How to learn to code

I just read a great post by Jessica Duarte on teaching beginners to code. It is all so true. Especially #5, making mistakes:

You [the instructor] have to ride out the mistakes. Make them often. Let the class fix them.

It’s essential for students to see and experience the process of working through mistakes. Right now, I am starting to use git and Github for our manakin research at the Smithsonian. A major benefit is that it allows us to make mistakes safely.

Duarte is organizing the 2017 National Learn to Code Day on Intro to Machine Learning and Artificial Intelligence. I look forward to helping out with the Ottawa chapter in on September 23!

Innovative, naturally

bluegill sunfish field work

Chandra Rodgers sampling bluegill sunfish on Lake Opinicon.

This spring I had the opportunity to write a feature article on the Queen’s University Biological Station, a site just north of Kingston where researchers have a long history of major scientific breakthroughs involving modest Ontario wildlife. Several of these discoveries have proved to be as useful as they are compelling. The story was published in the Kingston Whig Standard, and on the web through the Queen’s Alumni Review and Funding for photography was provided by the CFI’s 2011 Emerging Science Journalists Award.

Talking to scientists about their research was by far the best part of this project – much more fun than I expected! And even the toughest interviews were a gold mine of ideas. Thanks to everyone who participated. The full story is posted below…

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To save trees, major rethink is needed

When you stop to think about it, few things are weirder than a tree. Like us, they’re largish organisms made up of many cells, each with a central nucleus – but we have little else in common. Plants diverged from our early ancestors well before there was anything bigger than a single cell around. They split from the animal lineage even before fungi, which leads to a shocking conclusion. That spot of mould in the vegetable drawer? It’s more closely related to you than the plants upon which you both depend.

Small wonder, then, that plants don’t live and die by the same rules as animals – but this could have dire implications. That’s the message of a new study by Jonathan Davies of McGill University, published in PLoS Biology. Davies and his international collaborators have shown that the factors causing extinction in plants are entirely unexpected, and the upshot is that the current IUCN Red List criteria for listing endangered species – which are based on animal studies – might be useless when it comes to plants.

Davies and his team used the latest the comprehensive Red List data for all flowering plant species in two locations: the United Kingdom and the South African Cape. The Cape is a biodiversity hotspot with thousands of endemic species: plants that evolved there, and that can be found nowhere else. The UK flora, in contrast, is made up of species from other regions that moved in after the retreat of Pleistocene glaciers.

Previous work has shown that among mammals, we are most likely to lose species with large body sizes and long generation times – giant pandas and elephants are classic examples. But according to the new analysis, plants break the mold. Davies and coauthors found that the kinds of plants most at risk in the UK are different from those at risk of extinction in the Cape, indicating that basic traits like size have nothing to do with it. Using a detailed evolutionary history of the Cape species, the team also found evidence that extinction risk in plants is tightly linked to mode of speciation: the Cape species most at risk tend to be ones from the younger, rapidly-evolving lineages.

This implies that in plants, extinction is pruning the tips of the evolutionary tree. The authors suggest an explanation: unlike animals, new plant species tend to arise from small isolated populations that are at the extremes of a much larger ancestral range. Thus, a new plant starts off with a limited distribution, and because range size is an important criteria for Red List risk, it is also highly vulnerable.

The team’s analysis of anthropogenic factors turned up an additional surprise. For the Cape flora, human-induced habitat changes such as urbanization and agriculture cannot explain extinction risk of local plants. In other words, there is no simple geographic correspondence between human activity and plant decline. As the authors put it, places like the South African Cape might therefore be both “cradles and graveyards of diversity”, regardless of human activities.

This study suggests that a major strategy revision is in order if we want to conserve the world’s plants – a group that we all depend upon for oxygen and energy. More generally, risk criteria for one taxonomic group cannot necessarily be applied to another, since the pathways to rarity may be as foreign as the species themselves.

Further Reading

Davies, J. T. et al. 2011. PLoS Biology: 9(5): e1000620.

Identity evolves

Everyone is special.” The paradoxical refrain of baby boomer parents to their millenial offspring is true, so long as you’re a rodent living in a large, stable group of good communicators.

I recently wrote about the phenomenon of identity signals in animals, where variable colours and patchy-looking patterns can provide signatures of individuality, much like the human face. These are not limited to the visual domain. Think of how easily you can recognize a person’s voice – even someone you don’t know very well – from just a few lines of speech, like when a celebrity turns up in an animated movie.

But I didn’t have a chance to cover the latest news on this topic. In some very plain looking rodents, we now have evidence that individuality evolves1. Some of the plainest looking critters, like the Belding’s ground squirrel shown below, have the most distinctive snarfs and grumbles – and it all has to do with the number of group-mates they typically interact with.

Belding's ground squirrel pups

Two Belding’s ground squirrel pups peek out of a burrow. Photo by Alan Vernon from Wikimedia Commons.

The new results came out this month in the high profile journal Current Biology. Previously, researchers had looked for the evolution of individuality in a handful of bird and bat species. The prior studies examined distinctiveness in the begging calls offspring make to their parents, contrasting pairs of closely-related species that vary in the number of offspring in shared “crèche” or communal nest sites2,3. But nobody had tackled the evolution of individuality in a broad context.

Until Kim Pollard, that is. Pollard, a recent PhD graduate from UCLA, and her supervisor Dan Blumstein decided to look at this question in the social marmots. You might remember Blumstein from another recent post; his interests range from mammal conservation and environmental education to the bioacoustics of movie soundtracks.

