Science online, definitive gripes edition

Mimulus cardinalis #2 What’s living in your nectar supply? Photo by J.G. in S.F..

Happy Darwin Day!

Photo by jby.

Today would have been Charles Darwin‘s 204th birthday. For the occasion, I’m wearing my new t-shirt, which bears a most excellent and appropriate cartoon by Adam Korford. Here’s a snippet from The Origin of Species for your contemplation. It’s the opening salvo in Chapter IV, “Natural Selection”:

How will the struggle for existence, discussed too briefly in the last chapter, act in regard to variation? Can the principle of selection, which we have seen is so potent in the hands of man, apply in nature? I think we shall see that it can act most effectually. Let it be borne in mind in what an endless number of strange peculiarities our domestic productions, and, in a lesser degree, those under nature, vary; and how strong the hereditary tendency is. Under domestication, it may be truly said that the whole organisation becomes in some degree plastic. Let it be borne in mind how infinitely complex and close-fitting are the mutual relations of all organic beings to each other and to their physical conditions of life. Can it, then, be thought improbable, seeing that variations useful to man have undoubtedly occurred, that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of surviving and of procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favourable variations and the rejection of injurious variations, I call Natural Selection. Variations neither useful nor injurious would not be affected by natural selection, and would be left a fluctuating element, as perhaps we see in the species called polymorphic.

There’s so much packed into that verbose Victorian paragraph! From so simple a beginning, all of modern biology is descended.◼

Evolutionary psychology: You’re doing it wrong (but you could do it better!)

The Descent Of Man Well, it didn’t quite happen like that. Photo by Minette Layne.

Over at Scientific American, Kate Clancy sums up the scientific case against evolutionary psychology:

[Evolutionary psychology] is trying to take on an incredibly challenging task: understand what of human behavior is adaptive and why. We can better circumvent the conditions that lead to violence, war, and hatred if we know as much as we can about why we are the way we are. What motivates us, excites us, angers us, and how can evolutionary theory help us understand it all?

Because of this, there are consequences to a bad evolutionary psychology interpretation of the world. The biggest problem, to my mind, is that so often the conclusions of the bad sort of evolutionary psychology match the stereotypes and cultural expectations we already hold about the world: more feminine women are more beautiful, more masculine men more handsome; appearance is important to men while wealth is important to women; women are prone to flighty changes in political and partner preference depending on the phase of their menstrual cycles.

It may not always be evident, but biologists who get all shirty when we see the latest evo-psych study splashed across the headlines generally agree with the most basic premise of EP: that humans are evolved, biological organisms, and that our present behavior is a result of our evolutionary history. What drives us up the wall is the refusal of EP research to apply understanding developed over decades of work by evolutionary biologists—the discovery that there’s more to evolution than natural selection, that natural selection often acts on many traits simultaneously, and that there may be many ways to acheive the same level of reproductive success.

With modern genetic tools and a modern evolutionary perspective, biologists—including Kate, who studies human reproductive biology in an evolutionary context—have learned a lot about how natural selection and other evolutionary processes shaped current human diversity. Some of the best examples so far are in relation to diet (drinking milk and cultivating corn) and adaptation to low-oxygen conditions at high altitude; but there’s no reason the same methods can’t tackle other features of human nature, given sufficient quantities of the right data. Yet we rarely see EP studies based on the kind of data that could actually provide answers to the questions they ask. (And then, all too often, we see EP studies that are unmoored from basic biology altogether.)

So: The complaint that most evolutionary biologists have with EP isn’t that it’s asking the wrong questions, or asking questions it has no right to ask. It’s that EP is using the wrong tools to answer those questions. And, to the extent that we agree that those questions are important, it’s upsetting to see someone claim to have answered them using only surveys of undergraduates. We’re like plumbers expressing our exasperation with a guy who insists on intalling a new toilet using a nail file and a hot glue gun: dude, go buy a wrench!

Anyway, enough from me. Go read Kate’s post already.◼

Science online, wisdom of crowds of the stupid edition

school of yellow snappers Fish, schooling. Photo by otolithe (oliver roux).

Herd immunity, unfalsifiable hypotheses, and the search for the missing heritability

Image created with Pulp-O-Mizer.

It’s been a busy week at the other blogs with which I’m variously affiliated. So busy that I’m going to run down what’s up at Nothing in Biology Makes Sense! and The Molecular Ecologist in a single omnibus post.

First up, Nothing in Biology Makes Sense!: My younger brother Jon (@Bonovox1984), who’s in his third fourth year of medical school, led off with a post on a new study of “herd immunity”—the effect whereby people who haven’t been vaccinated benefit from reduced risk of disease if they’re living around lots of people who have been vaccinated. Then Prosanta Chakrabarty (@LSU_FISH) continued the NiB tradition of blasphemy by explaing why creationism is not—and can never be—science. And finally, we announced that Nothing in Biology will be hosting the March 2013 Carnival of Evolution—you can see how to submit your evolution-related blog posts and other online content right here.

Then, over at the Molecular Ecologist, Tim Vines posted Molecular Ecology‘s first-ever list of top reviewers to provide some recognition for the volunteer labor that goes into a good peer-review process. And I wrote about a cool new study that goes looking for the “missing” heritability in quantitative trait locus studies—and finds a lot of it, with the help of lots of statistical power. (It turns out that a lot of the missing heritability is hiding in genes of small effect, which is exactly what some folks have long speculated.)◼

Science online, plowing ahead edition

winter street Slow for snow. Photo by Andrew Ciscel.

First teaching experience: Final examination

2013.01.05 - Reem-Kayden Center The Reem-Kayden Center for Science, Bard College. Photo by jby.

