Category: opinion

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#overlyhonestsyllabi

About a week ago, I fired up Twitter in the evening to see what sort of interesting links my various contacts had posted during the day. As you would expect, due to my professional interests, I follow a fair number of academics ranging from undergraduates to graduate students to postdocs to professors. Many of them are scientists, and so I am usually able to find some good science reading in the evening as I wind down my day.

That evening was different, however, as I encountered a stream of #overlyhonestsyllabi-tagged tweets (mostly retweets, actually) in my feed.

I’m not going to analyze the phenomenon too deeply here, as others (e.g. here and here) have already done that very well. Rather, I’d like to sketch out my thoughts that evening, now that I’ve had a few days to let things percolate in my brain.

At first I was slightly amused. Some of the tweets were, indeed, funny in a ironic sort of way that tickled my Gen-X funny bone. But as I scrolled through the growing hashtag stream, I stopped feeling amused and began to understand that #overlyhonestsyllabi was becoming more of a “crasstag”  Or maybe even a bashtag. I began to feel more and more uneasy with each new tweet that appeared.

Then, burning through the hashfog, came this statement that suddenly crystalized my thoughts:

That was precisely it. Precisely.

It is vital to remember that the students in our classes are – in the vast majority – there because they appreciate the subject matter and want to learn more about it. Yes, there are always the minority that are only there for the grade, or because their parents made them, or…

Of course there are countless little stories – some humorous, some horrific – that accrue over the long semesters and long careers of teaching. But those stories represent the m-i-n-o-r-i-t-y of students. Given the fact that, these days, very few people are going to accumulate vast fame or immense fortune with a B.Sc. in biology (or most any other university degree), the fact is that most students are taking biology (or some other subject) because they have a burgeoning love for the subject matter.

Do you remember when you were at that same stage of life and were fascinated by the ants in your parents’ lawn, or by how a jet engine worked, or by Steinbeck’s genius? Do you remember that that was why you pursued the degree(s) that you did? Hopefully that fascination is still there and has grown and blossomed. And if it has (I won’t discuss what needs to happen if it hasn’t), then it is our job to cultivate that exact same seedling of fascination in our students.

I fully understand that most of the tweeters that evening were just having a bit of fun. But, unfortunately, it did not come across that way to the entire audience, as exemplified by the tweet above and a number of others that I read that evening as well.

Instead of careful cultivation it was, unfortunately, salting the fields.

So, here is my suggestion. As students return to classes and to the crisp-blue-sky promise of a new autumn semester, why not subvert the overall cynicism of #overlyhonestsyllabi to instead welcome them back to studying the subjects that they and you love so much.

I’ll start.

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Also, please don’t get me wrong. As I said above, I am sure that most #overlyhonestsyllabi tweeters were just trying to have a bit of fun.

And, of course, there were some gems that I noticed here and there in the hashtag stream. For instance:

 

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Kids, go outside… or maybe not?

My family is lucky enough to live in a city that is surrounded by vast tracts of wilderness. We’re also lucky to live in a city that has seen fit to preserve at least some of that wilderness within the urban boundaries. While Prince George has a long way to go in terms of truly being a green city (ahem… let’s at least start with a municipal recycling program instead of just talking about it), people here tend to love the nature that surrounds them. In fact, I would guess that many of the residents here – both longtime citizens and more recent arrivals – a big drawing point to life in central BC was the beauty of nature that surrounds us here. The city is surrounded by lakes. We’re at the junction of two rivers. Jasper National Park is just down the road. There is an awesome inland rainforest just to the east of us. And that’s just skimming the surface of what’s available to residents here.

Did I mention that we’re lucky?

I assume that many of you who read this blog (all six of you, not including my mom), enjoy spending time in nature too, wherever you may live. So think back to your own childhood for a moment. Did that love of nature emerge because you sat in the basement all day playing Atari? Or did you spend a lot of time out-of-doors, both with and without your parents or other relatives? I suspect that it’s safe to bet on the latter in most cases. Basement dwelling does not generally create lifelong naturalists.

However, today I get the impression that our municipal leaders would prefer that kids not get outside; or rather, if they do get outside, it’s only under strictly controlled conditions.

