Tuesday, November 30, 2010

Another inspirational video

This video touches all my buttons: teaching, education, collaboration, comics, story telling, science, humor.

Wednesday, November 24, 2010

Let's talk ... microbes

Amanda and Marina created a module to introduce Grade 1 kids to microbes for the program Let's talk science. They picked a very challenging subject to introduce something we cannot see to 6 year-olds. However, they pulled it off very successfully using pictures, glow-in-the-dark powder and black lights, and a couple of microscope. I joined them for the final presentation (in my son's class), and these are the pictures I took.



Next time, volcanos?

Saturday, November 20, 2010

Latest summary of Churchill Research

I recently gave a presentation at the University of Toronto - Mississauga, and that was the perfect opportunity to summarize the research results from our lab in Churchill of the last couple of years. Below you can see the slides of that presentation.


Friday, November 19, 2010

Empty Cups


Very occasionally, I will brave North American culture and go see a movie on a ridiculously big screen with a ridiculously big bag of popcorn. Last December, a friend convinced me to not only go see Avatar on the big screen, but to watch it in 3-D with her. I was blown away. Though I find the current 3-D craze to be, well, crazy, I have to admit that it brought a certain enchantment to the fantasy planet Pandora. The Pandoran world teems with all the weird and wonderful biota that make for an ecologist's paradise: giant plants that spiral and luminesce, majestic birds soaring and battling in the sky, delicate spores pulsing through the air like tiny jellyfish.

But special effects aside, the movie is first and foremost an insightful commentary on the danger and devastation of human arrogance. Writer and director James Cameron tells the classic and still-very-relevant tale of white man exploiting Native land for gold. A love story is central (of course), and it is the budding romance between American Jake Sully and Pandoran Neytiri that sparks complication and hope.

I won't spoil the movie, but what I want to focus on here is one of Jake's first encounters with the Native Pandoran people. (He was assigned to befriend them and learn their ways with the ultimate goal of pushing them off a desired tract of land.) Jake acquires the attention of Mo'at, the clan's matriarch. She is initially angry, demanding that he go away, expressing her frustration at how his people just don't understand. But Jake persists, imploring that she teach him and that maybe she can make him understand. I found the next bit of dialogue extremely telling:

Mo'at: It is hard to fill a cup that is already full.

Jake: My cup is empty. Trust me. Just ask Dr. Augustine. I'm no scientist.

Two points of interest emerge for me. The first is that scientists know. Jake makes it clear that scientists' cups may be full, but he doesn't fall under that camp (he is actually an ex-Marine). To be fair, a good scientist knows that they actually know very little. A good scientist knows that what they know today can be disproved tomorrow, and that uncertainty underlies the entire discipline. So I think there is a noteworthy disconnect between the public perception and the actual practice of science. But, that said, I think there is some truth to the stereotype, too. There is no denying that science is strictly rooted in the rational acquirement of knowledge. Scientists know what they are looking for (objective knowledge), and they know how to find it (through hypothetico-deductive reasoning). Their cups are definitely full in this sense.

This leads to the second point of interest: knowing can exclude possibilities. When one enters the world knowing what they are looking for and how to find it, they will not find anything else. When a scientist approaches the world as a scientist only, they will see scientific possibilities only. When "white man" enters Native land knowing what he wants--its riches, he will miss much of what's there--its richness.

To take another spin on this theme, we can turn to an environmental ethics paper by environmental philosophers Jim Cheney and Anthony Weston. They explore the relationship between what we know (epistemology) and how we act (ethics). They propose an "ethics-based epistemology" as an alternative to our traditional "epistemology-based ethics". This is a mouthful, but as my classmate Andy put it so succinctly, it boils down to the chicken-or-egg riddle about what comes first:


In the traditional view, epistemology comes first: what we know about something determines how we act towards it. For example, we know that some animals can feel pain, so we decide upon this fact that we should treat them ethically.

