considered for this piece on the effects of climate change on the wildlife of Yosemite National Park.
Mean monthly minimum temperatures in Yosemite have risen by 6 degrees Fahrenheit in the hundred years since the MVZ's first director, Joseph Grinnell, surveyed the wildlife there. Apparently in response, many of the wildlife species in the park have moved their upper and lower limits thousands of feet higher than they were.

The project is described in great detail here, and a subset of the Yosemite data were just published in Science. I wasn't involved in this work, in case you were wondering.

Thursday, October 09, 2008

Compresed Timeline

The Max Planck Society is a network of research institutes, mostly but not entirely in Germany. Many people consider it, to be the world's leading non-university research organization. The member institutes are more or less autonomous in terms of planning and executing research, as far as I understand, but all of them have the reputation for world-leading excellence.

A couple of years ago, at a conference on aging I had the pleasure of meeting the Executive Director of the Max Planck Institute for Demographic Research, Jim Vaupel. At the time, he and my professors, Ron Lee, discussed the possibility of me coming to MPIDR at some point. I was excited by the prospect. Here at Berkeley there is effectively no one outside of Ron's lab group who thinks much about the kinds of questions I do, while MPIDR has a whole Evolutionary Biodemography Lab, at which they think about and work on pretty much everything I do, plus a lot more.
But then I went off to PNG, and then I was injured, and pretty soon I figured the opportunity had passed. But then I got an email announcing that there was a fellowship available through the German Academic Exchange Service (better known by its German acronym, DAAD, for North American researchers to come work in Germany if they had the invitation of a German institution. The email conversation that followed was suprisingly short, spanning little more than 24 hours, and completely reorganized my timeline for finishing grad school. If I may paraphrase, it went something like this:

Me to Ron: Should I apply for a DAAD fellowship to work at MPIDR.
Ron to me: Do you want me to ask them?
Me: Yes, thank you.
Ron to Jim Vaupel: Dan is an excellent young biologist, should he apply for a DAAD fellowship to come work there?
Jim to Ron (to me): Yes, he should apply, but even if he doesn't get the fellowship he should come here as soon as is convenient, and we can support him.

Just like that, no application, no interview, I had a desirable post-doctoral position lined up at a time when the economy is tanking and most of my peers are wondering if there will be any positions for them at all. My deliberations consisted of describing the situation to my wife to make sure she didn't mind spending some time on the Baltic, and emailing Dr. Vaupel to make sure I understood him properly.

What this means for my grad-school timeline is that instead of 16 to 21 months, I have eight to ten months to finish. I was thinking I would finish December of 2009 or May of 2010. After the offer from MPIDR, I thought I would have to finish by August of 2009. Afer talking to my major proffessor today, it is clear I need to be pretty much done by May of 2009.

My department's commencment is May 23rd 2009, and I plan to walk then, if at all possible. I won't actually be finished at that point, but I will be finished enough to convince my faculty persons that I can file my disertation before the end of summer. My wife's graduation from UC Davis is mid-June 2009. That summer I will finish my dissertation, then we will pack up our lives, take the cat's to my sister's house, and fly to Germany.

That seems like a lot to accomplish in one year.


Student Researchers

I've added a Student Researcher section to my website, so all my students can have research sites. There will be more in the coming days.

Sunday, October 05, 2008

I wiggle my eyebrows ~1000 times a day.

I spend about eight hours a day in front of a microscope. I generally have a student on either side of me. I look at the first rotifer in our population and report how many eggs and juveniles it has, whether it is alive, and anything else notable about it. "Two forty six dash bee five is alive has three eggs, two juveniles and extended foot syndrome. The largest juvenile has one egg."
The student on my left, at the computer, enters all of this into the spreadsheet and tells me what to do with the juveniles, based on our established culling rules. "Put the biggest juvi in two forty eight dash a one, cull the other two."
I pick up the mom rotifer in a specially bent glass pipette and wiggle my eyebrows such that my glasses slide off my forehead and onto my nose so that I can see the student to my right. She uses her pipette to point at the hole where the rotifer is going. I squeeze the bulb at the end of my pipette to eject the rotifer into that hole. She looks through a second microscope to make sure the rotifer is actually there. I push my glasses back up, look through my microscope, pick up the juvenile, wiggle my eyebrows again, move it to the well where it needs to go, then move on. All of this takes 15 seconds to one minute, depending on the complexity and which students are working with me. We repeat this process 450 more times each day. By the end of each day we have gathered more demographic data than many field studies of long-lived vertebrates do in several decades. By the end of a month we can see significant evolutionary changes based on the selective pressures we apply through our decisions about who to cull and how much to feed them. It is not glamorous, but it is effective.

Monday, September 22, 2008

One foot in this world...

From my perspective as an evolutionary biologist, all of the social sciences are parts of the study of human behavior, which is a part of the study of animal behavior, which is a part of biology. I don't generally bring this up to the social scientists I know.

