Thursday, August 28, 2014

Carnival of Evolution #74

Well, it’s a couple of weeks late, but Carnival of Evolution #74 is now out.  Our contribution was Craig Benkman’s fascinating post about “A small mammal with an outsized impact”.  With more than 500 views already, it’s one of our most popular posts ever, and deservedly so.  So if you haven’t read it, check it out!  There are lots of other goodies in the carnival; I was very interested in the discussion of ring species by Jerry Coyne, for example.  Enjoy!

A ring species.

Saturday, August 16, 2014

The Divide: a survey about interactions between theoretical and empirical researchers

What is the proper role of theoretical versus empirical work in biology?  I self-identify as a theorist, and I do pretty much all of my work sitting at my Mac Pro.  However, I did my Ph.D. in Andrew Hendry’s lab, surrounded by empirical biologists working on stickleback, guppies, salmon, and other slimy real-world critters.  This was somewhat of an accident; initially, I was interested in doing an empirical Ph.D., but my past as a software engineer meant that I soon shifted into modeling.  (An early attempt at doing fieldwork on stickleback in British Columbia also convinced me that perhaps that was not my strongest suit.)  My position as the “token theorist” in the Hendry Lab worked out really well; I got a lot of exposure to empirical concerns and perspectives that informed my modeling work, both in what I chose to study and how I wrote about it.  At the same time, I provided a theoretical perspective that I hope was interesting and useful to the others in the lab.

This situation meant that I was often thinking about the way that theoretical and empirical approaches interact in ecology and evolutionary biology.  Should theoretical ideas drive new empirical work to look for the patterns and outcomes predicted by theoretical models?  Or should pure “natural history” observations of the real world drive new theoretical work to explain the patterns and outcomes observed?  Or is the ideal perhaps for the two perspectives to mutually drive each other, in a sort of ongoing feedback?  Do empiricists and theorists interact too little, too much, or just the right amount, in today’s world?  Which aspects of the interactions between these groups work, and which aspects are perhaps dysfunctional?  How do institutions such as journals, funding agencies, conferences, and universities influence (and perhaps hinder) such interactions?

My interest in such questions was whetted by discussions with Dan Bolnick, Andrew Hendry, Kiyoko Gotanda, Maria Servedio, and others too numerous to name, and the further along I got in my Ph.D., the more important these questions came to seem.  Some fascinating (and disturbing) papers came out on related topics, such as Fawcett & Higginson’s paper on the negative citation impact of equations in a paper, and Scheiner’s paper on the dearth of theoretical grounding in ecological research.  Eventually, I decided to conduct a survey of ecologists and evolutionary biologists to see what others thought about such questions.

And so that’s what I did, and the results of that survey are now published in BioScience.  I think the paper is quite accessible (it doesn’t contain a single equation!), so I won’t go into detail here about what I found.  In short, though, my results underscore three themes.  To quote from my abstract:

One theme is a widespread and mutual lack of trust, understanding, and interaction between empiricists and theorists. Another is a general desire, among almost all of the respondents, for greater understanding, more collaboration, and closer interactions between empirical and theoretical work. The final theme is that institutions, such as journals, funding agencies, and universities, are often seen as hindering such interactions. These results provide a clear mandate for institutional changes to improve interactions between theorists and empiricists in ecology and evolutionary biology.

That mention of a “clear mandate for institutional changes” in the last sentence is intended as a sort of clarion call, and although I didn’t devote much space in the article to my own personal opinions, this here is a blog post, so I will write a bit more frankly.

In the present institutional structure of science, attempts to collaborate and interact strongly across the theoretical–empirical divide generally go unrewarded; indeed, respondents to my survey often felt that such efforts were effectively punished, since such research is both harder to fund and harder to publish.  For this reason, it would be both unfair and unrealistic to ask individual researchers in the present climate to increase their interactions across the divide.  Instead, I think what we need are institutional reforms that provide incentives for greater interaction: funding programs specifically devoted to cross-divide research, editorial policies that encourage cross-divide publications, hiring policies in university biology departments that encourage the hiring of people with cross-divide publication records, and so forth.  Once the institutional incentives are in place, individual researchers will adjust their behavior; until then, individuals will continue to respond to the incentives as they presently exist.