In the alternative view, ethics come first: how we act towards something determines what we find out about it. In other words, we first act ethically, extending moral consideration and courtesy to even those that we know little about, and it is through this unconditional acceptance that we are allowed to really know the subject. So even if we cannot prove that snails feel pain, or that ecosystems exhibit stability, integrity, and beauty, or that wilderness matters intrinsically, we can show care and compassion for them anyway. We do not necessarily need to know all the facts before we can act in a caring manner. And, perhaps it is by caring first that knowledge and truth are revealed. By simply spending time and sharing space with other subjects, exercising mindfulness but resting our full minds, we invite unbridled discovery.

Essentially, the alternative view calls us to enter with empty cups. It calls us to let go of our need to know, to free ourselves of agendas, to quiet our preconceptions and open ourselves to surprise. Like the character Mo'at, Jim Cheney and Anthony Weston question our fixation with evidence, fact, and objectivity. They suggest emptying our cups so that other possibilities are free to flow in.


The alternative view has some implications for science and ecology. My thinking on this is still in-progress (and probably will continue to be for a long time), and I pose the following questions in the spirit of re-imagining ecology through open dialogue:

- When an ecologist conducts their research with a set agenda--to acquire objective, scientific knowledge--what possibilities are being excluded?

- Like the "white man" who enters wanting riches, is the ecologist, wanting objective knowledge, overlooking richness? (And by richness I of course mean something very different from "species richness".) Even if the scientist has the best of intentions in seeking objective knowledge, might he or she be (unknowingly) fueling arrogance and ignorance by fixating on one way of knowing?

- Of course, it is the ecologist's job to provide impartial knowledge. But this does not necessarily have to exclude other kinds of understandings that he or she may bear witness to. What if these other ways of knowing were embraced by the academic community, and offered a more central place in ecology than their current peripheral status?

- What if ecologists were encouraged to tell about scientific findings as well as other, more personal findings, whatever that may be? What if we openly raise the status of personal findings, embracing all the contradictions and mystery that may tag along? Might that contribute more truthfully and fruitfully (albeit more messily) to our on-going vital task of deciding how to value the environment?

- What if we, as an academic discipline, validated field work not just as a place to collect samples (i.e. the field is an object--"our study site"), but also as a place that you can form a relationship with (i.e. the field is a subject)? Like a relationship with any other subject, it takes time and a certain leap of faith before one can truly appreciate the other's depth, complexities, and value. Like any other loving relationship, sometimes the lover knows things that others do not. What if we took seriously the things that an ecologist knows about nature through love?

- It seems that many ecologists do feel an emotional connection with nature and value their time in the field for non-scientific reasons. But it is always the science that gets the professional stamp of approval, never the love or joy. Does it have to be this way? Might we be losing richness by always shelving love and joy in order to display objectivity?

- Ecologists and conservation biologists are valued in society for the impartial knowledge that they can contribute. They take part in environmental decision-making processes by providing the objective results of their research. However, it is often the case that the scientist cannot produce certain pieces of information, for a variety of reasons (lack of time, logistical problems, unforeseen circumstances, etc.). What if we implemented the alternative "ethics first" view, and chose the more caring and compassionate option despite not having all the facts?

- Ecologists are scientists, but are we just scientists? Might we benefit from trying to understand the world through other lenses besides the scientific one?

- If ecologists (and academics in general) more frequently approached the world with empty (or at least emptier) cups, I wonder what possibilities might flow in.

Monday, November 15, 2010

What can science learn from Google?