I recently attended a talk, in which the speaker was an historical economist, studying the marriage market in post-WWI France. The lack of marriageable men(due to combat fatalities) led to the surviving males having the ability to be much more choosy than they otherwise would. Many men were able to marry women from social classes higher than their own. Many women simply never married. This effect faded away as a new crop of young men got old enough to marry. At the end of his talk I raised my hand, and asked if he was aware of the biological literature on the effect of skewed operational sex ratios on mate choice and assortative mating. I believe that the idea of looking at the literature on the same phenomenon in other species hadn't occurred to him. To a natural scientist this is almost scandalous. To a social scientist, it is the standard and correct way to proceed. It is a very different world view.

But now my field of expertise is becoming evolutionary demography, which draws as much from social science as it does from natural science, and this has begun to affect my thinking. This afternoon I was presenting my research plans to my professor's lab group, and one of the biologists asked why everything I said kept relating back to humans. I told him that as I was studying post-reproductive lifespan, and humans have more PRLS than any other species we know of, and we know more about it in humans, and therefore it was inevitable that most of our questions and methods would relate back to humans. It took me a minute to realize this wasn't the whole truth. The broader answer was that I had started to think a bit like a social scientist, meaning anthropocentrically. In the social sciences one doesn't need an excuse to focus on humans, the social sciences are all about humans. Having a conversation with social scientists requires one to be able to understand anthropocentric thinking, and if one practices this enough, one can start to think like them.

There are times when anthropocentrism is absolutely necessary and proper. Most of human activity revolves around interactions with other humans, and many of the problems we face can only be understood by focusing deeply on understanding humans. Part of the reason I work on problems relating to humans is because that is what society values, and as I've said before, I think this is appropriate. But the reason society (through a grant to an economic demographer) is paying me, rather than an economist or a demographer to do this work, is because it is useful to have your conversation about humans be illuminated by knowledge of other species.

If I stay in this field, which I plan to, I will have to learn how to converse one moment with those for whom humans are almost everything, and the next with those for whom humans are just one very over-studied species.

Sunday, September 14, 2008

Whither hence?

My PhD is preparing me to be an expert in evolutionary demography.

The question is, what does one do with such expertise? There are maybe ten researchers in the world with a focus on evolutionary demography. How likely is it one of them will need a post-doctoral scholar when I need a post-doctoral position?

You want fries with that?

Saturday, September 13, 2008

Pompous Lab name needed

I need a door sign. My laboratory space is a tiny little nothing of a room directly across from the main elevators. Everyone walks right past it, even people who are looking for me, because it looks like it should be a janitor's closet or boiler room. I need a big sign on the door that lets everyone know it is a research space. I could just put up a sign saying "Dan's lab space." or "Rotifer Lab," but neither of those is entirely satisfying. I'm thinking more grandiose, more pompous. That and I'd like to have the conceptual idea Evolutionary Demography as part of the name. Here are some initial ideas.

Berkeley Evolutionary Demography Society (BEDS)
Berkeley Laboratory for Evolutionary Demography (BLED)
Berkeley Laboratory for Experimental Evolutionary Demography (BLEED)
Laboratory for Evolutionary Demography (LED)
Institute for Evolutionary Demography (IED)
Dan's Institute for Evolutionary Demography (DIED)
Levitis Institute for Evolutionary Demography (LIED)
Center on Evolutionary Demography (CoED)
Center for Evolutionary Demography and Rotifers (CEDaR)
Society for Experimental Evolutionary Demography (SEED)
Berkeley Evolutionary Demography Laboratory (BED Lab)

Suggestions and comments are welcome.

Sunday, September 07, 2008

Editorial of Science: No More Years

My work on the evolution of aging got started on the basis that the National Institute on Aging is better funded than almost any other non-military research branch of the government. Older people vote, politicians and administrators tend to be older, and our population is getting older, so we offer funding to researchers who will work on issues relating to aging. I happen to also find the topic fascinating, and think it raises wonderful evolutionary questions, but I would not have ended up pursuing it if there was no funding available. America cares about aging, so I study it.

In many ways, this is how it should be. If you hire a doctor or a lawyer, you are likely to have some specific benefits you are willing to individually pay for. Remove the cancer, fight the charges. When society hires an academic researcher, individual level benefits are likely to be few or far off, but society expects societal returns. Those who funded early research into the nature of electricity did not anticipate the particular technologies we enjoy based on that work, but they correctly predicted it would somehow be very useful to society.

Few objective observers could deny that for much of the twentieth century, American science and technology greatly outpaced most other developed countries, and much of our economic, military and diplomatic power was derived, at least in part, from this technical prowess. America was one of the best places to do science, and this drew many of the finest scientists from around the world to move their activities, and their intellectual contributions, to America. Einstein is one obvious example. The term "brain drain" was invented in part to describe the mass movement of scientists and academics from other countries to the US. The US government not only invested heavily in science, it valued science, honored scientists and encouraged its citizens to see scientific progress as vital to our national future.

How things have changed. Several of the most promising young American scientists I know have moved to other countries, because the US is no longer competitive in funding or respecting science. Why study evolution in the US when New Zealand will pay you more and take your work more seriously? Why work on alternative energy technology when Canada or Germany will give you many times the research funding and implement your advances more quickly? Scientists follow the priorities of their society, or they move to another society.