Twenty-one days, 12 schooldays, 24 class periods, 54 hours of class time … and now the 2013 Citizen Science course at Bard College, my first attempt at teaching all on my own is over. Actually, it’s been over for a couple days. I’ve flown back to Minneapolis, unpacked two suitcases full of laundry and books, spent a day at the office picking up the threads of work I left behind for a month, cleaned and restocked the kitchen, and posted photos from my weekend off in New York City.

Oh, and submitted the final grades.

But so now that it’s all over, how’d it go? Pretty well, on the overall. As much as Citizen Science is meant to be a crash course in scientific reasoning for Bard’s first-year students, it’s also a crash course in teaching for folks like me, who come to the job with experience as teaching assistants, but not in planning or executing a whole course. And judged solely on that level, Citizen Science is amazing.

Let me run through the numbers again: 12 four-and-a-half-hour days with the same 20 first-year students. I spent a fair bit of my Christmas holiday preparing lesson plans, and ended up reworking almost all of that planning in the last three days before class started. From there on, the average workday was something like:

  • 0700-0800h: Wake, shower, breakfast at cafeteria.
  • 0800-0900h: Last-minute lesson prep; classroom set-up, maybe some frantic final copy-making.
  • 0900-1130h: Morning class period. Ideally, no more than one hour of this is PowerPoint presentations and/or videos of TED talks.
  • 1130-1200h: Clean up, collect oneself, wait for the crush of students to move through the cafeteria.
  • 1200-1300h: Lunch at the cafeteria.
  • 1300-1500h: Afternoon class period. Only start this with a video if you want everyone to immediately fall asleep. Class debates are good in this time slot. Assign homework for the next day.
  • 1500-1600h: Clean up, collect oneself, adjust tomorrow’s plans based on what you covered today.
  • 1600-1730h: Exercise. (There’s a respectable campus gym, or nice trails if the weather’s not terrible.)
  • 1730-1900h: Dinner at the cafeteria.
  • 1900-whenever it’s done. Lesson planning and prep; printing and copying of handouts.
  • 2300h: Bedtime, one hopes.

With variations for a four-day rotation in the wet lab and another in the computer lab, plus a “civic engagement” day in which the first-year students go to a local public school to guest-teach science classes for half a day, that’s pretty much the shape of the course. It was exhausting. Boot camp for college teaching. Learning to swim by jumping into the middle of the Hudson River in January.

But that schedule leaves out a multitude of support. First and foremost, Citizen Science faculty have no other personal responsibility than the teaching. Meals are in the campus cafeteria, which provides just fine. Housing is on campus—yes, my dorm room was tiny and ill-equipped, but it was also right around the corner from my classrooms, the communal faculty workspace, the cafeteria, and the gym. So: no cooking, no commute.

Also, it must be said, the Bard student body is pretty great. There were the inevitable exceptions, but most of my class section were smart, friendly, and willing to at least try to tackle any topic I threw at them. Sometimes they were alarmingly informal, and I had to bend a little to accomodate the local concept of punctuality, but if a classroom full of unknown students is a cliff from which a rookie prof dives, these students were also the trampoline at the bottom.

But most importantly, Citizen Science teaching is collaborative. Intensely collaborative. From the moment I arrived on campus, most of my conversations with other faculty members were about lesson plans: what had worked last year, what spurred an amazing class discussion earlier today, what part of the lab procedure left every student confused and irritated. We all started with a six-inch-thick binder of readings, case studies, and worksheets, and then added our own ideas—and swapped, reworked, cut, and rejiggered each other’s ideas.

2013.01.14 - Running Running the campus trails. Photo by jby.

For me, the flagship example of this was the computer lab. The resource binder had some material on SIR models of disease spread in a population; I wanted to try and teach my students some of the programming language R. So why not build SIR simulations in R?

One faculty member had already developed a nifty interactive model of disease spread in a simulated social network, which included many of the basic concepts necessary to understand more general models, so I started the computer section with that. Next up was an intro-to-R worksheet I’d banged out over the holidays, which covered exactly the programming concepts necessary to code the model, and nothing more. A couple of other faculty members test-drove that worksheet in their own class sections, which had the computer lab earlier in the schedule than mine.

One night’s reading assignment was Anderson and May (1979) [PDF], the original SIR paper; the next day we walked through the math in class. Then I gave my students a worksheet covering some of the graphing capabilities of R, which another of the R-using faculty had developed as followup to my introduction worksheet. And finally, I walked them through the coding necessary to create a simple SIR recursion simulation, complete with a plot of populaiton dynamics over time.

The result wasn’t unqualified success, by a long shot. Some students bogged down in the programming; many glazed over when I started writing equations on the whiteboard. Almost everyone seemed to like drawing graphs in R, though a lot of folks got frustrated by the technicalities of programming syntax even in that context. In the end, most students were able to at least follow me through coding the SIR model, but that was all we had time to do. Given another go-around, I’d provide more structure in the final stretch, with a worksheet that walks through the model coding and how to use the finished model to test specific hypotheses about epidemic dynamics. Also, I’d probably lead with the graph-making, which was more engaging than just pushing variables around on the command line.

But on the whole, I think it worked. My students coded SIR simulations in R, which actually responded to parameter changes the way they were supposed to, and generated pretty graphs in the process. Several students even told me, afterward, that they’ll use R for graphing in the future.

That outcome was really only possible because there were other faculty working on similar ideas, testing things out for me, sharing their own experience and materials. From what I hear, that’s a resource I can’t expect to have when I start teaching my own “real” courses as a full-fledged faculty member. And yet it’s the biggest reason why Citizen Science left me feeling like, actually, I might be able to pull off this whole professor-ing thing after all.◼