That is the finishing sentence from this article. The author tries to argue that theory and the scientific method is getting obsolete in this day and age, using Google as a role model:
But faced with massive data, this approach to science — hypothesize, model, test — is becoming obsolete. [...] There is now a better way. Petabytes allow us to say: "Correlation is enough." We can stop looking for models. We can analyze the data without hypotheses about what it might show. We can throw the numbers into the biggest computing clusters the world has ever seen and let statistical algorithms find patterns where science cannot.
But what is the biggest problem about patterns? You will always find them, and nobody knows this better than Google. The irony of this article is that Google stands for everything that he claims is wrong with "conventional" science. Google test every new feature they implement, e.g. new gmail interface item (see contributions in the discussion by leggett.org, responsible for the new design), or this user interface design . This is not always completely successful (think Google Wave, duh), but based on some articles about how Google works, the scientific method is embedded in the core of their business model. This article, for instance, explains their overall strategy to improve their search algorithm:

At any moment, dozens of these changes are going through a well-oiled testing process. Google employs hundreds of people around the world to sit at their home computer and judge results for various queries, marking whether the tweaks return better or worse results than before. But Google also has a larger army of testers — its billions of users, virtually all of whom are unwittingly participating in its constant quality experiments. Every time engineers want to test a tweak, they run the new algorithm on a tiny percentage of random users, letting the rest of the site’s searchers serve as a massive control group. There are so many changes to measure that Google has discarded the traditional scientific nostrum that only one experiment should be conducted at a time. “On most Google queries, you’re actually in multiple control or experimental groups simultaneously,” says search quality engineer Patrick Riley. Then he corrects himself. “Essentially,” he says, “all the queries are involved in some test.” In other words, just about every time you search on Google, you’re a lab rat.

Google's strategy is probably the most successful implementation of the scientific method that does not involve technology at its core.

And what about the example that the author uses from biology?

The best practical example of this is the shotgun gene sequencing by J. Craig Venter. Enabled by high-speed sequencers and supercomputers that statistically analyze the data they produce, Venter went from sequencing individual organisms to sequencing entire ecosystems. In 2003, he started sequencing much of the ocean, retracing the voyage of Captain Cook. And in 2005 he started sequencing the air. In the process, he discovered thousands of previously unknown species of bacteria and other life-forms. If the words "discover a new species" call to mind Darwin and drawings of finches, you may be stuck in the old way of doing science. Venter can tell you almost nothing about the species he found. He doesn't know what they look like, how they live, or much of anything else about their morphology. He doesn't even have their entire genome. All he has is a statistical blip — a unique sequence that, being unlike any other sequence in the database, must represent a new species.
So what can biology learn from Google in this instance? First, that identifying these "unique sequences" as potential species is based on a hypothesis, because there probably are a staggering amount of unique sequences in each genome. Second, that these new species are nothing but a hypothesis that has to be tested. Sadly enough (or lucky enough, depending on your point of view), we biologists do not have 91 million searches per day at our disposal to test these hypotheses, but still have to get in our boat and get wet.

So should science learn the scientific method from Google? It turns out that for some science writers/scientists, the answer is "yes".

Saturday, November 13, 2010

Reduce + Simplify + Deepen + collaboration



Creating a concept map as a teaching/learning tool is all about what Chris Orwig refers to when he describes the poetics of pictures: it is not only about reducing and simplifying, but also (especially) about deepening (or synthesis in teaching terms). It is this last part that makes it very difficult, and rewarding. And to make this deepening work, it is all about dialogue and collaboration, which is why I believe that class room interactions are crucial in this day and age of moving more and more to digital interactions.

As an illustration, below are some pictures of the students in my class working on a problem ("Why did the development of late summer anoxic conditions in the hypolimnion of the central basin of Lake Erie frustrate attempts to reduce nutrient loading to the lake?").

This is the stage: Thursday class 8:30 am, during midterms. Only 1/3 of the students show up, which I anticipated by discussing that question since it is not a crucial part of the course. I have a starting concept map for the students, that has already taken care of the reduction and simplification part of a concept map (all the basic concepts are identified and extracted from the text book), the exercise for this class is to deepen the concept map by identifying and synthesizing the information to provide a complete answer to the question. I subdivide the class in 4 groups, and the students start by reading the question, initial concept map, text book. Of course half of the students are going over the notes for their various midterms they have that day, but there is some initial discussion going on. After 15 minutes, I ask the students to start writing their solution concept maps on whiteboards scattered throughout the class. Each group singles one person for this task, and they start the concept map.