So rather than suggesting that you ask “what can I, as an individual researcher, do to interact more across the divide?”, I suggest that you ask instead “What can I, as a faculty member, a journal editor, a manuscript reviewer, a conference organizer, a grant evaluator, a professor, a member of a professional society – a participant in creating the institutional structure of science – do to encourage everyone to interact more across the divide?”  And then please discuss this with others, and take action!


B.C. Haller.  (2014).  Theoretical and Empirical Perspectives in Ecology and Evolution: A survey.  BioScience (advance access).  DOI: 10.1093/biosci/biu131

Wednesday, August 13, 2014

Right beneath our feet: amazing nature in our backyards (Reign of Fire II?).

Our normal environs tend not to excite our scientific interest on a daily basis. They can instead become so familiar as to become boring and mundane – or just effectively invisible. We are instead more likely to be captivated and amazed when we go somewhere new – the Arctic, the Galapagos, the Amazon, the Negev Desert. On these trips, we tend to get excited about all sorts of critters, no matter how small or common. When visiting new countries, I find myself eagerly taking pictures of the most typical birds, birds that locals would never photograph, nor even notice, much as I treat a robin or starling or crow around my home.

Jumping spiders are awesome.
Yet our normal environs can become exciting and fresh again when we achieve a new perspective. Macro photography is a good example. Although I have long been interested in photography, I hadn’t spent much time on macro work until recently. Now, however, I often find myself at equestrian events and I need something to occupy myself and the kids in the hours between my wife’s performances. So the kids are tasked with running around in the bushes to find insects for me to photograph. Numerous times, I have been amazed by a cool new spider, mayfly, leaf hopper, lacewing, or any number of other spineless wonders. They were there all along, of course, right beneath my feet, but I simply hadn’t paid them much attention because I hadn’t previously been magnifying the world with a macro lens.

I only saw the parasites when I blew up this macro image of a lacewing.
A robber fly near my house
New perspectives can also be achieved by getting away from solid ground, such as going underwater or into the air. We recently bought my brother, Mike, a quadcopter on which he mounted his Go Pro to shot aerial footage of places we had seen countless times from the ground. We recently assembled a video aerial tour of the Wagner Natural Area, near Edmonton, Alberta, a site near our home that we had explored many times on foot or snowshoe or ski. Now, however, we were able to see patterns of diversity that were not apparent to us while walking on the ground – the trees no longer obscured the forest.

Mike and his quadcopter.
Or one can take a typical perspective and change its speed. Slow motion is a time shift we are used to from sports replays; but speeding things up, less so. I recently shot a time lapse video a sunset in Haida Gwaii, British Columbia. It shows the cool things a time lapse normally does, such as clouds zooming by – but then came a new insight: you can see very clearly the different layers of clouds going in different directions. I certainly already knew that winds go in different directions and different speeds at different altitudes, but here was the first time I could really SEE it so obviously. And, in my very first attempt to shoot a time lapse, I recorded of a wooly bear caterpillar building its cocoon. For the first time, I appreciated that they rip off their own hairs to form the basis for their cocoon.

New perspectives can also come just by chance through witnessing a rare event, like the time I watched an epic game of cat and mouse between a hawk and a squirrel in my backyard. The hawk would repeatedly swoop around the tree trying to get the squirrel on the opposite side only to fail when the squirrel dashed around again to the other side. The hawk eventually won the battle, but only when the squirrel tried to escape by dashing across a patch of lawn. As another example, barred owls are very conspicuous in many forests – to the point that they have become, if not common-place, at least not surprising. A few years ago, I was able to get very close to one in a tree by the side of a pond. I watched it for some time and eventually moved on, which was unfortunate because I was later told by someone else that it swooped down and caught a frog. (I went back and watched for hours but it didn’t happen again.)

