Tag / tutorial

by Roslyn

To kill bias, gather good data

I hate myself for this: I have the worst sense of direction.

For the entire year when I was living in my first apartment in Kingston, I would take a circuitous route along King Street and then up Princess on my way home from the Kingston Yacht Club. Nearly two kilometers, when walking up West Street would have got me home in half the time. As Charlie said when I revealed this to him, “Two sides of a triangle is always greater than one.”

It’s not that I didn’t know grade school geometry, or that I wanted a more scenic route. I just stuck to the path I knew would get me there.

I felt a bit triumphant when I realized how long it can take Charlie when you ask him to pick up the milk. The last time I dragged him to the grocery store, I left him alone for a few minutes to use the bathroom, and returned to find him loading pineapple after pineapple after pineapple – painfully slowly, into the cart. We laughed, but I don’t ask him to come with me anymore. Alone, I can collect a week’s worth of food in less than 20 minutes.

I’m not ashamed to admit my navigational failings, either. My field assistant Myra and I happily agreed that our best strategy driving around Los Angeles was that we should always do the opposite of whatever we both thought was correct. It worked.

What I hate is my sneaking suspicion that I’m just a lame stereotype. Maybe I’m a terrible navigator because of biology; female brains are just not suited for getting around.

Hunter, gatherer

Modified from this cartoon. Original source unknown.

Recently, psychologists looked at this sex difference in what seemed like a neat field study of human foraging behaviour – in a grocery store1. Joshua New from Yale University, and his coauthors from UC Santa Barbara, set up a unique experiment in a California farmers’ market: they led men and women around the market, giving them samples like apples, fennel, almonds and honey. Then they brought the subjects back to a central location and asked them to point in the direction of those same food items.

These researchers wanted to test the idea that women outperform men at certain kinds of spatial tasks: while men are thought to be better at vector-based navigation, women might excel at remembering the locations of objects, because of the way foraging roles were divided up when our brains were evolving. It’s thought that in our hunter-gatherer past, big game hunting meant that men had to figure out how to bring heavy prey home by the most direct route. Women foraging closer to home needed a much different set of spatial adaptations2. It’s not that men are better at spatial reasoning in general, you just have to choose the right task3.

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by Roslyn

A royal waste?

Giant pandas are in the news again, this time for their annual date night at the Smithsonian National Zoo in Washington DC. But hardly a day goes by without a report somewhere on the latest captive panda birth, strategic breeding attempt or panda relocation.

A blogger at the London Review of Books compared the bears to members of the British royal family: both are suffering from shrinking ecological niches and in serious danger of extinction, hanging on by virtue of their marketing potential. The similarities don’t end there. Giant pandas, like royals, are expensive to house, with a fee of over $1 million per year for a zoo to lease a pair from China. Naturally, the breeding activities of giant pandas are as intensely scrutinized as those of Prince William.

This entails some surprising efforts when it comes to the pandas. The history of captive breeding for Ailuropoda melanoleuca is no sordid royal affair. It’s long, and for the most part, pretty unfortunate; zoos have been failing to produce heirs to the panda legacy for decades.

For starters, it’s nearly impossible to get the bears to mate in captivity, and it’s not just their deficiency in the looks department, as comedian Mike Birbiglia suggests. Captive pandas can’t seem to figure out a working sexual position1. Females often start things off all wrong by lying down, but the males are just as clueless. This led to panda porn: zoos started making videos of pandas achieving copulatory success, as training tools for the more hapless bears2. Other attempts to use Viagra on pandas were less encouraging, but the porn worked – for females as well as males – leading to a boom in captive births in recent years3.

Giant panda cub

Visitors can pay to see the cubs at the Chengdu giant panda breeding centre. File photo modified from newssc.org.

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by Roslyn

Groupthink

Which animal would use Facebook most, if it could?

My poll in class last week was a popular one – a fact that I couldn’t properly enjoy, since Charlie came up with it for me in a fit of brain-dead incapacity. Charlie’s Facebook question elicited chirps of excitement, compliments and even a few drawings on the response sheets. Here are the results, ranked by favour among the students:

  • Chimpanzees: So they have opposable thumbs, and can “use the spacebar” (is this actually important in Facebook?). A number of students gave bonobos special mention, since they would probably want to keep track of all their casual sexual relationships.
  • Dolphins: Highly intelligent, social, and they might also be interested in monitoring multiple sexual conquests. Dolphins and migratory whales could use Facebook to keep in touch while roaming widely over the oceans – the long-distance relationships of the animal kingdom. For some reason, students in different tutorial groups who chose dolphins were inspired to draw them for me as well. Coincidence?
  • Parrots and other birds: Especially in species that have high levels of extra-pair paternity, birds could use Facebook as a form of mate-guarding to keep tabs on their social partner1,2. There are other reasons to think that songbirds might easily make the transition to internet gossip. Female black-capped chickadees, for instance, eavesdrop on the outcome of song contests between rival males, and use this information when deciding on a mate3.
  • Eusocial animals: Like ants or naked mole rats (the only known eusocial mammal). A couple of students also mentioned highly social meerkats, since living in groups of 10-40 individuals would require them to keep track of a lot of social information.
  • Other yappy follower-types: hyenas, seals, lemmings, and Yorkshire terriers all got a mention.