And then the magic happens: They start disagreeing, the second person comes up, erases part of the concept map, and starts her version, a third person does the same, the students start to look up from their midterm textbooks and pay attention, provide suggestions, more discussions, and before you know it...

... every single student is looking at the whiteboard, discussing, and thinking. 


My defining moment as a teacher (too bad I had to wait 5 years for this moment), and here are the pictures as proof. Afterwards, we used the different versions to explain the relative merits of the different solutions, and how these concept maps now can be used to identify fundamental solutions (or the lack thereof) for this eutrophication problem. I tried a similar approach later with the full class, and low and behold, worked again.







As a side note, you can see from the pictures that the concept map itself is deceptively simple: maybe 27 concepts in total, all fairly basic ones. It is the arrangement of them that showed a deeper and complete understanding of the problem, and as a class they needed 80 minutes to get to that point. The two main difficulties for this problem were 1) identifying the major hierarchy, and 2) 2 cross links between the two branches of the hierarchy. I could have just shown them the final concept map, and they would have learned nothing.

Thursday, November 4, 2010

And the discussion continues...

... on Amanda's blog: What do we do with all that science?

Ecofeminism: not just tree-hugging and hairy legs

In March 2009, the Women's Studies undergraduate program (among others) was cut at Guelph. I wasn't involved in the issue myself, but knew a few people who rallied against this decision. They cited it as ironic evidence that feminism is far from being a finished movement. At the time, I only saw a superficial link between the Women's Studies program cut and feminism; I didn't know what feminism really was.

Now that I am reading ecofeminist literature and gaining an understanding of this environmental philosophy, I am also beginning to really appreciate the feminist philosophy. Both ecofeminism and feminism have far broader impacts than the labels will have you perceive. In fact, they both have significant impacts for ecology and science.

The terms "ecofeminism" and "feminism" tend to put people off. There is a connotation of radical outburst and civil disobedience, reserved for the very passionate and very outraged. While these may be the most visible parts of the movement, at the heart of it is simply a powerful argument about value dualities.

The story begins with two familiar dualities: Male/Female, and Reason/Emotion. The dualities are commonly viewed in parallel, with men being typically associated with reason and thinking, and women with emotion and feeling.

There is nothing inherently wrong with noticing differences and contrasting two things that are different. The problem emerges when we start to value one more than the other. One is seen as superior, the other inferior. It becomes acceptable for one to dominate, control, and use the other. The problem emerges when we start treating the two as oppositional rather than complementary.

This happened to the Reason/Emotion duality, beginning with the advent of Western philosophy and carrying on (largely unnoticed) today. Western philosophy sees reason as the epitome of human existence. Reason is a sophisticated, high-order capacity, keeping us grounded from the whims of "animal" instinct and "mere" emotion. Without reason, we would be no better than our amoral (and inferior) counterparts on Earth--that is, animals. The ability to reason is essentially what defines us as humans.

Ecofeminist Val Plumwood questions this definition:

What is taken to be authentically and characteristically human, defining of the human, as well as the ideal for which humans should strive is not to be found in what is shared with the natural and animal (e.g., the body, sexuality, reproduction, emotionality, the senses, agency) but in what is thought to separate and distinguish them--especially reason and its offshoots. Hence humanity is defined not as part of nature (perhaps a special part) but as separate from and in oposition to it. Thus the relation of humans to nature is treated as an oppositional and value dualism.

Why do we emphasize the traits that distinguish us from animals, but ignore those that we share with animals? Besides being thinking creatures, are we not also bodily creatures and feeling creatures? It is this conception of human, stressing our reason, our separateness from other animals, that breeds another parallel divide: Human/Nature.

