Teaching mark-recapture with dor beetles

The key step in the planning of any good field course is to spend some time at the field site observing and asking questions. What is the habitat like, what lives there, what are the facilities, what are potential challenges or dangers to working there, etc? When I first went to do this at Svanninge Bjerge, the location of my zoology field course, I immediately started seeing big blue dung beetles all over the place. Bikuben Foundation, who operate the place, run cattle there. There is no lack of dung. These big plodding dor beetles (Geotrupidae) were all over the place, and it didn't take me long to decide I wanted to work them into the course. I wanted to introduce mark-recapture methods, and these seemed like perfect subjects. Mark-recapture methods involve catching animals, marking them in some way that would allow them to be recognized if re-sighted, letting them go, and then trying to recapture them. Such methods have a huge range of applications from tracking individual movements and estimating population sizes to monitoring growth and survival and studying behavior and sociality. To teach this in a field course, I wanted an invertebrate animal that wasn't too likely to leave the study area, that is easy to capture, mark and handle without damage, and that has enough charisma to capture students' attention. Dor beetles have all this. They are big and slow, and so easy to find and catch by hand. They don't bite or sting. They will collect in large numbers in pitfall traps baited with cow dung. They have big hard upper wings (elytra) that can be marked in any number or ways without harming them (we used this system with nail polish, but I've now got a battery-powered cautery). They are extremely numerous. They are shiny and blue. They can fly, but don't often do so.

Students mark a live beetle for release. Photo by Kim Lundgreen.

They make such an ideal intro to mark-recapture that I almost worry that I've given the student a false sense that this is easy, where in fact such studies are often very hard work. Still, if you want an efficient system for teaching mark-recapture methods and have beetles like this at your location, I strongly recommend them to you.

Ear to Ear

Yesterday, two students came to my office. They asked me to help them organize a BioBlitz, a rapid assessment of what species are present, at Svanninge Bjerge, the site where I taught my field course this spring. One of these students was in that course, the other I have seen around but don't really know. I asked all the basic questions. What do you envisage? Where will you do it? When? How will it be funded? We had a good long conversation, and I offered what support I can, while making clear I may no longer be in Denmark when this all happens. They frowned. I asked, "Where did you get the idea to do this? Why do you want to?" They looked at each other. The one I don't know, smiled sheepishly. "Well, I couldn't take your course last year. And after the course, all the students who did take it made all of us who couldn't fell incredibly jealous. They talked about it endlessly, like it was everything they could ever want in a course. Like we would go to a bar and instead of whatever we were talking about, they would be all about pinning beetles. Rather than fight about it, we agreed to try to organize something similar for ourselves. And it would really be great if you could be involved." I needed a moment to focus on maintaining my composure.

Picture show (in Danish)

This spring I taught a field course in terrestrial zoology at Svanninge Bjerge, a nature area owned and operated by the Bikuben Foundation. The foundation had Casper Tybjerg, a well known Danish photographer, join us and take photos. Bikubenfonden has featured the course on the Svanninge Bjerge website, including posting many of his photos (including the above). If you start here, and click to the right, most of the next several dozen photos are from our course, and all are beautiful. The accompany text is in Danish.

It makes me all happy and proud and sad-that-it-is-over to look through these and remember what amazing fun that course was.

Student scientists study sea stars, produce plaudable publication

A good university science education should give students the opportunity to engage in scientific research. This is widely agreed upon, and most of the biology position announcements I consider state that the successful applicant's research should present opportunities for student participation. The general model is that the professor has the research program, and a question that needs answering, and a plan for answering it, and the student gets to see how research happens by carrying out, or at best refining, that plan. I'm all in favor of this, but I'd like to take it a step further.

My first publication, way back in 2003, was with one of my professors at Bennington College, based on work that she planned, and I, as an undergraduate, helped carry out. I made alterations to the experimental protocols, did a lot of lab work with minimal supervision, and chose to work on this project rather than others that were available, but I can take no credit for any of the ideas in the publication. In retrospect the one thing I would add to my own undergraduate education, if I was to be my own professor, was working through the entire process of generating a primary paper, from initial observations and idea generation to publication.