Charlie and I discussed it over dinner at the Iron Duke. My first thought went to ants, for their extreme group lifestyle. The problem is that ants don’t really care about what other ants do or think about each other. Insect sociality is all about the greater good: worker ants toil away for the colony despite having no hope of reproducing on their own. Ok, so maybe the internet isn’t conducive to real reproduction either, but ants just don’t have the ego required. Plus, as one clever student pointed out, a colony of eusocial animals are all very close genetic relatives of one another – and she tends to block family members from Facebook.

Charlie mentioned peacocks for spending so much time on courtship and preening, but I rejected that one too.

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by Roslyn

Wherefore the mustache?

Ears, palms, toes, neck, and nose. In that order.

These are the grossest places for humans to have hair, according to Queen’s students. Ok, there were a few others that I didn’t mention. The upper lip, however, did not receive a single vote.

Last fall a number of men in the biology department grew competitive mustaches for “Movember” prostate cancer research fundraising. This required mass beard shaving on the first of November. Martin Mallet, known for his thick coat of fur, emphatic hand gestures and all-around intensity, suddenly transformed into a meek imposter. For the first time Martin had no probing questions for the speaker at the EEB seminar. I can’t help but wonder: if he did, would anyone have noticed?

I started to recognize Martin again when the hair on his upper lip attained visibility. Other men of Movember fared less well. It can’t be a good thing when the people who work in the same office as you don’t even notice your new, mustachioed face.

But what, if anything, is it for? My experience suggests that human facial hair serves as a male status signal. Is this why we evolved mustaches in the first place?

Inca Tern

Why do mustaches evolve? Inca tern, from Wikimedia Commons.

In class the other week we discussed Stephen Jay Gould and the trouble with adaptationism. Gould famously criticized the proliferation of sloppy adaptive reasoning in his 1979 paper “The Spandrels of San Marco and the Panglossian Paradigm“1. He took aim at scientists who apply adaptive “story-telling” to nearly anything – from the colour of our skin to the size of our noses – in an unverifiable, unfalsifiable way.

It can be easy to jump on the adaptationist bandwagon, since these stories are often quite plausible. This may have been especially true when “Spandrels” was written, due to the rise of some revolutionary ideas about how to apply evolutionary biology to the study of social behaviour. There was plenty of new research to be done. Of course, many of the people doing this research disagreed with Gould’s characterization2. At its worst, adaptationist thinking might lead to some bad science, especially when it comes to human behaviour (where confounds are especially hard to control). But speculation is a necessary part of the scientific method, and adaptive reasoning can be a good place to start.

It is worth noting that Gould’s paper has been enormously influential. “Spandrels” has been cited well over 3500 times. I’m still waiting on citation number 3 for my Master’s research.

And yet, the response of the research community to the “Spandrels” critique has largely been, “That’s well said, but let’s get back to our field work.”2 In that spirit, consider the mustache. Can we speculate about it in a reasonable way, avoiding the big adaptationist pitfalls?

First of all, is this question worth asking?

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by Roslyn

Science fictions

Fakery is not just for Hollywood films anymore.

Nature documentaries are full of it, from elegant narratives to some downright dirty tricks. This tradition goes back a long way: the myth that lemmings commit mass suicide to save their brethren from overpopulation was spread widely as as result of the 1958 Disney film White Wilderness. This is not trivial. The film won an Oscar for Best Documentary. The lemming story made it as far as a philosophy course I took in university (Science and Society PHIL203), where the instructor used it as an example of why we should doubt evolutionary explanations of human behaviour. The myth just won’t die, even though CBC exposed the lemming scam back in 19821. Journalists on The Fifth Estate proved that the mass suicide scene was actually filmed in downtown Calgary, not in the Arctic as Disney had claimed. The Disney crew used a rotating platform to push captive lemmings into the Bow River.

More recently, the BBC has come under fire for using captive animals to film some of the scenes in the Blue Planet series1. This seems justifiable to me, but some truly ugly practices have also been exposed, like baiting corpses with M&Ms to get footage for an IMAX documentary on wolves2.