Why do I say this? It turns out that someone in town, whose kids obviously enjoy playing outside in the yard, decided that a prudent and completely unobtrusive thing to do would be to post a small sign obtained from the British Columbia Automobile Association on their own front lawn to remind passing motorists that there were kids in the area. Sounds like a perfectly reasonable thing to me, both as a father of two boys and as a driver.

The city of Prince George, however, thought otherwise, and the family was sent a bylaw warning to remove their sign or face a fine. That, in itself, is well off the mark. But the part that really irked me was a comment from the city manager of transportation operations in response to a media inquiry:

“Parents should encourage their children to play in playgrounds as playing near the street is not the safest place to play.”

The thing that bugs me about this comment is its deeper implication that spontaneous play in a child’s own yard is not safe and that the only places that kids should be are in a playground (highly supervised, of course) or, presumably, in their house. This comment leaves the impression that, in the mind of our city officials, a yard is inherently unsafe.

This is not surprising, of course, since the notion of the “unsafe outdoors” is likely one of the main reasons that parents don’t let their kids play outside as much as they used to. But is keeping kids indoors most of the time and then shuttling them back and forth to tightly-monitored playground- or soccer-type situations really any safer in the long run? Is it really safer for them to learn to be sedentary as kids and head off into a sedentary adulthood, as modeled by their parents? Are the indoors really safer anyhow, in terms of overall household accidents? Does attempting to remove all dangers from kids teach them how to monitor, assess, and avoid real dangers when they inevitably encounter them? Is it safe for the local and global environment to be raising a generation of kids who don’t know anything about their local natural spaces because they never get out into them – and who thus have a mainly academic (if that) knowledge of nature?

So, to the good leaders of our fine city I say this:

Please take a serious look at our city’s bylaws and their enforcement and think about what they mean for parents who want their kids to spend time outdoors. You have done a great job in creating and maintaining natural spaces throughout our city, and for that I truly applaud you. But if we want the next generation to appreciate and work to protect those spaces – and to care about our environment in general – we need to find ways to encourage parents and kids to walk and play in the local environment. Messages that such play is somehow unsafe, combined with overzealous enforcement of bylaws that have the effect of stifling such childhood activity, need to be carefully reconsidered.

(On a side note: A great book on this very topic is Richard Louv‘s “Last Child in the Woods.” I highly recommend it to anyone who cares for children and who cares about their welfare and the welfare of our planet in general.)

(Another note – added 5-VII-13: I just noticed that the Nature Conservancy of Canada has a great little article in the Globe and Mail about a children spending time in nature. You can get it here.)

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Fear and loathing

Over the past few weeks, Prince George and other parts of British Columbia have seen a massive outbreak of tent caterpillars. And that, of course, means that people have been talking about insects. A lot. In fact almost everyone in town has become, at least for a short while, an amateur entomologist. In some cases, I have heard some pretty interesting observations from people. There have also been a few fascinating forays into applied economic entomology as well – my favorite being the lady who filled her Shop Vac half full of soapy water and used it to suck the caterpillars off of her shrubs.

Of course, an infestation of this size has unpleasant aspects. My wife and kids did not like going out in the backyard during the peak of the outbreak. And I don’t blame them, as I wasn’t too keen on it either. A short walk through our yard would leave us draped in zillions of invisible strands of caterpillar silk with a few of the creatures crawling up our necks. And even a simple task like coiling the garden hose would leave your hands covered in squished caterpillar goo. So, I fully understand not fully appreciating these creatures when they occur in vast numbers. Beyond making parts of our city look like autumn is already here, they have been just a general nuisance.

That said, I do not understand today’s editorial in the local newspaper. The editor spent a lot of column space writing about insects, pulling out some interesting and salient facts. Yes, insect biodiversity is astounding. Yes, some of them would likely survive even if an apocalyptic natural event wiped out all of human life. Yes, as implied, we share a more recent common ancestor with other vertebrates than we do with insects. All valid points.

Then these bits:

“Our hatred of caterpillars and other bugs also has a basis in evolution.”

and

“We’re right to fear and hate them as much as we do.”

Really?

