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.

Tuesday, July 22, 2008


I've spent the afternoon helping two of my best assistants move on to research that more closely matches their interests than what they have been doing with me. I'll still be helping to advise them, but I'll no longer have them on my project. They will be hard to replace, but after all the work they have done for me, I owed it to them to help advance their careers.
NN will be studying rotifer biomechanics in another lab (with me acting as rotifer expert), and MR will (if all goes as planned) be doing coral censuses in PNG (with me helping to urgently prepare her for her trip). My other long-term lab assistant, LZ, who is totally irreplaceable, is graduating in a week and moving to India two weeks after that to work in public health. Time to recruit more assistants.

Conservation inaction

A friend who runs a conservation organization in Papua New Guinea is visiting. She and I have been discussing whether, in the long run, there would be any meaningful change in long-term conservation outcomes if every western conservation organization in PNG were to up and leave. We are not convinced that there would be.


Thursday, July 17, 2008


One of my students, DC, emailed me, very confused. I had asked her to compile data on sex-baised dispersal in primates, and she has been doing a huge amount of work, digging through the literature, and has found data for about 50 species. Then in April, a paper came out in a high profile journal which, among other variables, examines sex-based dispersal in primates. DC student found the paper, but couldn't find the data on sex-biased dispersal. There are lots of references, and lots of supplemental materials, but nothing to our cause. So DC emailed me, and I read the paper and the supplemental materials. I also could find no data and no sources on sex biased dispersal, even though there were graphs (with 70 unlabeled diamonds, circles and squares labeled as male biased dispersers, female biased dispersers or both sexes dispers equally) and analyses based on those data. "Must have been left out by accident," I thought, and looked up the author's website to see if the data were posted there. Nope.
So I emailed the author, asked for either the data table or the references on which it was based, and got an almost immediate reply. She stated that:

A. The data and sources had been cut out to save space. This is fishy, as the journal has no space limits on supplemental online materials, and many papers come out in this same journal with far more appendixes than this paper has.

B. It would be too much work to track down all the references and sources again. This is fishy, as the paper came out only this year, and it would be truly remarkable to lose track of one's data set and all of its sources so quickly and thoroughly.

C. If I wanted information on a particular species, she would be glad to see what she could find. This too is fishy, as it implies that she would have to go to the library looking for the data that her published paper is already based on.

I can't help but wonder if there ever were data and sources. I would like to think of some innocuous explanation, but have not done so yet. I told my student to take this as an example of what not to do.

Wednesday, July 16, 2008

Snake self defence

Iris and I were on our way up Blake St from the BART station to our house.
At the corner of Walnut St, I exclaimed, "Oh!"
"What! What!? What?" Iris responded.
"A garter snake!"
The sleek black ribbon, two feet long and no more than half an inch wide, with a bright yellow strip up its back, was frantically trying to wriggle out of the street and onto the curb. That corner has no curb-cut, and its movements were too disorganized to allow it to climb the 6-inch curb.
Three facts jumped to mind:
1. It was clearly overheated by being on the black pavement in the sun, and would cook to death or get run-over unless we rescued it.
2. Garter snakes are not poisonous, but can bite.
3. It probably came from El Cerrito Hillside Natural Area, 200m up the street.

So I handed my cane and groceries to Iris and grabbed the snake with both hands. But I had forgotten that the hotter a snake is, the faster it can move. Before I could get a finger on it, my thumb was bleeding from multiple tiny punctures. I grabbed the little snot anyway and held firmly, but without squeezing, on the back of its skull. Then it hit me with a garter-snake's last line of defense: musk. A garter snake's musk glands are in its vent (a.k.a. cloaca, a.k.a. butt) and can rapidly discharge a surprising quantity of a fluid that smells somewhere between a port-a-potty and old gym-socks.

With one hand bleeding and the other clamped on a snake and stinking, I looked up at Iris. She handed me my cane and retreated up the street.

Thamnophis elegans - Western Terrestrial Gartersnake

Sunday, July 13, 2008

Catnip -> Olfaction -> Happy

My Friend Terry Johnson is a lecturer in Bioengeneering at UC Berkeley. He also writes the Ask a Biogeek column for Now he is one of the judges for their Mad Science Contest: Build a Lifeform. And, in investigating my idea for an artificial organism, I came across this abstract:

Hart BL, Leedy MG.1985. Analysis of the catnip reaction: mediation by olfactory system, not vomeronasal organ. Behav Neural Biol. 44(1):38-46.

Pet owners and behavioral scientists alike are fascinated by unique behavioral reactions that cats show in the presence of catnip. These experiments explored the possibility that the catnip reaction might be triggered by chemosensory stimulation of the vomeronasal organ. In the chewing and mouthing of the catnip source, substances might be dissolved in saliva and transported to the vomeronasal organ. The rolling and rubbing during a catnip reaction might be a sexual response activated by the accessory olfactory system since the system projects to parts of the brain involved in mediation of sexual behavior. However, removal of the vomeronasal organ did not attenuate any of the behavioral reactions to catnip. Olfactory bulbectomy immediately eliminated catnip responding, revealing that the chemosensory stimulus evoking the catnip reaction is undoubtedly mediated through the main olfactory system. Catnip activates behavioral elements associated with several species-specific behaviors, including sniffing and chewing as associated with oral appetitive behavior, rolling and rubbing characteristic of female sexual behavior, batting the catnip source characteristic of play behavior, and a type of kicking associated with predatory behavior. These behavioral reactions occur randomly and intermittently.

The moral of the story seems to be that:
A. Cats respond to catnip through their olfaction, the type of smelling that humans do fairly well, rather than through the vomeronasal organ, the part of smelling that humans don't seem to do at all.
B. Catnip elicits from cats behaviors associated with almost every active things cats enjoy (eating, playing, sex and hunting). Catnip does not elicit the calming and resting behaviors such as self-grooming and napping that cats also enjoy. Catnip also does not elict behavior associated with things cats don't enjoy (fighting, danger, housechoirs).

Based on this, and my own observations, it seems likely that catnip is a quick-acting stimulant, extremely pleasant to the cat and absorbed through the olfactory epithelium.

Stefanie Schwartz, in her book "Psychoactive Herbs in Veterinary Medicine" list some other useful facts. Catnip response is not associated with any know histological or physiological effect, (meaning that while it certainly does something in the body, it is something subtle) catnip is not toxic even at relatively high doses, and the physiological and psychological effects are very different in cats than in humans. In humans, catnip is mild sedative, and smoked catnip is said to have similar psychtrophic effects to smoke marijiana. In cats, it is clearly a stimulant. In neither species does it have any known side effects.

Nepetalactone, the active ingredient, is also aparrently a powerful insect repellant, driving off both lice and cockroaches many times more powerfully than does DEET.

Friday, July 11, 2008

Better Solar Cells

It is amazing how when one does research into a technology, that technology can get better.

Science 11 July 2008:
Vol. 321. no. 5886, pp. 226 - 228

High-Efficiency Organic Solar Concentrators for Photovoltaics
Michael J. Currie, Jonathan K. Mapel, Timothy D. Heidel, Shalom Goffri, Marc A. Baldo

The cost of photovoltaic power can be reduced with organic solar concentrators. These are planar waveguides with a thin-film organic coating on the face and inorganic solar cells attached to the edges. Light is absorbed by the coating and reemitted into waveguide modes for collection by the solar cells. We report single- and tandem-waveguide organic solar concentrators with quantum efficiencies exceeding 50% and projected power conversion efficiencies as high as 6.8%. The exploitation of near-field energy transfer, solid-state solvation, and phosphorescence enables 10-fold increases in the power obtained from photovoltaic cells, without the need for solar tracking.

Thursday, July 10, 2008

Sock of Science!

The Ozone Sock company employs my baby cousin David as National Sales Director, or some such title. He told me about their "My Socks are Your Socks Design Competition." Naturally I have been designing science themed socks.
Here is a sock I call, "Where's Pluto?"

Tuesday, July 08, 2008

The Velige People

One of the great pleasures of working with really talented undergraduates is that they know stuff I don't and make me learn stuff I would never otherwise have gotten to learn. Take NN. I met NN when I went to the Invertebrate Zoology class she was taking to ask if any of the students wanted to help me with my rotifer experiments. A couple of days later I got a resume from NN, and quickly realized that in addition to being a great assistant, she knows enormously more about aquatic invertebrates, and a bunch of other biological topics, than I do. A good start.

One of the topics she knows and I don't is biomechanics. She quickly developed an interest in rotifer fluid mechanics. So yesterday afternoon NN and I went up to the lab of Dr. Mimi Koehl, aquatic invertebrate biomechanician extraordinar and talked to her grad-student and my friend, Lindsay.

It turned out Lindsay and NN have a lot in common. They both are fascinated by aquatic invertebrates, biomechanics, fluids, and the interactions of these concepts. And they both know what a veliger is. In fact, they had quite a long discussion about veligers of different types, and how many of them have a range of similarities to rotifers. I, throughout this entire conversation, played the game of trying to take part in the discussion while also attempting to deduce what a veliger was.

I figured out this much: veligers are a subset of the larvae of aquatic invertebrates. They are motile plankton whose motive force and/or feeding is supplied by rings of compoud cilia, the same as one would find in a rotifer. They often grow up into forms that are not moved by cilia, like muscles and snails. When said quickly, veligers sounds a lot like villagers, which renders funny any conversation about what sorts of creatures eat veligers.

Today I looked up what a veliger actually is. I wasn't too far off the mark. A veliger is a young mollusk in a developmental stage provided with a velum, a membrane edged with clilia used for locomotion and feeding. Cilia are only a reasonable way to get around if one is small (a couple of millimeters at most) so once a veliger grows that big it generally moves on to other means of locomotion, losing its velum and thereby its veliger status. Veligers are found in the bivalves (clams, muscles etc) and the marine gastropods (snails and sea-slugs).

Lindsay says that several people have wanted to study how veligers use their cilia to feed and move, but that little progress has been made because of the difficulty of finding and keeping them. They die, they grow up, they don't reproduce quickly. So since I know how to provide a large number of the animals that most closely resemble veligers in their use of cilia, rotifers, and Nicole and Lindsay know about biomechanics and veligers and all that, it seems we have a good collaboration.

P.S. Here is a photo of a Fusitriton veliger that Lindsay sent me. I Photoshopped it to increase the contrast, to make the cilia more visible.