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by Roslyn

Field biology goes to Hollywood

One of the weirder things about my field site is that it is also a Hollywood set. A number of movies, TV shows and commercials have been filmed at the LA Arboretum, going back to Tarzan Escapes in the 1930s.

The Arboretum had a regular appearance in the popular 1970s show Fantasy Island. In the opening credits, a midget rings the bell in the Queen Anne Cottage. This is a historic building on the Arboretum grounds that was built in the by the same wealthy California businessman who started the peafowl population in the area.

You can catch the Arboretum in many other films, since it provides a convenient stand in for the jungle a short drive away from downtown Los Angeles. Examples: The Lord of the Flies, Anaconda, The Lost World, Congo, Terminator 2, The African Queen, and too many campy horror flicks to count (Attack of the Giant Leeches?).

Several things were filmed during my three seasons there, leading me to realize that making a movie is a lot like doing field biology. Here’s how:

1. The hours. Field biologists often have to keep the same hours as their study species, working for as long as the animals are active. For some ornithologists, this can mean starting at 4 am. We were lucky with peafowl. They are late risers, coming down from their roosts around 7-8 am. They also tend to take a long siesta in the middle of the day. This meant that we had to work two shifts, coming in for several hours in the morning and returning after lunch until sunset. It made for some long days.

Film crews also seem to work long hours based on the amount of light, since our schedules would often coincide.

2. Tedium and futility. Most of the time spent watching animal behaviour is watching them do very little. Here’s an example: we saw about 20 mating events in 2010, in 500 man-hours of observation time. That’s over 24 hours of sitting quietly for each copulation.

Catching the beasts can be a little bit more active, but you still feel completely useless 90% of the time. Your main activities include: waiting for the animals to show up, looking for the ones you haven’t caught yet, waiting around for your traps to work, and worrying about all the reasons why they aren’t.

A lot of jobs in Hollywood might not be so far off. When AT&T filmed a commercial at the Arboretum last year, we met a guy whose sole responsibility was to keep the peacocks away from the set. His boss gave him a bag of bird seed. It was the cusp of the breeding season, and the crew had decided to place their set right in the middle of one particularly dedicated male’s territory. The poor guy was literally playing tag with that bird all day.

3. Costumes. Important in Hollywood, but also useful when trying to catch birds. After a few weeks in the field, most tend to settle in to a uniform, wearing the same thing nearly every day. If it works and you’ll just be getting dirty again tomorrow, why change?

Field clothes

Waterproof jackets come in handy when catching large birds. From left: Will Roberts, Myra Burrell and Roz Dakin. Photo by Bonny Chan.

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by Roslyn

How to raise a science major

The newspapers have been abuzz lately about a controversial book: Battle Hymn of the Tiger Mother, by Amy Chua, is a memoir on the rewards and perils of stereotypically strict Asian-American parenting. This week I asked students in my 4th-year biology class to tell me about their earliest memory of being fascinated with something biological, information that could be useful for parents hoping to form their children into university science majors.

And so, some lessons learned:

1. Worms work. Let your kids get close to the ground, outside. At least two students listed earthworms appearing after the rain as their most important early memory. A large portion of the class described similar encounters with tadpoles, snails, caterpillars, ants, spiders and their webs, and other minutiae found on the lawn. Larger examples of charismatic megafauna barely got a mention. Perhaps opportunity plays a role. For instance, one student remembers being particularly enamoured with deer in the backyard.

2. Pain. A wise teacher once told me that “learning hurts”. The converse might also be true: harmful organisms can be educational. An encounter with razor-sharp zebra mussels was particularly salient for one student. Another recounted a family vacation in the New Mexico desert, where a first-hand experience with cacti led to an early lesson in adaptation.

Well-armed cacti

Hidden Valley, Joshua Tree National Park, California.

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by Roslyn

What should Stephen Harper know about biology?

I’m teaching again this semester, this time in Bob Montgomerie’s fourth-year course on the history and philosophy of biology. My job is to moderate group discussions and seminars in the tutorials. It will be a lot of work, since tutorials happen every week, but I’m excited at the prospect of using our debate as fuel for this blog.

I started by asking the class to answer three questions in an anonymous survey. First, I wanted them to tell me the most surprising thing they had recently learned about science.

My example of this was the nocebo effect. it’s the opposite of the placebo effect, with a bit of voodoo-witchcraft thrown in: apparently just believing in a negative outcome can be bad for your health. What I found surprising about it initially were the spooky anecdotal accounts of people diagnosed with terminal illness, and then dying within a few months just as the doctors predicted – only to have pathologists later realize that the original diagnosis was in error. Can we think ourselves to death?