Since the muse for the editorial seems to be the swarms of tent caterpillars in town, let’s start with some reasons not to “fear and hate” them.

First, although they cause a great deal of visible damage, they are unlikely to kill many trees at all. So on the “fear and hate” side of the ledger we are left with temporary cosmetic damage and a bit of hassle in the yard for a few weeks. On the other hand, they do have benefits. This article nicely summarizes many of them. For instance:

  • they are a natural part of a functioning forest ecosystem.
  • their removal of canopy leaves allows light to the forest floor, giving some plants down there a leg (or limb?) up.
  • caterpillars and the moths that they become provide food for other organisms.
  • caterpillar poop gives a burst of nutrients to the forest floor.
  • all of these things, over time and many cycles, make a forest what it is.

In other words, if there weren’t periodic outbreaks of defoliators, our forests would be much different from what we enjoy today both in terms of the forest structure and the plants and animals that live there.

But, even if you don’t believe me that the benefit side of the ledger is much more substantial than the detriment side for tent caterpillars, perhaps you’ll agree with me on some easier-to-prove examples:

If this recent caterpillar outbreak has shown us anything, it is that people are fascinated by insects – and by nature in general.

To give the editor the benefit of the doubt, as pointed out by a colleague of mine:

And perhaps that’s true; perhaps the editor meant “respect.” But, one way or the other, I would prefer more coverage of the wonders of nature and more encouragement for people to get outside and to see what’s really going on out there, than demonization of vast segments of the natural world with careless words – even if the intent of those words is mainly to amuse. If we want people to care about the global environment, it’s not wise to begin with making them think that they have reason to hate the local fauna and flora.

Rather show people why it’s so awesome out there, and they’ll begin to understand why we are all so intimately connected with those very insects that are buzzing around our yards and jogging paths.

And in time that will turn more people from being armchair environmentalists (at best) to being actual hands-in-the-soil and boots-on-the-ground naturalists who have a stake in real conservation.

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Baseball

A few of the many reasons that I love baseball:

1. Baseball is a sport in which you don’t run out of time, you run out of opportunities. Baseball doesn’t rely on massive bodily collisions or continual action. Baseball is all about suspense.

2. My dad used to take my mom, my sisters, and me to Calgary Cannons games when I was a kid. He would buy us each a hotdog, soda, and then ice cream cones for dessert. Dinner at the ballpark.

3. Winter is, alas, not my favorite season. Spring training, and then opening day, are the perfect markers of the end of snow and the beginning of sun.

4. There is nothing in the world like a lazy summer late-afternoon at the ballpark. And the crack of a bat.

5. Memories of my dad listening to baseball games on the radio in the evening. He is a San Francisco Giants fan and, if the weather was just right, he could pick up their broadcasts all they way up in Calgary. Of course, these days you can just listen on the internet (and I often do).

6. Speaking of that, baseball is the one sport that seems like it was completely made for radio. You can close your eyes while listening to a baseball broadcast and the entire game comes alive in your head. Try doing that with football, hockey, or basketball. This is particularly the case when listening to great play-by-play guys.

7. Baseball is the first professional sport that I remember watching live; watching Fernando Valenzuela pitch against the Montreal Expos at Dodger Stadium. And, being one excited little league kid, of course I brought my glove to the game.

8. Baseball has its own anthem, and everybody knows it by heart.

9. Baseball has many incredible stories.

 

AND, going into extra innings…

 

10. Baseball has deeply held traditions.

11. Baseball begets poetry.

12. Baseball has Yogi Berra.

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Open data

by Dezene Huber and Paul Fields, reblogged from the ESC-SEC Blog.

Have you ever read a paper and, after digesting it for a bit, thought: “I wish I could play with the data”?

Perhaps you thought that another statistical test was more appropriate for the data and would provide a different interpretation than the one given by the authors. Maybe you had completed a similar experiment and you wanted to conduct a deeper comparison of the results than would be possible by simply assessing a set of bar graphs or a table of statistical values. Maybe you were working on a meta-analysis and the entire data set would have been extremely useful in your work. Perhaps you thought that you had detected a flaw in the study, and you would have liked to test the data to see if your hunch was correct.