Implausible you say? Impracticable? If generating publishable science is so easy, why doesn't every professional scientist publish a paper a week? Well, I've just finished doing it with two of my students, and I'll tell you about it.

'Finished' is vague. We've submitted the paper, and I think it good, but we have to wait to hear if the reviewers agree. I'm not going to give you too much detail on what we found because you'll have to read the paper (or a future post) when it comes out.

It happened like this: At SDU, where I currently work, all natural science students in their second semester have to complete a group project. A group of students (four in my case) are assigned a faculty mentor who gives them a question to answer and guides them in answering it. In my case, the question was, "Can we use PIT-tags (like a vet puts in your cat) to mark starfish for a long-term demographic study?" We brought some starfish into the lab, talked about animal care and experimental design, showed them how to inject the tags and pretty much let them do their own thing.

They did great, but the tags just kept coming out. After a few weeks, all the tags were out. They answered my question with confidence: No, PIT-tags cannot be used to mark starfish long term. But the thing is, they didn't stop there. With no pay, no additional course credit, no requests for recommendation letters or such, two of the four students just decided to keep going. We met occasionally and I offered encouragement and comments, but little more.

They presented their results to the Evolutionary Demography Society, and long after the course was over they kept doing more experiments to figure out how the starfish were ejecting the tags. Notice that this is their own question. I asked, "Do the tags stay?" and my students answered this then asked, "How do they get rid of the tags?" And when we had an open house at the laboratory, they presented what they had learned to the public. Just by chance, one of the visitors they talked to had access to an ultrasound machine. This let them repeatedly image exactly where within the starfish the foreign body was moving. A year after they started, they convinced me that they had discovered, and had the data to back up, a previously unknown mechanism by which starfish can eliminate foreign objects from within their body cavities. "Okay," I said, "write it up for publication, and tell me now by what date you will have a finished draft." They missed their self-assigned deadline. They needed more help with data analysis than they expected. They put in all the wrong references in all the wrong places, and the flow of the article was terrible. English is not their first language. But not so long after they said they would, they sent me a draft that had most everything I needed to make it good. With the co-authorship of a couple of marine biologists (did I mention that I know next to nothing about starfish and have no other starfish research ongoing?) and with the continued input of these two students, we made a respectable manuscript out of it.

What lessons do I draw from this? Motivated undergraduates, with just enough guidance, can basically have their own successful research programs. The paper we produced still took a bit of my time to write up, and isn't the most important paper in the world, but they discovered something completely new (answering a question that someone who knew the literature would never think to ask), and they learned. They learned a lot. Refining questions. Starfish anatomy and function. Experimental design and practice. Ultrasound imaging. Cox regression in R. Scientific English. Literature searching and use. Collaboration. Communicating science to peers and the public. Preparing and submitting a manuscript for publication. Now they will get to see how peer review really works, or doesn't. These students, just starting their third year as undergraduates, have a fuller experience of what goes into making a scientific publication than I did when I started my third year as a doctoral student. Chew on that for a minute.

It is important here to think about these students' motivation. Judging by their grades, they are not academic stars. Neither of them has described a lifelong fascination with starfish. They did this, so far as I can tell, because it was their first chance to truly be scientists rather than just science students.

I told them early on that:
A) That they would have a strong say in the direction of the research and
B) that if they produced something publishable, I would help them submit it for publication.

These are not promises to be made lightly. Publishing things, especially things outside one's own central line of research, is time consuming. Giving first year undergraduates even this limited version of academic freedom in their research is, understandably, not common practice. But it seems to me to be damn good educational practice, and I plan to continue offering this type of opportunity to students when possible. Students will do much better, and more, work when they are exercising agency and following their own curiosity. Even if they don't choose careers in science, they know how science happens from start to finish, and that is surely something science students should be given the chance to learn.

Toddler naturalist

It was only 45 minutes until dinner and my girl was antsy. We decided to head out into the woods and see what we could see. We got on a bike brought along an almond and raisin snack, a water bottle, a doll, and stuffed orangutan. Five minutes later we were standing in the woods outside of town looking at this piece of wood. "This is a perfect cover object," I told Tigerlily. It was flat or even slightly concave underneath, it was on the soil but not in the soil, it was broad, and it was in the sunlight. "I want to look under it," she said. We lifted it up and found this shiny black toad.