Those who read the American press often hear about how America needs more scientists. But when I ask promising science majors why they are going into medicine or industrial engineering instead of science, they inevitably mention uncertainty about whether it is possible to make a decent living in science. Four years of college, two years of a masters degree and five years of doctoral study to qualify for a post-doctoral assistantship making $35K a year? No one smart enough to be a scientist thinks that's a financially desirable option. We can't have more scientists until we have more, and better paying, and better funded, and better respected, positions in science.

This national problem has gotten particularly bad over the past eight years. The right wing of the Republican Party takes a particularly low view of science. This is partly because they espouse a particularly anti-intellectual form of populism. In this view, normal people should only respect other normal people, and anyone who is too smart or too educated is not normal, but rather elite. The highly educated (who conveniently are overwhelmingly Democratic according to most polls) don't understand you and are keeping you down.
But the rightwing also dislikes science because science keeps producing answers that are contrary to the dictates of the far right. The far right knows that evolution does not occur, global warming is a naturally occurring hoax and trees are the primary cause of air pollution. The far right knows that Abstinence Only Sexual Education reduces pre-marital sex and teen pregnancy. The far right knows that homosexuality has no biological basis, that cities with more guns have fewer shootings, that we can drill our way to lower oil prices and that prayer is the most effective medicine. The far right knows that the lower our tax rates the higher our tax income. Science has the gall, the sheer pointy-headed elitist snobbery, to fail to support even one of these views, and to provide data directly contradicting most of them. The far right responds by treating science, and scientists, as somewhere between irrelevant and the enemy. Worse, under the Bush administration, there has been the consistent effort to bend, break or fabricate the conclusions of science to support every politically expedient fantasy. Research funding has been cut, science belittled and distorted and scientific reports edited, suppressed and distorted like never before.

This brings me to the current Republican ticket. John McCain has staked much of his campaign on the promise that drilling for oil in the US can bring down consumer fuel prices in the near future, a proposition one needs only simple arithmetic to disprove. Governor Palin is among the most anti-intellectual figures in her party, which is why the religious right so adores her. She strongly holds all of the fantasy-based, anti-intellectual views of the theocratic base. She has sworn to fight those who want evolution taught, those who want to do something about global warming, those who support sex-education policies that actually accomplish something and so on. Under a McCain-Palin administration, we can expect not only a continuation, but a strengthening of the Bush anti-science agenda. Should this happen the US faces a new brain drain, but in reverse. If science is not funded and not respected in the US, scientists in the US will have little choice but to give up science, or take their skills and knowledge elsewhere.
More immediately, and more importantly, we as a nation cannot afford to have another administration that so thoroughly rejects the foundational assumption of science: the best way to understand the world is by carefully observing it. The Bush-Cheney administration has consistently refused to allow observations of the world to influence their understanding of the world, or their strategies within it. Every sign points to a similar immunity to reality in any McCain-Palin administration. We can afford no more years of that.

Friday, September 05, 2008


This semester I am taking on the biggest and most complicated experiment I have ever attempted. Three populations of 150 rotifers, each population with different rules about how each individual is fed and which ones I cull. Frightening complexity just in planning the experiment, not to mention hiring an training enough undergraduates to staff 150 person-hours per week. This is not going to be an easy time, but I think it could produce a really significant paper. Lucky for me, my advisors think so too, and I should have enough funds to pull it all off.

Friday, August 29, 2008

Picture of Science! Steller's Jay

Many birds in the jay, crow and magpie family, the corvidae, are well known for successfully utilizing human provided resources in the form of handouts, garbage or unguarded food. This Steller's Jay, who followed us around a picnic area at Lassen National Park, is no exception.

Rotifer talk

I went into lab meeting this morning feeling like I didn't have much to say, and rather unprepared. After an hour of presenting one not quite done project after another, my professor asked, "Well, did you know rotifers were going to be such a rich and productive system when you started?" I realized everyone there but me was impressed by how much progress I've made on so many fronts. That was okay.

Wednesday, August 27, 2008

Picture of Science! Spider Hatchlings

One of the wonderful things about gardening is the opportunity to meet the creatures in my yard. I was very pleased this spring to find an empty nursery pot brimming with newly hatched spiders.
I have no idea what species they are. Within two days they had all dispersed to eat up garden pests.

Tuesday, August 26, 2008

Picture of Science! Tiger Salamander Larvae

My wife and I were walking up to Cecret Lake, at 10,000 ft. in Little Cottonwood Canyon, above Salt Lake City. When we got there, I said, "Oh fish!" Iris pointed out that they had too many dangley bits, and I took a closer look. "Tadpoles!" I said, but then I remembered that tadpoles don't have external gills along the back of the head like that. So I eventually figured out they must be salamander larvae. But what salamader has 6 inch long larvae? The tiger salamander, Ambystoma tigrinum.
This struck us as particularly fortuitous, as we only a month ago named a kitten Tigrinum, in honor of this species. Quite a resemblance, wouldn't you say?

Tiger salamanders often breed in mountain lakes and streams, and their populations often die out when fish are introduced to their previously fishless breeding grounds. Those big slow larvae are easy prey for predatory fish.

Picture of Science! American Dipper

I have far too many good nature/animal photos with no particular outlet, so I'm starting a new series here, which I call "Picture of Science!" even though most are pictures of nature, and not of science. Our first photo in the series is of an American Dipper.

Click photo for larger image.

I took this this past weekend at Manzanita Lake in Lassen Volcanic National Park. The wind and the overhanging trees made fantastic patterns on the water. The dipper was kind enough to stand in front of a relatively smooth spot where it's reflection would come through.

Dippers dip in two ways. First, they frequently bob from front to back to front to back, dipping their tail and belly feathers in the water as they do. Second, and more surprising, they will go completely underwater, walk along the bottom of a mountain stream or pond, and pick insect larvae as they go. They have clear nictitating membranes that act as dive goggles, and they have special movable scales that keep water out of their nostrils. Their numerous other adaptations for walking on the bottom of water bodies make them truely remarkable birds. They are sensitvie to degridation in water quality and have become rare through much of their range.

Thursday, August 21, 2008

So many data, so little time.

I first met Jerram Brown in 1999, when I was a senior at Bennington College. My adviser, Betsy Sherman, had been his student many years earlier. I was about to graduate from college and he was about to retire from a very long and extremely successful career in exactly the part of biology I was interested in. For the previous 30 some years he had been studying the behavior, ecology, demography and so forth of the Mexican Jay. I asked him about the possibility of working for him, but I was too late, his retirement plans were gathering momentum. He officially retired in 2002.
When I graduated, I went to work for Glen Woolfenden, who had an almost as long-term study of a very closely related bird, the Florida Scrub-Jay. Glen and Jerram, for reasons I don't know, had some sort of tension between them, and I had no further contact with Dr. Brown's group.

Looking through the program of the Animal Behavior Society Meeting I just attended, I was very excited to see that Jerram Brown would be momentarily be coming out of retirement to accept a distinguished researcher award and deliver a plenary address on his work. That talk was the last morning of the conference, and it turned out far more interesting than even I had suspected.

His data set on the Mexican Jays is shockingly extensive. In addition to the multi-decade highly detailed demographic data, he has an enormous number of ancillary data sets, many of which he had never gotten around to publishing, because he had not found any theoretically important question they could be used to answer. But as he heaped data upon data, I came to realize something. These data he had gathered because he could, rather than because he had a particular question in mind, were potentially exactly the data one of my advisors, Ron Lee, needed to test some of his hypotheses on the importance of intergenerational transfers of resources (in this case food) to the evolution of longevity and sociality. Dr. Brown had records of >26,000 individual food transfers, including who was transferring, to whom, how old each one of them was and how they were related to each other. My heart started thumping. I had to get Jerram's data and Ron's theoretical framework and analytical prowess together. But most scientists jealously guard the data sets they spent their lives gathering. And Ron is already terribly busy with far too many projects, would he even be interested?

Then Dr. Brown said, as part of his planned talk, something I have never heard any scientist say before, even though we probably should all say it sooner or later, "I will gladly turn over my entire dataset to anyone who can make good use of the data." There was a loud gasp. It was me, but not only me, several people gasped. He may as well have said, "I will turn over all this gold ore I have spent my life mining to anyone who can smelt it."

Immediately after his talk, I went up to speak to him. I shook his hand, told him that I was a former student of his former student (in case it helped) and began to tell him about Ron and his work. Another fellow, a Dr. Ha, came up and said that he would like to apply for NSF funds to hire a post-doc to work with Dr. Brown to make sure the data set is preserved and made available. He said that if Ron were involved, this would increase the chances of getting the funding, as NSF would want to know the data would be put to good use.

With some trepidation, I emailed Ron and told him all this. He wrote back almost instantly saying it sounded like a great opportunity, and he would love to join this collaboration, but would want, "some more junior researcher with more years of research ahead of him/her" to be involved, and suggested that I was the "leading candidate."

So this all raises the very real possibility that I may be spending a couple of years immediately after my doctorate applying Jerram Brown's data to Ron's hypotheses (and perhaps a few hypotheses of my own). I haven't yet figured out if this is something I actually want to do, and would be able to accomplish, but the prospect is very exciting all the same.

Tuesday, August 19, 2008

Chimp Politics

It is 8:30 AM on the second full day of the conference and I have already lost my name-tag. Things are going well. There are five people (with at least four PhDs among them) trying to deduce why the projector for the Keynote Address isn't working.
There are about 300 conference participants here, half of the usual ABS meeting. The reason, other than the scheduling conflict, seems to be that they are having it at the Snowbird Ski and Summer Resort. The problems with this are two. First, they had their meeting here in 2006, and a significant part of why many people decide to go to conferences is to have an excuse to visit a new and exciting place. The second problem is that the Resort is an industrial scale conspicuous consumption machine, meaning that it is overbuilt, overdone and overpriced. I have to admit that it is in a beautiful place, and I will be posting pictures of a moose and some marmots some time soon.

Looks like the projector is working, John Mitani is a well known expert on primate behavior, and has performed fieldwork on all five species of non-human apes. He is giving the Keynote Address, and I will try to convey in non-technical terms my understanding of his understanding of what he says (Or at least that part of it based on previously published work. I don't actually know, but I suspect it would be very rude to distribute the parts of his talk that he had not yet published.)

He has been studying the social behavior of the chimps of southwest Uganda for the last 14 years. Male chimps are more social than the females, form more lasting bonds, move more broadly over a group territory and more often cooperate in coalitions. Male coalitions seem to serve the function of supporting their members in conflicts with other males. The male with the most coalition support rises to the top of the social status, even if he is not the smartest, strongest etc. (A slide of Bush and Cheney somehow appeared in his talk.) The alpha male gets most of the mating opportunities, but in times of coalitional uncertainty, will cede those opportunities to other males whose coalitional support they need.

Chimps are also group hunters, especially of young monkeys. Most of the hunters are adult males. A large group of male chimps will surround a troop of monkeys, and are extremely frequently successful, even if the amount of food per hunter is very small. But group hunters are not necessarily cooperative hunters. If 50 guys all go for the same prey, they may successfully grab it, but that doesn't necessarily mean they are intentionally helping each other. Each individual may be trying to be the one who grabs the meat.

But the chimp who catches the monkey is likely to share it with others. Why? Males are the primary hunters, and hunt mostly when there are a bunch of other males around. It is suggested they may go hunting for male-bonding purposes. The meat seems to be used as a political tool. Males use meat to buy coalition support from other males.

Male coalitions will also make territorial patrols and raids into the territory of neighboring groups. They defend their own territories and grab more land, not infrequently resulting in serious injury or occasionally death. The larger the group patrolling together, the less the risk from any rival group encountered. Dr. Mitani's study group has killed 18 rival males in 10 years, because they are the largest group around. He wants to show us a video of chimps attacking each other, but is having technical difficulties. Now we see another video of a gang of male chimps beating another to death. The room is very still.

Female chimps disperse to other groups, males do not. So males are potentially living in groups of close relatives. And it turns out that males do preferentially help their maternally related brothers. It is easy to know if you have the same mother as another chimp. It is much harder in a non-monogamous species to know if you have the same father, and males don't preferentially help paternally related brothers.

He is finished telling us about the chimps in particular, and is going on to discuss the differences between those who study the behavior of primates and the broader animal behavior community. He says that primatologists can be overly focused on the primates, but that the broader behavioral biological community can be overly resistant to viewing the primates as relevant to their own work. This is apparently one shot in an arguement I was not aware of, and it seems odd to raise it here. One of the biologists sitting near me mutters that he regularly references primate papers, while he never sees primatologists reference the frog literature.

The address is over, time for bagels, juice and schmoozing. Then I'll try to take pictures of the marmot that hangs around on the hotel lawn, and find my name tag.

Sunday, August 17, 2008

On asking non-novel questions

One of my students, DC, wrote the following:

I started looking into the [student project that we discussed], and I found that there are already papers published about [that topic]. ... Since it seems like this topic has already been done, should I try to find another topic to look into? I've had the impression that if someone has already studied it, it doesn't work very well for a research topic but I know that must not be the case, otherwise no one would be able to prove theories wrong and there'd be nothing left to study... I suppose what I'm asking is if it's possible to still look into this, but in a way that doesn't only cover a portion of what another paper has already said (a paper that I'll have to cite, too)?
I responded as follows:
Hi DC-
An excellent question, and one that always needs to be asked. Very few people ever ask a truly novel question. Those who do are usually geniuses or lunatics or both. What we mostly do instead is try to ask the same question in a different context, or ask it better, or take a different and hopefully improved approach to answering it.
When LZ was hoping to design a project, she got interested in what caused mixis in rotifers, and I told her to go read the literature on that subject. She did, and came back upset because there were papers on the subject by respected rotifer experts, and they had already published answers to many of her questions. I told her to read those papers again with three questions in mind.
1. Which of her questions, or their own questions, had they failed to answer?
2. What areas of disagreement, apparent contradiction or uncertainty remained?
3. Where are the soft spots in the literature, meaning studies that could have been done better, analyses that are unconvincing or conclusions that aren't fully supported by the data they rest upon?

LZ, being both very hardworking and very clever, came back with answers to all these questions, and we used her answers, plus knowledge of our particular strengths, to design the study that became her senior honors thesis, and will become her first scientific publication.

Our strengths in terms of the primates, as compared to others who have written on this topic, are:
1. We have dispersal data on more species than they did.
2. We have longevity data for males and females of each species, where they did not.
3. We have their papers to use as references and examples of what to do (and what not to do) and they don't.

My suggestion to you is the same as what I suggested to LZ. I don't know if it is the best approach, but it worked for LZ.

Keep up the good work.

I wonder if my students know I make this stuff up as I go along?

Wednesday, August 13, 2008

Phylogeny schmylogeny

1. The generating and using of increasingly complex guesses as to how organisms are related to each other.
2. Something you have to do these days to study evolution.

That time has come. For five years in a heavily phylogenocentric lab in a museum mostly focussed on phylogeny in a department deeply into phylogenetics at a time when phylogenetics is nearing (I hope) the zenith of its trendiness, I have avoided really learning how to do phylogenetics. I can talk at length and in detail about the philosophical underpinnings of phylogenetics, I have read books and papers and taken classes on the subject, but I have never actually sat down and applied that knowledge. This is partly because of my inherent and unreasonable dislike for everything trendy and partly because I find that the most boring research talks in the universe are the straight phylogeny talks ("And then we sequenced 4327 base pairs of CR32.5 and SLD19423 from these twelve hundred taxa. Notice that on this taxa here there is a deletion, and I'll spend ten minutes talking about how we dealt with that. Now I'll spend half an hour talking about how we generated the priors for our Baysian analysis. And look, this taxon you have never heard of is closely related to this other taxon you have never heard of. Who would have thunk it? Someone wake that guy with the funny hair").

But my phylogenetic inexperience is based on more than simple obstinacy. I don't think that way. My predilection is to think of evolution in terms of selection, mutation, drift and so on. Phylogenetics at its core doesn't care WHY there are differences between organisms, phylogenetics is focussed on the methods for gathering and analyzing data on HOW these taxa are different from each other, and on drawing trees of relationships. In many papers, the tree itself is the goal, and maybe they do an analysis or two showing how useful their tree is.

I, knowing I needed to learn some phylogenetic software packages eventually, but deeply not wanting to, have backed myself into it. So I have taken a taxon for which the tree already exists (primates) and gathered from the literature (or had my students gather) a bunch of variables for as many species on that tree as possible. We have data on sex biased dispersal, social system, who provides care to the young and so on for about 90 species, and data on sex-biased longevity for 119. A huge amount of work over some years has gone into this, and there is no way I can weasel out of writing papers based on it. But there is also no way I can publish this in a decent journal without controlling for the effect of phylogeny. What "controlling for the effect of phylogeny" means takes a little bit of explaining. There is a tendency for related species to have similar traits, whether or not there is any adaptive mechanism driving that similarity. The common ancestor had that trait and both the descended populations inherited that trait from that ancestor. Humans and chimps have similar genetic sequences, and our common ancestor was surely very similar to both of us. This is termed 'phylogenetic inertia.'
Anytime one does a comparative analysis these days, one has to explain how we know that the observed pattern isn't just an example of phylogenetic inertia. Imagine one thought there was a causal relationship between being large and having hooves. One could find ten big species, notice they all have hooves, and ten species, notice none of them have hooves. But if those ten hooved species were all in the cow family, and the ten small species were all in the vole family, one would not have proved anything about hooves and largeness except that Bovidae have both and Cricetidae neither. So one has to make sure one is not being fooled by similarities due to evolutionary relatedness, or in the parlance, 'control for phylogeny.'
I need to control for phylogeny, and therefore will learn a few phylogenetics programs. But I don't have to like it, and I am going to make my students learn it too.

Stereotyping of students based on intended career

There is a commonly sited and widely believed in stereotype of a certain group of biology undergraduates, and this stereotype, I have reason to believe is frequently used in labs in my department to determine which students are desirable to have in one's class or section or lab, and how much responsibility and trust to give students. This stereotype is based not on race, sex, religion or socioeconomic background, but rather on intended career. I have heard faculty, grad-students and even other undergraduate students (including other pre-meds and pre-vets) rail against the pre-meds and pre-vets. At the new-grad student orientation last year the first response to the question, "What are the undergrads here like?" was, "too many pre-meds."

The stereotype goes something like this:
They only care about grades and letter of recommendation, they aren't interested in learning, they have no interest in science but will apply for any and every research position just to put it on their resumes. They will do a desultory job at any task you give them, so you may as well give them menial tasks. They are unpleasant to teach because they aren't interested and they spend all their time grade-grubbing. They are motivated to cheat by their fanatical devotion to getting A's.

This stereotype is, in my opinion, quite destructive. Not to say it has no basis in fact. I have had students who match the stereotype fairly well, both in classes and as lab assistants, and I will admit to finding myself hoping never to find myself or a member of my family in their medical offices. Our campus has both pre-medical and pre-vet undergraduate clubs, and while I have no direct knowledge of the advice these clubs give their members, the students who seem to be living up to the stereotype will occasionally say that they want the A or want the job because their pre-professional society told them so. (See here for my thoughts on how and why undergraduates should get involved in research. One important point, don't apply because your pre-med society told you you should, and if you do, don't admit to it, and if you do, expect menial tasks from most labs.) I suspect that some students really are led astray by receiving advice that emphasizes grades over learning and items on a resume over experience.

But honestly, the best undergraduates, bar-none, I have worked with have been pre-med and pre-vet. When I was a teaching assistant for Animal Behavior last year, the student in my section who asked the best questions, was the most enthusiastic and was the most helpful in explaining the material to her fellow students was a pre-vet student, very active in the pre-vet society. She also happened to get by far the highest grade in the course, but the high grade was clearly not her only reason for being there. My most accomplished lab assistant, whose thesis is nearly ready for publication, just applied to 20 med schools. I will admit to trying to talk her into a career in research, but I also have no doubt she would be an excellent physician. I could give as many examples of excellent pre-med and pre-vet students as I could examples of terrible ones.

Why do I think the stereotype is damaging though, if it is at least sometimes at least partly true? Partly because it colors interactions with undergrads. Some very large portion (well over half, I think) of students taking classes taught by my department are on pre-health career tracks. If one goes into interactions with more than half of one's students assuming that they are uninterested in learning, this affects one's teaching. If one offers only menial lab tasks to more than half of one's students, this affects their opportunity to learn about science. If instructors try to avoid teaching the classes that pre-med students flock toward, that doesn't say anything great about the educations of our pre-med students. It is also damaging if students feel compelled to live up to it. I had a pre-med students say to me that he was not interested in participating in anything that didn't contribute to his grade because that wasn't how pre-med students worked. I had the distinct impression he was striving to be the stereotype.

What actions do I suggest? The first would be for people on all levels of the department to be aware of this stereotype, and the biases it causes, and to be careful about how those biases affect their actions. The second would be for the pre-vet and pre-med clubs to make their members aware of this stereotype, and urge them to avoid being pigeon holed. Just as racism cannot be combated without acknowledging that it exists, I feel that carrerism must be exposed to the light of day.

Tuesday, August 12, 2008

What I'll be talking about at ABS.

The concept of "behavior" is central to the activities of the Animal Behavior Society and its members, but do we know what we mean by this term? Most published sources either do not include a definition of the word "behavior", or have definitions that both contradict each other or are either too broad or too narrow to be applied operationally.

We examined the range of available definitions, and finding no consensus, polled members of ABS as to their understanding of the term. Here again, we found surprisingly widespread disagreement as to what qualifies as behavior. This paper highlights the areas of agreement and disagreement, and proposes a definition intended to be operational and as free as possible of taxonomic bias.

Annual Review Extravaganza

Every grad student in my department is supposed to have an annual review with their advisers before Halloween of each year. The idea is that once a year we get our whole faculty committee in a single room for an hour to discuss our progress and future directions. This being my sixth year in grad school, I have decided that this year I am going to (for the first time) find a time when my whole committee is in town and make them come and sit down and talk to me. This is supposedly required every year, but last time I tried to comply, my committee chair said the effort was, "noble but fanciful." Every year I end up meeting with my committee members individually, or emailing with them, and getting only some of their signatures on the form I have to return to the department.

This year will be different.
My plan now is to communicate not with my major professor, but with his administrative assistant, who schedules his whole life. I already have a list of every time he is scheduled to be out of town, which is most of the time, and am working on getting such lists from my other three committee members. I plan on being a lot more persistent in trying to schedule a meeting this time than in the past, as this year I actually have product to show off, rather than simply a new plan for what I want to do in the future.
I've been working on a list of what to have ready by the meeting (which will be some time in September or October). Here is what I have so far.

Things to have ready:
1. Lauren's paper with completed data set.

2. Completed draft of defining behavior.

3. Primate variables mapped onto phylogeny.

4. Rough draft of comparative menopause paper.

5. Update on main rotifer experiment (draft of DDIG proposal?)

6. List of ongoing projects with one to two sentence summary of each.
.A. Rotifers
...1. Main Experiment
...2. Lauren's Thesis
...3. Sijie's Incest Avoidance project
...4. Rotifer Ethogram (Laura/Harmony)
...5. Polina's Egg Size Project
...6. Nicole's Biomechanics Project
...7. Rotifer/Chitrid
...8. Hamutahl's sickness project
.B. Comparative Primate studies
...1. Main analysis
...2. Comparative Menopause
...3. Sex biased dispersal (Darragh)
.C. Defining Behavior
.D. Thoughts on evolution of infant mortality (still nebulous)

Looking at this list, I see several items that I am confident can turn into publications, several others that could turn into publications if I ever get time for them, and others that are based on interesting ideas, but I am not entirely certain where I am going with them. My committee is inevitably going to tell me that I have too many projects and need to concentrate on just a few. I need to be prepared, before our meeting, to tell them which ones I will shelve or drop. Whenever that meeting is.

Sunday, August 10, 2008

Dueling Conferences

Most scientific societies have a conference every year or two. A chance to meet other scientists with similar research interests, hype your work, hear them hype their work, network and generally schmooze. This year the two big meetings most likely to draw American behavorists, the International Society for BehaviorAL Ecology, and the Animal Behavior Society, are almost overlapping. ISBE is, as the name implies, international, and have their meetings only every other year. Now they are having their meeting in Ithaca, at Cornell too good a chance for most American behaviorists to pass up. ABS is having their meeting a few days later at an overpriced resort in the mountains above Salt Lake City. A beautiful spot, to be sure, but not enough to convince many people who have just sat through a week of behavior talks to fly west and sit for another week. ISBE will have about three times as many attendants as ABS.

I am going to ABS, rather than ISBE, because it is easier to get to from here, because ISBE had their deadline for submission of abstracts before I got my act together, and because ABS is supposed to be more student friendly. I'm staying at a very affordable campsite some thousands of feet above the resort, and giving what I suspect will be the only philosophical talk of the meeting. I am not sure whether the ABS meeting will be more fun or less for being so much smaller than ISBE, but I shall try to liveblog the whole thing.

Sunday, August 03, 2008

The Draft

I spent my first few years as a graduate student taking classes, applying for funding, working on projects that didn't work out, teaching and similarly not producing papers. In the world of academic science, publishing papers is pretty much everything, which means that career-wise I was accomplishing pretty much nothing. In the last week I and my collaborators have finished first drafts of two papers that should be quite publishable once they are polished up a bit. And boy, does that feel good.