These three dualities (Reason/Emotion, Male/Female, and Human/Nature) are inextricably linked. And ecofeminists assert that Western society's obsession with reason has created the twin domination of women and nature. Obsession with reason has led us to highly value the "masculine" properties of thinking, distance, and abstraction, while degrading the "feminine" properties of feeling, affection, and experience. This oppressive framework results in the pervasive and subliminal message: nature and women cannot reason (at least not as well as men), therefore it is okay to dominate them.

This makes it okay for men to continually earn higher salaries than women. This makes it okay for humans to continually support animal abuse with every purchase of factory farmed meat. (I don't mean to fault anyone for what they earn or what they eat; social constructs have allowed for certain habits and conveniences, certain ethics.)

More invisibly, this makes it okay for, say, an ecology professor (probably male, teaching a class of probably mostly females) to heavily embed critical thinking into his curriculum, without any effort to nurture his students' emotional connection with nature. This makes it okay for, say, an ecologist to publish a paper on riparian buffers and water quality, without addressing (either publicly or privately) the instrumentalisation of forest and trees into "riparian buffers" and water and lake into "water quality".

Why do ecology students rarely get to go outside? Why are they only asked what they think about some ecosystem, community, or population, never what they feel for a particular place or subject? Why do ecologists study "natural resources" and not nature? (As if nature is only worth what it can provide for us.) Or "wildlife management" and not wildlife? (As if wildlife is ours to control, needing rules imposed on them when they show signs of disobedience.) These are real-world examples of our reason-dominated view, representing the widely accepted (even celebrated) norm in ecology.

Male-biased views entrench our education system, perhaps most blatantly in university science departments. Caring and love are cast aside. Professors, with the best of intentions, teach us that these are "merely" emotions, unreliable and untrustworthy. A good student will channel these passions into something productive and respectable--something rational.

It is not the ecofeminist or feminist's intention to reduce the prestige of reason in Western society. Rather, they question why this must come at the expense of the prestige of emotion. Reason is undebatably an important and powerful defense against myth, superstition, and propaganda. It allows us to evaluate, reveal, and construct. The "voice of reason" lets us look past individual desires to a more objective stance. Reason can serve as a friendly invitation to explore divergent views.

But emotion has much value, too. Ecofeminists and feminists validate the role of care, compassion, empathy, and inclusivity in our ethics and in our lives. These emotions are undebatably important and powerful antidotes for insensitivity, callousness, and apathy. Emotion, too, allows us to evaluate, reveal, and construct. Heartfelt emotions like sympathy and love carry us back from abstract theory to personal experience. Like reason, emotion can serve as a friendly invitation to explore divergent views.

To be human is to both think and feel. Thinking and feeling are different and complementary modes of knowing. They keep each other in check: thinking pulls us back from irrationality; feeling pulls us back from blind rationality. Western philosophy presents thinking and feeling as at war, with thinking being the favoured winner. Ecofeminism and feminism reject this oppositional value duality. Thinking and feeling feed each other. The complementarity of emotion and reason is our best toolkit for understanding the world and deciding how we ought to live.

The paradox of ecology is that it recognizes the importance of nature and the strain that humans impose on nature. Yet it insists on operating under a reason-dominated framework (i.e. science and the hypothetico-deductive method) that subliminally and continually oppresses nature. To truly value nature (and women), we must first seriously re-consider the oppositional value dualities that have led to this oppression. Borrowing a symbol from Buddhist philosophy, this shift must take place:


Caring and love should not be cast aside. They should be encouraged. I believe this encouragement can and should take place in an ecology classroom, right alongside encouraging critical thought and hypothetico-deductive reasoning. (Perhaps the traditional reason-dominated and male-biased classroom is a fundamental barrier against attracting and keeping women in science...but that is another posting altogether.)