We talked about toad poison and washing hands before eating. She hadn't finished her raisin and almond snack so only I held the toad.

Next we went for a little walk in the woods. She said she wanted to find insects. Instead, we found blackberries.

Or rather, she stumbled into them and I recognized what they were. I tried one just to make sure they were good, and they were. I didn't use my hands. Toad poison.

She left only the underripe ones. On our way back to our bike, she said, "what's this? An insect?" It was a beautiful dragonfly that I had walked right past. I couldn't get a good picture of it but you can get a sense of how colorful it was. 

Now it was dinner time and we walked straight back to our bike. My girl was tired and hungry but learning about the woods and was ready to come home.

Field Course!

I love field courses. I loved taking them, love teaching them and even enjoy the logistics of preparing for them. What could be better than teaching excited students about animals by taking them out to see the animals where they live? Nope, not better. Try again. Nope, not that either.

Our five day field-trip starts on Saturday. Me, three teaching assistants, twenty-four students and a small house out in the woods. Beetles, birds, frogs, snakes, newts, mice etc. Stinging nettle, ticks,  mosquitoes, vipers. Out late to record bats, up early to hear the dawn chorus. I love it.

More about the course is here.

While you should regret that you are not taking this course, you should take solace in the knowledge that you would not have enjoyed it as much as I will.

Friendly advice for writing your first grant application, actually first edition

As a first year graduate student studying birds in a university natural history museum, I largely failed to learn how to make a decent specimen out of a dead bird. While there are many reasons for my failure, including a lack of aptitude and a lack of effort, at the time it felt impossible in part because the ornithology curator who was teaching a group of us how to do it was just too good at it. She would hold up the dead bird, make a tiny incision in its belly, and then her hands would spin around it and the entire carcass of the bird would be outside of its now inverted skin, which she would hold up to show us. Then she’d grab some bits of wood and cotton, and again her hands would whirl around the bird for a few seconds, after which the bird would be right-side out and restored to a life-like shape, its feathers unruffled, its head turned to the side just so and toes overlapping, as though it was patiently listening for something. I would try to repeat this process on my assigned dead bird, would screw it up somehow, and she would come over, sigh, take the bird for a few seconds and hand it back to me, several steps ahead from where I was. Then she would say, “See?”

I never did learn, or make it in ornithology. From this I learned that of the great challenges of good teaching is that you have to know the topic well, be interested in it and have a strong aptitude for it, but you also have to be able remember what it was like to not know it at all empathize with those with less inherent aptitude.

At the time, I was also learning to write grant applications. I wrote several that first year in grad school, none of which were funded. This was partly because the ideas behind the proposal weren’t well worked out, but partly because I didn’t really know what I was doing as a grant-writer. I have now written a lot of different grant applications, lets guess 40, almost every one to a different funding source. I don’t know that I can claim to know the topic well enough to teach it, or to have a particularly strong aptitude, but I can well remember what it feels like to not know where to begin, which is a very good place to start. So with that in mind, I’m going to offer some thoughts for those trying to write their first research grant applications. I’ve recently written what I learned about applying for grants from NIH and ERC. This is going to be a lot more basic.

First, consider this picture of the time my wife turned into a giant and flattened part of southern Denmark. Pretty cool, huh? Not even Photoshopped.

Okay, now down to business.

1. Don't panic. There is a good chance it seems to you at this point like you are somehow supposed to know how grant-writing is done, and that everyone around you magically knows how to do it, but there is a good chance that no one has ever provided you with any guidance on the subject. Or at least that is where I was at when I was in your shoes. Ask for help and advice frequently. Several times during the process, have people read what you are doing so they can point out your mistakes. There is a whole culture that you haven't been initiated to, and you need a guide. The basic formula for a grant application goes like this: there is a fundamentally important question that we don't know enough about. Here is what the question is and why it is so important. Here is the piece of that question I can address, how I would address it, why that is the right way to do it, why it is feasible and why it won't fail to answer the question. Here is why I am the right person to do it. I need these resources for this part of the plan, and can't do the work without them. Reiterate the importance of the question and your future results.