Whatever your reason for wishing to access to the data, and this list probably just skims the surface of the sea of possibilities, you often only have one option for getting your hands on the spread sheets or other data outputs from the study – contacting the corresponding author.

Sometimes that works. Often times it does not.

  • The corresponding author may no longer be affiliated with the listed contact information. Tracking her down might not be easy, particularly if she has moved on from academic or government research.
  • The corresponding author may no longer be alive, the fate of us all.
  • You may be able to track down the author, but the data may no longer be available. Perhaps the student or postdoc that produced it is now out of contact with the PI. But even if efforts have been made to retain lab notebooks and similar items, is the data easily sharable?
  • And, even if it is potentially sharable (for instance, in an Excel file), are the PI’s records organized enough to find it?*
  • The author may be unwilling to share the data for one reason or another.

Molly (2011) covers many of the above points and also goes into much greater depth on the topic of open data than we are able to do here.

In many fields of study, the issues that we mention above are the rule rather than the exception. Some readers may note that a few fields have had policies to avoid issues like this for some time. For instance, genomics researchers have long used repositories such as NCBI to deposit data at the time of a study being published. And taxonomists have deposited labeled voucher specimens in curated collections for longer than any of us have been alive. Even in those cases, however, there are usually data outputs from studies associated with the deposited material that never again see the light of day. So even those exceptions that prove the rule are part of the rule of a lack of access to data.

But, what if things were different? What might a coherent open data policy look like? The Amsterdam Manifesto, which is still a work in progress, may be a good start. Its points are simple, but potentially paradigm-shifting. It states that:

  1. Data should be considered citable products of research.
  2. Such data should be held in persistent public repositories.
  3. If a publication is based on data not included in the text, those data should be cited in the publication.
  4. A data citation in a publication should resemble a bibliographic citation.
  5. A data citation should include a unique persistent identifier (a DataCite DOI recommended, unless other persistent identifiers are in use within the community).
  6. The identifier should resolve to provide either direct access to the data or information on accessibility.
  7. If data citation supports versioning of the data set, it should provide a method to access all the versions.
  8. Data citation should support attribution of credit to all contributors.

This line of reasoning is no longer just left to back-of-napkin scrawls. Open access to long term, citable data is slowly becoming the norm rather than the exception. Several journals have begun require, or at least strongly suggest, deposition of all data associated with a study at the time of submission. These include PeerJ and various PLoS journals. It is more than likely that other journals will do the same, now that this ball is rolling.

The benefits of open data are numerous (Molloy, 2011). They include the fact that full disclosure of data allows for verification of your results by others. Openness also allows others to use your data in ways that you may not have anticipated. It ensures that the data reside alongside the papers that stemmed from them. It reduces the likelihood that your data may be lost due to various common circumstances. Above all it takes the most common of scientific outputs – the peer reviewed paper – and adds lasting value for ongoing use by others. We believe that these benefits outweigh the two main costs:  the time taken to organize the data and the effort involved in posting in an online data repository.

If this interests you, and we hope that it does, the next question on your mind is probably “where can I deposit the data for my next paper?” There are a number of options available that allow citable

(DOI) archiving of all sorts of data types (text, spreadsheets, photographs, videos, even that poster or presentation file from your last conference presentation). These include figshare, Dryad, various institutional repositories, and others. You can search for specific repositories at OpenDOAR using a number of criteria. When choosing a data repository, it is important that you ensure that it is backed up by a system such as CLOCKSS.

Along with the ongoing expansion of open access publishing options, open data archiving is beginning to come into its own. Perhaps you can think of novel ways to prepare and share the data from your next manuscript, talk, or poster presentation for use by a wide and diverse audience.

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* To illustrate this point, one of us (DH) still has access to the data for the papers that stemmed from his Ph.D. thesis research. Or at least he thinks that he does. They currently reside on the hard drive of the Bondi blue iMac that he used to write his thesis, and that is now stored in a crawlspace under the stairs at his house. Maybe it still works and maybe the data could be retrieved. But it would entail a fair bit of work to do that (not to mention trying to remember the file structure more than a decade later). And digital media have a shelf life, so data retrieval may be out of the question at this point anyhow.