For Kim Pollard’s study of identity signalling, marmots were an ideal choice. Marmota is a large genus of 14 different species in the squirrel family, all social, and all with their own alarm calls that they use to warn neighbours and family members about nearby predators. Species like the yellow-bellied marmot and Richardson’s ground squirrel also have the ability to recognize each other based on the unique sound of these calls4,5.

Crucially for Pollard and Blumstein, social group size also varies in the genus, ranging from about 5 to 15 individuals per clan or family group. This allowed the authors to test the hypothesis that group size has been an important factor in the evolution of distinctiveness, since, as they put it, “The bigger the crowd, the more it takes to stand out.”

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You are what you feed

What makes you you?

The problem of identity – and its flip-side, change – has been vexing philosophers ever since the discipline got started in ancient Greece. As early as 500 years BC, Heraclitus was musing about the ever-changing nature of a flowing river, recorded by his contemporary Plato with the enduring line, “You cannot step in the same river twice.”

This issue comes up everywhere. In an astronomy course I took at university, the professor gave us a mind-boggling assignment: calculate the number of atoms in your body that were once part of a living dinosaur. The answer was a lot, and though I don’t recall the exact number, the question could have just as easily been about sharing atoms with Heraclitus, or Plato, for that matter. The point is that most of the molecules in our bodies are being replaced and recycled, all of the time1. Like a flowing river, you are literally not the same bag of stuff that you were last year, or even last week; although a more accurate way to put it might be that you are a bag of somewhat different stuff than you contained before.

This raises a tough question. If a different collection of matter can be the same person, how much has to change before you aren’t yourself anymore? The implications are nearer than you might think. Organ transplants, bionic limbs and electronic implants – including devices implanted in the brain – are all within the range of current medicine. How much of a person’s body can we replace and still consider them to be the same person?

I don’t have the answer, and I’m not sure anyone ever will, although some would argue that it is a mistake to assume that there is anything like a constant “you” in the first place. For example, the philosopher Daniel Dennett contends that the idea of a continuous self is really just an illusion produced by the brain2.

Biology has a thing or two to say about the matter. It turns out that part of what makes you you is other species. Specifically, the ones living inside you: the veritable ecosystem of bacteria and other microscopic organisms inside your gut. Evidence is mounting that the microcosm within is an important part of who we are: it provides a unique signature of individuality. It can also determine future health. It might even be part of what defines us as human, since a new study shows that as we evolved from ape ancestors, so did our inner ecosystems3.

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A case of mistaken celebrity

They all look the same to us. Celebrities, that is. And by us, I mean academics.

The proof starts with peacocks. Last fall, I was working on some measurements I took of the crest ornament in these birds. Peafowl have this funky little fan of feathers on top of their heads, and though it’s not that small in the grand scheme of fancy bird plumage ornaments, the peacock’s five centimetre crest looks a bit ridiculous next to the metre-and-a-half long train.

Why bother having a crest when you also have a big train? And why do females wear crests too? In this species, the crest appears to be the only plumage ornament shared by both sexes. Here are some of my pictures from the field, taken on the cusp of the breeding season:

Crest ornaments of male and female peafowl

Crests of (a) male and (b-c) female peafowl. Scale bars are 10 cm. Photos by Roslyn Dakin.

Over the years, I’ve measured the crests of close to 150 birds. These data lend some support to the idea that the crest is a signal of health in both males and females, although it might work in slightly different ways for the two sexes1. As you can see from the picture above, there is a lot of variation in how the crests look – and it’s mostly on the female side of the equation. Almost all adult males have tidy looking crests like the one shown in (a), but females often have crests with a lot of new feathers growing in (c). It turns out that males in better condition tend to have fuller, wider crests. The healthiest females, on the other hand, have crests that look most like those of males, with all feathers grown out to the top level (b).

The extreme variability among females leads to an additional hypothesis, and it’s one that I can’t rule out at this time. Perhaps the crest is a signal of individual identity that the birds use to sort out who’s who in their social groups – just as faces do for us. A clue that this could potentially work for peahens is that my field assistants and I can do it. Once you spend enough time hanging around with these birds, you find yourself recognizing certain females that haven’t been captured yet (and that therefore lack identifying leg bands). Your first clue? Usually a unique pattern of crest feathers.

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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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Reaching the other side, in synchrony

It’s a familiar site on campus here during the first week of class: packs of jaywalkers moving in tight co-ordination, in sync with the flow of oncoming cars. From traffic lights and power grids to stereo sound and cinema, synchrony is so common in our environment that we usually only notice it when it fails. Not so with nature: the examples of synchrony in living things tend to be much more surprising to people studying animal behaviour.

Group courtship displays are a classic example. Think of chorusing songbirds in the morning or calling frogs gathered around a pool of water at night. Readers of my blog on peacock field work might be familiar with lek-mating birds gathered around a clearing to wait for females. Peacock train displays also tend to happen in sync. One traditional explanation for these co-ordinated displays is that, by synchronizing their most conspicuous behaviour, animals might gain some protection from predation1. Another possibility is constructive interference: co-ordinated timing might allow a pair of animals to spread the message farther than either one could on its own2. Two innovative new studies on animal courtship have added to this list. The first, on firefly displays, shows that synchrony might help insects recognize members of their own species by getting rid of visual clutter.

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