2. The place to start with a grant application is to have a question you need money to answer. While that may seem horrendously obvious, I have known a fair number of graduate students who were told to apply for a certain grant, or many grants, but didn’t have a clear conception of what they needed the money for. Either the question was ill-defined (as was mine that first year) or it wasn’t really clear what the money was needed for.

3. Writing grants is a pain in the ass, and there are very few academics who wouldn’t rather be spending their time on research. We do it because we need to. That said, writing grant applications is tremendously useful to your research planning, because it gives you a hard-deadline and strict format in which you have to clearly state your research plans in a succinct and clear way. My research plans have often improved dramatically through the process of writing them into an application. Some universities require graduate students to submit a detailed research proposal before starting work on their theses. This serves the same purpose.

4. The two most common types of funding you may be applying for are for research costs and for your own stipend or salary. Small grants available to students usually focus on research costs, fellowships usually fund only stipend or salary and related costs, although some do both or are for funding travel to conferences or other specific costs. Every granting agency has rules for what each grant can or can’t be used for, and so what you apply for depends on what you need to fund.

5. There are an effectively infinite number of organizations that at least occasionally give research grants, but the chance that any one of them is the one you need to apply for is almost infinitely small. This makes finding the grants you should be applying for very difficult. The way to go about this is to avoid doing what I did. I wasted a huge amount of time online looking at listing of things I could apply for, examining the websites of various foundations, etc. Instead, ask people at your university what other students have applied for successfully. Ask faculty, other students, and the administrative staff. Most every university has people whose job it is to shepherd grant applications.

6. Whenever possible, get a copy of someone's successful grant application. Get several if you can. The instructions for every grant are different, so it is best if the application you are reading is for the same grant you are applying for. That said, there is a certain grant-like style that you will find in most applications.

7. Know your audience. Most research grants are evaluated by a small group of very busy researchers who have to get through a big pile of applications and find just a few to fund. Find out as much as you can about who these people are, and design your grant to grab their interest, and tailor it to (or slightly below) their level of knowledge of your field.

8. You need to convince them that your ideas are compelling and sound, your goals achievable and the whole thing in line with the purpose for which the grant is given. You also need to convince them that you are the person to do it. Doing all of this is harder in less space than in more. When you only have a page or two, as is often the case with the grants available to students, you can't get bogged down in the details. Your writing needs to be crisp and to the point. I often write much more than I need and then edit it down repeatedly. No matter how much time you put into writing a section, if you find it isn't necessary, cut it.

9. Beware of giving too much methodological detail. The committee reviewing the grants generally won't care what concentration your solution will be at, where you will order the food pellets or what software package you will use to analyze your data. That said, if one of those details is key to understanding what you plan to do, of course you need to include it.

10. Try to write it long enough in advance that you can set it aside and come back to it a few days later, perhaps more than once. Once you've worked it over more than a few times, you need some time away from it before you can really see it again. Very good writers can produce very bad writing when they've lost their ability to take a step back and just read.

That's my ten cents (inflation). I'm sure there are things I've missed, but those are the main lessons that I can remember learning. Good luck. Now quit browsing the internet and get back to writing.

Authorship code

I'm writing a paper with two of my students. Well, I'm writing it with one of them and another one did a lot of work on the statistics. But today we had to straighten out the order that the authors would be listed in on the paper. This can be a contentious issue, and I know of cases in which papers did not getting written at all because the authors couldn't agree on who got to be listed first. Some big multi-author papers simply list everyone in alphabetical order to avoid the fuss, but then Dr. Aardvark always gets to be first author. Some journals have a little section where each author's contribution is described, but they usually end up saying something uninformative and false like "all authors contributed equally."