Returning to the issue of the Women's Studies program at Guelph, it is ironic indeed that a program giving voice to the value of emotion was single-handedly silenced by a reason-dominated institution. At the time, I was hard at work completing my Master of Science degree, writing about "riparian buffers" and "water quality" within the impenetrable walls of the new Science Complex. I had no idea that I, too, was fueling the twin domination of women and nature. I found the loss of Women's Studies unfortunate, but was largely oblivious to its heavy social implications.

Reading ecofeminist philosophy has really opened my eyes. Ecofeminism is only superficially about stopping animal cruelty and championing for women's rights. It digs far deeper, revealing the oppositional value dualities that underscore our societal prejudices. This story does not only apply to women and nature, but virtually to every group that has faced discrimination (Aboriginal communities, disabled persons, LGBT, etc.). Ecofeminism sheds light on the shared history and shared challenges of many social and environmental problems.

For me, I am astonished to learn the tight links between social and environmental problems. I am also astonished to learn how much I did not learn in my years of science education. Thus, I am ever more convinced that we need stronger commitment to interdisciplinary education and research. Disconcertingly...guess what other undergraduate program was cut at Guelph in March 2009? Arts and Science.

Tuesday, November 2, 2010

A remedy for inaccessible science?

One of the most common complaints about the world of science is it's inaccessibility to the everyday person. Carl Zimmer has put together an "Index of Banned Words". Words that should be vanquished from the vocabulary of scientists everywhere. The list includes the taboos "elucidate", "predation", "mechanism", and (gasp!) "community ecology".

Reading through the list has made me realize how incredibly predictable my choice of words has become when writing in my science courses.

What is it that makes scientists so scared to write in everyday language? Does that fact that only a tiny percentage of the general population understand our writing make us feel like we belong to an exclusive club? Are we scared that we will lose our street cred among fellow scientists if our writing is not "abstract" enough? But then again, since when is our target audience the general public? In a recent post, Ingrid made some great points about the changing role of scientists, and our need to communicate with non-scientists. Ecologists need to start talking more effectively with non-scientists about environmental issues. The days of writing exclusively for our peers are over, and writing in a way that is coherent to the layperson may be a great first step to bridging the divide. After all, if we expect non-scientists to get on board with what we have to say, shouldn't they at least have an idea of what we are saying?

How do we strike a balance between writing accessibly and maintaining the technical aspects that are required for communicating abstract ideas and the scientific method? No one has taught me how to do that.

Monday, November 1, 2010

Eelgrass communities - An update

I recently gave a brief project update to the gang. Here are the nuts and bolts of my undergrad thesis (I’ll try to stay brief):

-Eelgrass meadows are important. They provide habitat for dozens of fish and invertebrate species, stabilize sediment, and cycle carbon and nutrients. Meadows are found in shallow coastal waters on the East and West coasts of North America. Seagrass meadows are globally threatened.

-The community dynamics of eelgrass meadows in temperate zones are largely not understood. In tropical zones, there is evidence that seagrass is often the victim of coastal eutrophication.

-Gulf Islands National Park Reserve consists of several islands off the southern tip of Vancouver Island. The park was established in 2003 and has been collecting data on fish and invertebrate communities in eelgrass meadows in the park. Data is collected as part of the park’s ecological integrity monitoring initiative. Parks Canada has a mandate to ensure that the ecological integrity of park lands is maintained.

Here is a bit of footage from field sampling:

video

So what could be influencing community dynamics?

-Proximity to Fraser River estuary as well as cool nutrient rich summer upwelling which results in a temperature and salinity gradient across sites as well as summer eutrophic conditions.

-Recent El Niño/La Niña oscillations may be influencing community dynamics.

-Using published fish and invertebrate diet data, a food web will be constructed. I will then explore site differences in community structure and then attempt to determine if community dynamics as consumer or producer driven. Analysis will be done in R using RDA analysis.

At this point in the semester my “who eats who” section of the project is complete (graphical representation coming soon) and am currently beginning “real” data analysis—mostly fiddling in R, trying to determine how the community composition of the various sample site sites differ.

An interpretation of regression: