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.