I came up with most of the ideas in the current paper, put things together, decided who would do what, etc. My student did much of the lab work and is doing much of the actual writing. Given this, most biologists would propose what I did, and what my student objected to: She (as the person doing the writing) should come first, I (as the senior person on the paper) should come last, and everyone else (in this case meaning the statistics student) gets sandwiched in between. This was very counterintuitive for my student; she thought I was trying to minimize my own role by putting myself last. In fact, it is a step up for me to be writing papers in which I am in that last position. I remember this being counterintuitive for me the first time it was explained to me. I was a college student, and a boss said that he'd make me second author on a paper. I said something to the effect that I'd be glad to be even last author, which I thought was being humble, but he took it as me saying the paper had been my idea. We straightened out the miscommunication but I didn't end up being listed as author on the paper. That the last author spot (at least in biology) signifies the senior author is a code biologists internalize, and I had to think back a long way to figure out why my student objected to me being last author. I explained, she reluctantly believed, and now it is settled.

Excited to teach again

Summer Semester 2011

IMPRSD 189
Introduction to Evolutionary Demography

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Start:	4 July 2011
End:	9 July 2011
Location:	Max Planck Institute for Demographic Research (MPIDR), Rostock, Germany

Instructors:

• Daniel Levitis, MPIDR
• Hal Caswell, Woods Hole Oceanographic Institution
• David Thomson, University of Hong Kong
• Annette Baudisch, MPIDR
• Alexander Scheuerlein, MPIDR
• Oskar Burger, MPIDR
• Maren Rebke, MPIDR

Course description:

Understanding survival, reproduction and other life-history events is central to the study of both demography and evolutionary biology, and each field has developed methods and concepts to observe patterns and elucidate principles. The growing field of evolutionary demography treats demographic variables (patterns of survival, reproduction, and development) as properties of organisms that reflect evolutionary processes, just as morphology, behavior, and physiology do. It draws on both disciplines to search for evolutionary explanations of demographic patterns in terms of adaptation, genetics, phylogeny, and the environment. Further, it applies demographic methods and reasoning to answering evolutionary questions. Demography and evolutionary biology are conceptually unified and inextricably linked, so the questions we want to answer can best be tackled by traversing traditional disciplinary boundaries. This course is intended to introduce early career researchers from both fields to the concepts, methods, challenges and questions of evolutionary demography.

Course structure:

We will begin with an introduction to classical evolutionary demography and the motivations for combing evolution and demography, incorporating enough basic evolutionary theory and demographic theory to get everyone on the same page. We will then focus on current topics in evolutionary demography, including:

• Aging across the Tree of Life: Measures and Patterns
• Sex-specific differences in mortality patterns: Evolution in action
• Modes of adaptive explanation of demographic patterns: a survey
• The pace and shape of aging
• The evolution of mortality of the young
• Age specific reproduction in the wild
• Life-history allometry and Charnovian invariants

Finally, pairs of students will be asked to spend the afternoons of the 7th and 8th preparing short presentations, to be presented on July 9th. Each pair will discuss the evolutionary basis of a different demographic trait or phenomenon, what is known about it and how it can be investigated.

Organization:

For July 4-8, each morning will consist of two lectures (one hour each) and each afternoon will have a one hour lab. Then the afternoon of July 9th will be occupied with short presentations by pairs of students.

Prerequisites:

Students should be familiar either with the basics of demographic life-table methods, or with evolutionary theory. Familiarity with Stata or R software will be very helpful.

Examination:

Students will be evaluated on participation in class and on short presentations.

Financial support:

There is no tuition fee for this course. Students are expected to pay their own transportation and living costs. However, a limited number of scholarships are available on a competitive basis for outstanding candidates.

Recruitment of students:

• Applicants should either be enrolled in a PhD program or have received their PhD.
• A maximum of 16 students will be admitted.
• The selection will be made by the MPIDR based on the applicants’ scientific qualifications.

How to apply:

Applications should be sent by email to the MPIDR. Please begin your email message with a statement saying that you apply for course IMPRSD 189 - Introduction to Evolutionary Demography.

• You also need to include the following three documents, either in the text of the email or as attached documents. (1) A two-page curriculum vitae, including a list of your scholarly publications. (2) A one-page letter from your supervisor at your home institution supporting your application. (3) A one-page statement of your research and how it relates to course IMPRSD 189. Please indicate whether you would like to be considered for financial support.
• Send your email to Heiner Maier (office@imprs-demogr.mpg.de).
• Application deadline is 31 March 2011.
• Applicants will be informed whether they will be admitted by 15 April 2011.