Hawk 1. Squirrel 0.
The barred owl before he went fishing.
My brother, Mike, had a barred owl experience several times better. Seeing some owls low in the trees at a remote fishing camp in BC, he wondered if perhaps he could entice them to come down for proffered prey. The camp had a trap that produced five or so freshly-dead mice every day and so he started the process of training the owls to take them. It started with a rubber band attaching the mouse to the end of a fishing line, with the mouse then reeled in in a presumably tempting manner. After several attempts, the owls started swooping down upon the “fleeing” mice, grabbing them and flying off to feast on their perch. Eventually, they were able to get the owl to take mice right out of their hands. Mike made an awesome VIDEO of the experience.

Finally, a new perspective can result from a happenstance shift in the environment that exposes something previously hidden. Just imagine all of the fossils beneath our feet that we will never see unless a rockslide occurs, we dig a new septic tank, or a stream floods and cuts into the bank. The proof is in those numerous construction projects or mines that have uncovered cool new fossils or amazing archeological sites (or those dragons in the movie Reign of Fire). Closer to home, every time they disc the soil in our family vineyard in California, they turn up a slew of obsidian arrowheads that generates a family competition to find the best pieces.

Just last week, Mike, the kids, and I were visiting my mother in Edmonton, where we were helping her move from her home of 30 years into a condo. On the very last day we were all together (we won’t be back before Mom moves out), we were taking the quadcopter for some aerial shots when we crossed a creek we had crossed thousands of times before. Mike, looking down, noticed a bone and sent the kids after it. Upon retrieval, it was clearly a very old bone that had been buried in the ground and recently exposed by high creek flows. Old bones found in the forest are always fun but hardly novel, and so we set it aside and continued on our way.

The site of the find.
On the way back from filming, Mike hopped down into the creek and almost immediately found a piece of skull that seemed to be from the same animal as the leg bone. A bit further along, he found another skull fragment with the bony base of a horn attached – a bison. Now it was time to get excited: bison hadn’t populated this area for at least 140 years.

Bison and moose bones
Then the mad hunt began. Mike and the kids found another 15 or so bones right away – of all shapes and sizes and types. Then, the next day after Mike left, the kids went off to find more. They took a walkie talkie and had great fun reporting their finds back to me as I was working on the house. At one point they had so many bones that they had filled their pail and so called me to come and replace the bucket so they would have room for more bones. And, then, of course, I had to take my own turn through the creek, finding a few more bones in places kids wouldn’t normally look. By the end, we had quite a pile of bones, which were certainly from a number of bison (and a few moose).

Grandma and the kids show off their find.
Now we need to solve the puzzle. The previous day we visited a friend to look at mammoth bones that had been collected in the Arctic. Now we immediately began hoping we were looking Pleistocene bison, which were larger than modern bison. However, comparison to various skull images online suggested the latter; but why so many in this one place? Our neighbour, a taxidermist who had worked for the Royal Alberta Museum, came over to look and told us that he too had found bison bones when digging a new pond. He suggested they might be 300 to 600 years old and were from a boggy area in which plains bison not used to soggy conditions had become mired. It is a good hypothesis and now we aim to test it, starting by dating some teeth we brought back to Montreal. These discoveries and questions and projects have brought a completely new perspective on our childhood home that was revealed to us out of the blue on the very last day we were all there together.

Big bison bones
Many amazing things are just beneath our feet right in our own backyards, awaiting only a new perspective. Sometimes we need to actively engage that perspective with an underwater camera or a quadcopter or a microscope or a fishing rod and a mouse. Sometimes we merely need to wait for the right moment when new conditions expose previously invisible phenomena (those bones were there the whole time!). Other times (indeed, all times), we have to keep our eyes open for when rare events finally happen (when that owl dives for that frog). Natural history, ecology, evolution, and biodiversity are just as fascinating at home as they are in the Antarctic or the tropics, sometimes we just have to shift our perspective to see it.

Quite literally beneath our feet - under the flagging stones near the fire pit.

Wednesday, August 6, 2014

Standing and flowing

Our paper on "The genomic signature of parallel adaptation from shared genetic variation" is finally out in print. Check out the funky cover they used.

The paper is also subject of a News and Views by John Welch and Chris Jiggins:

Here is the paper:

Here is the original blog post:

A 25-year quest for the Holy Grail of evolutionary biology

When I started my postdoc in 1998, I think it is safe to say that the Holy Grail (or maybe Rosetta Stone) for many evolutionary biologists w...