But maybe this was a bad example. In general, the power of negative thinking isn’t all that surprising. Why shouldn’t there be a flip side of the coin for the placebo effect? After all, the negative effects of stress and anxiety on health are well-documented by the medical community. For example, this Washington Post article describes a study on blood thinning drugs where doctors showed that just by giving patients a warning about gastrointestinal side effects, you can make it much more likely that they will experience those negative symptoms. Other documented nocebo effects in the Skeptic’s Dictionary range from headaches to allergic reactions. Again, the power of thought to affect us via our own immune systems is perhaps not so surprising.

Voodoo may have lost its magic too: according to this article from Salon, there is some debate as to whether examples of death by curse in tribal societies are really due to starvation and dehydration, since feeding the doomed individual is often seen as a waste of scarce resources. And of course, the medical anecdotes of death by false diagnosis are good stories, but probably not much more than eerie and highly memorable coincidences.

What do the students find hard to believe? Out of 28 responses, 4 had to do with the paradoxical nature of modern physics. There was 1 response on lemmings that was certainly hard to believe, because it was just plain wrong (more on that later, but lemmings do not jump off of cliffs in a form of altruistic mass suicide. That is a myth). The majority, at 14, were on marvels of adaptive evolution (e.g., the complexity of the brain, venomous mammals like the platypus, bowerbirds, examples of rapid evolution).

This is proof that majoring in biology does not diminish the sense of wonder we have about living things. If anything, it probably enhances it. Here are two student responses that sum it up nicely: the “diversity that surrounds us” and “just how much there is out there to learn”. It may be the hardest thing about biology to really wrap your mind around, but it sure is fun to try.

The second question: What should Stephen Harper know about biology?

The most popular category here was the environment, with 13 students listing principles of ecology and environmental science that Harper could use. After that, 4 wanted Harper to have a basic grasp of evolution and natural selection, especially given the strange opinions of his science minister Gary Goodyear. There were 2 shameless requests for more research funding. Sadly, 2 left this one blank – hopefully not because they think Harper doesn’t need any biology. At the other extreme, 1 complained that there is a lot Harper should know about “any matter really”. One student wants him to have “a dangerous idea like Charles Darwin”.

I would tell Stephen Harper that Taq polymerase comes from Yellowstone National Park. Everyone should know this one – I’m sure I learned it during undergraduate, but forgot, only to be reminded of it again recently.

Here’s the story: Taq polymerase is a chemical we use to study DNA. A workhorse of the modern genetics lab, this enzyme makes it possible to turn a minuscule amount of DNA into a much larger sample by rapidly copying the molecules at high temperatures in the polymerase chain reaction (PCR). Countless techniques are made possible as a result: forensic DNA fingerprinting, diagnosis of genetic diseases, unraveling gene functions, sequencing whole genomes, and filling in the branches on the tree of life that describes how all living things are related to one another.

Taq polymerase works at high temperatures because it comes from Thermus aquaticus, a heat-loving bacteria. Up until the 1960s, the temperature threshold for life was thought to be around 73 degrees Celsius (which is the limit for photosynthetic bacteria). However, in 1967 Thomas D. Brock and Hudson Freeze reported finding bacteria that could withstand temperatures a lot higher than that in the hot springs of Yellowstone. This was revolutionary. Years later, when people were working out the chemical procedures necessary for DNA analysis, it was knowledge of the earlier Yellowstone discovery that made efficient DNA copying at high temperatures possible.

I also asked the students what they hoped to get out of the course. Only 1 claimed a good mark, which was surprising for an anonymous survey. Some emphasized novelty: to learn “something new in biology for once”, “something stimulating and eyebrow raising” and “ideas never thought of before”. Others hope to learn some personal and biographical details of the iconic figures in science: “what inspired them” and “what was going through their heads when their ideas were opposing the popular belief of their time”. I hope I can learn from this group about what goes on in the heads of students and the public in Canada.

by Roslyn

Biology 210 Magazine Article

Popular science writing style

Olivia Judson’s blog for the New York Times is an excellent example of the sharp-but-accurate style you should aim for, although the posts are much shorter and don’t into as much detail as you will for the assignment. Here are a couple of quick reads for inspiration:

An Evolve-By Date

Laboratory Life

Judson also lists her primary sources at the end, as further readings.

Feature-length articles

Examples of longer feature articles. This one from the New York Times covers research from the lab of Meredith Chivers, a Queen’s professor in the Psychology Department who works on sexuality and gender:

What Do Women Want?

More examples from New Scientist magazine. The first article is on sexual conflict down to the level of gametes, and the second is on same-sex behaviour in animals:

Dad vs. Mom: The Ultimate Battle of the Sexes

Homosexual Selection

And finally, another feature-length piece from Science News magazine covering the latest research and opinions about sex differences in science and math aptitude:

Showdown at Sex Gap