Thursday, July 31, 2008

Down to the wire

One of my professors, RL has this habit of being uncannily right most of the time. My student, LZ, and I were working on analyzing our data this afternoon. The first draft of her senior thesis is due tomorrow, and we decided we may as well try one last thing, calculating a variable that RL had suggested. We plugged it into our model and BAM! highly statistically significant, much more so than anything else. And, in retrospect, it makes beautiful biological sense. Of course it all depends on cumulative lay order across generations! Any brilliant biodemographer would have seen that at once.

Now LZ has at least 12 hours to rewrite her paper.

Tuesday, July 29, 2008

Cleaning Data

My studies of rotifer demography and evolution would not be possible without extensive student participation. I need three people working together for four hours every day just to get the census done. Most of the time I have six or seven students on my team. Only one student, LZ, has been working with me the whole time. She started last year as an Undergraduate Research Apprentice and this spring and summer has been working on her Senior Thesis. She decided, quite independently, that she was going to study which demographic factors affect the probability of a rotifer reproducing sexually, rather than asexually. She is a fabulous student, has become a talented researcher, and I hate to see her go.
A rough draft of her thesis is due this Friday, and as we have been trying to analyze our data, we have instead been spending most of our time fixing typos and errors in the data. We've been finding mistakes ranging from recording a rotifer as being in plate 1111 instead of 111 to the same information recorded quite differently in two different places. LZ and I spent ten hours yesterday going through our data line by line and cleaning up errors. Some sections were perfect, others awful, and we couldn't help but wonder which students had taken the clean data and which had gotten sloppy, lazy or confused.
Doing this has brought into sharp relief both the good and the bad of having such student-powered research. Relying on students is extremely useful and motivating and inspiring, but can also be frustrating and time-munching. Which way it goes depends enormously on the students I choose. I am very shortly going to be needing to find another couple of assistants, and will have this experience in mind.

Friday, July 25, 2008

Question Creep

If a billion scientists studied life on earth for a billion years, they would leave more unanswered questions than we now know exist.

Every project I have ever been involved with, or heard of, has generated far more questions than it has answered, not because the researchers were doing a bad job, but because one can't study any organism in detail without realizing how little one knows about it. Humans are the favorite research subject of humans, and we have published literally billions of articles on us, every aspect of our biology and behavior has been the topic of intense research, and yet there is still a huge amount we don't understand about ourselves, neurologically, chemically, socially, medically, you-name-it-ly.
And after all this research, we have succeeded in creating whole new fields of study to generate more questions. Genomics being an obvious example of a new field that is question rich.

That level of research (at least on the biological and chemical sides) could be applied to any of the hundreds of millions of life forms out there, and we would still be generating questions about that species. And then their are all the questions about the differences and similarities between species, the way that life has changed over time, the evolutionary, ecological and social interactions between species, and so on and so forth, ad infinitum.

This plays out quite clearly in my own little lab. As a grad student, I am lucky to have a very small lab space that I share with another student and my ~$25K worth of borrowed equipment. Oh but the use that tiny little room gets. Any day of the year there are at least three people in there looking at rotifers for four hours. I got into studying rotifers to answer a question about humans, why our females have such a long post-reproductive lifespan. But now that I need data on rotifer demographics, and have a horde of undergraduates studying them, my students and I have raised a huge range of related questions. To give you a sense, here is a short list of the projects currently under way, or in planning:

1. I started with the question, will rotifers evolve a post-reproductive lifespan if exposed to selective pressures similar to those thought to have caused human females to survive well past menopause?

2. I brought on LZ as an assistant, and she wondered what demographic factors influence when a rotifer reproduces sexually as opposed to asexually?

3. I hired PB as a work-study student, and she is working on an assigned side project, looking at how the size of a rotifer's eggs vary based on her size and age. This arose out of discussion with LZ in which we wondered if egg size could be affecting mode of reproduction.

4. Another student, NN, came on as a volunteer and got fascinated with rotifer biomechanics. Her senior honors thesis will ask how rotifers use their cilia for movement and feeding, and how does this vary with size and between males and females?

5. We noticed that when we do get sexually competent rotifers, they generally won't mate with their own sons. I asked a former student of mine, SM, to join the rotifer lab and investigate incest avoidance in rotifers. Now she is in the lab most afternoons taking video of rotifers mating, or choosing not to mate.

6. In studying the demography, we found that we could often visually identify when a rotifer was 'sick.' We wondered if we could categorize these 'sick' behaviors, and use our demographic data set to test whether our perceptions of sickness consistently presage death. HC, who came on as a volunteer, is working on this.

7. With all these projects looking at rotifer behavior, I decided it was important to have a unified terminology to describe the behaviors we were seeing. So I have two students, LF and HL, working on an ethogram, a list of behaviors with a description and diagram of each.

8. One of my lab mates in the Moritz lab is studying how water filtration affects the progression of the Chytrid disease that is killing off large numbers of amphibian species. It occurred to me that rotifers live in the same habitats as amphibians, and eat things the size of the Chytrid zoospores, the mobile cells that cause infections and reinfections. A former rotifer rangler, CW, is planning experiments to ask whether rotifers will eat chytrid zoospores, and if so whether that information can be applied to amphibian conservation. (Chytrid Experiment).

Every one of these projects is doable, and all of them will generate far more questions than they answer. I have my billion years work cut out for me.