Readings:

The course will make use of readings from:

• Baudisch, A. 2011. The pace and shape of ageing. Methods in Ecology and Evolution. DOI: 10.1111/j.2041-210X.2010.00087.x
• Caswell, H. 2001. Chapter 11, Matrix population models. Sinauer.
• Jones, O. R., Gaillard, J. M., Tuljapurkar, S., Alho, J. S., Armitage, K. B., Becker, P. H., Bize, P., Brommer, J., Charmantier, A. & Charpentier, M. 2008 Senescence rates are determined by ranking on the fast-slow life history continuum. Ecology Letters 11, 664-673.
• Levitis, D. A. 2011 Before senescence: the evolutionary demography of ontogenesis. Proceedings of the Royal Society B: Biological Sciences 278, 801-809.
• Metcalf, C. J. E. & Pavard, S. 2007 Why evolutionary biologists should be demographers. Trends in Ecology & Evolution 22, 205-212.
• Rebke, M., Coulson, T., Becker, P. H. & Vaupel, J. W. 2010 Reproductive improvement and senescence in a long-lived bird. Proceedings of the National Academy of Sciences 107, 7841-7846.
• Vaupel, J. W., Baudisch, A., Dolling, M., Roach, D. A. & Gampe, J. 2004 The case for negative senescence. Theoretical Population Biology 65, 339-351.

Additional reading material will be provided at the beginning of the course.

Decide what your point is before you write

I have spent most of my time recently writing papers for publication, and I have come to a realization. It is one of those realizations where I knew it all along, but had forgotten, or had never considered how important it was. What I realized is this: every paper should have a point, expressible in a sentence or two, and everything in the paper should be relevant to understanding and evaluating that point. Analyze the data, read the literature, analyze the data some more, but before one actually starts writing, one should have a pretty good sense of what one's point is. I've taken to making the point of the paper also be the title of the paper. Here are three titles I've written recently:

• Post-fertile survival in comparative perspective: humans are qualitatively different
• Behavioral biologists don't agree on what constitutes behavior
• The grandmother hypothesis is supported, but only in humans

I don't know that these will be the titles these papers actually have when they get published, but they serve to remind me that there is a point I am trying to make, and I'm not just spilling out everything that I've done or found out or thought. In many cases the point changes somewhat once I start writing the paper, and then I change the title. But in those cases where I start writing not really having a point in mind, I end up in a morass, casting about, writing several pages and then deleting them because they don't really say anything, the bits don't go together into a single logical argument.

The null assumption of many paper writers is that one starts writing at the beginning of the paper, writes until one gets to the end, then stops. In some forms of writing, (e.g. writing a short essay for one's blog) this is probably the most reasonable approach. I have heard it suggested that in writing a scientific paper, one should write the sections in revers order. Compile the list of references one needs to mention, write the conclusion, then the discussion, the results, the methods, the intro and only very last the abstract. I am think that what works well for me in creating a first draft is more like this: Reference, title, abstract, decide what journal I hope to submit to, methods, results, discussion, conclusion, add more references and then re-write the abstract and then write the introduction last, putting in only that information necessary for readers to understand the rest of the paper. These are arranged into the document in the order the journal demands, but I write them in the order that I feel leads to an efficient writing process. Of course I then end up going back and reading it in the final order to make sure the document does not read as disjointed.

Now that I've come to this realization, and begun to implement it in my writing, I need to also impress it upon my students. I have more than one very talented student struggling somewhat in writing a paper for publication, and in some cases I think what the papers lack most is a clear and central point. We need to rectify that. New rule for the lab: decide what your point is first, then continue writing after that.

Students

One of the great things about having lots of students involved in my research over the last few semesters is that the ones who aren't that interested tend to drift away and the ones who are really interested and energetic keep coming back for more. It is like a distillation process where now, my last semester in grad school, I have this awesome group of highly motivated students and very few who are just along for the ride. It makes me happy.

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.

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.

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.

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.

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.

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.

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.

Best,
Dan

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

Phylogeny schmylogeny

Phylogenetics-
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.